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Sample records for cattle genetic introgression

  1. INTROGRESIÓN GENÉTICA DE Bos indicus (BOVIDAE EN BOVINOS CRIOLLOS COLOMBIANOS DE ORIGEN Bos taurus Genetic Introgression of Bos indicus (Bovidae in Colombian Creole Cattle Bos taurus

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    CARLOS ARTURO SÁNCHEZ ISAZA

    Full Text Available El presente trabajo evidencia desde el punto de vista citogenético la introgresión genética, de origen paterno, de Bos indicus en ganado criollo colombiano descendiente de Bos taurus. Para este estudio se realizó el análisis cariológico de la morfología del cromosoma Y a partir de muestras de sangre heparinizada de 67 bovinos machos pertenecientes a siete razas criollas colombianas. Se reporta la presencia de cuatro ejemplares pertenecientes a la raza Romosinuano (40% y 10 toros de la raza Casanareña (100% con cromosoma Y de tipo acrocéntrico característico de Bos indicus, lo cual estaría evidenciando un alto grado de introgresión genética, en estas dos razas, posiblemente originada por la intensiva introducción de sementales de la raza Cebú en la ganadería criolla colombiana. En las otras cinco razas (Blanco Orejinegro (BON, Chino santandereano, Costeño con cuernos, Hartón del valle y Sanmartinero, los toros presentaron el cromosoma Y submetacéntrico, característico de Bos taurus.This work evidenced, using a cytogenetics approach, that Bos indicus exerted a genetic introgression of paternal origin on Creole Colombian cattle descendent from Bos taurus. Analysis of chromosome Y morphology was carried out in heparinized blood samples of 67 bulls belonging to seven Colombian breeds. We report 4 sires belonging to the Romosinuano breed (40% and 10 bulls of the Casanareño breed (100% with acrocentric Y chromosome which is characteristic of Bos taurus. This finding indicates a high degree of genetic introgression in these two breeds probably caused by the continuous input of zebu stallions in the Colombian Creole breeds. In other five Creole breeds (Blanco Orejinegro -BON-, Chino Santandereano, Costeño con Cuernos, Hartón del Valle and Sanmartinero, the bulls had a submetacentric Y chromosome characteristic of Bos taurus.

  2. On the History of Cattle Genetic Resources

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    Marleen Felius

    2014-11-01

    Full Text Available Cattle are our most important livestock species because of their production and role in human culture. Many breeds that differ in appearance, performance and environmental adaptation are kept on all inhabited continents, but the historic origin of the diverse phenotypes is not always clear. We give an account of the history of cattle by integrating archaeological record and pictorial or written sources, scarce until 300 years ago, with the recent contributions of DNA analysis. We describe the domestication of their wild ancestor, migrations to eventually all inhabited continents, the developments during prehistory, the antiquity and the Middle Ages, the relatively recent breed formation, the industrial cattle husbandry in the Old and New World and the current efforts to preserve the cattle genetic resources. Surveying the available information, we propose three main and overlapping phases during the development of the present genetic diversity: (i domestication and subsequent wild introgression; (ii natural adaptation to a diverse agricultural habitat; and (iii breed development.

  3. Comparative Transmission Genetics of Introgressed Chromatin in Gossypium Species

    Institute of Scientific and Technical Information of China (English)

    WAGHMARE Vijay N; RONG Jun-kang; ROGERS Carl J; BOWERS John E; PATERSON Andrew H

    2008-01-01

    @@ Wild relatives and un-adapted germplasm of crop species harbors several adaptive traits.Introgression of genes for economic and adaptive traits brings in novel genetic variation into the gene pools of many crops including cotton.We compared patterns of introgression into polyploid Gossypium hirsuture from its sister G.tomentosum,and from G.barbadense representing a different clade tracing to the same polyploidization.Advanced-generation populations,resulting from recurrent backcrossing to G.hirsutum,show a paucity of G.tomentosum alleles and severe deficiencies of homozygotes.

  4. Genetic Introgression and the Survival of Florida Panther Kittens.

    Science.gov (United States)

    Hostetler, Jeffrey A; Onorato, David P; Nichols, James D; Johnson, Warren E; Roelke, Melody E; O'Brien, Stephen J; Jansen, Deborah; Oli, Madan K

    2010-11-01

    Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982-2008 and a live recapture-dead recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0 - 1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F(1) admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data. PMID:21113436

  5. Indigenous cattle in Sri Lanka: production systems and genetic diversity

    International Nuclear Information System (INIS)

    Production status, farming systems and genetic diversity of indigenous cattle in Sri Lanka were evaluated using six geographically distinct populations. The indigenous cattle population of the country is considered as a nondescript mixture of genotypes, and represents more than half of the total cattle population of 1.2 million heads. Five distinct indigenous populations were investigated for morphological analysis, and four were included in evaluating genetic differences. Farming systems were analysed using a pre-tested structured questionnaire. The genetic variation was assessed within and between populations using 15 autosomal and two Y-specific microsatellite markers, and compared with two indigenous populations from the African region. Farming system analysis revealed that indigenous cattle rearing was based on traditional mixed-crop integration practices and operates under limited or no input basis. The contribution of indigenous cattle to total tangible income ranged from zero to 90% reflecting the high variation in the purpose of keeping. Morphometric measurements explained specific phenotypic characteristics arising from geographical isolation and selective breeding. Though varying according to the region, the compact body, narrow face, small horns and humps with shades of brown and black coat colour described the indigenous cattle phenotype in general. Genetic analysis indicated that indigenous cattle in Sri Lanka have high diversity with average number of alleles per locus ranging from 7.9 to 8.5. Average heterozygosity of different regions varied within a narrow range (0.72 ± 0.04 to 0.76 ± 0.03). Genetic distances between regions were low (0.085 and 0.066) suggesting a similar mixture of genotypes across regions. Y-specific analysis indicated a possible introgression of Taurine cattle in one of the cattle populations. (author)

  6. West African cattle breeds characterizations: Review of CIRDES genetic works

    International Nuclear Information System (INIS)

    Full text: The improvement of domestical animal breeds productivity or the animal genetic diversity maintenance to allow breeders to select animals or to create new breeds in order to adapt to environmental modifications, new diseases and societies needs, requires first a detailed inventory and, secondly, a genetic characterization of domestic animal breeds. Indeed, in developing countries, the notion of breed is not clear; visual parameters are often used even if these procedures are subjective. So it is necessary to complete this phenotypic approach by a genomic one in order to contribute to an efficient characterization. At CIRDES, a regional center for subhumid livestock research and development, these studies have been conducted during the past ten years. They permitted (i) to describe the cattle phenotypic traits and their geographical localization and to highlight the breeds threatened with extinction, (ii) to determine zebu introgression level in taurine trypanotolerant cattle (iii) to identify specific alleles of different cattle breeds, and (iv) to quantify the importance of Robertson translocation in livestock production. Data collection has been realized using a bibliography study, completed by investigations in seven countries of West Africa. Blood collection has been also done for an analysis of 4 categories of genome markers (11 blood group systems, 3 blood protein loci, microsatellites and chromosomes). According to phenotypic description and to the conceptions of autochtone human population, 13 local cattle breeds have been identified: Ndama, Kouri, the group Baoule-Somba, the group Lagoon cattle, zebu Azawak, zebu Maure, zebu Touareg, zebu Goudali, zebu Bororo, zebu White Fulani, zebu Djelli, zebu peuhl soudanien, zebu Gobra, and their crossbreds (Zebu x Ndama and Zebu x West African Shorthorns). Nine exotic breeds have been also identified: American Brahman, Gir, Girolando, Droughtmaster, Santa Gertrudis, Holstein, Montbeliarde, Jersey and Brown

  7. Genetic Introgression and Species Boundary of Two Geographically Overlapping Pine Species Revealed by Molecular Markers

    OpenAIRE

    Zhang, Defang; Xia, Tao; Yan, Maomao; Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

    2014-01-01

    Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine tre...

  8. Intentional genetic introgression influences survival of adults and subadults in a small, inbred felid population.

    Science.gov (United States)

    Benson, John F; Hostetler, Jeffrey A; Onorato, David P; Johnson, Warren E; Roelke, Melody E; O'Brien, Stephen J; Jansen, Deborah; Oli, Madan K

    2011-09-01

    1. Inbreeding and low genetic diversity can cause reductions in individual fitness and increase extinction risk in animal populations. Intentional introgression, achieved by releasing genetically diverse individuals into inbred populations, has been used as a conservation tool to improve demographic performance in endangered populations. 2. By the 1980s, Florida panthers (Puma concolor coryi) had been reduced to a small, inbred population that appeared to be on the brink of extinction. In 1995, female pumas from Texas (P. c. stanleyana) were released in occupied panther range as part of an intentional introgression programme to restore genetic variability and improve demographic performance of panthers. 3. We used 25 years (1981-2006) of continuous radiotelemetry and genetic data to estimate and model subadult and adult panther survival and cause-specific mortality to provide rigorous sex and age class-specific survival estimates and evaluate the effect of the introgression programme on these parameters. 4. Genetic ancestry influenced annual survival of subadults and adults after introgression, as F(1) generation admixed panthers ( = 0·98) survived better than pre-introgression type panthers ( = 0·77) and other admixed individuals ( = 0·82). Furthermore, heterozygosity was higher for admixed panthers relative to pre-introgression type panthers and positively influenced survival. 5. Our results are consistent with hybrid vigour; however, extrinsic factors such as low density of males in some areas of panther range may also have contributed to higher survival of F(1) panthers. Regardless, improved survival of F(1) subadults and adults likely contributed to the numerical increase in panthers following introgression, and our results indicate that intentional admixture, achieved here by releasing individuals from another population, appears to have been successful in improving demographic performance in this highly endangered population. PMID:21338353

  9. Characterization of Genetic Variation in Icelandic Cattle

    DEFF Research Database (Denmark)

    Holm, Lars-Erik; Das, Ashutosh; Momeni, Jamal;

    Identification of genetic variation in cattle breeds using next-generation sequencing technology has focused on the modern production cattle breeds. We focused on one of the oldest indigenous breeds, the Icelandic cattle breed. Sequencing of two individuals enabled identification of more than 8...... million SNPs and more than one million short indels. Annotation of the genetic variants identified a substantial number of functional SNPs and variants. The number of genetic variants identified in the Icelandic cattle breed is on the same level as previously seen in other studies on Holstein cattle...

  10. Does genetic introgression improve female reproductive performance? A test on the endangered Florida panther.

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    Hostetler, Jeffrey A; Onorato, David P; Bolker, Benjamin M; Johnson, Warren E; O'Brien, Stephen J; Jansen, Deborah; Oli, Madan K

    2012-01-01

    Genetic introgression has been suggested as a management tool for mitigating detrimental effects of inbreeding depression, but the role of introgression in species conservation has been controversial, partly because population-level impacts of genetic introgressions are not well understood. Concerns about potential inbreeding depression in the endangered Florida panther (Puma concolor coryi) led to the release of eight female Texas pumas (P. c. stanleyana) into the Florida panther population in 1995. We used long-term reproductive data (1995-2008) collected from 61 female Florida panthers to estimate and model reproduction probability (probability of producing a litter) and litter size, and to investigate the influence of intentional genetic introgression on these parameters. Overall, 6-month probability of reproduction (±1SE) was 0.232 ± 0.021 and average litter size was 2.60 ± 0.09. Although F(1) admixed females had a lower reproduction probability than females with other ancestries, this was most likely because kittens born to F(1) females survive better; consequently, these females are unavailable for breeding until kittens are independent. There was no evidence for the effect of ancestry on litter size or of heterozygosity on probability of reproduction or litter size. In contrast, earlier studies have shown that genetic introgression positively affected Florida panther survival. Our results, along with those of earlier studies, clearly suggest that genetic introgression can have differential effects on components of fitness and highlight the importance of examining multiple demographic parameters when evaluating the effects of management actions. PMID:21805300

  11. Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers.

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    Zhang, Defang; Xia, Tao; Yan, Maomao; Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

    2014-01-01

    Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids. PMID:24977711

  12. Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers.

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    Defang Zhang

    Full Text Available Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids.

  13. Introgression of transgenic crop alleles: Its evolutionary impacts on conserving genetic diversity of crop wild relatives

    Institute of Scientific and Technical Information of China (English)

    Bao-Rong LU

    2013-01-01

    Effective conservation of crop wild relative (CWR) species is essential for the sustainable use and genetic improvement of crop varieties,which offers greater opportunities for world food security,particularly in modem agroecosystems where CWR diversity is under severe threat.Factors such as habitat fragmentation,human disturbances,global climate change,and invasion of harmful alien species have been identified to be responsible for losses and threats to CWR diversity.However,a neglected factor,gene introgression from domesticated species through repeated outcrossing,may have a significant impact on CWR diversity.Introgression can influence genetic diversity and evolutionary processes of CWR populations through effects such as demographic swarming,genetic assimilation,and selective sweep.When largely enhancing or reducing fitness of wild plants,the introgression of crop genes will impose more significant genetic and evolutionary impacts on CWR populations,leading to undesired consequences for conserved CWR populations and species.This situation is particularly true when genetically engineered (GE) crops are deployed for commercial cultivation.It is argued that a GE crop usually contains transgenes with strong natural selection advantages,and such transgenes introgressed into CWR populations may have strong impacts on their genetic diversity and evolutionary processes,threatening their conservation.This article reviews the challenge of crop-wild gene flow,and particularly transgene introgression from GE crops,for the in situ conservation of wild relative species.The design of effective management strategies for conserving CWR species under the scenario of extensive cultivation of GE crops is also discussed.

  14. Molecular Markers Allow to Remove Introgressed Genetic Background: A Simulation Study

    OpenAIRE

    Carmen Amador; Miguel Ángel Toro; Jesús Fernández

    2012-01-01

    The maintenance of genetically differentiated populations can be important for several reasons (whether for wild species or domestic breeds of economic interest). When those populations are introgressed by foreign individuals, methods to eliminate the exogenous alleles can be implemented to recover the native genetic background. This study used computer simulations to explore the usefulness of several molecular based diagnostic approaches to recover of a native population after suffering an i...

  15. Genetic and epigenetic changes in somatic hybrid introgression lines between wheat and tall wheatgrass.

    Science.gov (United States)

    Liu, Shuwei; Li, Fei; Kong, Lina; Sun, Yang; Qin, Lumin; Chen, Suiyun; Cui, Haifeng; Huang, Yinghua; Xia, Guangmin

    2015-04-01

    Broad phenotypic variations were induced in derivatives of an asymmetric somatic hybridization of bread wheat (Triticum aestivum) and tall wheatgrass (Thinopyrum ponticum Podp); however, how these variations occurred was unknown. We explored the nature of these variations by cytogenetic assays and DNA profiling techniques to characterize six genetically stable somatic introgression lines. Karyotyping results show the six lines similar to their wheat parent, but GISH analysis identified the presence of a number of short introgressed tall wheatgrass chromatin segments. DNA profiling revealed many genetic and epigenetic differences, including sequences deletions, altered regulation of gene expression, changed patterns of cytosine methylation, and the reactivation of retrotransposons. Phenotypic variations appear to result from altered repetitive sequences combined with the epigenetic regulation of gene expression and/or retrotransposon transposition. The extent of genetic and epigenetic variation due to the maintenance of parent wheat cells in tissue culture was assessed and shown to be considerably lower than had been induced in the introgression lines. Asymmetric somatic hybridization provides appropriate material to explore the nature of the genetic and epigenetic variations induced by genomic shock. PMID:25670745

  16. Indigenous cattle in Sri Lanka: Production systems and genetic diversity

    International Nuclear Information System (INIS)

    feature in systems across the regions. Morphometric measurements identified the specific phenotypic characteristics resulted by geographical isolation and selective breeding. Though vary according to the regional preferences, the compact body, narrow face, small horns and humps with shades of brown and black coat colour described the indigenous cattle phenotype in general. The diversity analysis based on microsatellite genotyping indicated that indigenous cattle in Sri Lanka has a high genetic diversity with average number of alleles per locus ranging from 7.9 to 8.5. Average heterozygosity of different regions varied within a narrow range (0.72 ± 0.04 to 0.76 ± 0.03). The genetic distances (DA) between regions were low (ranged between 0.085 and 0.066) suggesting a similar mixture of genotypes across regions despite the geographical isolation. However, two genetic clusters were visible though no relationship of those clusters with the geographical distribution of different regions could be observed. Introgression of taurine cattle was evidenced in one of the cattle populations (NC) as suggested by the Y-specific microsatellite analysis (author)

  17. Genetic and Epigenetic Changes in Somatic Hybrid Introgression Lines Between Wheat and Tall Wheatgrass

    OpenAIRE

    Liu, Shuwei; Li, Fei; Kong, Lina; Sun, Yang; Qin, Lumin; Chen, Suiyun; Cui, Haifeng; Huang, Yinghua; Xia, Guangmin

    2015-01-01

    Broad phenotypic variations were induced in derivatives of an asymmetric somatic hybridization of bread wheat (Triticum aestivum) and tall wheatgrass (Thinopyrum ponticum Podp); however, how these variations occurred was unknown. We explored the nature of these variations by cytogenetic assays and DNA profiling techniques to characterize six genetically stable somatic introgression lines. Karyotyping results show the six lines similar to their wheat parent, but GISH analysis identified the pr...

  18. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil

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    Almeida Leonardo D

    2007-12-01

    Full Text Available Abstract Background Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists on the Brazilian Creole breeds very little is known on their genetic composition. The objective of this study was to assess the levels of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture among ten cattle breeds raised in Brazil. Results Significant reduction of heterozygosity exists due both to within-population inbreeding and to breed differentiation in both subspecies (taurine and zebuine. For taurine breeds the number of markers that contribute to breed differentiation is larger than for zebuine. A consistently similar number of alleles was seen in both subspecies for all microsatellites. Four Creole breeds were the most genetically diverse followed by the zebuine breeds, the two specialized taurine breeds and the Creole Caracu. Pairwise genetic differentiation were all significant indicating that all breeds can be considered as genetically independent entities. A STRUCTURE based diagram indicated introgression of indicine genes in the local Creole breeds and suggested that occasional Creole introgression can be detected in some Zebuine animals. Conclusion This study reports on a comprehensive study of the genetic structure and diversity of cattle breeds in Brazil. A significant amount of genetic variation is maintained in the local cattle populations. The genetic data show that Brazilian Creole breeds constitute an important and diverse reservoir of genetic diversity for bovine breeding and conservation. The

  19. A deterministic model of admixture and genetic introgression: the case of Neanderthal and Cro-Magnon.

    Science.gov (United States)

    Forhan, Gerald; Martiel, Jean-Louis; Blum, Michael G B

    2008-11-01

    There is an ongoing debate in the field of human evolution about the possible contribution of Neanderthals to the modern human gene pool. To study how the Neanderthal private alleles may have spread over the genes of Homo sapiens, we propose a deterministic model based on recursive equations and ordinary differential equations. If the Neanderthal population was large compared to the Homo sapiens population at the beginning of the contact period, we show that genetic introgression should have been fast and complete meaning that most of the Neanderthal private alleles should be found in the modern human gene pool in case of ancient admixture. In order to test/reject ancient admixture from genome-wide data, we incorporate the model of genetic introgression into a statistical hypothesis-testing framework. We show that the power to reject ancient admixture increases as the ratio, at the time of putative admixture, of the population size of Homo sapiens over that of Neanderthal decreases. We find that the power to reject ancient admixture might be particularly low if the population size of Homo sapiens was comparable to the Neanderthal population size. PMID:18768141

  20. Genetic diversity and elite gene introgression reveal the japonica rice breeding in northern China

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    LIU Dan; WANG Jia-yu; WANG Xiao-xue; YANG Xian-li; SUN Jian; CHEN Wen-fu

    2015-01-01

    Abundant genetic diversity and rational population structure of germplasm beneift crop breeding greatly. To investigate genetic variation among geographical y diverse set of japonica germplasm, we analyzed 233 japonica rice cultivars col-lected from Liaoning, Jilin and Heilongjiang provinces of China, which were released from 1970 to 2011 by using 62 simple sequence repeat (SSR) markers and 8 functional gene tags related to yield. A total of 195 al eles (Na) were detected with an average of 3.61 per locus, indicating a low level of genetic diversity level among al individuals. The genetic diversity of the cultivars from Jilin Province was the highest among the three geographic distribution zones. Moreover, the genetic diversity was increased slightly with the released period of cultivars from 1970 to 2011. The analysis of molecular variance (AMOVA) revealed that genetic differentiation was more diverse within the populations than that among the populations. The neighbor-joining (NJ) tree indicated that cultivar clusters based on geographic distribution represented three independent groups, among which the cluster of cultivars from Heilongjiang is distinctly different to the cluster of cultivars from Liaoning. For the examined functional genes, two or three al elic variations for each were detected, except for IPA1 and GW2, and most of elite genes had been introgressed in modern japonica rice varieties. These results provide a valuable evaluation for genetic backgrounds of current japonica rice and wil be used directly for japonica rice breeding in future.

  1. Analysis of genetic diversity and population structure in Argentine and Bolivian Creole cattle using five loci related to milk production

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    Lirón J.P.

    2002-01-01

    Full Text Available Data from five protein-coding loci related to dairy production were used to study the genetic diversity and population structure of Argentine and Bolivian Creole cattle breeds. Genomic DNA was extracted from blood samples of six Creole cattle breeds: Argentine (n = 230, Patagonian (n = 25; "Saavedreño" (n = 140, "Chaqueño Boliviano" (n = 30, "Yacumeño" (n = 27, and "Chusco" (n = 11. kappa-casein, beta-lactoglobulin, growth hormone and prolactin were measured by PCR-RFLP, while alphaS1-casein was typed by PCR-ASO. The results are discussed, focusing on: historical origin, recent differentiation and selection events, Zebu gene introgression, and population structure. This work shows that: (i For the studied genes, the observed gene frequency profiles of Argentine and Bolivian Creole cattle breeds were close to the data reported for Iberian breeds and for other South-American Creole cattle breeds which are historically related; (ii although Zebu gene introgression has been reported at the studied loci, these breeds seem to be far from the Zebu gene frequency profiles; and (iii the Argentine and Bolivian Creole cattle showed significant levels of subdivision, but each population has maintained its degree of genetic variability.

  2. The eastern migratory caribou: the role of genetic introgression in ecotype evolution

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    Klütsch, Cornelya F. C.; Manseau, Micheline; Trim, Vicki; Polfus, Jean; Wilson, Paul J.

    2016-01-01

    Understanding the evolutionary history of contemporary animal groups is essential for conservation and management of endangered species like caribou (Rangifer tarandus). In central Canada, the ranges of two caribou subspecies (barren-ground/woodland caribou) and two woodland caribou ecotypes (boreal/eastern migratory) overlap. Our objectives were to reconstruct the evolutionary history of the eastern migratory ecotype and to assess the potential role of introgression in ecotype evolution. STRUCTURE analyses identified five higher order groups (i.e. three boreal caribou populations, eastern migratory ecotype and barren-ground). The evolutionary history of the eastern migratory ecotype was best explained by an early genetic introgression from barren-ground into a woodland caribou lineage during the Late Pleistocene and subsequent divergence of the eastern migratory ecotype during the Holocene. These results are consistent with the retreat of the Laurentide ice sheet and the colonization of the Hudson Bay coastal areas subsequent to the establishment of forest tundra vegetation approximately 7000 years ago. This historical reconstruction of the eastern migratory ecotype further supports its current classification as a conservation unit, specifically a Designatable Unit, under Canada’s Species at Risk Act. These findings have implications for other sub-specific contact zones for caribou and other North American species in conservation unit delineation. PMID:26998320

  3. The complex biogeography of the plant pathogen Xylella fastidiosa: genetic evidence of introductions and Subspecific introgression in Central America.

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    Leonard Nunney

    Full Text Available The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST of isolates from Costa Rica. Six (five from oleander, one from coffee defined a new sequence type (ST53 that carried alleles at six of the eight loci sequenced (five of the seven MLST loci diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa.

  4. The complex biogeography of the plant pathogen Xylella fastidiosa: genetic evidence of introductions and Subspecific introgression in Central America.

    Science.gov (United States)

    Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A; Ruiz Sánchez, Rebeca; Stouthamer, Richard

    2014-01-01

    The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa. PMID:25379725

  5. Genetics of hybrid inviability and sterility in Drosophila: dissection of introgression of D. simulans genes in D. melanogaster genome.

    Science.gov (United States)

    Sawamura, Kyoichi; Karr, Timothy L; Yamamoto, Masa-Toshi

    2004-03-01

    Interspecific crosses between Drosophila melanogaster and Drosophila simulans usually produce sterile unisexual hybrids. The barrier preventing genetic analysis of hybrid inviability and sterility has been taken away by the discovery of a D. simulans strain which produces fertile female hybrids. D. simulans genes in the cytological locations of 21A1 to 22C1-23B1 and 30F3-31C5 to 36A2-7 have been introgressed into the D. melanogaster genetic background by consecutive backcrosses. Flies heterozygous for the introgression are fertile, while homozygotes are sterile both in females and males. The genes responsible for the sterility have been mapped in the introgression. The male sterility is caused by the synergistic effect of multiple genes, while the female sterility genes have been localized to a 170 kb region (32D2 to 32E4) containing 20 open reading frames. Thus, the female sterility might be attributed to a single gene with a large effect. We have also found that the Lethal hybrid rescue mutation which prevents the inviability of male hybrids from the cross of D. melanogaster females and D. simulans males cannot rescue those carrying the introgression, suggesting that D. simulans genes maybe non-functional in this hybrid genotype. The genes responsible for the inviability have not been separated from the female sterility genes by recombination.

  6. Adaptive introgression as a resource for management and genetic conservation in a changing climate.

    Science.gov (United States)

    Hamilton, Jill A; Miller, Joshua M

    2016-02-01

    Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species' and populations' ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species' ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced-generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate.

  7. Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid

    Directory of Open Access Journals (Sweden)

    Glaszmann Jean-Christophe

    2009-08-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is widely used as a food and cash crop around the world. It is considered to be an allotetraploid (2n = 4x = 40 originated from a single hybridization event between two wild diploids. The most probable hypothesis gave A. duranensis as the wild donor of the A genome and A. ipaënsis as the wild donor of the B genome. A low level of molecular polymorphism is found in cultivated germplasm and up to date few genetic linkage maps have been published. The utilization of wild germplasm in breeding programs has received little attention due to the reproductive barriers between wild and cultivated species and to the technical difficulties encountered in making large number of crosses. We report here the development of a SSR based genetic map and the analysis of genome-wide segment introgressions into the background of a cultivated variety through the utilization of a synthetic amphidiploid between A. duranensis and A. ipaënsis. Results Two hundred ninety eight (298 loci were mapped in 21 linkage groups (LGs, spanning a total map distance of 1843.7 cM with an average distance of 6.1 cM between adjacent markers. The level of polymorphism observed between the parent of the amphidiploid and the cultivated variety is consistent with A. duranensis and A. ipaënsis being the most probable donor of the A and B genomes respectively. The synteny analysis between the A and B genomes revealed an overall good collinearity of the homeologous LGs. The comparison with the diploid and tetraploid maps shed new light on the evolutionary forces that contributed to the divergence of the A and B genome species and raised the question of the classification of the B genome species. Structural modifications such as chromosomal segment inversions and a major translocation event prior to the tetraploidisation of the cultivated species were revealed. Marker assisted selection of BC1F1 and then BC2F1 lines carrying the desirable donor

  8. Genetic Dissection of Low Phosphorus Tolerance Related Traits Using Selected Introgression Lines in Rice

    Institute of Scientific and Technical Information of China (English)

    XIANG Chao; PANG Yun-long; GAO Yong-ming; SHI Ying-yao; REN Jie; ZHAO Xiu-qin; DING Zai-song; ZHANG Jing; WANG Chao; ZHANGJun-wei; Charles Augustino JOSEPH; ZHANG Qiang

    2015-01-01

    To dissect the genetic basis of low phosphorus tolerance (LPT), 114 BC2F4 introgression lines (ILs) were developed from Shuhui 527 and Minghui 86 (recurrent parents), and Yetuozai (donor parent). The progenies were tested for 11 quantitative traits under three treatments including normal fertilization in normal soil (as control), normal fertilization in barren soil and low phosphorus stress in barren soil in Langfang, Hebei Province, China. Moreover, the ILs were investigated at the seedling stage using nutrient solution culture method in greenhouse in Beijing, China. A total of 49 main-effect quantitative trait loci (QTLs) underlying yield related traits were identified in Langfang, and their contributions to phenotypic variations ranged from 6.7% to 16.5%. Among them, 25 (51.0%) QTLs had favorable alleles from donor parent. A total of 48 main-effect QTLs were identified for LPT-related traits in Beijing, and their contributions to phenotypic variations ranged from 7.7% to 16.6%. Among them, 21 (43.8%) QTLs had favorable alleles from donor parent. About 79.6% of the QTLs can be detected repeatedly under two or more treatments, especially QTLs associated with spikelet number per panicle, spikelet fertility and 1000-grain weight, displaying consistent phenotypic effects. Among all the detected QTLs, eight QTLs were simultaneously identified under low phosphorus stress across two environments. These results can provide useful information for the genetic dissection of LPT in rice.

  9. Genetic Analysis of Kernel Traits in Maize-Teosinte Introgression Populations

    Directory of Open Access Journals (Sweden)

    Zhengbin Liu

    2016-08-01

    Full Text Available Seed traits have been targeted by human selection during the domestication of crop species as a way to increase the caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays kernel weight has increased more than 10-fold in the 9000 years since domestication from its wild ancestor, teosinte (Z. mays ssp. parviglumis. In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of 10 maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTL for kernel area and length with moderate allelic effects that colocalize with kernel weight QTL. Several genomic regions with strong effects during maize domestication were detected, and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects, enabling future research into the genetic basis of these traits.

  10. Detection of genetic diversity and selective gene introgression in coffee using RAPD markers.

    Science.gov (United States)

    Orozco-Castillo, C; Chalmers, K J; Waugh, R; Powell, W

    1994-03-01

    RAPD (randomly amplified polymorphic DNA) markers generated by arbitary decamers have been successfully employed to detect genetic polymorphisms between coffee species and between Coffea arabica genotypes. The RAPD profiles were used to construct dendrograms and these were consistent with the known history and evolution of Coffea arabica. Material originating from Ethiopia and the arabica sub-groups - C. arabica var. typica and C. arabica var. bourbon - were clearly distinguished. RAPD analysis therefore reflects morphological differences between the sub-groups and the geographical origin of the coffee material. Species-specific amplification products were also identified, but, more importantly, amplification products specific to C. canephora were identified in two C. arabica genotypes, Rume Sudan and Catimor 5175. This diagnostic product is therefore indicative of interspecific gene flow in coffee and has biological implications for selective introgressive hybridisation in coffee. Our study demonstrates the power of the polymerase chain reaction technology for the generation of genetic markers for long-lived perennial tree and bush crops. PMID:24190527

  11. The Genetic Diversity and Phylogenetic Status of Luxi Cattle

    Institute of Scientific and Technical Information of China (English)

    MAO Yong-jiang; CHANG Hong; YANG Zhang-ping; XU Ming; ZHANG Liu; CHANG Guo-bin; SONG Wei-tao; WANG Dong-lei

    2006-01-01

    A total of 87 individuals of Luxi cattle from Juanchen and Liangshan counties, Shangdong Province, China, were sampled by simple random sampling in typical colony. Twenty-one blood proteins and enzymes loci were detected by polyacrylamide gel electrophoresis (PAGE) and starch gel electrophoresis (SGE). In the meantime, the data of 7 loci of 13 cattle populations in China and other countries were collected and phylogeny relationships were studied. The results indicated that 9 out of 21 loci showed polymorphism (42.86%); the level of genetic variation in Luxi cattle population was relatively high, the mean heterozygosity was 0.1416. The Luxi cattle have a close phylogenetic relationship with the cattle populations of east and south of Asia, and this further confirmed the fact that Luxi cattle were the cross-breed between the Bos taurus and Bos indicus in China, but it is impossible that yellow cattle contained the blood of of Bali.

  12. Genetic diversity and relationship of Yunnan native cattle breeds and introduced beef cattle breeds.

    Science.gov (United States)

    Yu, Ying; Lian, Lin-Sheng; Wen, Ji-Kun; Shi, Xian-Wei; Zhu, Fang-Xian; Nie, Long; Zhang, Ya-Ping

    2004-02-01

    In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and relationship in 134 samples belonging to two native cattle breeds from the Yunnan province of China (DeHong cattle and DiQing cattle) and four introduced beef cattle breeds (Brahman, Simmental, MurryGrey, and ShortHorn). Ten primers were used, and a total of 84 bands were scored, of which 63 bands (75.0%) were polymorphic. The genetic distance matrix was obtained by proportions of shared fragment. The results indicate that the Yunnnan DeHong cattle breed is closely related to the Brahman (Bos indicus), and the Yunnan DiQing cattle breed is closely related to the Simmental, ShortHorn, and MurryGrey (Bos taurus) breeds. Our results imply that Bos indicus and Bos taurus were the two main origins of Yunnan native cattle. The results also provide the basic genetic materials for conservation of cattle resources and crossbreeding of beef cattle breeds in South China. PMID:15068334

  13. Genetic background of claw health in dairy cattle

    NARCIS (Netherlands)

    Spek, van der D.

    2015-01-01

    Abstract Van der Spek, D. (2015). Genetic background of claw health in dairy cattle. PhD thesis, Wageningen University, the Netherlands. Claw disorders affect cow welfare and profitability of farms and as such are important traits relevant to dairy cattle breeding. Aim of this thesi

  14. Genetic diversity in mazandaranian native cattle: a comparison with Holstein cattle, using ISSR marker.

    Science.gov (United States)

    Pashaei, S; Azari, M A; Hasani, S; Khanahmadi, A; Rostamzadeh, J

    2009-05-01

    This study was carried out to investigate genetic diversity in Mazandaranian native cattle population comparised to the Holstein breed, using Inter Simple Sequence Repeats (ISSR) marker. A total of 175 animals, including 71 native and 104 cattle of Holstein breed were screened. The extraction of DNA samples were carried out, using modified salting out method. A 19-mer oligonucleotide, (GA)9C, was used as primer in PCR reactions. The PCR products showed 15 different fragments with length ranged from 120 to 1600 bp in the two breeds.. Genetic variation indexes, including effective number of alleles, Shannon index, Nei's gene diversity and standard genetic distance were estimated, using POPGene software. Generally, the estimated genetic variation indexes showed low levels of diversity in the two breeds. However, Nei's gene diversity and Shannon index estimation was observed almost two folds in native cattle compared to Holstein breed. Less levels of diversity in Holstein cattle may be because of applying intensive selection programs. Conversely, native cattle have been less affected by selection. Therefore, it seems that Mazandaranian native cattle probably are better for breeding programs than Holstein cattle. Results showed that ISSR Markers are reliable and can be used in genetic diversity investigations. PMID:19634477

  15. Commercial aspects of cloning and genetic modification in cattle

    DEFF Research Database (Denmark)

    Lewis, I M; French, A J; Tecirlioglu, R T;

    2004-01-01

    A range of potential commercial applications of cloning and genetic modification in cattle has been suggested over the last decade. It includes the rapid multiplication of elite genotypes, production of valuable human proteins, altered production characteristics, increased disease resistance...

  16. Heritability and genetic advance studies for biochemical traits in F2-3 introgressed families of Brassica

    International Nuclear Information System (INIS)

    Higher heritability estimates along with high genetic advance values are effective in envisaging gain under selection in developing genotypes. The objective of the present study was to evaluate variability, heritability and genetic advance in 10 interspecific F2-3 families of Brassica species (B. napus * B. juncea, B. napus * B. rapa). These families were studied for heterospecific introgression of biochemical traits. Low to high heritability estimates were recorded for seed quality traits. Considerable variations within F2-3 families were observed for biochemical traits. Most of the F2-3 families for oil content and erucic showed moderate to high heritability indicating the slightest influence of environment thus modification of trait by selection would be more effective. Among F2-3 introgressed families Bn-510 x Bj-109 produced high oil i.e., 49.5% while Bn-532 x Br-118 (24.4%), Bn-533 x Bj-109 (24.1%) and high protein percentage in terms of mean performance. In the present research, individual segregating progenies of interspecific cross populations i.e., which possessed combination of desirable traits, were identified which could be incorporated in the future Breeding programs and it may facilitate varietal development. (author)

  17. Interspecific Hybridization in Pilot Whales and Asymmetric Genetic Introgression in Northern Globicephala melas under the Scenario of Global Warming.

    Science.gov (United States)

    Miralles, Laura; Oremus, Marc; Silva, Mónica A; Planes, Serge; Garcia-Vazquez, Eva

    2016-01-01

    Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas. PMID:27508496

  18. Introgression of genetic material from Zea mays ssp. Mexicana into cultivated maize was facilitated by tissue culture

    International Nuclear Information System (INIS)

    Zea mays ssp. mexicana, a wild relative of cultivated maize (Z. mays ssp. mays), is a useful gene resource for maize breeding. In this study, two populations were generated by conventional breeding scheme (population I) or tissue culture regime (population II), respectively, to introgress genetic material of Z. mays ssp. mexicana into maize. Karyotype analysis showed that the arm ratios of 10 pairs of chromosomes in parent maize Ye515 and derivative lines from 2 different populations with 26% and 38% chromosome variation frequencies, respectively. Alien chromatin was detected in the root tip cells of progeny plants through genomic in situ hybridization (GISH). There were 3.3 chromosomes carrying alien chromatin on average in population I and 6.5 in population II. The hybridization signals were located mainly at the terminal or sub terminal regions of the chromosomes and the sizes were notably variant among lines. Based on those results, it is concluded that the introgression of genetic material from Z. mays ssp. mexicana into cultivated maize was facilitated by tissue culture, and subsequently some excellent materials for maize breeding were created. (author)

  19. Interspecific Hybridization in Pilot Whales and Asymmetric Genetic Introgression in Northern Globicephala melas under the Scenario of Global Warming

    Science.gov (United States)

    Miralles, Laura; Oremus, Marc; Silva, Mónica A.; Planes, Serge; Garcia-Vazquez, Eva

    2016-01-01

    Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas. PMID:27508496

  20. The genetic architecture of climatic adaptation of tropical cattle.

    Science.gov (United States)

    Porto-Neto, Laercio R; Reverter, Antonio; Prayaga, Kishore C; Chan, Eva K F; Johnston, David J; Hawken, Rachel J; Fordyce, Geoffry; Garcia, Jose Fernando; Sonstegard, Tad S; Bolormaa, Sunduimijid; Goddard, Michael E; Burrow, Heather M; Henshall, John M; Lehnert, Sigrid A; Barendse, William

    2014-01-01

    Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity. PMID:25419663

  1. Genetics of animal health and disease in cattle

    Directory of Open Access Journals (Sweden)

    Berry Donagh P

    2011-03-01

    Full Text Available Abstract There have been considerable recent advancements in animal breeding and genetics relevant to disease control in cattle, which can now be utilised as part of an overall programme for improved cattle health. This review summarises the contribution of genetic makeup to differences in resistance to many diseases affecting cattle. Significant genetic variation in susceptibility to disease does exist among cattle suggesting that genetic selection for improved resistance to disease will be fruitful. Deficiencies in accurately recorded data on individual animal susceptibility to disease are, however, currently hindering the inclusion of health and disease resistance traits in national breeding goals. Developments in 'omics' technologies, such as genomic selection, may help overcome some of the limitations of traditional breeding programmes and will be especially beneficial in breeding for lowly heritable disease traits that only manifest themselves following exposure to pathogens or environmental stressors in adulthood. However, access to large databases of phenotypes on health and disease will still be necessary. This review clearly shows that genetics make a significant contribution to the overall health and resistance to disease in cattle. Therefore, breeding programmes for improved animal health and disease resistance should be seen as an integral part of any overall national disease control strategy.

  2. Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact.

    Science.gov (United States)

    Le Moan, A; Gagnaire, P-A; Bonhomme, F

    2016-07-01

    Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300 kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions.

  3. Reduced SNP Panels for Genetic Identification and Introgression Analysis in the Dark Honey Bee (Apis mellifera mellifera)

    DEFF Research Database (Denmark)

    Muñoz, Irene; Henriques, Dora; Johnston, J. Spencer;

    2015-01-01

    Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m...... and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can...... individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs....

  4. Genetic and Epigenetic Alterations of Brassica nigra Introgression Lines from Somatic Hybridization: A Resource for Cauliflower Improvement.

    Science.gov (United States)

    Wang, Gui-Xiang; Lv, Jing; Zhang, Jie; Han, Shuo; Zong, Mei; Guo, Ning; Zeng, Xing-Ying; Zhang, Yue-Yun; Wang, You-Ping; Liu, Fan

    2016-01-01

    Broad phenotypic variations were obtained previously in derivatives from the asymmetric somatic hybridization of cauliflower "Korso" (Brassica oleracea var. botrytis, 2n = 18, CC genome) and black mustard "G1/1" (Brassica nigra, 2n = 16, BB genome). However, the mechanisms underlying these variations were unknown. In this study, 28 putative introgression lines (ILs) were pre-selected according to a series of morphological (leaf shape and color, plant height and branching, curd features, and flower traits) and physiological (black rot/club root resistance) characters. Multi-color fluorescence in situ hybridization revealed that these plants contained 18 chromosomes derived from "Korso." Molecular marker (65 simple sequence repeats and 77 amplified fragment length polymorphisms) analysis identified the presence of "G1/1" DNA segments (average 7.5%). Additionally, DNA profiling revealed many genetic and epigenetic differences among the ILs, including sequence alterations, deletions, and variation in patterns of cytosine methylation. The frequency of fragments lost (5.1%) was higher than presence of novel bands (1.4%), and the presence of fragments specific to Brassica carinata (BBCC 2n = 34) were common (average 15.5%). Methylation-sensitive amplified polymorphism analysis indicated that methylation changes were common and that hypermethylation (12.4%) was more frequent than hypomethylation (4.8%). Our results suggested that asymmetric somatic hybridization and alien DNA introgression induced genetic and epigenetic alterations. Thus, these ILs represent an important, novel germplasm resource for cauliflower improvement that can be mined for diverse traits of interest to breeders and researchers. PMID:27625659

  5. On the history of cattle genetic resources

    NARCIS (Netherlands)

    Felius, Marleen; Beerling, Marie Louise; Buchanan, David S.; Theunissen, Bert; Koolmees, Peter A.; Lenstra, Johannes A.

    2014-01-01

    Cattle are our most important livestock species because of their production and role in human culture. Many breeds that differ in appearance, performance and environmental adaptation are kept on all inhabited continents, but the historic origin of the diverse phenotypes is not always clear. We give

  6. Criollo cattle: Heritage genetics for arid landscapes

    Science.gov (United States)

    Thirty cows and three bulls from the Chinipas region in the state of Chihuahua, Mexico, were introduced onto the US Department of Agriculture – Agricultural Research Service’s Jornada Experimental Range (JER) in 2005. Since then behavioral research has revealed these cattle, most accurately referre...

  7. Generation of a multi-locus chicken introgression line to study the effects of genetic interactions on metabolic phenotypes in chickens

    Directory of Open Access Journals (Sweden)

    Weronica eEk

    2012-03-01

    Full Text Available Most biological traits are regulated by a complex interplay between genetic and environmental factors. By intercrossing divergent lines, it is possible to identify individual and interacting QTL involved in the genetic architecture of these traits. When the loci have been mapped, alternative strategies are needed for fine-mapping and studying the individual and interactive effects of the QTL in detail. We have previously identified, replicated and fine-mapped a four-locus QTL network that determines nearly half of the eight-fold difference in body-weight at 56 days of age between two divergently selected chicken lines. Here, we describe, to our knowledge, the first generation of a three-locus QTL introgression line in chickens to further study the effect of three of the interacting loci in this network on metabolic phenotypes. Recurrent marker assisted backcrossing was used to simultaneously transfer QTL alleles from the low-weight selected line into the high-weight selected line. Three generations of backcrossing and one generation of intercrossing resulted in an introgression line where all three introgressed QTL and several unlinked and linked control-loci were segregating at nearly expected allele frequencies. We show that marker-based sexing is an efficient method for sexing breeding populations and how intensive selection can be applied using artificial insemination to generate large half-sib families. Based on our empirical observations, we provide recommendations for future introgression-line breeding experiments. In the future, use of this confirmed introgression line will facilitate detailed studies of the effects of genetic interactions on complex traits.

  8. Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact.

    Science.gov (United States)

    Le Moan, A; Gagnaire, P-A; Bonhomme, F

    2016-07-01

    Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300 kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions. PMID:27027737

  9. Genetic dissection of tetraploid cotton resistant to Verticillium wilt using interspecific chromosome segment introgression lines

    Institute of Scientific and Technical Information of China (English)

    Peng; Wang; Zhiyuan; Ning; Ling; Lin; Hong; Chen; Hongxian; Mei; Jun; Zhao; Bingliang; Liu; Xin; Zhang; Wangzhen; Guo; Tianzhen; Zhang

    2014-01-01

    Verticillium wilt(caused by the pathogen Verticillium dahliae) is of high concern for cotton producers and consumers. The major strategy for controlling this disease is the development of resistant cotton(Gossypium spp.) cultivars. We used interspecific chromosome segment introgression lines(CSILs) to identify quantitative trait loci(QTL) associated with resistance to Verticillium wilt in cotton grown in greenhouse and inoculated with three defoliating V. dahliae isolates. A total of 42 QTL, including 23 with resistance-increasing and 19 with resistancedecreasing, influenced host resistance against the three isolates. These QTL were identified and mapped on 18 chromosomes(chromosomes A1, A3, A4, A5, A7, A8, A9, A12, A13, D1, D2,D3, D4, D5, D7, D8, D11, and D12), with LOD values ranging from 3.00 to 9.29. Among the positive QTL with resistance-increasing effect, 21 conferred resistance to only one V. dahliae isolate, suggesting that resistance to V. dahliae conferred by most QTL is pathogen isolate-specific. The At subgenome of cotton had greater effect on resistance to Verticillium wilt than the Dt subgenome. We conclude that pyramiding different resistant QTL could be used to breed cotton cultivars with broad-spectrum resistance to Verticillium wilt.

  10. Mining of lethal recessive genetic variation in Danish cattle

    DEFF Research Database (Denmark)

    Das, Ashutosh

    2015-01-01

    The widespread use of artificial insemination in cattle breeding Worldwide leads to reduced effective population sizes and increased inbreeding levels. Increased inbreeding result in increased probalility of expression of recessive defective alleles, which probably is reflected in a decline...... in fertility. The primary objective of this PhD projekt was to identify recessive lethal gentic variants in the main Danish dairy cattle breed. Holstein-Friesian utilzing next generation sequencing (NGS) data. This study shows a potential for the use of the NGS-based reverse genetic approach in identifying...... lethal or semi-lethal recessive gentic variation...

  11. Genetic Architecture of clinical mastitis traits in dairy cattle

    DEFF Research Database (Denmark)

    Sahana, Goutam; Guldbrandtsen, Bernt; Lund, Mogens Sandø

    2012-01-01

    investigate the genetic architecture of clinical mastitis and somatic cell score traits in dairy cattle using a high density (HD) SNP panel. Mastitis, an inflammation of the mammary gland most commonly caused by bacterial infection, is a frequent disease in dairy cattle. Clinical mastitis and somatic cell...... mixed model analysis. After Bonferroni correction 12, 372 SNP exhibited genome-wide significant associations with mastitis related traits. A total 61 QTL regions on 22 chromosomes associated with mastitis related traits were identified. The SNP with highest effect explained 5.6% of the variance...... of the predicted breeding values for the first lactation clinical mastitis...

  12. National Genetic Evaluation (System) of Hanwoo (Korean Native Cattle)

    OpenAIRE

    Park, B; Choi, T; Kim, S.; Oh, S.-H.

    2013-01-01

    Hanwoo (Also known as Korean native cattle; Bos taurus coreanae) have been used for transportation and farming for a long time in South Korea. It has been about 30 yrs since Hanwoo improvement began in earnest as beef cattle for meat yield. The purpose of this study was to determine the trend of improvement as well as to estimate genetic parameters of the traits being used for seedstock selection based on the data collected from the past. Hanwoo proven bulls in South Korea are currently selec...

  13. International genetic evaluation for fertility traits in dairy cattle

    Directory of Open Access Journals (Sweden)

    F. Canavesi

    2010-04-01

    Full Text Available The objective of this study was to review and discuss the results of the first international evaluation for female fertility of Holstein dairy cattle. Fifteen countries, including Italy, provided breeding values of bulls and joined the evaluation. Four trait groups were used to analyze animal’s ability to became pregnant and animal’s ability to recycle after calving. Italy submitted three traits: days to first service (DTFS, non-return rate at 56 days (NR56 and calving interval (CI. Genetic correlation between Italy and the other countries ranged from 0.72 to 0.94 for DTFS, from 0.25 to 0.90 for NR56 and from 0.67 to 0.87 for CI. Results represent another step forward in the international trade of dairy cattle genetic material.

  14. Multivariate Outlier Detection in Genetic Evaluation in Nordic Jersey Cattle

    OpenAIRE

    Gao, Hongding; Madsen, Per; Pösö, Jukka; Pedersen, Jørn; Lidauer, Martin H; Jensen, Just

    2014-01-01

    A procedure was developed for detection of multivariate outliers based on an approximation for Mahanalobis Distance (MD) and was implemented in the Nordic Jersey population. Evaluations are carried out by Nordic Cattle Genetic Evaluation (NAV), who uses a 9 trait model for milk, protein and fat in the first 3 lactations. It is based on the phenotypic correlation structure as a function of days in milk (DIM) and on computation of trait means and standard deviations (SDs) within classes of prod...

  15. Genetic polymorphism of milk protein loci in Argentinian Holstein cattle

    Directory of Open Access Journals (Sweden)

    Bonvillani Adriana Gloria

    2000-01-01

    Full Text Available Some alleles of milk protein loci are associated with superior cheese production characteristics. The genetic polymorphism of the milk protein loci alphas1-casein, beta-casein, k-casein and beta-lactoglobulin was examined in Argentinian Holstein cattle. Samples from 12 herds of four regions of Córdoba were analyzed by starch gel electrophoresis. The chi² test was used to assess whether the populations were in Hardy-Weinberg equilibrium. Genotypic diversity was analyzed by the Shannon-Weaver index. The observed genotypic frequencies were analyzed by Hedrick's genetic identity and the genetic distance of Balakrishnan and Sanghvi. The allelic and genotypic frequencies were similar to those of other Holstein populations. The genotypic frequencies of the alphas1-casein and beta-casein loci were in equilibrium, whereas in some populations the k-casein and beta-lactoglobulin loci were not. According to the Shannon-Weaver index the total genetic diversity within each herd was greater than 96%. The high values of identity agreed with the low genetic distances among populations. We conclude that there is extensive genetic homogeneity in Holstein cattle in Córdoba Province and that it would be feasible to select for B alleles at the k-casein and b-lactoglobulin loci in order to improve the quality of milk available for cheese manufacturing.

  16. Introgression and genetic characterization of alien Fusarium head blight resistance in wheat

    Science.gov (United States)

    Alien species are an important source of genetic variability in wheat (Triticum spp.) and carry genes for resistance to numerous pathogens, including Fusarium graminearum Schwabe, the causal agent of Fusarium head blight (FHB). The goal of this project was to develop breeder-friendly, FHB-resistant ...

  17. Genetic diversity studies of Kherigarh cattle based on microsatellite markers

    Indian Academy of Sciences (India)

    A. K. Pandey; Rekha Sharma; Yatender Singh; B. B. Prakash; S. P. S. Ahlawat

    2006-08-01

    We report a genetic diversity study of Kherigarh cattle, a utility draught-purpose breed of India, currently declining at a startling rate, by use of microsatellite markers recommended by the Food and Agriculture Organization. Microsatellite genotypes were derived, and allelic and genotypic frequencies, heterozygosities and gene diversity were estimated. A total of 131 alleles were distinguished by the 21 microsatellite markers used. All the microsatellites were highly polymorphic, with mean (± s.e.) allelic number of 6.24 ± 1.7, ranging 4–10 per locus. The observed heterozygosity in the population ranged between 0.261 and 0.809, with mean (± s.e.) of 0.574 ± 0.131, indicating considerable genetic variation in this population. Genetic bottleneck hypotheses were also explored. Our data suggest that the Kherigarh breed has not experienced a genetic bottleneck in the recent past.

  18. Rangewide genetic analysis of Lesser Prairie-Chicken reveals population structure, range expansion, and possible introgression

    Science.gov (United States)

    Oyler-McCance, Sara J.; DeYoung, Randall W; Fike, Jennifer; Hagen, Christian A.; Johnson, Jeff A.; Larsson, Lena C; Patten, Michael

    2016-01-01

    The distribution of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) has been markedly reduced due to loss and fragmentation of habitat. Portions of the historical range, however, have been recolonized and even expanded due to planting of conservation reserve program (CRP) fields that provide favorable vegetation structure for Lesser Prairie-Chickens. The source population(s) feeding the range expansion is unknown, yet has resulted in overlap between Lesser and Greater Prairie-Chickens (T. cupido) increasing the potential for hybridization. Our objectives were to characterize connectivity and genetic diversity among populations, identify source population(s) of recent range expansion, and examine hybridization with the Greater Prairie-Chicken. We analyzed 640 samples from across the range using 13 microsatellites. We identified three to four populations corresponding largely to ecoregions. The Shinnery Oak Prairie and Sand Sagebrush Prairie represented genetically distinct populations (F ST > 0.034 and F ST > 0.023 respectively). The Shortgrass/CRP Mosaic and Mixed Grass ecoregions appeared admixed (F ST = 0.009). Genetic diversity was similar among ecoregions and N e ranged from 142 (95 % CI 99–236) for the Shortgrass/CRP Mosaic to 296 (95 % CI 233–396) in the Mixed Grass Prairie. No recent migration was detected among ecoregions, except asymmetric dispersal from both the Mixed Grass Prairie and to a lesser extent the Sand Sagebrush Prairie north into adjacent Shortgrass/CRP Mosaic (m = 0.207, 95 % CI 0.116–0.298, m = 0.097, 95 % CI 0.010–0.183, respectively). Indices investigating potential hybridization in the Shortgrass/CRP Mosaic revealed that six of the 13 individuals with hybrid phenotypes were significantly admixed suggesting hybridization. Continued monitoring of diversity within and among ecoregions is warranted as are actions promoting genetic connectivity and range expansion.

  19. Partitioning of Genetic Trends by Origin in Croatian Simmental Cattle

    Directory of Open Access Journals (Sweden)

    Marija Špehar

    2011-12-01

    Full Text Available The objective of this study was to partition genetic trend for milk (protein yield and meat (net daily gain traits by the origin of selection in Croatian Simmental cattle. In order to evaluate overall genetic trend, breeding values were averaged by the year of birth and origin. Origin was defined as a country where animal was initially registered. Overall genetic trend for protein yield was positive. The relative effect of three origins on the overall genetic trend for protein yield was 43.5% for Germany, 33.9% for Croatia, and 22.1% for Austria at the end of analysed period. Genetic trend for net daily gain was also positive. The Croatian and German partitions had large contribution to the overall genetic trend, while small partition was attributed to the Austrian origin. At the end of analysed period, the relative effect of these three origins on the overall genetic trend for net daily gain was 57.0% for Croatia, 38.5% for Germany, and 4.5% for Austria. Selection work originated from Austria, Croatia, and Germany had effect on genetic trend in Croatia. Other origins did not contribute notably to the overall genetic trend of both traits.

  20. Partitioning of Genetic Trends by Origin in Croatian Simmental Cattle

    Directory of Open Access Journals (Sweden)

    Marija Špehar

    2011-10-01

    Full Text Available The objective of this study was to partition genetic trend for milk (protein yield and meat (net daily gain traits by the origin of selection in Croatian Simmental cattle. In order to evaluate overall genetic trend, breeding values were averaged by the year of birth and origin. Origin was defined as a country where animal was initially registered. Overall genetic trend for protein yield was positive. The relative effect of three origins on the overall genetic trend for protein yield was 43.5% for Germany, 33.9% for Croatia, and 22.1% for Austria at the end of analysed period. Genetic trend for net daily gain was also positive. The Croatian and German partitions had large contribution to the overall genetic trend, while small partition was attributed to the Austrian origin. At the end of analysed period, the relative effect of these three origins on the overall genetic trend for net daily gain was 57.0% for Croatia, 38.5% for Germany, and 4.5% for Austria. Selection work originated from Austria, Croatia, and Germany had effect on genetic trend in Croatia. Other origins did not contribute notably to the overall genetic trend of both traits.

  1. Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice

    Institute of Scientific and Technical Information of China (English)

    ZANG JinPing; XU JianLong; LI ZhiKang; SUN Yong; WANG Yun; YANG Jing; LI Fang; ZHOU YongLi; ZHU LingHua; Reys JESSICA; Fotokian MOHAMMADHOSEIN

    2008-01-01

    QTLs for salt-tolerance (ST) related traits at the seedling and tillering stages were identified using 99 BC2F8 introgression lines (IL) derived from a cross between IR64 (indica) as a recurrent parent and Bi-nam (japonica) from Iran as the donor parent. Thirteen QTLs affecting survival days of seedlings (SDS), score of salt toxicity of leaves (SST), shoot K+ concentration (SKC) and shoot Na+ concentration (SNC) at the seedling stage and 22 QTLs underlying fresh weight of shoots (FW), tiller number per plant (TN) and plant height (PH) at the tillering stage were identified. Most QTLs detected at the tillering stage showed obvious differential expression to salt stress and were classified into three types based on their differential behaviors. Type Ⅰ included 11 QTLs which were expressed only under the non-stress condition. Type Ⅱ included five QTLs expressed in the control and the salt stress conditions, and three of them (QPh5, QPh8 and QTn9) had similar quantity and the same direction of gene effect, suggesting their expression was less influenced by salt stress. Type Ⅲ included six QTLs which were detectable only under salt stress, suggesting that these QTLs were apparently induced by the stress. Thirteen QTLs affecting trait difference or trait stability of Ils between the stress and non-stress conditions were identified and the Binam alleles at all loci except QPh4, QTn2 and QFw2a decreased trait difference. The three QTLs less influenced by the stress and 13 QTLs affecting trait stability were considered as ST QTLs which contributed to ST. Comparing the distribution of QTLs detected at the seedling and tillering stages, most (69%) of them were genetically independent. Only four were the same or adjacent regions on chromosomes 1, 2, 8 and 11 harboring ST QTLs detected at the two stages, suggesting that partial genetic overlap of ST across the two stages occurs. It is likely, therefore, to develop ST rice variety for both stages by pyramiding of ST QTLs

  2. Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    QTLs for salt-tolerance(ST)related traits at the seedling and tillering stages were identified using 99 BC2F8 introgression lines(IL)derived from a cross between IR64(indica)as a recurrent parent and Binam(japonica)from Iran as the donor parent.Thirteen QTLs affecting survival days of seedlings(SDS), score of salt toxicity of leaves(SST),shoot K + concentration(SKC)and shoot Na + concentration(SNC) at the seedling stage and 22 QTLs underlying fresh weight of shoots(FW),tiller number per plant(TN) and plant height(PH)at the tillering stage were identified.Most QTLs detected at the tillering stage showed obvious differential expression to salt stress and were classified into three types based on their differential behaviors.Type I included 11 QTLs which were expressed only under the non-stress condition.Type II included five QTLs expressed in the control and the salt stress conditions,and three of them(QPh5,QPh8 and QTn9)had similar quantity and the same direction of gene effect,suggesting their expression was less influenced by salt stress.Type III included six QTLs which were detectable only under salt stress,suggesting that these QTLs were apparently induced by the stress.Thirteen QTLs affecting trait difference or trait stability of ILs between the stress and non-stress conditions were identified and the Binam alleles at all loci except QPh4,QTn2 and QFw2a decreased trait difference.The three QTLs less influenced by the stress and 13 QTLs affecting trait stability were considered as ST QTLs which contributed to ST.Comparing the distribution of QTLs detected at the seedling and tillering stages,most(69%)of them were genetically independent.Only four were the same or adjacent regions on chromosomes 1,2,8 and 11 harboring ST QTLs detected at the two stages,suggesting that partial genetic overlap of ST across the two stages occurs.It is likely,therefore,to develop ST rice variety for both stages by pyramiding of ST QTLs of different stages or selection against the

  3. Genetic characterization of Aberdeen Angus cattle using molecular markers

    Directory of Open Access Journals (Sweden)

    Vasconcellos Luciana Pimentel de Mello Klocker

    2003-01-01

    Full Text Available Aberdeen Angus beef cattle from the Brazilian herd were studied genetically using restriction fragment length polymorphism (RFLP of the kappa-casein - HinfI (CSN3 - HinfI, beta-lactoglobulin - HaeIII (LGB - HaeIII and growth hormone AluI (GH- AluI genes, as well as four microsatellites (TEXAN15, CSFM50, BM1224 and BM7160. The RFLP genotypes were determined using the polymerase chain reaction (PCR followed by digestion with restriction endonucleases and electrophoresis in agarose gels. With the exception of the microsatellite BM7160, which was analyzed in an automatic sequencer, the PCR products were genotyped by silver staining. The allele and genotype frequencies, heterozygosities and gene diversity were estimated. The values for these parameters of variability were comparable to other cattle breeds. The genetic relationship of the Aberdeen Angus to other breeds (Caracu, Canchim, Charolais, Guzerath, Gyr, Nelore, Santa Gertrudis and Simmental was investigated using Nei's genetic distance. Cluster analysis placed the Aberdeen Angus in an isolated group in the Bos taurus breeds branch. This fact is in agreement with the geographic origin of this breed.

  4. Multivariate Outlier Detection in Genetic Evaluation in Nordic Jersey Cattle

    DEFF Research Database (Denmark)

    Gao, Hongding; Madsen, Per; Pösö, Jukka;

    A procedure was developed for detection of multivariate outliers based on an approximation for Mahanalobis Distance (MD) and was implemented in the Nordic Jersey population. Evaluations are carried out by Nordic Cattle Genetic Evaluation (NAV), who uses a 9 trait model for milk, protein and fat...... in the first 3 lactations. It is based on the phenotypic correlation structure as a function of days in milk (DIM) and on computation of trait means and standard deviations (SDs) within classes of production year (PY), lactation and days in milk (DIM). For each record in the data, MD is computed based on trait...

  5. Genetic evaluation of retail product percentage in Simmental cattle.

    Science.gov (United States)

    Crews, D H; Enns, R M; Rumph, J M; Pollak, E J

    2008-02-01

    The objective of this study was to estimate genetic parameters required for genetic evaluation of retail product percentage (RPP) in Simmental cattle. Carcass weight (HCW), subcutaneous fat thickness (FAT), longissimus muscle area (REA) and kidney, pelvic, and heart fat (KPH) records were available to compute RPP on steers (n = 5171) and heifers (n = 1400) from the American Simmental Association database; animals were sired by 561 Simmental bulls and out of 5886 crossbred dams. Genetic parameters were estimated using residual maximal likelihood and a four trait animal model for the components of RPP including fixed harvest contemporary group effects, random animal genetic effects, and a linear covariate for age at harvest. Heritability estimates were 0.51 +/- 0.05, 0.36 +/- 0.05, 0.46 +/- 0.05, and 0.18 +/- 0.05 for HCW, FAT, REA and KPH respectively. Non-zero genetic correlations were estimated between HCW and REA (rg = 0.51 +/- 0.06) and between REA and FAT (rg = -0.43 +/- 0.08), but other genetic correlation estimates among the component traits were low. As a linear function of its components, heritability and genetic correlations involving RPP were estimated using index methods. The heritability estimate for RPP was 0.41, and genetic correlations were -0.17, -0.83, 0.67, and 0.01 with HCW, FAT, REA and KPH respectively. Therefore, RPP was strongly associated with muscle and fat deposition, but essentially independent of carcass weight and internal body cavity fat. Genetic evaluation of RPP would be straightforward using multiple trait index methods and genetic regression, although the inclusion of KPH would be of marginal value. PMID:18254821

  6. Genetic parameters for pre-weaning traits in Braunvieh cattle.

    Science.gov (United States)

    Cucco, D C; Ferraz, J B S; Pinto, L F B; Eler, J P; Balieiro, J C C; Mattos, E C

    2009-01-01

    The objective of this study was to estimate genetic parameters for pre-weaning traits of Braunvieh cattle raised under tropical conditions in Brazil. The weight and weight gain parameters were birth weight (BW, N = 9955), weight at 120 days of age (W120, N = 5901), weaning weight at 205 days (WW, N = 6970), weight gain from birth to 205 days (GAIN205, N = 6013), weight gain from birth to 120 days (GAIN120, N = 5135), and weight gain from 120 to 205 days (GAIN85, N = 4482). Variance components were estimated using the animal model with the MTDFREML software. The relationship matrix included 35,188 animals; phenotypic measures were available for 18,688. Direct and maternal heritability increased from birth to weaning, with estimates of 0.23 +/- 0.037, 0.25+/- 0.050, 0.41+/- 0.059 for direct heritability for BW, W120 and WW, respectively, 0.08 +/- 0.012, 0.15 +/- 0.032, 0.22 +/- 0.036 for maternal genetic effects, and 0.18, 0.14 and 0.16 for total heritability estimates. For pre-weaning gains, estimates of heritability were 0.36 +/- 0.059, 0.30+/- 0.059, 0.12 +/- 0.035 for direct genetic effects of the traits GAIN205, GAIN120 and GAIN85, respectively, 0.23 +/- 0.038, 0.17 +/- 0.037, 0.03 +/- 0.029 for estimates of maternal heritability, and 0.12, 0.13, 0.16 for total heritability, respectively. Genetic correlations between weights were greater between measures taken at shorter intervals. This information can be used to optimize the design of programs for genetic improvement of Braunvieh cattle raised under tropical conditions.

  7. Genetic diversity in cattle of eight regions in Costa Rica.

    Directory of Open Access Journals (Sweden)

    Juan Miguel Cordero-Solórzano

    2015-06-01

    Full Text Available The aim of this study was to explore the extent of inter-regional genetic diversity present in the cattle of Costa Rica. 1498 DNA samples were collected (year 2013 from eight different regions within the country. Allelic frequencies and major population genetic parameters were determined for eighteen microsatellite markers. An analysis of molecular variance was also carried out and genetic distances were calculated between cattle from different regions. At the national level, a high allelic diversity was found, with an average of 14.6±1.01 observed alleles and 5.6+0.37 effective alleles per marker. Observed (Ho and expected (He heterozygosities were 0.76±0.01 and 0.81±01, respectively. Polymorphic Information Content (PIC and Coefficient of Inbreeding (FIS were 0.79±0.06 and 0.06±0.004, respectively. At the regional level, Ho ranged between 0.73±0.02 in the South Central region to 0.78±0.01 in the North Huetar region. The dendrogram showed three clearly distinct groups, Metropolitan Central and West Central regions in one group, Caribbean Huetar, South Central, Central Pacific and Chorotega regions in a second group; and North Huetar and Brunca regions in a third intermediate group. Estimates of genetic differentiation (RST were significant between regions from different groups and non-significant for regions within the same group. Genetic differences between regions are related to differential proliferation of breed groups based on their adaptability to the agro-ecological conditions and production systems prevailing in each region.

  8. MLST subtypes and population genetic structure of Cryptosporidium andersoni from dairy cattle and beef cattle in northeastern China's Heilongjiang Province.

    Directory of Open Access Journals (Sweden)

    Wei Zhao

    Full Text Available Cattle are the main reservoir host of C. andersoni, which shows a predominance in yearlings and adults of cattle. To understand the subtypes of C. andersoni and the population genetic structure in Heilongjiang Province, fecal specimens were collected from 420 dairy cattle and 405 beef cattle at the age of 12-14 months in eight cattle farms in five areas within this province and were screened for the presence of Cryptosporidium oocysts by microscopy after Sheather's sugar flotation technique. The average prevalence of Cryptosporidium spp. was 19.15% (158/825 and all the Cryptosporidium isolates were identified as C. andersoni by the SSU rRNA gene nested PCR-RFLP using SspI, VspI and MboII restriction enzymes. A total of 50 C. andersoni isolates were randomly selected and sequenced to confirm the RFLP results before they were subtyped by multilocus sequence typing (MLST at the four microsatellite/minisatellite loci (MS1, MS2, MS3 and MS16. Four, one, two and one haplotypes were obtained at the four loci, respectively. The MLST subtype A4,A4,A4,A1 showed an absolute predominance and a wide distribution among the six MLST subtypes obtained in the investigated areas. Linkage disequilibrium analysis showed the presence of a clonal population genetic structure of C. andersoni in cattle, suggesting the absence of recombination among lineages. The finding of a clonal population genetic structure indicated that the prevalence of C. andersoni in cattle in Heilongjiang Province is not attributed to the introduction of cattle. Thus, prevention and control strategies should be focused on making stricter measures to avoid the occurrence of cross-transmission and re-infection between cattle individuals. These molecular data will also be helpful to explore the source attribution of infection/contamination of C. andersoni and to elucidate its transmission dynamics in Heilongjiang Province, even in China.

  9. Genetic structure of Miscanthus sinensis and M. sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression

    DEFF Research Database (Denmark)

    Clark, Lindsay V; Stewart, J Ryan; Nishiwaki, Aya;

    2015-01-01

    high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid Miscanthus sinensis are common, and occasionally hybridize. In this study, 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan were characterized using 20 704 SNPs and ten plastid microsatellites....... Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated through autopolyploidy. Structure analysis indicated a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M....... sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1–39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6–27% M. sacchariflorus ancestry. Population...

  10. Physiological basis of genetic variation in leaf photosynthesis among rice (Oryza sativa L.) introgression lines under drought and well-watered conditions.

    Science.gov (United States)

    Gu, Junfei; Yin, Xinyou; Stomph, Tjeerd-Jan; Wang, Huaqi; Struik, Paul C

    2012-09-01

    To understand the physiological basis of genetic variation and resulting quantitative trait loci (QTLs) for photosynthesis in a rice (Oryza sativa L.) introgression line population, 13 lines were studied under drought and well-watered conditions, at flowering and grain filling. Simultaneous gas exchange and chlorophyll fluorescence measurements were conducted at various levels of incident irradiance and ambient CO(2) to estimate parameters of a model that dissects photosynthesis into stomatal conductance (g(s)), mesophyll conductance (g(m)), electron transport capacity (J(max)), and Rubisco carboxylation capacity (V(cmax)). Significant genetic variation in these parameters was found, although drought and leaf age accounted for larger proportions of the total variation. Genetic variation in light-saturated photosynthesis and transpiration efficiency (TE) were mainly associated with variation in g(s) and g(m). One previously mapped major QTL of photosynthesis was associated with variation in g(s) and g(m), but also in J(max) and V(cmax) at flowering. Thus, g(s) and g(m), which were demonstrated in the literature to be responsible for environmental variation in photosynthesis, were found also to be associated with genetic variation in photosynthesis. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area, which were previously found across environmental treatments, were shown to be valid for variation across genotypes. Finally, the extent to which photosynthesis rate and TE can be improved was evaluated. Virtual ideotypes were estimated to have 17.0% higher photosynthesis and 25.1% higher TE compared with the best genotype investigated. This analysis using introgression lines highlights possibilities of improving both photosynthesis and TE within the same genetic background.

  11. PRODUCTIVITY AND GENETIC DIVERSITY OF LOCAL CATTLE IN CIAMIS-WEST JAVA

    Directory of Open Access Journals (Sweden)

    N. Hilmia

    2013-03-01

    Full Text Available The objectives of this study were to identify the productivity and genetic diversity of local cattle in Ciamis West Java based on DNA microsatellite, in order to provide the basic information for its rearing, conservation and development. Eighteen of local cattle were kept for 58 days by feeding concentrates and rice straw. The measured parameters were weekly body weight as well as carcass percentage. The percentage of comparing carcass was taken from PO, Bali and crossbred cattle from local cattle with Limousin, Simmental, Brahman and Angus cattle. Data were analyzed using Excel software and SAS (2004. Blood samples were taken from two subpopulations i.e., 46 and 52 samples from Tambaksari and Cijulang areas, respectively. Other DNA samples were collected from Bali, PO, Limousin, Simental, Brahman and Angus cattle. Genetic diversity and phylogenetic analysis were analyzed using 3 microsatellite loci, that were INRA35, HEL9 and BM2113. The genotyping data were analyzed using POPGENE.32 program, while phylogenetic trees were analyzed by MEGA 4. Average daily gain (ADG of local cattle in Ciamis was 0.62±0.23 kg/head/day with a carcass percentage was 51.62±1.80%. The carcasses percentage of local cattle in Ciamis was not significantly different from those of Bali, PO, and crossbred cattle. The genetic diversity of local cattle in Ciamis was categorized in the medium level, the diversity of local cattle in Tambaksari subpopulation was higher than in Cijulang subpopulation. Local cattle in Ciamis had a closer genetic distance with the PO cattle.

  12. Improvement of beef cattle genetics provided increasing sustainability of beef cattle production and protein consumption in Thailand

    International Nuclear Information System (INIS)

    The rural innovation research and development (R and D) in beef cattle genetics, biotechnology, climate science and production systems, supported profitable and sustainable beef cattle production in Thailand. Department of Livestock Development (DLD) undertakes R and D to achieve continuous improvement in genetics, production technologies to improve productivity, profitability and sustainability of beef cattle production and quality of products. Efficiencies were achieved through improvements in genetics, nutrition and grazing management, use of information, meat science, and reduction in ruminant methane production. This function was essential to maintain long-term production competitiveness and achieve sustained economic growth in rural Thailand, where the beef cattle production was the important livestock production, accounting for 36.99% of the value of livestock production in Thailand. Molecular, quantitative genetics, and biotechnology tool were being combined in the development of genetic improvement. In 2006, beef meat was imported 1,842.53 thousand tons (0.41% of all consumption, 120.84 baht/kg). For the big size cattle, such as Tak cattle, Kabinburi cattle (Thai synthetic breeds by DLD, Tak = 62.5 Charoles-Brahman, Kabinburi = 50 Simental- Brahman), and cross breed cattle, they were in fattening period for 6-12 month. Fattening group, they were raised for restaurant, hotel, super market, and steak house. Data were collected from 2 parts: 1) 354 cattle of experimental trial in DLD part, and 2) 492 fattening cattle of small holders in Tak province and Nakorn Pathom province during October 2004-September 2007. Data collecting was separated into 2 parts (performance data and reference). Data were adjusted by group location month and year to analyze for growth, carcass performance and economic performances). There were 5 breeds of fattening beef cattle: 1) Thai Native, 2) Thai Brahman, 3) Kabinburi, 4) Tak, and 5) Tajima-Native. The first group was around 41

  13. Genetic evaluation of reproductive performance in Canadian dairy cattle

    Directory of Open Access Journals (Sweden)

    F. Miglior

    2010-04-01

    Full Text Available A new genetic evaluation system for the reproductive performance of dairy cattle has been developed in Canada. The evaluation system includes all traits related to reproductive performance, namely age at first service as a heifer trait, interval from calving to first service for cows and 7 traits each for both heifers and cows (56-days non return rate, interval from first service to conception, number of services to conception, gestation length, direct and maternal calving ease, direct and maternal calf survival and direct and maternal calf size. The model of analysis is a 16-trait animal model with different fixed effects according to the analyzed trait. Two indices for daughter fertility and calving performance have been developed. The impact of including the two indices in the national selection index was assessed.

  14. PRODUCTIVITY AND GENETIC DIVERSITY OF LOCAL CATTLE IN CIAMIS-WEST JAVA

    OpenAIRE

    N. Hilmia; R. R. Noor; C. Sumantri; R.E. Gurnadi; R. Priyanto

    2014-01-01

    The objectives of this study were to identify the productivity and genetic diversity of local cattle inCiamis West Java based on DNA microsatellite, in order to provide the basic information for its rearing,conservation and development. Eighteen of local cattle were kept for 58 days by feeding concentratesand rice straw. The measured parameters were weekly body weight as well as carcass percentage. Thepercentage of comparing carcass was taken from PO, Bali and crossbred cattle from local catt...

  15. PRODUCTIVITY AND GENETIC DIVERSITY OF LOCAL CATTLE IN CIAMIS-WEST JAVA

    OpenAIRE

    N. Hilmia; R. R. Noor; C. Sumantri; R.E. Gurnadi; R. Priyanto

    2013-01-01

    The objectives of this study were to identify the productivity and genetic diversity of local cattle in Ciamis West Java based on DNA microsatellite, in order to provide the basic information for its rearing, conservation and development. Eighteen of local cattle were kept for 58 days by feeding concentrates and rice straw. The measured parameters were weekly body weight as well as carcass percentage. The percentage of comparing carcass was taken from PO, Bali and crossbred cattle from local ...

  16. PRODUCTIVITY AND GENETIC DIVERSITY OF LOCAL CATTLE IN CIAMIS-WEST JAVA

    Directory of Open Access Journals (Sweden)

    N. Hilmia

    2014-10-01

    Full Text Available The objectives of this study were to identify the productivity and genetic diversity of local cattle inCiamis West Java based on DNA microsatellite, in order to provide the basic information for its rearing,conservation and development. Eighteen of local cattle were kept for 58 days by feeding concentratesand rice straw. The measured parameters were weekly body weight as well as carcass percentage. Thepercentage of comparing carcass was taken from PO, Bali and crossbred cattle from local cattle withLimousin, Simmental, Brahman and Angus cattle. Data were analyzed using Excel software and SAS(2004. Blood samples were taken from two subpopulations i.e., 46 and 52 samples from Tambaksariand Cijulang areas, respectively. Other DNA samples were collected from Bali, PO, Limousin, Simental,Brahman and Angus cattle. Genetic diversity and phylogenetic analysis were analyzed using 3microsatellite loci, that were INRA35, HEL9 and BM2113. The genotyping data were analyzed usingPOPGENE.32 program, while phylogenetic trees were analyzed by MEGA 4. Average daily gain (ADGof local cattle in Ciamis was 0.62±0.23 kg/head/day with a carcass percentage was 51.62±1.80%. Thecarcasses percentage of local cattle in Ciamis was not significantly different from those of Bali, PO, andcrossbred cattle. The genetic diversity of local cattle in Ciamis was categorized in the medium level, thediversity of local cattle in Tambaksari subpopulation was higher than in Cijulang subpopulation. Localcattle in Ciamis had a closer genetic distance with the PO cattle.

  17. On the origin of Indonesian cattle.

    Directory of Open Access Journals (Sweden)

    Kusdiantoro Mohamad

    Full Text Available BACKGROUND: Two bovine species contribute to the Indonesian livestock, zebu (Bos indicus and banteng (Bos javanicus, respectively. Although male hybrid offspring of these species is not fertile, Indonesian cattle breeds are supposed to be of mixed species origin. However, this has not been documented and is so far only supported by preliminary molecular analysis. METHODS AND FINDINGS: Analysis of mitochondrial, Y-chromosomal and microsatellite DNA showed a banteng introgression of 10-16% in Indonesian zebu breeds. East-Javanese Madura and Galekan cattle have higher levels of autosomal banteng introgression (20-30% and combine a zebu paternal lineage with a predominant (Madura or even complete (Galekan maternal banteng origin. Two Madura bulls carried taurine Y-chromosomal haplotypes, presumably of French Limousin origin. In contrast, we did not find evidence for zebu introgression in five populations of the Bali cattle, a domestic form of the banteng. CONCLUSIONS: Because of their unique species composition Indonesian cattle represent a valuable genetic resource, which potentially may also be exploited in other tropical regions.

  18. A REVIEW ON INDIGENOUS CATTLE GENETIC RESOURCES IN ETHIOPIA: ADAPTATION, STATUS AND SURVIVAL

    Directory of Open Access Journals (Sweden)

    Getinet MEKURIAW

    2015-09-01

    Full Text Available Ethiopia is endowed with different Indigenous cattle genetic resources with millions of people directly depending on them. However, despite the potentials of these diversified genetic resources, the huge loss of cattle genetic diversity is becoming a prominent challenge these days. The aim of this review is to show the current status and performance of some selected indigenous cattle breeds of Ethiopia for better understanding of the situation of these breeds for the collective efforts towards conserving and improving the breeds. Based on the review, there are persuasive evidences on the critical situation of the selected indigenous cattle breeds. The facts and figures of the past and current situation of the selected indigenous cattle of Ethiopia showed that the situation of these breeds is very critical. This situation therefore demands the need to devise strategies to conserve and improve the cattle breeds based on the challenges that threatens them. Use of new biological and information technologies is also imperative to facilitate the genetic restoration process. Besides, use of new biological and information technologies which can enhance the conservation and improvement program are crucial. Various ongoing development interventions like Artificial Insemination and introduction of genotypes into new environments that are exacerbating threat of the breeds should totally be avoided by revising and designing sound approaches for cattle Conservation and improvement programs. Strict regulations and by laws should also be in place for illegal movement of breeding cattle to the neighboring countries.

  19. Genetic Diversity of Bali Cattle Based on Microsatellite Marker in Indonesian Breeding Centre

    Directory of Open Access Journals (Sweden)

    W. A. Septian

    2015-04-01

    Full Text Available Genetics characterization in livestock based on microsatellite has been widely implemented including for Bali cattle in three different breeding centres in Indonesia. This study aimed to determine diversity of Bali cattle microsatellites in three breeding centers namely BPTU Bali cattle in Bali, BPT-HMT Serading Sumbawa in West Nusa Tenggara, and Village Breeding Center in South Sulawesi. The number of animals used in this study was 95 head of cattle consisted of 32 heads from BPTU Bali Province, 32 heads from BPT-HMT Serading Sumbawa, and 31 heads from Village Barru Breeding Center Barru distric. Microsatellite loci used to determine the diversity was the locus SPS115, INRA037, MM12, and ETH185 based on flourescently labeled fragment method. Data analysis of microsatellite in Bali cattle at three different locations was performed by using POPGEN 1.2, Cervus, and POPTREE2 programs. The results showed that microsatellite diversity in Bali cattle detected 32 alleles from three different locations, and there were specific alleles at each location. Average values of observed heterozygosity (Ho and expected heterozygosity (He were 0.418 and 0.604 respectively, while the average value of polymorphism informative content (PIC was 0.579. The Hardy-Weinberg equilibrium in general suggested that the loci used in the Bali cattle in three populations were in equilibrium, except INRA037 and ETH185. The genetic diversity between populations of Bali cattle was 0.033 (3%, while the inbreeding coefficient index in all populations was 0.296 (29.6 %. Bali cattle phylogeny tree with three populations showed that the populations of Bali cattle in BPTU Bali and VBC Barru had close genetic distance compared to the population of Bali cattle in BPT-HMT Serading Sumbawa. The results of this study provide information that the characteristics of Bali cattle breeding centers in three locations are different, so we need a directed breeding program in each population.

  20. Intervention of genetic flow of the foreign cattle toward diversity of phenotype expressions of local cattle in the District of Banyuwangi

    Directory of Open Access Journals (Sweden)

    MOHAMAD AMIN

    2010-04-01

    Full Text Available Amin M (2010 Intervention of genetic flow of the foreign cattle toward diversity of phenotype expressions of local cattle in the District of Banyuwangi. Biodiversitas 10: 69-74. The aims of the present research are two folds: to know the phenotypic diversity and to reconstruct the cross-breeding pattern of local cattle in Banyuwangi. Based on three sampling areas, it was found that there were 32 phenotypic cattle (10 in the sub districts of Rogojampi, 16 in Tegaldlimo and 6 in Glagah areas. The phenotypic varieties were caused by two factors, namely the flow of genetic intervention of the other local cattle (Bali, Ongole, and Brahman cattle and the artificial insemination program using the semen of Limousine, Simmental, Aberdeen Angus and Santa Gertrudis cattle.

  1. Transgenic dairy cattle: genetic engineering on a large scale.

    Science.gov (United States)

    Wall, R J; Kerr, D E; Bondioli, K R

    1997-09-01

    Amid the explosion of fundamental knowledge generated from transgenic animal models, a small group of scientists has been producing transgenic livestock with goals of improving animal production efficiency and generating new products. The ability to modify mammary-specific genes provides an opportunity to pursue several distinctly different avenues of research. The objective of the emerging gene "pharming" industry is to produce pharmaceuticals for treating human diseases. It is argued that mammary glands are an ideal site for producing complex bioactive proteins that can be cost effectively harvested and purified. Consequently, during the past decade, approximately a dozen companies have been created to capture the US market for pharmaceuticals produced from transgenic bioreactors estimated at $3 billion annually. Several products produced in this way are now in human clinical trials. Another research direction, which has been widely discussed but has received less attention in the laboratory, is genetic engineering of the bovine mammary gland to alter the composition of milk destined for human consumption. Proposals include increasing or altering endogenous proteins, decreasing fat, and altering milk composition to resemble that of human milk. Initial studies using transgenic mice to investigate the feasibility of enhancing manufacturing properties of milk have been encouraging. The potential profitability of gene "pharming" seems clear, as do the benefits of transgenic cows producing milk that has been optimized for food products. To take full advantage of enhanced milk, it may be desirable to restructure the method by which dairy producers are compensated. However, the cost of producing functional transgenic cattle will remain a severe limitation to realizing the potential of transgenic cattle until inefficiencies of transgenic technology are overcome. These inefficiencies include low rates of gene integration, poor embryo survival, and unpredictable transgene

  2. Genetic selection for temperament traits in dairy and beef cattle.

    Science.gov (United States)

    Haskell, Marie J; Simm, Geoff; Turner, Simon P

    2014-01-01

    Animal temperament can be defined as a response to environmental or social stimuli. There are a number of temperament traits in cattle that contribute to their welfare, including their response to handling or milking, response to challenge such as human approach or intervention at calving, and response to conspecifics. In a number of these areas, the genetic basis of the trait has been studied. Heritabilities have been estimated and in some cases quantitative trait loci (QTL) have been identified. The variation is sometimes considerable and moderate heritabilities have been found for the major handling temperament traits, making them amenable to selection. Studies have also investigated the correlations between temperament and other traits, such as productivity and meat quality. Despite this, there are relatively few examples of temperament traits being used in selection programmes. Most often, animals are screened for aggression or excessive fear during handling or milking, with extreme animals being culled, or EBVs for temperament are estimated, but these traits are not commonly included routinely in selection indices, despite there being economic, welfare and human safety drivers for their. There may be a number of constraints and barriers. For some traits and breeds, there may be difficulties in collecting behavioral data on sufficiently large populations of animals to estimate genetic parameters. Most selection indices require estimates of economic values, and it is often difficult to assign an economic value to a temperament trait. The effects of selection primarily for productivity traits on temperament and welfare are discussed. Future opportunities include automated data collection methods and the wider use of genomic information in selection.

  3. Oocyte development in cattle: physiological and genetic aspects

    Directory of Open Access Journals (Sweden)

    Jack H. Britt

    2008-07-01

    Full Text Available Oocytes in cattle are formed during embryogenesis and develop within individual follicles in the cortex of the ovary. Dormant primordial follicles become active and undergo progressive development at regular intervals commencing during the late fetal stage and continuing throughout adulthood. Once activated, follicles and oocytes in a cohort either grow to maturation and ovulation or undergo atresia, ultimately depleting the ovaries of germ cells. It takes an estimated 100 days for a follicle and its oocyte to reach the mature ovulatory stage. Within an individual, number of follicles in one ovary is similar to number in the other ovary; however, there are large differences among individuals in total number of follicles present in both ovaries. In follicles that are recruited into the preovulatory pool, the fluid filled antrum enlarges and growth can be monitored by ultrasonography. Preovulatory follicles grow in waves rather than in a continuous stream, and number of follicles detected in a wave is related positively to number of microscopic follicles populating the ovarian cortex. Number of follicles in a wave is highly repeatable and the estimated heritability of number of follicles in heifers is approximately 0.35. Monitoring preovulatory follicle numbers by ultrasonography can be used to identify females that produce more embryos following superovulation or more natural twin births. Number of follicles in a wave can be influenced by energy balance and exogenous hormones, and quality of oocytes within those follicles can be influenced environmental factors, hormones and vitamins. The potential exists to increase genetic progress through repeatedly harvesting oocytes from preovulatory follicles of genetically superior females.

  4. Genetic parameters for postweaning traits in Braunvieh cattle.

    Science.gov (United States)

    Cucco, D C; Ferraz, J B S; Eler, J P; Balieiro, J C C; Mattos, E C; Varona, L

    2010-01-01

    Genetic parameters for traits related to postweaning growth in Braunvieh cattle, reared under tropical and sub-tropical conditions in Brazil, were studied. Weight traits were weight at 365 days of age (W365, N = 4055), at 450 days (W450, N = 3453), and at 550 days (W550, N = 1946), while weight gains were gain from weaning to 365 days of age (WGW365, N = 3060), from weaning to 450 days (WGW450, N = 2764), from weaning to 550 days (WGW550, N = 1531), from 365 to 550 days of age (WG365550, N = 1528), from 365 to 450 days (WG365450, N = 2401), and from 450 to 550 days (WG450550, N = 1563). A full animal model was used for estimating the variance components, using the MTDFREML software. The dataset contained 18,688 animals with phenotypic measures and 35,188 animals in the relationship matrix. Heritability estimates for postweaning weights decreased with age. For W365, W450 and W550, respectively, the direct heritability estimates were 0.29 +/- 0.061, 0.25 +/- 0.057, 0.16 +/- 0.060, maternal heritability was 0.20 +/- 0.035, 0.18 +/- 0.035, 0.13 +/- 0.052, and total heritability was 0.30, 0.35, 0.26. In this breed, maternal influence was found to be important up to 550 days of age. The greater genetic correlations between weights were observed for weights measured at shorter intervals. A large environmental effect was observed for weight gain between weaning and 550 days; this effect was greater for the gains between 365 and 550 days.

  5. Genetic selection for temperament traits in dairy and beef cattle

    Directory of Open Access Journals (Sweden)

    Marie J Haskell

    2014-10-01

    Full Text Available Animal temperament can be defined as a response to environmental or social stimuli. There are a number of temperament traits in cattle that contribute to their welfare, including their response to handling or milking, response to challenge such as human approach or intervention at calving, and response to conspecifics. In a number of these areas, the genetic basis of the trait has been studied. Heritabilities have been estimated and in some cases quantitative trait loci (QTL have been identified. The variation is sometimes considerable and moderate heritabilities have been found for the major handling temperament traits, making them amenable to selection. Studies have also investigated the correlations between temperament and other traits, such as productivity and meat quality. Despite this, there are relatively few examples of temperament traits being used in selection programmes. Most often, animals are screened for aggression or excessive fear during handling or milking, with extreme animals being culled, or EBVs for temperament are estimated, but these traits are not commonly included routinely in selection indices, despite there being economic, welfare and human safety drivers for their. There may be a number of constraints and barriers. For some traits and breeds, there may be difficulties in collecting behavioral data on sufficiently large populations of animals to estimate genetic parameters. Most selection indices require estimates of economic values, and it is often difficult to assign an economic value to a temperament trait. The effects of selection primarily for productivity traits on temperament and welfare are discussed. Future opportunities include automated data collection methods and the wider use of genomic information in selection.

  6. Conservation genetics of an endangered Catalonian cattle breed ("Alberes"

    Directory of Open Access Journals (Sweden)

    J. Jordana

    1999-09-01

    Full Text Available We biochemically analyzed and characterized the genetic structure of a population in danger of extinction ,"Alberes", a local cattle breed of the Catalonian Pyrenees (Spain and France. Ninety-two individuals were analyzed for five polymorphic genetic loci (Hb, Alb, Tf, Gc and Ptf2. The animals were grouped according to coat color: Fagina Alberes variety (N = 39 and Black Alberes variety (N = 53. The genetic structures and relationships between these subpopulations and one "outgroup" breed ("Bruna dels Pirineus" were analyzed and compared by using F-statistics. We determined that inbreeding in the Alberes breed is not significant, since negative and nonsignificant FIT and FIS values were obtained. The average genetic differentiation between subpopulations within the Alberes breed was 1.5% (FST = 0.015; P A estrutura génetica de uma população de Alberes, uma raça de gado dos Pirineus catalônicos (Espanha e França em risco de extinção, foi analisada e caracterizada bioquimicamente. Noventa e dois indivíduos foram analisados para 5 loci genéticos polimórficos (Hb, Alb, Tf, Gc e Ptf2. Os animais foram agrupados de acordo com a cor do pêlo: variedade Fagina Alberes (N = 39 e Black Alberes (N = 53. As estruturas genéticas e as relações entre estas subpopulações e uma raça extra ("Bruna dels Pirineus" foram analisadas e comparadas pela estatística F. A endogamia na raça Alberes não foi significante, pois foram obtidos valores FIT e FIS negativos e não significantes. A diferenciação genética média entre as subpopulações dentro da raça Alberes foi 1,5% (FST = 0,015; P < 0,05, com um número efetivo de 4,1 indivíduos trocados entre as subpopulações por geração (fluxo de gene. Os resultados obtidos neste estudo confirmaram o perigo potencial de extinção da raça. A variedade Black Alberes é sugerida como o principal núcleo de conservação genética para esta raça, pois parece mostrar maior grau de isolamento gen

  7. The genetic integrity of the ex situ population of the European wildcat (Felis silvestris silvestris) is seriously threatened by introgression from domestic cats (Felis silvestris catus).

    Science.gov (United States)

    Witzenberger, Kathrin A; Hochkirch, Axel

    2014-01-01

    Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction. PMID:25162450

  8. The genetic integrity of the ex situ population of the European wildcat (Felis silvestris silvestris) is seriously threatened by introgression from domestic cats (Felis silvestris catus).

    Science.gov (United States)

    Witzenberger, Kathrin A; Hochkirch, Axel

    2014-01-01

    Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction.

  9. Studies on the value of incorporating the effect of dominance in genetic evaluations of dairy cattle, beef cattle and swine

    Directory of Open Access Journals (Sweden)

    Van Tassel CP.

    1998-01-01

    Full Text Available Nonadditive genetic effects are currently ignored in national genetic evaluations of farm animals because of ignorance of thelevel of dominance variance for traits of interest and the difficult computational problems involved. Potential gains fromincluding the effects of dominance in genetic evaluations include “purification” of additive values and availability ofpredictions of specific combining abilities for each pair of prospective parents. This study focused on making evaluation withdominance effects feasible computationally and on ascertaining benefits of such an evaluation for dairy cattle, beef cattle,and swine. Using iteration on data, computing costs for evaluation with dominance effects included costs could be less thantwice expensive as with only an additive model. With Method Â, variance components could be estimated for problemsinvolving up to 10 millions equations. Dominance effects accounted for up to 10% of phenotypic variance; estimates werelarger for growth traits. As a percentage of additive variance, the estimate of dominance variance reached 78% for 21-d litterweight of swine and 47% for post weaning weight of beef cattle. When dominance effects are ignored, additive evaluationsare “contaminated”; effects are greatest for evaluations of dams in a single large family. These changes in ranking wereimportant for dairy cattle, especially for dams of full-sibs, but were less important for swine. Specific combining abilitiescannot be included in sire evaluations and need to be computed separately for each set of parents. The predictions of specificcombining abilities could be used in computerized mating programs via the Internet. Gains from including the dominanceeffect in genetic evaluations would be moderate but would outweigh expenditures to produce those evaluations.

  10. Genetic Analysis of the Henry Mountains Bison Herd.

    Directory of Open Access Journals (Sweden)

    Dustin H Ranglack

    Full Text Available Wild American plains bison (Bison bison populations virtually disappeared in the late 1800s, with some remnant animals retained in what would become Yellowstone National Park and on private ranches. Some of these private bison were intentionally crossbred with cattle for commercial purposes. This forced hybridization resulted in both mitochondrial and nuclear introgression of cattle genes into some of the extant bison genome. As the private populations grew, excess animals, along with their history of cattle genetics, provided founders for newly established public bison populations. Of the US public bison herds, only those in Yellowstone and Wind Cave National Parks (YNP and WCNP appear to be free of detectable levels of cattle introgression. However, a small free-ranging population (~350 animals exists on public land, along with domestic cattle, in the Henry Mountains (HM of southern Utah. This isolated bison herd originated from a founder group translocated from YNP in the 1940s. Using genetic samples from 129 individuals, we examined the genetic status of the HM population and found no evidence of mitochondrial or nuclear introgression of cattle genes. This new information confirms it is highly unlikely for free-living bison to crossbreed with cattle, and this disease-free HM bison herd is valuable for the long-term conservation of the species. This bison herd is a subpopulation of the YNP/WCNP/HM metapopulation, within which it can contribute significantly to national efforts to restore the American plains bison to more of its native range.

  11. Morphological and genetic evidence for early Holocene cattle management in northeastern China

    DEFF Research Database (Denmark)

    Zhang, Hucai; Paijmans, Johanna L A; Chang, Fengqin;

    2013-01-01

    The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological...... and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent (14)C dates. Using Illumina high-throughput sequencing coupled with DNA...... hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate...

  12. Genetic effects on beef tenderness in Bos indicus composite and Bos taurus cattle.

    Science.gov (United States)

    O'Connor, S F; Tatum, J D; Wulf, D M; Green, R D; Smith, G C

    1997-07-01

    Bos indicus composite and Bos taurus cattle, originating from diverse production environments, were used to quantify genetic variation in marbling, 24-h calpastatin activity, and beef tenderness and to identify strategies for prevention of beef tenderness problems in Bos indicus composite cattle. Comparisons among 3/8 Bos indicus breeds (Braford, Red Brangus, Simbrah) revealed significant differences in marbling and 24-h calpastatin activity, but not in tenderness. Compared with Bos taurus cattle, 3/ 8 Bos indicus cattle had similar marbling scores but higher 24-h calpastatin activities. Also, beef from 3/8 Bos indicus composites aged more slowly from 1 to 7 d and was less tender at 4, 7, 14, 21, and 35 d postmortem than beef from Bos taurus cattle. However, beef from 3/8 Bos indicus cattle was relatively tender if it was aged for a sufficient period of time (21 d). The delayed response to aging and greater toughness of beef from 3/8 Bos indicus cattle was associated with Brahman breed effects and was not related to the Bos taurus germplasm source. Marbling was moderately heritable (.52 +/- .21) but exhibited positive genetic correlations with shear force at d 1 through 14 of aging, suggesting that, in these cattle, selection for increased marbling would have an unfavorable effect on beef tenderness. A low heritability estimate for 24-h calpastatin activity (.15 +/- .15), coupled with low genetic correlations between calpastatin activity and shear force at 7, 14, and 35 d, suggested that selection for low calpastatin activity would have little effect on aged beef tenderness. Panel tenderness and shear force at 7, 14, and 21 d were moderately heritable (.27 to .47), indicating that aged beef tenderness could be improved by direct selection (via progeny testing). Comparisons among Simbrah, Senegus x Simbrah, and Red Angus x Simmental steers showed that inclusion of a tropically adapted Bos taurus breed (Senepol) could be an effective strategy for preventing beef

  13. Genetic effects on beef tenderness in Bos indicus composite and Bos taurus cattle.

    Science.gov (United States)

    O'Connor, S F; Tatum, J D; Wulf, D M; Green, R D; Smith, G C

    1997-07-01

    Bos indicus composite and Bos taurus cattle, originating from diverse production environments, were used to quantify genetic variation in marbling, 24-h calpastatin activity, and beef tenderness and to identify strategies for prevention of beef tenderness problems in Bos indicus composite cattle. Comparisons among 3/8 Bos indicus breeds (Braford, Red Brangus, Simbrah) revealed significant differences in marbling and 24-h calpastatin activity, but not in tenderness. Compared with Bos taurus cattle, 3/ 8 Bos indicus cattle had similar marbling scores but higher 24-h calpastatin activities. Also, beef from 3/8 Bos indicus composites aged more slowly from 1 to 7 d and was less tender at 4, 7, 14, 21, and 35 d postmortem than beef from Bos taurus cattle. However, beef from 3/8 Bos indicus cattle was relatively tender if it was aged for a sufficient period of time (21 d). The delayed response to aging and greater toughness of beef from 3/8 Bos indicus cattle was associated with Brahman breed effects and was not related to the Bos taurus germplasm source. Marbling was moderately heritable (.52 +/- .21) but exhibited positive genetic correlations with shear force at d 1 through 14 of aging, suggesting that, in these cattle, selection for increased marbling would have an unfavorable effect on beef tenderness. A low heritability estimate for 24-h calpastatin activity (.15 +/- .15), coupled with low genetic correlations between calpastatin activity and shear force at 7, 14, and 35 d, suggested that selection for low calpastatin activity would have little effect on aged beef tenderness. Panel tenderness and shear force at 7, 14, and 21 d were moderately heritable (.27 to .47), indicating that aged beef tenderness could be improved by direct selection (via progeny testing). Comparisons among Simbrah, Senegus x Simbrah, and Red Angus x Simmental steers showed that inclusion of a tropically adapted Bos taurus breed (Senepol) could be an effective strategy for preventing beef

  14. Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle

    Science.gov (United States)

    Heat stress affects production and reproduction in dairy cattle. Genetic selection for body temperature might help to decrease the effects of heat stress on those traits. Objectives of the current study were a) to estimate genetic parameters of rectal temperature in dairy cows under heat stress cond...

  15. Genetic predisposition to pass the standard SICCT test for bovine tuberculosis in British cattle.

    Directory of Open Access Journals (Sweden)

    William Amos

    Full Text Available Bovine tuberculosis (bTB imposes an important financial burden on the British cattle industry, yet despite intense efforts to control its spread, incidence is currently rising. Surveillance for bTB is based on a skin test that measures an immunological response to tuberculin. Cattle that fail the test are classified as "reactors" and slaughtered. Recent studies have identified genetic markers associated with the reaction of cattle to the tuberculin test. At marker INRA111 a relatively common '22' genotype occurs significantly more frequently in non-reactor cattle. Here we test the possibility that the putative protective '22' genotype does not confer resistance but instead causes cattle that carry it to react less strongly to the prescribed test, and hence avoid slaughter, potentially even though they are infected. We show that, after controlling for age and breed, '22' cattle react less strongly to the immunological challenge and may therefore be less likely to be classified as a reactor. These results highlight the potential discrepancy between infection and test status and imply that the effectiveness of the test-and-slaughter policy may be being compromised by selection for cattle that are genetically predisposed to react less strongly to tuberculin.

  16. African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World.

    Science.gov (United States)

    Mwai, Okeyo; Hanotte, Olivier; Kwon, Young-Jun; Cho, Seoae

    2015-07-01

    At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers. PMID:26104394

  17. Genetic Investigations Using Immuno-biochemical Markers in a Maramureş Brown Cattle Population

    Directory of Open Access Journals (Sweden)

    Nicoleta Isfan

    2011-05-01

    Full Text Available The study of the genetic markers and identifying new markers involves an increasing number of research projects in the fields of genetics of immunology, biochemical genetics, molecular genetics, quantity genetics and the genetic improvement of animals. Some studies on genes frequency determining the red cells specificity and for whey hemoglobin are approached in the present report. In this way, some blood factors, most of them belonging to B system (the most complex system in cattle have been evidenced. The lowest gene frequency was present in K factor (7%, and highest one in, O1, G’ , W and F1 (100%. In addition to basic importance on knowledge and determination of cattle population genetic structure for studied protein loci, another theme proposed to correlate hemoglobin type with some traits of economical importance: milk yield, fat and protein content, fat and protein yield. Higher performance was recorded by HbA/HbA individuals.

  18. Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers.

    Science.gov (United States)

    Sanarana, Yandisiwe; Visser, Carina; Bosman, Lydia; Nephawe, Khathutshelo; Maiwashe, Azwihangwisi; van Marle-Köster, Este

    2016-02-01

    The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study, molecular characterisation was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from the University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69 % (UFH) to 72 % (PED) with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8 % of the total genetic variation was due to the genetic differentiation between the populations and 92.2 % accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.

  19. Intervention of genetic flow of the foreign cattle toward diversity of phenotype expressions of local cattle in the District of Banyuwangi

    OpenAIRE

    MOHAMAD AMIN

    2010-01-01

    Amin M (2010) Intervention of genetic flow of the foreign cattle toward diversity of phenotype expressions of local cattle in the District of Banyuwangi. Biodiversitas 10: 69-74. The aims of the present research are two folds: to know the phenotypic diversity and to reconstruct the cross-breeding pattern of local cattle in Banyuwangi. Based on three sampling areas, it was found that there were 32 phenotypic cattle (10 in the sub districts of Rogojampi, 16 in Tegaldlimo and 6 in Glagah areas)....

  20. Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds.

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    Mathieu Gautier

    Full Text Available BACKGROUND: Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time. METHODOLOGY/PRINCIPAL FINDINGS: This study gives a detailed assessment of cattle genetic diversity based on 1,121 individuals sampled in 47 populations from different parts of the world (with a special focus on French cattle genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of new genotypes for 296 individuals representing 14 French cattle breeds which were combined to those available from three previously published studies. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. We further searched for spatial patterns of genetic diversity among 23 European populations, most of them being of French origin, under the recently developed spatial Principal Component analysis framework. CONCLUSIONS/SIGNIFICANCE: Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. In addition, patterns of differentiation among the three main groups of populations--the African taurine, the European taurine and zebus--may provide some additional support for three distinct domestication centres. Finally, among the European cattle breeds investigated, spatial patterns of genetic diversity were found in good agreement with the two main migration routes towards France, initially postulated based on archeological evidence.

  1. SELECTIVE BREEDING, HERITABLE CHARACTERISTICS AND GENETIC-BASED TECHNOLOGICAL CHANGE IN THE CANADIAN BEEF CATTLE INDUSTRY

    OpenAIRE

    Kerr, William A.

    1984-01-01

    The paper presents an examination of genetic-based technological change in the Canadian beef cattle industry. A model of technological change is explicitly developed in characteristics space. Production functions with genetic characteristics as arguments are estimated and two forms of technological change identified. Shadow values for characteristics are then calculated and actual genetic improvements are compared to the improvements suggested by the shadow prices. It is concluded that market...

  2. [Development and study of spring bread wheat variety Pamyati Maystrenko with introgression of genetic material from synthetic hexaploid Triticum timopheevii zhuk. x Aegilops tauschii Coss].

    Science.gov (United States)

    Laikova, L I; Belan, I A; Badaeva, E D; Posseeva, L P; Shepelev, S S; Shumny, V K; Pershina, L A

    2013-01-01

    Synthetic hexaploids are bridges for transferring new genes that determine resistance to stress factors from wild-type species to bread wheat. In the present work, the method of developing the spring bread wheat variety Pamyati Maystrenko and the results of its study are described. This variety was obtained using one of the immune lines produced earlier via the hybridization of the spring bread wheat variety Saratovskaya 29 with the synthetic hexaploid T. timopheevii Zhuk. x Ae. tauschii Coss. The C-staining of chromosomes in the Pamyati Maystrenko variety revealed substitutions of 2B and 6B chromosomes by the homeologous chromosomes of the G genome of T. timopheevii and the substitution of chromosome 1D by an orthologous chromosome ofAe. tauschii. It was found that this variety is characterized by resistance to leaf and stem rust, powdery mildew, and loose smut as well as by high grain and bread-making qualities. The role of the alien genetic material introgressed into the bread-wheat genome in the expression of adaptive and economically valuable traits in the Pamyati Maystrenko variety is discussed.

  3. Genetic introgression of ethylene-suppressed transgenic tomatoes with higher-polyamines trait overcomes many unintended effects due to reduced ethylene on the primary metabolome

    Directory of Open Access Journals (Sweden)

    Anatoly P Sobolev

    2014-12-01

    Full Text Available Ethylene regulates a myriad physiological and biochemical processes in ripening fruits and is accepted as the ripening hormone for the climacteric fruits. However, its effects on metabolome and resulting fruit quality are not yet fully understood, particularly when some of the ripening-associated biochemical changes are independent of ethylene action. We have generated a homozygous transgenic tomato genotype (2AS-AS that exhibits reduced ethylene production as a result of impaired expression of 1-aminocyclopropane-1-carboxylate synthase 2 gene by its antisense RNA and had a longer shelf life. Double transgenic hybrid (2AS-AS x 579HO developed through a genetic cross between 2AS-AS and 579HO (Mehta et al., 2002 lines resulted in significantly higher ethylene production than either the WT or 2AS-AS fruit. To determine the effects of reduced ethylene and introgression of higher polyamines’ trait, the metabolic profiles of ripening fruits from WT (556AZ, 2AS-AS, and 2AS-AS x 579HO lines were determined using 1H-NMR spectroscopy. The levels of Glu, Asp, AMP, Adenosine, Nucl1 and Nucl2 increased during ripening of the WT fruit. The increases in Glu, Asp, and AMP levels were attenuated in 2AS-AS fruit but recovered in the double hybrid with higher ethylene and polyamine levels. The ripening-associated decreases in Ala, Tyr, Val, Ile, Phe, malate and myo-inositol levels in the 2AS-AS line were not reversed in the double hybrid line suggesting a developmental/ripening regulated accumulation of these metabolites independent of ethylene. Significant increases in the levels of fumarate, formate, choline, Nucl1 and Nucl2 at most stages of ripening fruit were found in the double transgenic line due to introgression with higher-polyamines trait. Taken together these results show that the ripening-associated metabolic changes are both ethylene dependent and independent, and that the fruit metabolome is under the control of multiple regulators, including

  4. Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.

    Science.gov (United States)

    Simčič, Mojca; Smetko, Anamarija; Sölkner, Johann; Seichter, Doris; Gorjanc, Gregor; Kompan, Dragomir; Medugorac, Ivica

    2015-01-01

    The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had

  5. Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.

    Directory of Open Access Journals (Sweden)

    Mojca Simčič

    Full Text Available The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which

  6. Broadening the genetic base of Abyssinian mustard (Brassica carinata A. Braun) through introgression of genes from related allotetraploid species

    OpenAIRE

    Farooq A. Sheikh; Sashi Banga; Surindar S. Banga

    2014-01-01

    Brassica carinata (BBCC, 2n=34) has still to emerge as a major oilseed crop owing to poor agronomic attributes like long stature, long maturity duration and low seed yield. The restricted amount of genetic variability available in natural B. carinata necessitates utilization of new sources of variability for broadening its genetic base. Interspecific hybridization followed by selection in selfed and back cross progenies was employed to generate useful variability into B. carinata cv ˈPC5ˈ fro...

  7. Genetic polymorphism of β-lactoglobulin and κ-casein of cattle breeds in Croatia

    Directory of Open Access Journals (Sweden)

    Ante Ivanković

    2011-12-01

    Full Text Available Profitable milk production respects the interests of producers, processing industries, consumer requirements and welfare of animals. Development of new methods of direct gene analysis responsible for milk proteins polymorphism provide new tools to raise the profitability of milk production and dairy products through implementation of breed genetic profile in breeding program. Because of necessity to determinate genetic profiles of cattle breeds in Croatia using new analytical methods, the ratio of dominant allelic polymorphic variants of beta-lactoglobulin (β-Lg and kappa-casein (κ-CN is defined. The share of beta-lactoglobulin B variant is dominant in all investigated cattle breeds (>52.9 %. Kappa- casein allelic variant A is dominant in selected cattle breeds (60.7-76.4 %, while the share of B variant is significantly more presented in autochthonous cattle breeds (48.2-84.1 %. Knowledge about genetic profile of breeds due to studied polymorphic variants of milk proteins is useful in further breeding development and economic reaffirmation of cattle breeds, especially autochthonous ones.

  8. Genetic dissection of milk yield traits and mastitis resistance QTL on chromosome 20 in dairy cattle

    DEFF Research Database (Denmark)

    Kadri, Naveen Kumar; Guldbrandtsen, Bernt; Lund, Mogens Sandø;

    2015-01-01

    , there was indication on differences in the causal factor(s) across breeds. A previously reported F279Y mutation (rs385640152) within the growth hormone receptor (GHR) gene showed strong association with milk, fat, protein yields. In HOL, the highest peaks for milk yield and susceptibility to mastitis were separated......Intense selection to increase milk yield has had negative consequences for mastitis incidence in dairy cattle. Due to low heritability of mastitis resistance and an unfavorable genetic correlation with milk yield, a reduction in mastitis through traditional breeding has been difficult to achieve...... but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle...

  9. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    Directory of Open Access Journals (Sweden)

    Rocío Pineda-Martos

    2014-01-01

    Full Text Available Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms.

  10. Short communication: Genetic evaluation of mobility for Brown Swiss dairy cattle

    Science.gov (United States)

    Genetic parameters were estimated for mobility score and 16 linear type traits of Brown Swiss dairy cattle. Mobility is an overall assessment trait that measures a cow’s ability to move as well as the structure of her feet, pasterns, and legs. Scores from 50 to 99 were assigned by appraisers for the...

  11. Genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle

    Science.gov (United States)

    Stillbirth (SB) has been associated with reduced milk yield, compromised reproductive performance, and decreased dam longevity. Genetic evaluations for stillbirth were initiated in 2006 for Holsteins (HO) in the US, but evaluations for Brown Swiss (BS) and Jersey (JE) cattle were not feasible at tha...

  12. Genetic analysis of superovulation and embryo transfer traits in Holstein cattle

    Science.gov (United States)

    The objectives of this study were to estimate variance components and investigate genomic regions of interest associated with superovulation and embryo transfer in dairy cattle. Superovulation and embryo transfer are methods commonly used by dairy producers to increase the rate of genetic gain achie...

  13. Cattle sex-specific recombination and genetic control from a very large pedigree

    Science.gov (United States)

    Meiotic recombination is an essential biological process that generates novel genetic variants and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half million genotyped animals, we extracted 186,927 three-generation families, identified ov...

  14. Genetic relationships between calving performance and beef production traits in Piemontese cattle

    NARCIS (Netherlands)

    Albera, A.; Groen, A.F.; Carnier, P.

    2004-01-01

    The aim of the study was to obtain estimates of genetic correlations between direct and maternal calving performance of heifers and cows and beef production traits in Piemontese cattle. Beef production traits were daily gain, live fleshiness, and bone thinness measured on 1,602 young bulls tested at

  15. Impact of transgenic insect resistance in introgressed wild Brassica populations

    OpenAIRE

    Liu, Yong-Bo; Wei, Wei; Tang, Zhi Xi; Stewart, C. Neal Jr.; Ma, Ke-Ping; Darmency, Henri

    2012-01-01

    Gene flow between crops and their wild relatives may lead to interspecific hybrids and result in the introgression in weed populations of any novel trait breeded in the crop. Transgenes are typically novel genetic constructions aimed to improve agronomic quality of crops. Consequently, introgression from genetically modified crops to their relatives might increase the fitness of receiving plants and impact the dynamics and invasiveness of related weeds. In particular, it is a concern in the c...

  16. Oocyte development in cattle: physiological and genetic aspects

    OpenAIRE

    Jack H. Britt

    2008-01-01

    Oocytes in cattle are formed during embryogenesis and develop within individual follicles in the cortex of the ovary. Dormant primordial follicles become active and undergo progressive development at regular intervals commencing during the late fetal stage and continuing throughout adulthood. Once activated, follicles and oocytes in a cohort either grow to maturation and ovulation or undergo atresia, ultimately depleting the ovaries of germ cells. It takes an estimated 100 days for a follicle...

  17. Characterizing the physical and genetic structure of the lodgepole pine × jack pine hybrid zone: mosaic structure and differential introgression

    OpenAIRE

    Cullingham, Catherine I; James, Patrick M. A.; Cooke, Janice E.K.; Coltman, David W

    2012-01-01

    Understanding the physical and genetic structure of hybrid zones can illuminate factors affecting their formation and stability. In north-central Alberta, lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia) and jack pine (Pinus banksiana Lamb) form a complex and poorly defined hybrid zone. Better knowledge of this zone is relevant, given the recent host expansion of mountain pine beetle into jack pine. We characterized the zone by genotyping 1998 lodgepole, jack pine, and hybrids f...

  18. Characterizing the physical and genetic structure of the lodgepole pine × jack pine hybrid zone: mosaic structure and differential introgression.

    Science.gov (United States)

    Cullingham, Catherine I; James, Patrick M A; Cooke, Janice E K; Coltman, David W

    2012-12-01

    Understanding the physical and genetic structure of hybrid zones can illuminate factors affecting their formation and stability. In north-central Alberta, lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia) and jack pine (Pinus banksiana Lamb) form a complex and poorly defined hybrid zone. Better knowledge of this zone is relevant, given the recent host expansion of mountain pine beetle into jack pine. We characterized the zone by genotyping 1998 lodgepole, jack pine, and hybrids from British Columbia, Alberta, Saskatchewan, Ontario, and Minnesota at 11 microsatellites. Using Bayesian algorithms, we calculated genetic ancestry and used this to model the relationship between species occurrence and environment. In addition, we analyzed the ancestry of hybrids to calculate the genetic contribution of lodgepole and jack pine. Finally, we measured the amount of gene flow between the pure species. We found the distribution of the pine classes is explained by environmental variables, and these distributions differ from classic distribution maps. Hybrid ancestry was biased toward lodgepole pine; however, gene flow between the two species was equal. The results of this study suggest that the hybrid zone is complex and influenced by environmental constraints. As a result of this analysis, range limits should be redefined. PMID:23346232

  19. Genetic diversity measures of local European beef cattle breeds for conservation purposes

    Directory of Open Access Journals (Sweden)

    Pereira Albano

    2001-05-01

    Full Text Available Abstract This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean Fst = 0.07; P

  20. [Genetic variation and phylogeography of the bank vole (Clethrionomys glareolus, Arvicolinae, Rodentia) in Russia with special reference to the introgression of the mtDNA of a closely related species, red-backed vole (C. rutilus)].

    Science.gov (United States)

    Abramson, N I; Rodchenkova, E N; Kostygov, A Iu

    2009-05-01

    Totally, 294 bank voles (Clethrionomys glareolus) and 18 red-backed voles (C. rutilus) from 62 sites of European Russia were studied. Incomplete sequences (967 bp) of the mitochondrial cytochrome b gene were determined for 93 C. glareolus individuals from 56 sites and 18 C. rutilus individuals from the same habitats. Analysis of the cytochrome b gene variation has demonstrated that practically the entire European part of Russia, Ural, and a considerable part of Western Europe are inhabited by bank voles of the same phylogroup, displaying an extremely low genetic differentiation. Our data suggest that C. glareolus very rapidly colonized over the presently occupied territory in the post-Pleistocene period from no more than two (central European and western European) refugia for ancestral populations with a small efficient size. PCR typing of the mitochondrial cytochrome b gene allowed us to assess the scale of mtDNA introgression from a closely related species, C. rutilus, and to outline the geographical zone of this introgression. Comparison with the red-backed vole haplotypes in the habitats shared by both species favors the hypothesis of an ancient hybridization event (mid-Holocene) and a subsequent introgression. These results suggest that the hybridization took place in the southern and middle Pre-Ural region. PMID:19534420

  1. Genetic background effects on QTL and QTL × environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice

    Institute of Scientific and Technical Information of China (English)

    Xiaoqian; Wang; Yunlong; Pang; Jian; Zhang; Qiang; Zhang; Yonghong; Tao; Bo; Feng; Tianqing; Zheng; Jianlong; Xu; Zhikang; Li

    2014-01-01

    QTLs for quantitative traits are influenced by genetic background(GB) and environment.Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection(MAS). In this study, QTLs and QTL × environment interactions affecting grain yield per plant(GY) and its component traits, filled grain number per panicle(FGN), panicle number per plant(PN) and 1000-grain weight(TGW) across six environments were dissected using two sets of reciprocal introgression lines(ILs) derived from the cross Lemont × Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs(87.4%) showed significant QTL × environment interactions(QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15(20.8%) QTLs and 12(16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail.

  2. Mycobacterium bovis in Burkina Faso: epidemiologic and genetic links between human and cattle isolates.

    Directory of Open Access Journals (Sweden)

    Adama Sanou

    2014-10-01

    Full Text Available In sub-Saharan Africa, bovine tuberculosis (bTB is a potential hazard for animals and humans health. The goal of this study was to improve our understanding of bTB epidemiology in Burkina Faso and especially Mycobacterium bovis transmission within and between the bovine and human populations.Twenty six M. bovis strains were isolated from 101 cattle carcasses with suspected bTB lesions during routine meat inspections at the Bobo Dioulasso and Ouagadougou slaughterhouses. In addition, 7 M. bovis strains were isolated from 576 patients with pulmonary tuberculosis. Spoligotyping, RDAf1 deletion and MIRU-VNTR typing were used for strains genotyping. The isolation of M. bovis strains was confirmed by spoligotyping and 12 spoligotype signatures were detected. Together, the spoligotyping and MIRU-VNTR data allowed grouping the 33 M. bovis isolates in seven clusters including isolates exclusively from cattle (5 or humans (1 or from both (1. Moreover, these data (genetic analyses and phenetic tree showed that the M. bovis isolates belonged to the African 1 (Af1 clonal complex (81.8% and the putative African 5 (Af5 clonal complex (18.2%, in agreement with the results of RDAf1 deletion typing.This is the first detailed molecular characterization of M. bovis strains from humans and cattle in Burkina Faso. The distribution of the two Af1 and putative Af5 clonal complexes is comparable to what has been reported in neighbouring countries. Furthermore, the strain genetic profiles suggest that M. bovis circulates across the borders and that the Burkina Faso strains originate from different countries, but have a country-specific evolution. The genetic characterization suggests that, currently, M. bovis transmission occurs mainly between cattle, occasionally between cattle and humans and potentially between humans. This study emphasizes the bTB risk in cattle but also in humans and the difficulty to set up proper disease control strategies in Burkina Faso.

  3. Prevalence, quantitative load and genetic diversity of Campylobacter spp. in dairy cattle herds in Lithuania

    Science.gov (United States)

    2013-01-01

    Background Campylobacteriosis is a zoonotic disease, and animals such as poultry, pigs and cattle may act as reservoirs for Campylobacter spp. Cattle shed Campylobacter spp. into the environment and they can act as a reservoir for human infection directly via contact with cattle or their faeces or indirectly by consumption of contaminated food. The aim of this study was to determine the prevalence, the quantitative load and the genetic strain diversity of Campylobacter spp. in dairy cattle of different age groups. Results Faecal samples of 200 dairy cattle from three farms in the central part of Lithuania were collected and examined for Campylobacter. Cattle herds of all three farms were Campylobacter spp. positive, with a prevalence ranging from 75% (farm I), 77.5% (farm II) to 83.3% (farm III). Overall, the highest prevalence was detected in calves (86.5%) and heifers (86.2%). In contrast, the lowest Campylobacter prevalence was detectable in dairy cows (60.6%). C. jejuni, C. coli, C. lari and C. fetus subsp. fetus were identified in faecal samples of dairy cattle. C. upsaliensis was not detectable in any sample. The high counts of Campylobacter spp. were observed in faecal material of dairy cattle (average 4.5 log10 cfu/g). The highest numbers of Campylobacter spp. were found in faecal samples from calves (average 5.3 log10 cfu/g), whereas, faecal samples from cows harboured the lowest number of Campylobacter spp. (average 3.7 log10 cfu/g). Genotyping by flaA PCR-RFLP analysis of selected C. jejuni isolates showed that some genotypes were present in all farms and all age groups. However, farm or age specific genotypes were also identified. Conclusions Future studies are needed to investigate risk factors related to the degree of colonisation in cattle. Based on that, possible measures to reduce the colonisation and subsequent shedding of Campylobacter in cattle could be established. It is important to further investigate the epidemiology of Campylobacter in the

  4. Occurrence and genetic characterization of Echinococcus granulosus in naturally infected adult sheep and cattle in Romania.

    Science.gov (United States)

    Mitrea, Ioan Liviu; Ionita, Mariana; Costin, Irina Ioana; Predoi, Gabriel; Avram, Eugeniu; Rinaldi, Laura; Maurelli, Maria Paola; Cringoli, Giuseppe; Genchi, Claudio

    2014-12-15

    An epidemiological and molecular study was conducted to investigate the occurrence and genetic diversity of Echinococcus granulosus isolates from adult sheep and cattle in Romania. Overall, 642 sheep (aged over 3 years) and 1878 cattle (aged over 5 years) from 16 counties were examined for hydatid cysts. Of them, 421 (65.6%) sheep and 754 (40.1%) cattle were found infected by cystic echinococcosis (CE). Germinal layers were collected from 98 individual cysts (one cyst per animal; 31 from sheep and 67 from cattle), DNA was extracted and two different mitochondrial DNA genes, namely cytochrome c oxidase subunits 1 (CO1) and 12S ribosomal DNA (12S rDNA) were used as genetic markers. The assessment of the genetic diversity of the Echinococcus strains showed the presence of the E. granulosus sensu stricto complex and disclosed an apparent dominance of the G1 genotype within the G1–G3 complex. Furthermore, several mitochondrial variants were identified for the G1 and G2 genotypes of E. granulosus s.s. complex. Overall, the findings were of epidemiological relevance and highlighted a high potential risk of zoonotic infection.

  5. Systems Genetics and Transcriptomics of Feed Efficiency in Dairy Cattle

    DEFF Research Database (Denmark)

    Salleh, Suraya Binti Mohamad; Hoglund, J.; Løvendahl, P.;

    Feed is the largest variable cost in milk production industries, thus improving feed efficiency will give better use of resources. This project works closely on definitions of feed efficiency in dairy cattle and uses advanced integrated genomics, bioinformatics and systems biology methods linking...... are of high or low efficiency. mRNA will be extracted from liver biopsies samples for RNA-sequencing which will be performed on the Illumina HiSeq2500. Blood samples will be collected for genotyping and plasma. Plasma will be extracted from the blood for analysis of glucose, NEFA, β...

  6. Nuclear introgression without mitochondrial introgression in two turtle species exhibiting sex-specific trophic differentiation.

    Science.gov (United States)

    Mitchell, Sarah M; Muehlbauer, Laura K; Freedberg, Steven

    2016-05-01

    Despite the presence of reproductive barriers between species, interspecific gene introgression has been documented in a range of natural systems. Comparing patterns of genetic introgression in biparental versus matrilineal markers can potentially reveal sex-specific barriers to interspecific gene flow. Hybridization has been documented in the freshwater turtles Graptemys geographica and G. pseudogeographica, whose ranges are largely sympatric. Morphological differentiation between the species is restricted to females, with female G. geographica possessing large heads and jaws compared to the narrow heads of G. pseudogeographica females. If hybrid females are morphologically intermediate, they may be less successful at exploiting parental feeding niches, thereby limiting the introgression of maternally inherited, but not biparental, molecular markers. We paired sequence data with stable isotope analysis and examined sex-specific genetic introgression and trophic differentiation in sympatric populations of G. geographica and G. pseudogeographica. We observed introgression from G. pseudogeographica into G. geographica at three nuclear loci, but not at the mitochondrial locus. Analysis of ∂(15)N and ∂(13)C was consistent with species differences in trophic positioning in females, but not males. These results suggest that ecological divergence in females may reduce the opportunity for gene flow in this system. PMID:27252833

  7. Genetic parameter estimation for pre- and post-weaning traits in Brahman cattle in Brazil.

    Science.gov (United States)

    Vargas, Giovana; Buzanskas, Marcos Eli; Guidolin, Diego Gomes Freire; Grossi, Daniela do Amaral; Bonifácio, Alexandre da Silva; Lôbo, Raysildo Barbosa; da Fonseca, Ricardo; Oliveira, João Ademir de; Munari, Danísio Prado

    2014-10-01

    Beef cattle producers in Brazil use body weight traits as breeding program selection criteria due to their great economic importance. The objectives of this study were to evaluate different animal models, estimate genetic parameters, and define the most fitting model for Brahman cattle body weight standardized at 120 (BW120), 210 (BW210), 365 (BW365), 450 (BW450), and 550 (BW550) days of age. To estimate genetic parameters, single-, two-, and multi-trait analyses were performed using the animal model. The likelihood ratio test was verified between all models. For BW120 and BW210, additive direct genetic, maternal genetic, maternal permanent environment, and residual effects were considered, while for BW365 and BW450, additive direct genetic, maternal genetic, and residual effects were considered. Finally, for BW550, additive direct genetic and residual effects were considered. Estimates of direct heritability for BW120 were similar in all analyses; however, for the other traits, multi-trait analysis resulted in higher estimates. The maternal heritability and proportion of maternal permanent environmental variance to total variance were minimal in multi-trait analyses. Genetic, environmental, and phenotypic correlations were of high magnitude between all traits. Multi-trait analyses would aid in the parameter estimation for body weight at older ages because they are usually affected by a lower number of animals with phenotypic information due to culling and mortality. PMID:25037588

  8. Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens.

    Science.gov (United States)

    Chen, Jie; Moinard, Magalie; Xu, Jianping; Wang, Shouxian; Foulongne-Oriol, Marie; Zhao, Ruilin; Hyde, Kevin D; Callac, Philippe

    2016-01-01

    The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated. PMID:27228131

  9. Effects of introgression on the genetic population structure of two ecologically and economically important conifer species: lodgepole pine (Pinus contorta var. latifolia) and jack pine (Pinus banksiana).

    Science.gov (United States)

    Cullingham, Catherine I; Cooke, Janice E K; Coltman, David W

    2013-10-01

    Forest trees exhibit a remarkable range of adaptations to their environment, but as a result of frequent and long-distance gene flow, populations are often only weakly differentiated. Lodgepole and jack pine hybridize in western Canada, which adds the opportunity for introgression through hybridization to contribute to population structure and (or) adaptive variation. Access to large sample size, high density SNP datasets for these species would improve our ability to resolve population structure, parameterize introgression, and separate the influence of demography from adaptation. To accomplish this, 454 transcriptome reads for lodgepole and jack pine were assembled using Newbler and MIRA, the assemblies mined for SNPs, and 1536 SNPs were selected for typing on lodgepole pine, jack pine, and their hybrids (N = 536). We identified population structure using both Bayesian clustering and discriminate analysis of principle components. Introgressed SNP loci were identified and their influence on observed population structure was assessed. We found that introgressed loci resulted in increased differentiation both within lodgepole and jack pine populations. These findings are timely given the recent mountain pine beetle population expansion in the hybrid zone, and will facilitate future studies of adaptive traits in these ecologically important species. PMID:24237338

  10. Genetics and genomics of reproductive performance in dairy and beef cattle.

    Science.gov (United States)

    Berry, D P; Wall, E; Pryce, J E

    2014-05-01

    Excellent reproductive performance in both males and females is fundamental to profitable dairy and beef production systems. In this review we undertook a meta-analysis of genetic parameters for female reproductive performance across 55 dairy studies or populations and 12 beef studies or populations as well as across 28 different studies or populations for male reproductive performance. A plethora of reproductive phenotypes exist in dairy and beef cattle and a meta-analysis of the literature suggests that most of the female reproductive traits in dairy and beef cattle tend to be lowly heritable (0.02 to 0.04). Reproductive-related phenotypes in male animals (e.g. semen quality) tend to be more heritable than female reproductive phenotypes with mean heritability estimates of between 0.05 and 0.22 for semen-related traits with the exception of scrotal circumference (0.42) and field non-return rate (0.001). The low heritability of reproductive traits, in females in particular, does not however imply that genetic selection cannot alter phenotypic performance as evidenced by the decline until recently in dairy cow reproductive performance attributable in part to aggressive selection for increased milk production. Moreover, the antagonistic genetic correlations among reproductive traits and both milk (dairy cattle) and meat (beef cattle) yield is not unity thereby implying that simultaneous genetic selection for both increased (milk and meat) yield and reproductive performance is indeed possible. The required emphasis on reproductive traits within a breeding goal to halt deterioration will vary based on the underlying assumptions and is discussed using examples for Ireland, the United Kingdom and Australia as well as quantifying the impact on genetic gain for milk production. Advancements in genomic technologies can aid in increasing the accuracy of selection for especially reproductive traits and thus genetic gain. Elucidation of the underlying genomic mechanisms for

  11. Calving Performance in the Endangered Murboden Cattle Breed: Genetic Parameters and Inbreeding Depression

    Directory of Open Access Journals (Sweden)

    Sophie A.e. Eaglen

    2013-09-01

    Full Text Available Calving is a key event on any cattle farm, with both economic and animal welfare consequences when complications arise. Although mostly reported in highly selected breeds, problematic calving performance is also a worry to the unselected dualpurpose Murboden breed, local to Austria. This study presents genetic parameter estimates for calving ease and stillbirth in Murboden cattle. Furthermore, a potential effect of inbreeding on the breeds’ calving performance is evaluated. Results show a moderate direct and maternal heritability (0.18±0.04; 0.11±0.02 and a significant negative direct-maternal genetic correlation for calving ease (-0.41±0.10. Heritabilities of stillbirth are low yet significant (0.048±0.01; 0.018±0.007. A significant effect of inbreeding was detected on maternal calving ease i.e. the ease with which a dam calves. By categorizing the inbreeding coefficients of the dam in six ascending classes it was shown that calving ease worsens as inbreeding coefficients become larger. Results of this study reveal significant genetic variation in calving performance of the Murboden breed which opens doors for genetic selection. An additional important aspect of this study is that its result on inbreeding depression gives counterweight to the general intuitive notion in literature that high selection for production traits is the major contributor to calving difficulty in dairy and beef cattle breeds worldwide.

  12. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle.

    Science.gov (United States)

    Bickhart, Derek M; Xu, Lingyang; Hutchison, Jana L; Cole, John B; Null, Daniel J; Schroeder, Steven G; Song, Jiuzhou; Garcia, Jose Fernando; Sonstegard, Tad S; Van Tassell, Curtis P; Schnabel, Robert D; Taylor, Jeremy F; Lewin, Harris A; Liu, George E

    2016-06-01

    The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1 Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future. PMID:27085184

  13. Genetic polymorphisms at the leptin receptor gene in three beef cattle breeds

    Directory of Open Access Journals (Sweden)

    Sabrina E.M. Almeida

    2008-01-01

    Full Text Available The genetic diversity of a single nucleotide polymorphism (SNP at the exon 20 (T945M of the leptin receptor gene (LEPR and of three short tandem repeats (STRs BM7225, BMS694, and BMS2145 linked to LEPR was investigated in three beef cattle herds (Brangus Ibagé, Charolais, and Aberdeen Angus. A cheap and effective new method to analyze the T945M polymorphism in cattle populations was developed and the possible role of these polymorphisms in reproduction and weight gain of postpartum cows was evaluated. High levels of genetic diversity were observed with the average heterozygosity of STRs ranging from 0.71 to 0.81. No significant association was detected between LEPR markers and reproductive parameters or daily weight gain. These negative results suggest that the LEPR gene polymorphisms, at least those herein described, do not influence postpartum cows production.

  14. Genomic contributions in livestock gene introgression programmes

    Directory of Open Access Journals (Sweden)

    Hospital Frédéric

    2005-05-01

    Full Text Available Abstract The composition of the genome after introgression of a marker gene from a donor to a recipient breed was studied using analytical and simulation methods. Theoretical predictions of proportional genomic contributions, including donor linkage drag, from ancestors used at each generation of crossing after an introgression programme agreed closely with simulated results. The obligate drag, the donor genome surrounding the target locus that cannot be removed by subsequent selection, was also studied. It was shown that the number of backcross generations and the length of the chromosome affected proportional genomic contributions to the carrier chromosomes. Population structure had no significant effect on ancestral contributions and linkage drag but it did have an effect on the obligate drag whereby larger offspring groups resulted in smaller obligate drag. The implications for an introgression programme of the number of backcross generations, the population structure and the carrier chromosome length are discussed. The equations derived describing contributions to the genome from individuals from a given generation provide a framework to predict the genomic composition of a population after the introgression of a favourable donor allele. These ancestral contributions can be assigned a value and therefore allow the prediction of genetic lag.

  15. Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle

    DEFF Research Database (Denmark)

    Ali, A.; O'Neill, C.J.; Thomson, P.C.;

    2012-01-01

    Background: Infectious bovine keratoconjunctivitis (IBK) or 'pinkeye' is an economically important ocular disease that significantly impacts animal performance. Genetic parameters for IBK infection and its genetic and phenotypic correlations with cattle tick counts, number of helminth (unspecified...... species) eggs per gram of faeces and growth traits in Australian tropically adapted Bos taurus cattle were estimated. Methods: Animals were clinically examined for the presence of IBK infection before and after weaning when the calves were 3 to 6 months and 15 to 18 months old, respectively and were also...... counts. Conclusions: Our results suggest that genetic selection against IBK incidence in tropical cattle is feasible and that calves genetically prone to acquire IBK infection could also be genetically prone to have a slower growth. The positive genetic correlations among weight traits and between tick...

  16. Genetic analysis on accumulated productivity and calving intervals in Nelore cattle.

    Science.gov (United States)

    Grossi, Daniela do Amaral; Berton, Mariana Piatto; Buzanskas, Marcos Eli; Chud, Tatiane Cristina Seleguim; Grupioni, Natália Vinhal; de Paz, Claudia Cristina Paro; Lôbo, Raysildo Barbosa; Munari, Danísio Prado

    2016-01-01

    The aim of this study was to estimate genetic parameters for accumulated productivity (ACP), first calving interval (CI1), second calving interval (CI2), and mean calving interval (MCI) in Nelore beef cattle. The ACP trait is a reproduction index and comprises the total number of calves born per dam, weight of weaned calves, and age of the dam at calving. Genetic parameters were estimated by the average information restricted maximum likelihood method in two-trait analyses. The average heritability estimate for ACP was 0.17 (0.03). For CI1, CI2, and MCI, the heritability estimates were 0.02, 0.02, and 0.06, respectively. Genetic correlations between ACP with CI1, CI2, and MCI were -0.16 ± 0.47, -0.29 ± 0.53, and -0.40 ± 0.27, respectively. Despite of the low heritability estimates obtained in our study, reproduction traits should be further studied and their inclusion in the selection criteria must be evaluated in order to improve the performance of females because these traits are of great economic importance in beef cattle. Accumulated productivity could contribute to decrease the mean calving interval in Nelore cattle.

  17. Genetic parameters for carcass cut weight in Irish beef cattle.

    Science.gov (United States)

    Pabiou, T; Fikse, W F; Näsholm, A; Cromie, A R; Drennan, M J; Keane, M G; Berry, D P

    2009-12-01

    The objective of this study was to estimate genetic parameters for the weights of different wholesale cuts, using an experimental and a commercial data set. The experimental and commercial data sets included 413 and 635 crossbred Belgian Blue, Charolais, Limousin, Angus, Holstein, and Simmental animals, respectively. Univariate analyses using a mixed linear animal model with relationships were undertaken to estimate the heritability of cold carcass weight, carcass conformation and fat, and the cut weights, whereas a series of bivariate analyses was used to estimate the phenotypic and genetic correlations between carcass weight, carcass conformation, carcass fat, and the major primal cuts. Heritability estimates for cold carcass weight in both data sets were moderate (>0.48), whereas heritability estimates for carcass conformation and fat grading were greater in the commercial data set (>0.63) than in the experimental study (>0.33). Across both data sets, heritability estimates for wholesale cut weight in the forequarter varied from 0.03 to 0.79, whereas heritability estimates of carcass cut weight in the hindquarter varied from 0.14 to 0.86. Heritability estimates for cut weights expressed as a proportion of the entire carcass weight varied from 0.04 to 0.91. Genetic correlations were strong among the different carcass cut weights within the experimental and the commercial studies. Genetic correlations between the weights of selected carcass cuts and carcass weight were moderate to high (minimum 0.45; maximum 0.88) in both data sets. Positive genetic correlations were observed in the commercial data set between the different wholesale cut weights and carcass conformation, whereas these were positive and negative in the experimental data set. Selection for increased carcass weight will, on average, increase the weight of each cut. However, the genetic correlations were less than unity, suggesting a benefit of more direct selection on high value cuts. PMID:19717761

  18. Genetic parameters for docility, weaning weight, yearling weight, and intramuscular fat percentage in Hereford cattle.

    Science.gov (United States)

    Torres-Vázquez, J A; Spangler, M L

    2016-01-01

    Cattle behavior, including measures of docility, is important to beef cattle producers not only from a human safety perspective but also due to potential correlations to economically relevant traits. Field data from the American Hereford Association was used to estimate genetic parameters for chute score (CS; = 25,037), weaning weight (WW; = 24,908), yearling weight (YW; = 23,978), and intramuscular fat percentage (IMF; = 12,566). Single-trait and bivariate animal models were used to estimate heritabilities and genetic correlations. All models included fixed effects of sex and contemporary group, defined as herd-year-season, and direct genetic and residual components were included as random effects. For CS and WW, additional random effects of maternal genetic and maternal permanent environment were also fitted. For CS, WW, YW, and IMF, heritability estimates were 0.27 ± 0.02, 0.35 ± 0.03, 0.36 ± 0.02, and 0.27 ± 0.02, respectively. Genetic correlations between CS and WW, CS and YW, CS and IMF, WW and YW, WW and IMF, and YW and IMF were -0.12 ± 0.06, -0.10 ± 0.05, -0.08 ± 0.06, 0.47 ± 0.05, -0.19 ± 0.09, and -0.41 ± 0.05, respectively. Heritability estimates for all traits suggest that they would respond favorably to selection and that selection for increased WW or YW could decrease marbling. Genetic correlations between CS and WW, YW, and IMF were all favorable but weak, suggesting that selection for improved docility will not have negative consequences on growth or carcass quality. Furthermore, maternal additive and maternal permanent environmental variances for CS were near 0, suggesting that their inclusion in National Cattle Evaluations is not warranted.

  19. Association of genetic markers in cattle receiving differing implant protocols

    Science.gov (United States)

    The potential interaction of growth-promoting implants and genetic markers previously reported to be associated with growth, carcass traits, and tenderness was evaluated. Two implant protocols were applied to subsets of steers (n=383) and heifers (n=65) that were also genotyped for 47 SNP reported ...

  20. Short communication: Genetic variants of Sarcocystis cruzi in infected Malaysian cattle based on 18S rDNA.

    Science.gov (United States)

    Ng, Yit Han; Fong, Mun Yik; Subramaniam, Vellayan; Shahari, Shahhaziq; Lau, Yee Ling

    2015-12-01

    Sarcocystis species are pathogenic parasites that infect a wide range of animals, including cattle. A high prevalence of cattle sarcocystosis has been reported worldwide, but its status is unknown in Malaysia. This study focused on utilizing 18S rDNA to identify Sarcocystis species in Malaysian cattle and to determine their genetic variants. In this study, only Sarcocystis cruzi was detected in Malaysian cattle. The intra-species S. cruzi phylogenetic tree analysis and principal coordinate analysis (PCoA), respectively displayed two minor groups among the parasite isolates. This finding was supported by high Wright FST value (FST=0.647). The definitive hosts (dogs) may play a fundamental role in the development of S. cruzi genetic variants. Additionally, the existence of microheterogeneity within the S. cruzi merozoites and/or distinct genetic variants arisen from independent merozoites in mature sarcocysts, possibly contributed to the existence of intra-species variations within the population.

  1. Genetic Architecture of Milk, Fat, Protein, Mastitis and Fertility Studied using NGS Data in Holstein Cattle

    DEFF Research Database (Denmark)

    Sahana, Goutam; Janss, Luc; Guldbrandtsen, Bernt;

    cattle using NGS variants. The analysis was done using a linear mixed model (LMM) and a Bayesian mixture model (BMM). The top 10 QTL identified by LMM analyses explained 22.61, 23.86, 10.88, 18.58 and 14.83% of the total genetic variance for these traits respectively. Trait-specific sets of 4,964 SNPs...... from NGS variants (most ‘associated’ SNP for each 0.5 Mbp bin) explained 81.0, 81.6, 85.0, 60.4 and 70.9% of total genetic variance for milk, fat, protein, mastitis and fertility indices when analyzed simultaneously by BMM...

  2. Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression

    OpenAIRE

    Murray, Gemma GR; Woolhouse, Mark EJ; Tapio, Miika; Mary N Mbole-Kariuki; Tad S. Sonstegard; Thumbi, Samuel M; Jennings, Amy E.; VAN WYK, ILANA CONRADIE; Chase-Topping, Margo; Kiara, Henry; TOYE, PHIL; Coetzer, Koos; deC Bronsvoort, Barend M; Hanotte, Olivier

    2013-01-01

    Background Positive multi-locus heterozygosity-fitness correlations have been observed in a number of natural populations. They have been explained by the correlation between heterozygosity and inbreeding, and the negative effect of inbreeding on fitness (inbreeding depression). Exotic introgression in a locally adapted population has also been found to reduce fitness (outbreeding depression) through the breaking-up of co-adapted genes, or the introduction of non-locally adapted gene variants...

  3. Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression

    OpenAIRE

    Murray, Gemma G. R.; Woolhouse, Mark; Tapio, Miika; Mbole-Kariuki, Mary Ndila; Thumbi, Samuel Mwangi; Jennings, Amy; Conradie van Wyk, Ilana; Kiara, Henry; Toye, Philip G.; Coetzer, J.A.W.; Bronsvoort, Mark; Hanotte, Olivier; Sonstegard, Tad; Chase-Topping, Margo

    2013-01-01

    BackgroundPositive multi-locus heterozygosity-fitness correlations have been observed in a number of natural populations. They have been explained by the correlation between heterozygosity and inbreeding, and the negative effect of inbreeding on fitness (inbreeding depression). Exotic introgression in a locally adapted population has also been found to reduce fitness (outbreeding depression) through the breaking-up of co-adapted genes, or the introduction of non-locally adapted gene variants....

  4. Genetic selection strategies to improve longevity in Chianina beef cattle

    Directory of Open Access Journals (Sweden)

    Piter Bijma

    2010-01-01

    Full Text Available Longevity in beef cattle is an important economic trait. Including this trait in a breeding scheme increases profit and has a positive impact on the well-being and welfare of the animals. The aim of the present study was to evaluate the conse- quences of alternative selection strategies to include longevity in different breeding schemes using deterministic simula- tion. Different schemes were compared and economic (EcW and empirical weights (EmW were used to evaluate the responses. The empirical weights of average daily gain (ADG and muscularity (MU were identical because both traits have an identical importance for the breeders. Economic weights have been derived from profit equations. Traits used in the Basescenarios were: average daily gain pre-performance test (ADG1, average daily gain during the performance test (ADG2 and muscularity (MU; longevity (L was included in the alternative schemes. When longevity was included both in the breeding index and in the breeding goal (scenario A-2, the total longevity response using EmW and EcW was +2.97 d/yr and +4.92 d/yr, respectively. The total economic response for scenario A-2 using EmW and EcW were 3.020 €/yr and 3.342 €/yr, respectively, and the total response in units of Bull Selection Index were +0.699 and +0.678, respectively. Longevity decreased when it was not included in either the breeding goal or in the breeding index (scenario Base, and economic response was the lowest found. The results of the current study indicate that the highest total response using either economic weights or empirical weights was found when information on longevity was included both in the breeding index and in the breeding goal (scenario A-2.

  5. Genetic relationships between internal diseases diagnosed at slaughter and carcass traits in Japanese Black cattle.

    Science.gov (United States)

    Inoue, K; Honda, T; Oyama, K

    2015-06-01

    The objective of this paper was to estimate the genetic parameters of certain internal diseases (multifocal necrosis in the liver [MNL], bovine abdominal fat necrosis [BFN], and inflammation of the large intestine [ILI]) and to investigate relationships between the internal diseases and carcass traits (carcass weight [CW], rib eye area [REA], rib thickness [RT], subcutaneous fat thickness, and beef marbling score [BMS]). Records of the internal diseases and the carcass traits of 5,788 Japanese Black cattle were used for this study. The data for all the diseases were recorded as binary data as to whether the disease was observed (1) or not (0). Genetic parameters were estimated using linear and threshold animal models. The prevalence rates of MNL, BFN, and ILI were 16.1, 23.0, and 6.8%, respectively, and heritability estimates ± posterior SD were 0.18 ± 0.06, 0.28 ± 0.06, and 0.18 ± 0.06, respectively. The genetic correlations of MNL with BFN and ILI were -0.23 (P = 0.19) and -0.49 (P genetic correlations of MNL with the carcass traits were all weak and not significant. In contrast, the genetic correlations of BFN and ILI with CW, REA, and RT were all negative and significant (P genetic correlations for BFN and ILI with BMS were all positive at 0.21 P( = 0.16) and 0.39 (P genetically improved. Genetic relationships of BFN and ILI with meat quantity traits were favorable for beef cattle breeding, because lower disease liabilities were associated with improved CW, REA, and RT for BFN and ILI. However, rather strong and unfavorable genetic relationships were found between BFN or ILI and BMS, which is related to meat quality. This suggests that selection for animals with superior BMS would increasingly lead to animals with higher liability to the internal diseases.

  6. Genetic parameter estimates for carcass and yearling ultrasound measurements in Brangus cattle.

    Science.gov (United States)

    Moser, D W; Bertrand, J K; Misztal, I; Kriese, L A; Benyshek, L L

    1998-10-01

    Carcass measurements of 12th-rib fat thickness (CARCFAT), longissimus muscle area (CARCLMA), and weight (CARCWT) on 2,028 Brangus and Brangus-sired fed steers and heifers, as well as yearling weights (YWT) and ultrasound measures of 12th-rib fat thickness (USFAT) and longissimus muscle area (USLMA) on 3,583 Brangus bulls and heifers were analyzed to estimate genetic parameters. Data were analyzed using a six-trait animal model and an average information REML algorithm. The model included fixed effects for contemporary group and breed of dam, covariates for age at slaughter or measurement, and random animal and residual effects. Heritabilities for CARCFAT, CARCLMA, CARCWT, USFAT, USLMA, and YWT were .27+/-.05, .39+/-.05, .59+/-.06, .11+/-.03, .29+/-.04, and .40+/-.04, respectively. Genetic correlations between CARCFAT and USFAT, CARCLMA and USLMA, and CARCWT and YWT were .69+/-.18, .66+/-.14, and .61+/-.11, respectively. The favorable and moderately strong genetic correlations between carcass measurements and similar yearling breeding-animal ultrasound measurements indicate that such measurements of 12th-rib fat and longissimus muscle area are useful in predicting genetic values for carcass leanness and longissimus muscle area. Selection using yearling ultrasound measurements of breeding cattle should result in predictable genetic improvement for carcass characteristics. Inclusion of yearling ultrasound measurements for fat thickness and longissimus muscle area should enhance national cattle evaluation programs. PMID:9814892

  7. REVIEW: The Characteristics of Genetic Resource of Bali Cattle (Bos-bibos banteng and the Alternative of It's Conservation Methods

    Directory of Open Access Journals (Sweden)

    ACHMAD NUR CHAMDI

    2005-01-01

    Full Text Available Bali cattle is an Indonesian native beef cattle, the result of domestication of Banteng (Bos-bibos banteng. The main problem faced in the development of Bali cattle is the low quality of breed, which is predicted as the effect of inbreeding or raising management. The affects of genetic and cross breeding which usually inflict a loss are the decreasing of cattle’s endurance, fertility and birth weight. Seeing the fact, the government effort to introduce a quality bull to the breed source areas, the determination of cattle release including the controll on the cutting of productive female cattle, and to exactly count the number of Bali cattle which can be released in order to do not disturb its population balance, so it is necessary to do conservation attempt by in-situ and ex-situ. The result of this study shows that the characteristics on genetic resource of Bali cattle which comprises documentation, evaluation on reproduction and production, and attempt in increasing Bali cattle’s genetic quality in Indonesia have been done, eventhough those are still limited.

  8. Genetic Factors Affecting Performance Traits of Sahiwal Cattle in Pakistan

    Directory of Open Access Journals (Sweden)

    Z. Rehman*§ and M. S. Khan1

    2012-06-01

    Full Text Available Data on 23925 lactations of 5897 Sahiwal cows in five Government herds of Punjab province were collected to estimate the genetic control and genetic correlations among performance traits. A repeatability animal model having herd-year-season and parity was used for this purpose. The repeatability estimates for 305-d milk yield, total milk yield, lactation length, dry period, calving interval and service period were 0.40±0.015, 0.40±0.016, 0.33±0.013, 0.14±0.005, 0.15±0.004, and 0.14±0.005 respectively. The heritability estimates for these traits were 0.10±0.016, 0.09±0.016, 0.06±0.013, 0.14±0.009, 0.15±0.010, and 0.14±0.010, respectively. The phenotypic, genetic and environmental correlation of 305-d milk yield with lactation length was 0.71, 0.48 and 0.70, respectively, with dry period was -0.31, -0.43 and -0.22, respectively while with calving interval and service period exhibited similar pattern (0.08, 0.25 and 0.08, respectively. The estimated breeding values ranged from -447 to 1254 kg, -442 to 1265 kg, -24 to 38, -78 to 116, -84 to 107 and -81 to 91, days for 305-day milk yield, total milk yield, lactation length, dry period, calving interval and service period, respectively. No specific genetic trend was observed for performance traits during the period under study. Cows have not improved in their ability to perform in various economic traits. Accurate recording of pedigree and performance is necessary for improving the performance traits of Sahiwal. Due to high repeatability estimates of yield traits selection or culling may be practised from first few records.

  9. Genetics of health and lameness in dairy cattle

    OpenAIRE

    Obike, Onyemauchechi Mercy

    2009-01-01

    For the modern dairy cow, advances in genetics and breeding for productivity has resulted in an increasing incidence of health disorders and reduced longevity. One of the most important health problems is lameness, which has led to significant economic, production and welfare consequences. A reduction in lameness will improve the economic future of the dairy industry through increased profitability and decreased welfare-related problems. Although positive attempts have been mad...

  10. Estimated genetic parameters for carcass traits of Brahman cattle.

    Science.gov (United States)

    Riley, D G; Chase, C C; Hammond, A C; West, R L; Johnson, D D; Olson, T A; Coleman, S W

    2002-04-01

    Heritabilities and genetic and phenotypic correlations were estimated from feedlot and carcass data collected from Brahman calves (n = 504) in central Florida from 1996 to 2000. Data were analyzed using animal models in MTDFREML. Models included contemporary group (n = 44; groups of calves of the same sex, fed in the same pen, slaughtered on the same day) as a fixed effect and calf age in days at slaughter as a continuous variable. Estimated feedlot trait heritabilities were 0.64, 0.67, 0.47, and 0.26 for ADG, hip height at slaughter, slaughter weight, and shrink. The USDA yield grade estimated heritability was 0.71; heritabilities for component traits of yield grade, including hot carcass weight, adjusted 12th rib backfat thickness, loin muscle area, and percentage kidney, pelvic, and heart fat were 0.55, 0.63, 0.44, and 0.46, respectively. Heritability estimates for dressing percentage, marbling score, USDA quality grade, cutability, retail yield, and carcass hump height were 0.77, 0.44, 0.47, 0.71, 0.5, and 0.54, respectively. Estimated genetic correlations of adjusted 12th rib backfat thickness with ADG, slaughter weight, marbling score, percentage kidney, pelvic, and heart fat, and yield grade (0.49, 0.46, 0.56, 0.63, and 0.93, respectively) were generally larger than most literature estimates. Estimated genetic correlations of marbling score with ADG, percentage shrink, loin muscle area, percentage kidney, pelvic, and heart fat, USDA yield grade, cutability, retail yield, and carcass hump height were 0.28, 0.49, 0.44, 0.27, 0.45, -0.43, 0.27, and 0.43, respectively. Results indicate that sufficient genetic variation exists within the Brahman breed for design and implementation of effective selection programs for important carcass quality and yield traits. PMID:12008662

  11. Estimated genetic parameters for carcass traits of Brahman cattle.

    Science.gov (United States)

    Riley, D G; Chase, C C; Hammond, A C; West, R L; Johnson, D D; Olson, T A; Coleman, S W

    2002-04-01

    Heritabilities and genetic and phenotypic correlations were estimated from feedlot and carcass data collected from Brahman calves (n = 504) in central Florida from 1996 to 2000. Data were analyzed using animal models in MTDFREML. Models included contemporary group (n = 44; groups of calves of the same sex, fed in the same pen, slaughtered on the same day) as a fixed effect and calf age in days at slaughter as a continuous variable. Estimated feedlot trait heritabilities were 0.64, 0.67, 0.47, and 0.26 for ADG, hip height at slaughter, slaughter weight, and shrink. The USDA yield grade estimated heritability was 0.71; heritabilities for component traits of yield grade, including hot carcass weight, adjusted 12th rib backfat thickness, loin muscle area, and percentage kidney, pelvic, and heart fat were 0.55, 0.63, 0.44, and 0.46, respectively. Heritability estimates for dressing percentage, marbling score, USDA quality grade, cutability, retail yield, and carcass hump height were 0.77, 0.44, 0.47, 0.71, 0.5, and 0.54, respectively. Estimated genetic correlations of adjusted 12th rib backfat thickness with ADG, slaughter weight, marbling score, percentage kidney, pelvic, and heart fat, and yield grade (0.49, 0.46, 0.56, 0.63, and 0.93, respectively) were generally larger than most literature estimates. Estimated genetic correlations of marbling score with ADG, percentage shrink, loin muscle area, percentage kidney, pelvic, and heart fat, USDA yield grade, cutability, retail yield, and carcass hump height were 0.28, 0.49, 0.44, 0.27, 0.45, -0.43, 0.27, and 0.43, respectively. Results indicate that sufficient genetic variation exists within the Brahman breed for design and implementation of effective selection programs for important carcass quality and yield traits.

  12. Estimates of genetic parameters for growth traits in Brahman cattle using random regression and multitrait models.

    Science.gov (United States)

    Bertipaglia, T S; Carreño, L O D; Aspilcueta-Borquis, R R; Boligon, A A; Farah, M M; Gomes, F J; Machado, C H C; Rey, F S B; da Fonseca, R

    2015-08-01

    Random regression models (RRM) and multitrait models (MTM) were used to estimate genetic parameters for growth traits in Brazilian Brahman cattle and to compare the estimated breeding values obtained by these 2 methodologies. For RRM, 78,641 weight records taken between 60 and 550 d of age from 16,204 cattle were analyzed, and for MTM, the analysis consisted of 17,385 weight records taken at the same ages from 12,925 cattle. All models included the fixed effects of contemporary group and the additive genetic, maternal genetic, and animal permanent environmental effects and the quadratic effect of age at calving (AAC) as covariate. For RRM, the AAC was nested in the animal's age class. The best RRM considered cubic polynomials and the residual variance heterogeneity (5 levels). For MTM, the weights were adjusted for standard ages. For RRM, additive heritability estimates ranged from 0.42 to 0.75, and for MTM, the estimates ranged from 0.44 to 0.72 for both models at 60, 120, 205, 365, and 550 d of age. The maximum maternal heritability estimate (0.08) was at 140 d for RRM, but for MTM, it was highest at weaning (0.09). The magnitude of the genetic correlations was generally from moderate to high. The RRM adequately modeled changes in variance or covariance with age, and provided there was sufficient number of samples, increased accuracy in the estimation of the genetic parameters can be expected. Correlation of bull classifications were different in both methods and at all the ages evaluated, especially at high selection intensities, which could affect the response to selection. PMID:26440161

  13. Relationship between physical attributes and heat stress in dairy cattle from different genetic groups

    Science.gov (United States)

    Alfonzo, Evelyn Priscila München; Barbosa da Silva, Marcos Vinicius Gualberto; dos Santos Daltro, Darlene; Stumpf, Marcelo Tempel; Dalcin, Vanessa Calderaro; Kolling, Giovani; Fischer, Vivian; McManus, Concepta Margaret

    2016-02-01

    Dairy cattle raised under harsh conditions have to adapt and prevent heat stress. The aim of this study was to evaluate physical characteristics and their association with heat tolerance in different genetic groups of dairy cattle. Thickness of the skin and coat, length and number of hairs, body measurements, as well as physiological parameters and body temperatures by infrared thermography were determined in 19 Holstein and 19 Girolando (½ and ¾ Holstein) cows. The Holstein cattle were less tolerant to heat stress than Girolando (GH50 and GH75 Holstein), because of the difficulty in dissipating heat due to the larger body size, as well as thicker and longer hairs. The correlations between physical characteristics, physiological parameters, and thermographic measurements prove to be inconsistent among genetic groups and therefore are not predictive of heat tolerance, while the regressions of morphometric characteristics on physiological and thermographic measures were not significant. Thus, the physical characteristics were not good predictors of physiological indices and thermographic temperature and so should not be used.

  14. Genetic variations among Mycoplasma bovis strains isolated from Danish cattle

    DEFF Research Database (Denmark)

    Kusiluka, L.J.M.; Kokotovic, Branko; Ojeniyi, B.;

    2000-01-01

    The genetic heterogeneity of Mycoplasma bovis strains isolated in Denmark over a 17-year period was investigated. Forty-two field strains isolated from different geographic locations and specimens, including strains from 21 herds involved in two outbreaks of M. bovis-induced mastitis, and the type....... Among the analyzed strains, 18 different AFLP profiles were detected. The similarity between individual fingerprints, calculated by Dice similarity coefficient, ranged from 0.9 to 1.0. Twenty-five strains, including 23 which were isolated during two outbreaks of M. bovis-induced mastitis which occurred...

  15. Non-genetic effects on growth characteristics of Brahman cattle

    Directory of Open Access Journals (Sweden)

    Nicacia Hernández-Hernández

    2015-01-01

    Full Text Available Objective. To determine how some non-genetic factors influence weights at birth (BW, weaning (WW and yearling (YW of Brahman calves. Materials and methods. Data corresponding to 58257, 57045 and 40364 for BW, WW and YW, respectively, were analyzed. The models included the effects of year and season of birth and sex, and were considered simple interactions. Results. All effects were significant (p0.05 on WW. The average general BW, WW and YW were 32±3.2, 188±37.7 and 291±56.8 kg, respectively. Variables evaluated that take into account the year of birth show a trend to increase weight each year. In relation to the birth season on BW and YW, it was observed that calves born during the rainy season were heavier than those born during the dry season. Similarly, male calves were heavier than females at birth, weaning and one year of age. The effects of the analyzed interactions were significant (p0.05 for BW and WW. Conclusions. The studied non-genetic factors were important and should be taken into account in management strategies when striving to increase the efficiency of the productive system.

  16. An alternative approach to modeling genetic merit of feed efficiency in dairy cattle.

    Science.gov (United States)

    Lu, Y; Vandehaar, M J; Spurlock, D M; Weigel, K A; Armentano, L E; Staples, C R; Connor, E E; Wang, Z; Bello, N M; Tempelman, R J

    2015-09-01

    Genetic improvement of feed efficiency (FE) in dairy cattle requires greater attention given increasingly important resource constraint issues. A widely accepted yet occasionally contested measure of FE in dairy cattle is residual feed intake (RFI). The use of RFI is limiting for several reasons, including interpretation, differences in recording frequencies between the various component traits that define RFI, and potential differences in genetic versus nongenetic relationships between dry matter intake (DMI) and FE component traits. Hence, analyses focusing on DMI as the response are often preferred. We propose an alternative multiple-trait (MT) modeling strategy that exploits the Cholesky decomposition to provide a potentially more robust measure of FE. We demonstrate that our proposed FE measure is identical to RFI provided that genetic and nongenetic relationships between DMI and component traits of FE are identical. We assessed both approaches (MT and RFI) by simulation as well as by application to 26,383 weekly records from 50 to 200 d in milk on 2,470 cows from a dairy FE consortium study involving 7 institutions. Although the proposed MT model fared better than the RFI model when simulated genetic and nongenetic associations between DMI and FE component traits were substantially different from each other, no meaningful differences were found in predictive performance between the 2 models when applied to the consortium data. PMID:26210274

  17. Heritabilities and genetic trends for reproductive traits in a population of Romosinuano cattle in Colombia

    Directory of Open Access Journals (Sweden)

    Oscar Vergara G.

    2015-12-01

    Full Text Available Objective. The aim of this study was to estimate heritabilities and genetic trends for reproductive traits in a beef cattle population Romosinuano. Material and methods. Age at first calving (AFC, first calving interval (FCI, and second calving interval (SCI were evaluated from a database generated from 1951 to 2011 by Research Center Turipana. Unicaracter animal model was used, which included fixed of contemporary group (year-season, random direct genetic additives effects and residual. Estimates of variance components and genetic parameters were obtained through Restricted Maximum Likelihood procedure, using AIREMLF90 program. Genetic trends were calculated as a linear regression of weighted averages of breeding values over the years, using the REG procedure of Statistical Analysis System. Results. The indices of heritability for additive genetic effects were 0.04 ± 0.05 for AFC, 0.06 ± 0.06 for FCI, and 0.09 ± 0.06 for SCI. Conclusions. Low heritabilities indicating that should improve nutritional and management conditions in the herd, so that they can better express the traits evaluated. The estimated genetic trends were near zero, which shows that the objective of the CI Turipaná regarding this population has complied fully preserving the genetic variability of the breed Romosinuano.

  18. The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by(δμ)2 and DA distances, and the divergence times between populations were estimated by (δμ)2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles (10), whereas,Bohai black and Buffalo had the smallest number of private alleles (2). Chinese Holstein showed the highest genetic variability. Its observed number of alleles (Na), mean effective number of alleles (MNA), and mean heterozygosity (He) were 7.7500, 4.9722, and 0.7719,respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first,followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations.Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago (MYA), however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600MYA, respectively.

  19. Additive and nonadditive genetic variances for milk yield, fertility, and lifetime performance traits of dairy cattle.

    Science.gov (United States)

    Fuerst, C; Sölkner, J

    1994-04-01

    Additive and nonadditive genetic variances were estimated for yield traits and fertility for three subsequent lactations and for lifetime performance traits of purebred and crossbred dairy cattle populations. Traits were milk yield, energy-corrected milk yield, fat percentage, protein percentage, calving interval, length of productive life, and lifetime FCM of purebred Simmental, Simmental including crossbreds, and Braunvieh crossed with Brown Swiss. Data files ranged from 66,740 to 375,093 records. An approach based on pedigree information for sire and maternal grandsire was used and included additive, dominance, and additive by additive genetic effects. Variances were estimated using the tildehat approximation to REML. Heritability estimated without nonadditive effects in the model was overestimated, particularly in presence of additive by additive variance. Dominance variance was important for most traits; for the lifetime performance traits, dominance was clearly higher than additive variance. Additive by additive variance was very high for milk yield and energy-corrected milk yield, especially for data including crossbreds. Effect of inbreeding was low in most cases. Inclusion of nonadditive effects in genetic evaluation models might improve estimation of additive effects and may require consideration for dairy cattle breeding programs.

  20. 黄牛Y染色体分子遗传多样性研究进展%Progress on Molecular Genetic Diversity of Cattle Y Chromosome

    Institute of Scientific and Technical Information of China (English)

    李冉; 常振华; 徐苹; 黄洁萍; 陈宏; 雷初朝

    2012-01-01

    Y chromosome molecular genetic diversity is an important tool for tracing animal origin, do- mestication history and migrating routines and it can also be used to analyze the paternal genetic diversity of a certain population or investigate the male-mediated introgression between populations. Y chromosome haplotype diversity can be revealed by Y chromosome single nucleotide polymorphism (Y-SNP) and Y chromosome mierosatellite (Y-STR) respectively or by combination of these two kinds of markers together to obtain more specific Y chromosome haplotypes. Cattle have three paternal origins (Y1 ,Y2 in Bos taurus and Y3 in Bos indicus) which can be distinguished by Y-SNP markers, while the abundant specific haplo- types in Y1,Y2 and Y3 haplogroup respectively can be further identified by using Y-STR markers. This paper reviewed the research progress on cattle Y chromosome diversity and paternal origins in China and other foreign countries.%Y染色体分子遗传多样性是追溯动物起源、驯化历史和迁徙路线的重要工具,也可以用来反映动物的父系遗传多样性及用于研究群体间父系介导的杂交情况。Y染色体单倍型多样性可以分别通过Y染色体单核苷酸多态性(Y-SNP)和Y染色体微卫星多态性(Y-STR)或这二者结合起来构建精确的Y染色体单倍型。黄牛有3种父系起源(普通牛Y1、Y2和瘤牛Y3单倍型组),可以通过Y-SNP来区分,通过-STR标记可以区分Y1、Y2和Y3所具有的丰富的精细单倍型。本文汇集了包括中国在内的国内外黄牛Y染色体遗传多样性与起源进化的研究进展。

  1. Genetic analysis of carcass traits in beef cattle using random regression models.

    Science.gov (United States)

    Englishby, T M; Banos, G; Moore, K L; Coffey, M P; Evans, R D; Berry, D P

    2016-04-01

    Livestock mature at different rates depending, in part, on their genetic merit; therefore, the optimal age at slaughter for progeny of certain sires may differ. The objective of the present study was to examine sire-level genetic profiles for carcass weight, carcass conformation, and carcass fat in cattle of multiple beef and dairy breeds, including crossbreeds. Slaughter records from 126,214 heifers and 124,641 steers aged between 360 and 1,200 d and from 86,089 young bulls aged between 360 and 720 d were used in the analysis; animals were from 15,127 sires. Variance components for each trait across age at slaughter were generated using sire random regression models that included quadratic polynomials for fixed and random effects; heterogeneous residual variances were assumed across ages. Heritability estimates across genders ranged from 0.08 (±0.02) to 0.34 (±0.02) for carcass weight, from 0.24 (±0.02) to 0.42 (±0.01) for conformation, and from 0.16 (±0.03) to 0.40 (±0.02) for fat score. Genetic correlations within each trait across ages weakened as the interval between ages compared lengthened but were all >0.64, suggesting a similar genetic background for each trait across different ages. Eigenvalues and eigenfunctions of the additive genetic covariance matrix revealed genetic variability among animals in their growth profiles for carcass traits, although most of the genetic variability was associated with the height of the growth profile. At the same age, a positive genetic correlation (0.60 to 0.78; SE ranged from 0.01 to 0.04) existed between carcass weight and conformation, whereas negative genetic correlations existed between fatness and both conformation (-0.46 to 0.08; SE ranged from 0.02 to 0.09) and carcass weight (-0.48 to -0.16; SE ranged from 0.02 to 0.14) at the same age. The estimated genetic parameters in the present study indicate genetic variability in the growth trajectory in cattle, which can be exploited through breeding programs and

  2. ESTIMATION OF GENETIC PARAMETERS FOR CARCASS TRAITS FOR SIMMENTAL CATTLE IN CROATIA

    OpenAIRE

    Marija Špehar; Špela Malovrh; Vesna Bulić; Ivkić, Z.; Milena Kovač

    2007-01-01

    The objective of this paper was an estimation of genetic parameters for carcass weight, conformation, fatness class and net gain for Simmental cattle in Croatia. Data of young bulls slaughtered in years 2005 and 2006 with 12 to 24 months of age was taken from the central database of the Croatian Livestock Centre. Three data sets were constructed as follows: 1) data set 1 (DS1) included 80462 records of bulls with known and unknown parents; 2) data set 2 (DS2) had 26245 records of bulls wi...

  3. Mitochondrial control region genetic diversity and maternal ancestry of a Brangus-Ibage cattle populations

    OpenAIRE

    Luiz Ernani Henkes; Wilson Araújo Silva Jr; José Carlos Ferrugem Moraes; Tania de Azevedo Weimer

    2005-01-01

    The genetic diversity of 277 nucleotides in the mitochondrial DNA control region (nt 15,964 to 16,240 in reference sequence) was analyzed in crossbreed beef cattle (Brangus-Ibage, 5/8 Bos primigenius taurus x 3/8 Bos primigenius indicus) as well as in some Nellore samples (B. p. indicus). Fifty-seven mutations were found in Brangus-Ibage comprising 18 haplotypes (haplotype diversity, h = 0.851 ± 0.041 and nucleotide diversity, ntd = 0.009 ± 0.006) and 66 in Nellore (h = 1.00 ± 0.27, ntd = 0.0...

  4. Age and lactation specific disposal pattern in Sahiwal cattle and influence of various genetic and non-genetic factors

    Directory of Open Access Journals (Sweden)

    A. Upadhyay

    2014-10-01

    Full Text Available Premature disposal of female calves before reaching milch herd and undesirable disposal of lactating cows are the major constraints in achieving larger herd size. During the early lactations, younger cows are supposed to give higher milk yield and undesirable disposal of early calvers, thereby, greatly hampers profitability of a dairy farm. Knowledge of the incidence of disposal along with reasons in various age groups and at various parities is essential to identify which age group or parity is more vulnerable for disposal. Moreover, knowledge of various genetic and non-genetic factors associated with disposal of animals may also be helpful in developing breeding and management strategies to reduce the incidence of disposal. In most of the studies, it was found that major reasons of disposal of dairy cattle were mortality among female calves and involuntary culling among adult lactating cows. Maximum mortality in female calves was observed during earlier ages and pneumonia, gastro-enteritis and debility were major reasons of female calf mortality. Whereas, most of the adult cows left the herd, due to teat and udder and reproductive problems. Moreover, indigenous breeds were found to be more adapted to Indian tropical climatic conditions in comparison to crossbred and exotic cattle breeds.

  5. Genetic and environmental causes of variation in gestation length of Jersey crossbred cattle

    Directory of Open Access Journals (Sweden)

    Anshuman Kumar

    2016-04-01

    Full Text Available Aim: The objective of this study was to investigate the effect of genetic and non-genetic factors and estimate the genetic parameter for gestation length (GL of Jersey crossbred cattle. Materials and Methods: The data included the 986 parturition records on Jersey crossbred cattle maintained at the Eastern Regional Station of ICAR-National Dairy Research Institute, Kalyani, West Bengal, India during 36 years (1978-2013. The data were analyzed applying mixed model least square technique considering the fixed effects of genetic group, season of calving, period of calving, parity of animal, birth weight, and sex of calf born from animal. The effect of sire was included as a random effect in the model. Results: The genetic group of animal, season of calving, parity of animal, and birth weight of calf born were found to be a significant source of variation in the GL, whereas the period of calving and sex of calf did not affect this trait. Cows with 62.5% Jersey inheritance had the shortest and longest GLs, respectively. Cows calved in summer and rainy season had shorter GL than those calved in the winter season. Older cows in 4th parity carried calves for longer days than the cows in 1st parity. The increase in calf birth weight significantly (p<0.01 contributed to a linear increase in GL value in this study. The heritability estimate of GL was 0.24±0.08. Conclusion: It can be concluded that selection for lower GL without distressing future growth of calf can be used to reduce calving difficulty, but a very small standard deviation of GL limits the benefit. Moreover, more accurate prediction of calving date will help in better management and health care of pregnant animals.

  6. Genetic diversity among Angus, American Brahman, Senepol and Romosinuano cattle breeds.

    Science.gov (United States)

    Brenneman, R A; Chase, C C; Olson, T A; Riley, D G; Coleman, S W

    2007-02-01

    The objective of this study was to quantify the genetic diversity among breeds under evaluation for tropical adaptability traits that affect the performance of beef cattle at the USDA/ARS SubTropical Agricultural Research Station (STARS) near Brooksville, FL, USA. Twenty-six microsatellite loci were used to estimate parameters of genetic diversity among the breeds American Brahman, Angus, Senepol and Romosinuano; the latter was comprised of two distinct bloodlines (Costa Rican and Venezuelan). Genotypes of 47 animals from each of these STARS herds were analysed for genetic diversity and genetic distance. Using two methods, the greatest genetic distance was detected between the Costa Rican line of Romosinuano and the Senepol. Gene diversity ranged between 0.64 (Costa Rican line of Romosinuano) and 0.75 (American Brahman). The breed relationship inferences, which are based on genetic distance, provide additional tools for consideration in future crossbreeding studies and for testing the relationship between quantified breed diversity and observed heterosis. PMID:17257188

  7. The genetic variability of the Podolica cattle breed from the Gargano area. Preliminary results

    Directory of Open Access Journals (Sweden)

    Dario Cianci

    2010-01-01

    Full Text Available The Podolica cattle breed is autochthonous of Southern Italy and denoted by its particular rusticity. This study presents the preliminary results of the genetic characterization of the Podolica breed using DNA STR markers. A total of 20 microsatellite loci were analysed in 79 individuals reared in the Gargano area. Number of polymorphisms, allele fre- quencies, deviations from Hardy-Weinberg proportions, linkage disequilibrium between loci and genetic similarities between animals were calculated. The results showed a high deficiency of heterozygotes, the observed mean of het- erozygosis being 0.449, whereas the expected mean was 0.766. Many markers showed also deviations from the Hardy- Weinberg proportions and significant linkage disequilibrium between loci. However the genetic similarity within the pop- ulation was low (0.281 and the average number of alleles per locus was high (10, representing a high genetic vari- ability. In order to explain these results, a stratification of the breed in sub-populations with a high interior genetic homo- geneity but markedly differentiated one from each other could be hypothesized; this situation probably derived from non- random mating within each herd (consanguinity and from the lack of exchange of genetic material between the herds. A further study is needed on a wider sample and extending the analysis to FAO-ISAG microsatellite panel in order to con- firm this hypothesis. This could eventually provide the information necessary for the correct management of the repro- ductive schemes and for genomic traceability of meat production.

  8. Genetic parameters for EUROP carcass traits within different groups of cattle in Ireland.

    Science.gov (United States)

    Hickey, J M; Keane, M G; Kenny, D A; Cromie, A R; Veerkamp, R F

    2007-02-01

    The first objective of this study was to test the ability of systems of weighing and classifying bovine carcasses used in commercial abattoirs in Ireland to provide information that can be used for the purposes of genetic evaluation of carcass weight, carcass fatness class, and carcass conformation class. Secondly, the study aimed to test whether genetic and phenotypic variances differed by breed of sire. Variance components for carcass traits were estimated for crosses between dairy cows and 8 breeds of sire commonly found in the Irish cattle population. These 8 breeds were Aberdeen Angus, Belgian Blue, Charolais, Friesian, Hereford, Holstein, Limousin, and Simmental. A multivariate animal model was used to estimate genetic parameters within the Holstein sire breed group. Univariate analyses were used to estimate variance components for the remaining 7 sire breed groups. Multivariate sire models were used to formally test differences in genetic variances in sire breed groups. Field data on 64,443 animals, which were slaughtered in commercial abattoirs between the ages of 300 and 875 d, were analyzed in 8 analyses. Carcass fat class and carcass conformation class were measured using the European Union beef carcass classification system (EUROP) scale. For all 3 traits, the sire breed group with the greatest genetic variance had a value of more than 8 times the sire breed group with least genetic variance. Heritabilities ranged from zero to moderate for carcass fatness class (0.00 to 0.40), from low to moderate for carcass conformation class (0.04 to 0.36), and from low to high for carcass weight (0.06 to 0.65). Carcass weight was the most heritable (0.26) of the 3 traits. Carcass conformation class and carcass fatness class were equally heritable (0.17). Genetic and phenotypic correlations were all positive in the Holstein sire breed group. The genetic correlations varied from 0.11 for the relationship between carcass weight and carcass fatness class to 0.44 for the

  9. Artificial infestation of Boophilus microplus in beef cattle heifers of four genetic groups

    Directory of Open Access Journals (Sweden)

    Ana Mary da Silva

    2007-01-01

    Full Text Available Resistance of beef cattle heifers to the cattle tick Boophilus microplus was evaluated by artificial infestation of 66 beef cattle heifers of the following genetic groups: 16 Nelore (NE, 18 Canchim x Nelore (CN, 16 Angus x Nelore (AN and 16 Simmental x Nelore (SN. The animals, with a mean age of 16.5 months, were maintained with no chemical tick control in a Brachiaria decumbens pasture. Four artificial infestations with 20,000 B. microplus larvae were carried out 14 days apart and from day 18 to day 22 of each infestation the number of engorged female ticks (> 4.5 mm was counted on the left side of each heifer. Data were analyzed as the percentage of return (PR = percentage of ticks counted relative to the number infested, transformed to (PR¼, and as log10 (Cij + 1, in which Cij is the number of ticks in each infestation, using the least squares method with a model that included the effects of genetic group (GG, animal within GG (error a, infestation number (I, GG x I and the residual (error b. Results indicated a significant GG x I interaction, because AN and SN heifers had a higher percentage of return than CN and NE heifers, while CN heifers showed a higher percentage of return than the NE heifers only in infestations 3 and 4. Transformed percentages of return were NE = 0.35 ± 0.06, AN = 0.89 ± 0.06, CN = 0.54 ± 0.05 and SN = 0.85 ± 0.06.

  10. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

    Directory of Open Access Journals (Sweden)

    Rangel-Figueiredo Teresa

    2010-06-01

    Full Text Available Abstract Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95. With breed information, 30 cows and three bulls were identified (q > 0.95 that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10 relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P st = 0.028, P > 0.05. Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50 to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that

  11. Genetic variation of the weaning weight of beef cattle as a function of accumulated heat stress.

    Science.gov (United States)

    Santana, M L; Bignardi, A B; Eler, J P; Ferraz, J B S

    2016-04-01

    The objective of this study was to identify the genetic variation in the weaning weight (WW) of beef cattle as a function of heat stress. The WWs were recorded at approximately 205 days of age in three Brazilian beef cattle populations: Nelore (93,616), Brangus (18,906) and Tropical Composite (62,679). In view of the cumulative nature of WW, the effect of heat stress was considered as the accumulation of temperature and humidity index units (ACTHI) from the animal's birth to weaning. A reaction norm model was used to estimate the (co)variance components of WW across the ACTHI scale. The accumulation of THI units from birth to weaning negatively affected the WW. The definition of accumulated THI units as an environmental descriptor permitted to identify important genetic variation in the WW as a function of heat stress. As evidence of genotype by environment interaction, substantial heterogeneity was observed in the (co)variance components for WW across the environmental gradient. In this respect, the best animals in less stressful environments are not necessarily the best animals in more stressful environments. Furthermore, the response to selection for WW is expected to be lower in more stressful environments. PMID:26061790

  12. Estimates of genetic parameters for reproductive traits in Brahman cattle breed.

    Science.gov (United States)

    Cavani, L; Garcia, D A; Carreño, L O D; Ono, R K; Pires, M P; Farah, M M; Ventura, H T; Millen, D D; Fonseca, R

    2015-07-01

    This study was designed to estimate genetic parameters for the following traits of Brahman cattle in Brazil: age at first calving (AFC), calving interval (CI), rebreeding (REB), and stayability (STAY). For REB, the value 1 was assigned to heifers that rebred and calved after first calving and the value 0 was assigned to heifers that failed to rebreed after first calving. Likewise, for STAY, the value 1 was assigned to cows that calved at least 3 times by the time they reach 6 yr of age; otherwise, the value 0 was assigned. A bivariate analysis was used to estimate covariances components by using linear animal model for CI and AFC and threshold animal model for REB and STAY. The mean h(2) were 0.10, 0.02, 0.22, and 0.10 for AFC, CI, REB, and STAY, respectively. The genetic correlations were –0.13 between AFC and CI, –0.35 between AFC and REB, –0.57 between AFC and STAY, and 0.32 between REB and STAY, which reveal that cows that remain productive for longer periods in the herd also start breeding younger and present greater chances to REB. The selection of Brahman cattle for reproductive traits, such as AFC, CI, REB, and STAY, will render low magnitude and long-term responses. PMID:26439997

  13. Genetic characterization of a noncytopathic bovine viral diarrhea virus 2b isolated from cattle in China.

    Science.gov (United States)

    Wang, Wei; Shi, Xinchuan; Chen, Chaoyang; Wu, Hua

    2014-10-01

    In January 2013, several clinical signs of cattle with diarrhea, cough, nasal discharge, and fever were reported in Jilin province, China. One virus named SD1301 was isolated and identified. Complete genome of the virus is 12258nt in length and contains a 5'UTR, one open reading frame encoding a polyprotein of 3,897 amino acids and a 3'UTR. Phylogenetic analysis of 5'UTR, N(pro), E1 and E2 gene demonstrated the virus belonged to BVDV 2b, and genetically related to the BVDV strain Hokudai-Lab/09 from Japan in 2010. This bovine viral diarrhea virus displays a unique genetic signature with 27-nucleotide deletion in the 5'UTR, which is similar to the bovine viral diarrhea virus C413 (AF002227). This was the first confirmed isolation of ncp BVDV2b circulating in bovine herd of China.

  14. Genetic parameters for carcass traits and body weight using a Bayesian approach in the Canchim cattle.

    Science.gov (United States)

    Meirelles, S L C; Mokry, F B; Espasandín, A C; Dias, M A D; Baena, M M; de A Regitano, L C

    2016-06-10

    Correlation between genetic parameters and factors such as backfat thickness (BFT), rib eye area (REA), and body weight (BW) were estimated for Canchim beef cattle raised in natural pastures of Brazil. Data from 1648 animals were analyzed using multi-trait (BFT, REA, and BW) animal models by the Bayesian approach. This model included the effects of contemporary group, age, and individual heterozygosity as covariates. In addition, direct additive genetic and random residual effects were also analyzed. Heritability estimated for BFT (0.16), REA (0.50), and BW (0.44) indicated their potential for genetic improvements and response to selection processes. Furthermore, genetic correlations between BW and the remaining traits were high (P > 0.50), suggesting that selection for BW could improve REA and BFT. On the other hand, genetic correlation between BFT and REA was low (P = 0.39 ± 0.17), and included considerable variations, suggesting that these traits can be jointly included as selection criteria without influencing each other. We found that REA and BFT responded to the selection processes, as measured by ultrasound. Therefore, selection for yearling weight results in changes in REA and BFT.

  15. Analysis of genetic and cultural conservation value of three indigenous Croatian cattle breeds in a local and global context.

    Science.gov (United States)

    Ramljak, J; Ivanković, A; Veit-Kensch, C E; Förster, M; Medugorac, I

    2011-02-01

    It is widely accepted that autochthonous cattle breeds can be important genetic resources for unforeseeable environmental conditions in the future. Apart from that, they often represent local culture and tradition and thus assist in the awareness of ethnic identity of a country. In Croatia, there are only three indigenous cattle breeds, Croatian Buša, Slavonian Syrmian Podolian and Istrian Cattle. All of them are threatened but specialized in a particular habitat and production system. We analysed 93 microsatellites in 51 animals of each breed to get thorough information about genetic diversity and population structure. We further set them within an existing frame of additional 16 breeds that have been genotyped for the same marker set and cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the north-west of Europe. The cultural value was evaluated regarding the role in landscape, gastronomy, folklore and handicraft. The overall results recognize Croatian Buša being partly admixed but harbouring an enormous genetic diversity comparable with other traditional unselected Buša breeds in the Anatolian and Balkan areas. The Podolian cattle showed the lowest genetic diversity at the highest genetic distance to all remaining breeds but are playing an important role as part of the cultural landscape and thus contribute to the tourist industry. The genetic diversity of the Istrian cattle was found in the middle range of this study. It is already included in the tourist industry as a local food speciality. Current and future conservation strategies are discussed.

  16. Analysis of genetic and cultural conservation value of three indigenous Croatian cattle breeds in a local and global context.

    Science.gov (United States)

    Ramljak, J; Ivanković, A; Veit-Kensch, C E; Förster, M; Medugorac, I

    2011-02-01

    It is widely accepted that autochthonous cattle breeds can be important genetic resources for unforeseeable environmental conditions in the future. Apart from that, they often represent local culture and tradition and thus assist in the awareness of ethnic identity of a country. In Croatia, there are only three indigenous cattle breeds, Croatian Buša, Slavonian Syrmian Podolian and Istrian Cattle. All of them are threatened but specialized in a particular habitat and production system. We analysed 93 microsatellites in 51 animals of each breed to get thorough information about genetic diversity and population structure. We further set them within an existing frame of additional 16 breeds that have been genotyped for the same marker set and cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the north-west of Europe. The cultural value was evaluated regarding the role in landscape, gastronomy, folklore and handicraft. The overall results recognize Croatian Buša being partly admixed but harbouring an enormous genetic diversity comparable with other traditional unselected Buša breeds in the Anatolian and Balkan areas. The Podolian cattle showed the lowest genetic diversity at the highest genetic distance to all remaining breeds but are playing an important role as part of the cultural landscape and thus contribute to the tourist industry. The genetic diversity of the Istrian cattle was found in the middle range of this study. It is already included in the tourist industry as a local food speciality. Current and future conservation strategies are discussed. PMID:21214647

  17. Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip.

    Science.gov (United States)

    Cañas-Álvarez, J J; González-Rodríguez, A; Munilla, S; Varona, L; Díaz, C; Baro, J A; Altarriba, J; Molina, A; Piedrafita, J

    2015-11-01

    The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD BeadChip genotyping array was used to describe the genetic variability and divergence among 7 important autochthonous Spanish beef cattle breeds. The within-breed genetic diversity, measured as the marker expected heterozygosity, was around 0.30, similar to other European cattle breeds. The analysis of molecular variance revealed that 94.22% of the total variance was explained by differences within individuals whereas only 4.46% was the result of differences among populations. The degree of genetic differentiation was small to moderate as the pairwise fixation index of genetic differentiation among breeds (F) estimates ranged from 0.026 to 0.068 and the Nei's D genetic distances ranged from 0.009 to 0.016. A neighbor joining (N-J) phylogenetic tree showed 2 main groups of breeds: Pirenaica, Bruna dels Pirineus, and Rubia Gallega on the one hand and Avileña-Negra Ibérica, Morucha, and Retinta on the other. In turn, Asturiana de los Valles occupied an independent and intermediate position. A principal component analysis (PCA) applied to a distance matrix based on marker identity by state, in which the first 2 axes explained up to 17.3% of the variance, showed a grouping of animals that was similar to the one observed in the N-J tree. Finally, a cluster analysis for ancestries allowed assigning all the individuals to the breed they belong to, although it revealed some degree of admixture among breeds. Our results indicate large within-breed diversity and a low degree of divergence among the autochthonous Spanish beef cattle breeds studied. Both N-J and PCA groupings fit quite well to the ancestral trunks from which the Spanish beef cattle breeds were supposed to derive.

  18. Genetic association of growth traits with carcass and meat traits in Nellore cattle.

    Science.gov (United States)

    Tonussi, R L; Espigolan, R; Gordo, D G M; Magalhães, A F B; Venturini, G C; Baldi, F; de Oliveira, H N; Chardulo, L A L; Tonhati, H; de Albuquerque, L G

    2015-01-01

    The aim of this study was to estimate genetic and phenotypic associations of growth traits with carcass and meat traits in Nellore cattle. Data from male and female animals were used for weaning weight (WW; N = 241,416), yearling weight (YW, N = 126,596), weight gain from weaning to yearling (GWY, N = 78,687), and yearling hip height (YHH, N = 90,720), respectively; 877 male animals were used for hot carcass weight (HCW) and 884 for longissimus muscle area (LMA), backfat thickness (BT), marbling score (MS), and shear force (SF). The variance components were estimated by the restricted maximum likelihood method using three-trait animal models that included WW. The model for WW included direct and maternal additive genetic, maternal permanent environmental, and residual effects as random effects; contemporary group as fixed effects; and age of dam at calving and age of animal as covariates (linear and quadratic effects). For the other traits, maternal effects and the effect of age of dam at calving were excluded from the model. Heritability ranged from 0.10 ± 0.12 (LMA) to 0.44 ± 0.007 (YW). Genetic correlations ranged from -0.40 ± 0.38 (WW x LMA) to 0.55 ± 0.10 (HCW x YW). Growth, carcass, and meat traits have sufficient genetic variability to be included as selection criteria in animal breeding programs. PMID:26782521

  19. Genetic parameters across lactation for feed intake, fat and protein corrected milk, and live weight in first parity Holstein cattle

    NARCIS (Netherlands)

    Manzanilla Pech, C.I.V.; Veerkamp, R.F.; Calus, M.P.L.; Zom, R.L.G.; Knegsel, van A.; Pryce, J.E.; Haas, de Y.

    2014-01-01

    Breeding values for dry matter intake (DMI) are important to optimize dairy cattle breeding goals for feed efficiency. However, generally, only small data sets are available for feed intake, due to the cost and difficulty of measuring DMI, which makes understanding the genetic associations between t

  20. Genetic and phenotypic variance and covariance components for methane emission and postweaning traits in Angus cattle.

    Science.gov (United States)

    Donoghue, K A; Bird-Gardiner, T; Arthur, P F; Herd, R M; Hegarty, R F

    2016-04-01

    Ruminants contribute 80% of the global livestock greenhouse gas (GHG) emissions mainly through the production of methane, a byproduct of enteric microbial fermentation primarily in the rumen. Hence, reducing enteric methane production is essential in any GHG emissions reduction strategy in livestock. Data on 1,046 young bulls and heifers from 2 performance-recording research herds of Angus cattle were analyzed to provide genetic and phenotypic variance and covariance estimates for methane emissions and production traits and to examine the interrelationships among these traits. The cattle were fed a roughage diet at 1.2 times their estimated maintenance energy requirements and measured for methane production rate (MPR) in open circuit respiration chambers for 48 h. Traits studied included DMI during the methane measurement period, MPR, and methane yield (MY; MPR/DMI), with means of 6.1 kg/d (SD 1.3), 132 g/d (SD 25), and 22.0 g/kg (SD 2.3) DMI, respectively. Four forms of residual methane production (RMP), which is a measure of actual minus predicted MPR, were evaluated. For the first 3 forms, predicted MPR was calculated using published equations. For the fourth (RMP), predicted MPR was obtained by regression of MPR on DMI. Growth and body composition traits evaluated were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), final weight (FWT), and ultrasound measures of eye muscle area, rump fat depth, rib fat depth, and intramuscular fat. Heritability estimates were moderate for MPR (0.27 [SE 0.07]), MY (0.22 [SE 0.06]), and the RMP traits (0.19 [SE 0.06] for each), indicating that genetic improvement to reduce methane emissions is possible. The RMP traits and MY were strongly genetically correlated with each other (0.99 ± 0.01). The genetic correlation of MPR with MY as well as with the RMP traits was moderate (0.32 to 0.63). The genetic correlation between MPR and the growth traits (except BWT) was strong (0.79 to 0.86). These results indicate that

  1. Introgression browser: high-throughput whole-genome SNP visualization

    NARCIS (Netherlands)

    S. Alves Aflitos; G. Sanchez-Perez; D. de Ridder; P. Fransz; M.E. Schranz; H. de Jong; S.A. Peters

    2015-01-01

    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

  2. Genetic analysis of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore cattle.

    Science.gov (United States)

    Passafaro, Tiago Luciano; Carrera, Juan Pablo Botero; dos Santos, Livia Loiola; Raidan, Fernanda Santos Silva; dos Santos, Dalinne Chrystian Carvalho; Cardoso, Eduardo Penteado; Leite, Romário Cerqueira; Toral, Fabio Luiz Buranelo

    2015-06-15

    The aim of the present study was to obtain genetic parameters for resistance to ticks, gastrointestinal nematodes (worms) and Eimeria spp. in Nellore cattle, analyze the inclusion of resistance traits in Nellore breeding programs and evaluate genetic selection as a complementary tool in parasite control programs. Counting of ticks, gastrointestinal nematode eggs and Eimeria spp. oocysts per gram of feces totaling 4270; 3872 and 3872 records from 1188; 1142 and 1142 animals, respectively, aged 146 to 597 days were used. The animals were classified as resistant (counts equal to zero) or susceptible (counts above zero) to each parasite. The statistical models included systematics effects of contemporary groups and the mean trajectory. The random effects included additive genetic effects, direct permanent environmental effects and residual. The mean trajectory and random effects were modeled with linear Legendre polynomials for all traits except for the mean trajectory of resistance to Eimeria spp., which employed the cubic polynomial. Heritability estimates were of low to moderate magnitude and ranged from 0.06 to 0.30, 0.06 to 0.33 and 0.04 to 0.33 for resistance to ticks, gastrointestinal nematodes and Eimeria spp., respectively. The posterior mean of genetic and environmental correlations for the same trait at different ages (205, 365, 450 and 550 days) were favorable at adjacent ages and unfavorable at distant ages. In general, the posterior mean of the genetic and environmental correlations between traits of resistance were low and high-density intervals were large and included zero in many cases. The heritability estimates support the inclusion of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore breeding programs. Genetic selection can increase the frequency of resistant animals and be used as a complementary tool in parasite control programs. PMID:25899078

  3. Genetic analysis of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore cattle.

    Science.gov (United States)

    Passafaro, Tiago Luciano; Carrera, Juan Pablo Botero; dos Santos, Livia Loiola; Raidan, Fernanda Santos Silva; dos Santos, Dalinne Chrystian Carvalho; Cardoso, Eduardo Penteado; Leite, Romário Cerqueira; Toral, Fabio Luiz Buranelo

    2015-06-15

    The aim of the present study was to obtain genetic parameters for resistance to ticks, gastrointestinal nematodes (worms) and Eimeria spp. in Nellore cattle, analyze the inclusion of resistance traits in Nellore breeding programs and evaluate genetic selection as a complementary tool in parasite control programs. Counting of ticks, gastrointestinal nematode eggs and Eimeria spp. oocysts per gram of feces totaling 4270; 3872 and 3872 records from 1188; 1142 and 1142 animals, respectively, aged 146 to 597 days were used. The animals were classified as resistant (counts equal to zero) or susceptible (counts above zero) to each parasite. The statistical models included systematics effects of contemporary groups and the mean trajectory. The random effects included additive genetic effects, direct permanent environmental effects and residual. The mean trajectory and random effects were modeled with linear Legendre polynomials for all traits except for the mean trajectory of resistance to Eimeria spp., which employed the cubic polynomial. Heritability estimates were of low to moderate magnitude and ranged from 0.06 to 0.30, 0.06 to 0.33 and 0.04 to 0.33 for resistance to ticks, gastrointestinal nematodes and Eimeria spp., respectively. The posterior mean of genetic and environmental correlations for the same trait at different ages (205, 365, 450 and 550 days) were favorable at adjacent ages and unfavorable at distant ages. In general, the posterior mean of the genetic and environmental correlations between traits of resistance were low and high-density intervals were large and included zero in many cases. The heritability estimates support the inclusion of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore breeding programs. Genetic selection can increase the frequency of resistant animals and be used as a complementary tool in parasite control programs.

  4. Possibilities of direct introgression from Brassica napus to B. juncea and indirect introgression from B. napus to related Brassicaceae through B. juncea.

    Science.gov (United States)

    Tsuda, Mai; Ohsawa, Ryo; Tabei, Yutaka

    2014-05-01

    The impact of genetically modified canola (Brassica napus) on biodiversity has been examined since its initial stage of commercialization. Various research groups have extensively investigated crossability and introgression among species of Brassicaceae. B. rapa and B. juncea are ranked first and second as the recipients of cross-pollination and introgression from B. napus, respectively. Crossability between B. napus and B. rapa has been examined, specifically in terms of introgression from B. napus to B. rapa, which is mainly considered a weed in America and European countries. On the other hand, knowledge on introgression from B. napus to B. juncea is insufficient, although B. juncea is recognized as the main Brassicaceae weed species in Asia. It is therefore essential to gather information regarding the direct introgression of B. napus into B. juncea and indirect introgression of B. napus into other species of Brassicaceae through B. juncea to evaluate the influence of genetically modified canola on biodiversity. We review information on crossability and introgression between B. juncea and other related Brassicaseae in this report. PMID:24987292

  5. DEMAND FOR BEEF FROM CATTLE ADMINISTERED GROWTH HORMONES OR FED GENETICALLY MODIFIED CORN: A COMPARISON OF CONSUMERS IN FRANCE, GERMANY, THE UNITED KINGDOM, AND THE UNITED STATES

    OpenAIRE

    Jayson L Lusk; Roosen, Jutta; Fox, John A.

    2001-01-01

    This study compares consumer valuations of beef steaks from cattle produced without growth hormones or genetically modified corn in France, Germany, the United Kingdom, and the United States. In general, European consumers place a higher value on beef from cattle that have not been administered growth hormones and/or fed genetically modified corn than United States consumers. There is a larger divergence between the two cultures with regard to the issue of biotechnology and genetic engineerin...

  6. Genetic Variability of Bovine Viral Diarrhea Virus and Evidence for a Possible Genetic Bottleneck during Vertical Transmission in Persistently Infected Cattle.

    Science.gov (United States)

    Dow, Natalie; Chernick, Adam; Orsel, Karin; van Marle, Guido; van der Meer, Frank

    2015-01-01

    Bovine viral diarrhea virus (BVDV), a Pestivirus in the family Flaviviridae, is an economically important pathogen of cattle worldwide. The primary propagators of the virus are immunotolerant persistently infected (PI) cattle, which shed large quantities of virus throughout life. Despite the absence of an acquired immunity against BVDV in these PI cattle there are strong indications of viral variability that are of clinical and epidemiological importance. In this study the variability of E2 and NS5B sequences in multiple body compartments of PI cattle were characterized using clonal sequencing. Phylogenetic analyses revealed that BVDV exists as a quasispecies within PI cattle. Viral variants were clustered by tissue compartment significantly more often than expected by chance alone with the central nervous system appearing to be a particularly important viral reservoir. We also found strong indications for a genetic bottleneck during vertical transmission from PI animals to their offspring. These quasispecies analyses within PI cattle exemplify the role of the PI host in viral propagation and highlight the complex dynamics of BVDV pathogenesis, transmission and evolution.

  7. Genetic Variability of Bovine Viral Diarrhea Virus and Evidence for a Possible Genetic Bottleneck during Vertical Transmission in Persistently Infected Cattle.

    Directory of Open Access Journals (Sweden)

    Natalie Dow

    Full Text Available Bovine viral diarrhea virus (BVDV, a Pestivirus in the family Flaviviridae, is an economically important pathogen of cattle worldwide. The primary propagators of the virus are immunotolerant persistently infected (PI cattle, which shed large quantities of virus throughout life. Despite the absence of an acquired immunity against BVDV in these PI cattle there are strong indications of viral variability that are of clinical and epidemiological importance. In this study the variability of E2 and NS5B sequences in multiple body compartments of PI cattle were characterized using clonal sequencing. Phylogenetic analyses revealed that BVDV exists as a quasispecies within PI cattle. Viral variants were clustered by tissue compartment significantly more often than expected by chance alone with the central nervous system appearing to be a particularly important viral reservoir. We also found strong indications for a genetic bottleneck during vertical transmission from PI animals to their offspring. These quasispecies analyses within PI cattle exemplify the role of the PI host in viral propagation and highlight the complex dynamics of BVDV pathogenesis, transmission and evolution.

  8. Clinical and biochemical signs in Fleckvieh cattle with genetically confirmed Fanconi-Bickel syndrome (cattle homozygous for Fleckvieh haplotype 2).

    Science.gov (United States)

    Burgstaller, Johann; Url, Angelika; Pausch, Hubert; Schwarzenbacher, Hermann; Egerbacher, Monika; Wittek, Thomas

    2016-01-01

    Fanconi-Bickel Syndrome (FBS) is an autosomal recessive disorder of the carbohydrate metabolism, which has been reported in human and some animals (OMIA 000366-9913). In Fleckvieh cattle it is caused by mutations in SLC2A2, a gene encoding for glucose transporter protein 2 (GLUT2), which is primarily expressed in liver, kidney, pancreas and intestines. The causal mutation resides in a previously reported Fleckvieh Haplotype 2 (FH-2). FH-2 homozygous individuals are rare, but due to widespread use of heterozygous bulls in artificial insemination, heterozygous animals are likely to be present in a larger number in the cattle population. Two clinical cases of Fleckvieh cattle with a syndrome resembling the phenotypic appearance of FBS are presented in the present study describing the association between the clinical manifestations of FBS and the postulated frameshift mutation in bovine SLC2A2. Clinical examination showed poor growth, retarded development, polyuria, and polydipsia. Laboratory analyses showed an increased plasma glucose but normal insulin concentration and increased renal glucose excretion. Histopathological examination of kidney and liver samples revealed massively increased liver glycogen storage and nephrosis. Sires of both cases were tested positive for being heterozygous carriers for the same frameshift mutation in SLC2A2 as was originally reported in Fleckvieh cattle. DNA of both cases described was analyzed and Sanger sequencing confirmed homozygosity for the frameshift mutation in SLC2A2.

  9. Clinical and biochemical signs in Fleckvieh cattle with genetically confirmed Fanconi-Bickel syndrome (cattle homozygous for Fleckvieh haplotype 2).

    Science.gov (United States)

    Burgstaller, Johann; Url, Angelika; Pausch, Hubert; Schwarzenbacher, Hermann; Egerbacher, Monika; Wittek, Thomas

    2016-01-01

    Fanconi-Bickel Syndrome (FBS) is an autosomal recessive disorder of the carbohydrate metabolism, which has been reported in human and some animals (OMIA 000366-9913). In Fleckvieh cattle it is caused by mutations in SLC2A2, a gene encoding for glucose transporter protein 2 (GLUT2), which is primarily expressed in liver, kidney, pancreas and intestines. The causal mutation resides in a previously reported Fleckvieh Haplotype 2 (FH-2). FH-2 homozygous individuals are rare, but due to widespread use of heterozygous bulls in artificial insemination, heterozygous animals are likely to be present in a larger number in the cattle population. Two clinical cases of Fleckvieh cattle with a syndrome resembling the phenotypic appearance of FBS are presented in the present study describing the association between the clinical manifestations of FBS and the postulated frameshift mutation in bovine SLC2A2. Clinical examination showed poor growth, retarded development, polyuria, and polydipsia. Laboratory analyses showed an increased plasma glucose but normal insulin concentration and increased renal glucose excretion. Histopathological examination of kidney and liver samples revealed massively increased liver glycogen storage and nephrosis. Sires of both cases were tested positive for being heterozygous carriers for the same frameshift mutation in SLC2A2 as was originally reported in Fleckvieh cattle. DNA of both cases described was analyzed and Sanger sequencing confirmed homozygosity for the frameshift mutation in SLC2A2. PMID:27169150

  10. Genetic correlations between visual slaughter conformation scores and growth and reproductive traits in Canchim cattle.

    Science.gov (United States)

    Borba, L H F; Baldi, F; Feitosa, F L B; da Silva, L O C; Pereira, A S C; Alencar, M M

    2016-01-01

    We obtained heritability and (co)variance component estimates for slaughter conformation scores at 420 days of age (SCS420), age at calving (first, AFC; second, ASC), calving occurrence until 38 months of age (CP38), weight at 420 days of age (W420), and scrotal circumference at 420 days (SC420) in Canchim (5/8 Charolais + 3/8 Zebu) cattle. A total of 23,168 records of Canchim animals, including 12,493 females and 10,675 males, were analyzed. SCS420 indicated carcass structure, muscle development, and subcutaneous fat deposition. The slaughter conformation score of each animal was relative to the whole contemporary group; 1 corresponded to the lowest expression of the trait and 6 to the highest. Heritabilities, and genetic and residual correlation estimates between SCS420 and reproductive and weight traits, were estimated by multitrait analyses using an animal model with Bayesian inference, employing a linear model for AFC, ASC, SC420, and W420 and a threshold model for CP38 and SCS420. Heritability estimates for SCS420, AFC, ASC, CP38, W420, and SC420 were 0.11, 0.15, 0.15, 0.15, 0.30, and 0.30, respectively. Genetic correlation estimates between SCS420 and the other traits were 0.08 (AFC), 0.58 (ASC), 0.08 (CP38), 0.43 (W420), and 0.17 (SC420). Visual slaughter conformation scores respond to individual selection and can be used as selection criteria in Canchim cattle. Selection to improve sexual precocity would not be effective in improving carcass conformation and composition, and selection for animals with high breeding values for yearling weight may improve slaughter conformation at the yearling stage. PMID:27323049

  11. Genetic and phenotypic parameters of productivity traits on the first three lactations in Gyr cattle herds

    Directory of Open Access Journals (Sweden)

    Albuquerque Maria do Socorro Maués

    1999-01-01

    Full Text Available Records of Gyr cows selected for milk production were obtained from the National Gyr Dairy Cattle Breeding Program (Embrapa/CNPGL and analyzed, in order to estimate genetic parameters for the first three lactations and to verify the effects of some environmental factors on milk production from 1979 to 1994. Genetic parameters were estimated by REML with an animal model and a group of fixed effects that included classes of herd, year, season and age at calving. Milk production means and standard deviations were 2,183 kg, 707 kg; 2,682 kg, 762 kg and 2,638 kg, 851 kg, for first, second, and third lactations, respectively. Heritability estimates were 0.20, 0.12, and 0.19 for first, second, and third lactations, respectively, and repeatability was 0.44. Genetic correlation estimates were: 0.68 between first and second lactations, 0.84 between first and third lactations and 1.0 between second and third lactations. Results confirm other research for specialized dairy breeds and firmly suggest that even in breeds of Indian origin the best time to make selection decisions is during the first lactation.

  12. Genetic parameters for gestation length and pre- and postweaning growth traits in Nellore cattle

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    Heverton Luis Moreira

    2015-07-01

    Full Text Available The objective of this study was to estimate heritabilities and genetic and phenotypic correlations for gestation length as calf trait (GLcalf and preweaning [birth weight (BW and weights at 120 (W120 and 210 (W210 days] and postweaning performance traits [weights at 365 (W365 and 450 (W450 days] in Nellore cattle participating in the Nellore Brazil Program coordinated by the National Association of Breeders and Researchers (Associação Nacional de Criadores e Pesquisadores - ANCP. The parameters were estimated by the restricted maximum likelihood method under an animal model using the WOMBAT software. The genetic correlation between GLcalf and BW was 0.15, indicating a favorable association between the two traits which, however, was of small magnitude. GLcalf showed low positive genetic correlations (0.06 to 0.10 with the other weights, indicating that selection to reduce gestation length would not result in significant losses in weights at older ages. Furthermore, it is possible to infer that selection for higher W365 will not expressively increase gestation length.

  13. Genetic parameter estimates of yearling live animal ultrasonic measurements in Brangus cattle.

    Science.gov (United States)

    Stelzleni, A M; Perkins, T L; Brown, A H; Pohlman, F W; Johnson, Z B; Sandelin, B A

    2002-12-01

    The objective of this study was to estimate genetic parameters for real-time ultrasound measurements of longissimus muscle area (LMA), 12th rib backfat thickness (FT), percent intramuscular fat (IMF), and yearling weight (YW) for 1,299 yearling Brangus bulls and heifers. A single ultrasound technician performed all measurements. The number of observations was 1,298, 1,298, 1,215, and 1,170 for LMA, FT, IMF, and YW, respectively. Genetic parameters were estimated for each trait using single- and multiple-trait derivative-free restricted maximal likelihood. Fixed effects were contemporary group (defined as same sex, same age within six months, and same environment), and days of age as a covariate. Correlations were estimated from two-trait models. Heritabilities for LMA, FT, IMF, and YW were 0.31, 0.26, 0.16, and 0.53, respectively. Genetic correlations between LMA and FT, LMA and IMF, LMA and YW, FT and IMF, FT and YW, and IMF and YW were 0.09, 0.25, 0.44, 0.36, 0.42, and 0.31, respectively. Yearling live animal ultrasonic measurements can be used as a selection tool in breeding cattle for the improvement of carcass traits. PMID:12542155

  14. Genetic parameters for carcass weight, conformation and fat in five beef cattle breeds.

    Science.gov (United States)

    Kause, A; Mikkola, L; Strandén, I; Sirkko, K

    2015-01-01

    Profitability of beef production can be increased by genetically improving carcass traits. To construct breeding value evaluations for carcass traits, breed-specific genetic parameters were estimated for carcass weight, carcass conformation and carcass fat in five beef cattle breeds in Finland (Hereford, Aberdeen Angus, Simmental, Charolais and Limousin). Conformation and fat were visually scored using the EUROP carcass classification. Each breed was separately analyzed using a multitrait animal model. A total of 6879-19 539 animals per breed had phenotypes. For the five breeds, heritabilities were moderate for carcass weight (h 2=0.39 to 0.48, s.e.=0.02 to 0.04) and slightly lower for conformation (h 2=0.30 to 0.44, s.e.=0.02 to 0.04) and carcass fat (h 2=0.29 to 0.44, s.e.=0.02 to 0.04). The genetic correlation between carcass weight and conformation was favorable in all breeds (r G=0.37 to 0.53, s.e.=0.04 to 0.05), heavy carcasses being genetically more conformed. The phenotypic correlation between carcass weight and carcass fat was moderately positive in all breeds (r P=0.21 to 0.32), implying that increasing carcass weight was related to increasing fat levels. The respective genetic correlation was the strongest in Hereford (r G=0.28, s.e.=0.05) and Angus (r G=0.15, s.e.=0.05), the two small body-sized British breeds with the lowest conformation and the highest fat level. The correlation was weaker in the other breeds (r G=0.08 to 0.14). For Hereford, Angus and Simmental, more conformed carcasses were phenotypically fatter (r P=0.11 to 0.15), but the respective genetic correlations were close to zero (r G=-0.05 to 0.04). In contrast, in the two large body-sized and muscular French breeds, the genetic correlation between conformation and fat was negative and the phenotypic correlation was close to zero or negative (Charolais: r G=-0.18, s.e.=0.06, r P=0.02; Limousin: r G=-0.56, s.e.=0.04, r P=-0.13). The results indicate genetic variation for the genetic

  15. Genotype by climate interaction in the genetic evaluation for growing traits of Braunvieh cattle in Mexico.

    Science.gov (United States)

    Saavedra-Jiménez, Luis A; Ramírez-Valverde, Rodolfo; Núñez-Domínguez, Rafael; García-Muñiz, José G; Lopez-Villalobos, Nicolas; Ruíz-Flores, Agustín

    2013-10-01

    The objective of this study was to determine the magnitude of genotype by climate interaction (GCI) in the national genetic evaluation for weaning (WW) and yearling (YW) weights of Mexican Braunvieh cattle. The numbers of performance records and animals in the pedigree were 12,364 and 25,173 for WW, and 7,991 and 18,072 for YW, respectively. Performance records were clustered based on climatological variables into: dry tropic (DT), wet tropic (WT), and temperate (TE) climates. Animal models were used to estimate genetic parameters and predict breeding values in each of the climates. Bivariate analyses were carried out for pairwise combinations of climates on each trait, considering the same trait in different climates as a different trait. Criteria to evaluate GCI were genetic correlations (r g), correlations between predicted breeding values (r BV), and frequencies of coincidence (FC) in the ranking of the top 25 sires. Results of comparisons between pairs of climates were variable, depending on specific cases. For WW, the r g, r BV, and FC ranged from -0.36 to 0.84, -0.60 to 0.97, and 0.16 to 0.92, respectively; whereas for YW, they fluctuated between 0.23 and 0.99, 0.33 and 1.00, and 0.60 and 1.00, respectively. For both traits, the results suggest absence of GCI between DT and TE; however, GCI was detected in the other pairs of climates, where WT was involved. To maximize genetic progress, the joint genetic evaluation should be performed only for animals with performance data in DT and TE, whereas a separated evaluation is suggested for animals with performance records generated under WT conditions.

  16. Effects of genetic variants in the promoter region of the bovine adiponectin (ADIPOQ) gene on marbling of Hanwoo beef cattle.

    Science.gov (United States)

    Choi, Yoonjeong; Davis, Michael E; Chung, Hoyoung

    2015-07-01

    This study aimed to verify genetic effects of the bovine adiponectin (ADIPOQ) gene on carcass traits of Hanwoo cattle. The measured carcass traits were marbling score (MAR), backfat thickness (BFT), loineye area (LEA), and carcass weight (CAW). Selection of primers was based on the bovine ADIPOQ sequence, and the analysis amplified approximately 267 and 333 bp genomic segments, including 67 bp of insertions in the promoter region. Sequencing analysis confirmed genetic variants (g.81966235C>T, g.81966377T>C, and g.81966364D>I) that showed significant effects on MAR. The present results suggest that the identified SNPs are useful genetic markers for the improvement of carcass traits in Hanwoo cattle.

  17. Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus and current genetic status of this species in Vietnam

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    Renard Jean-Paul

    2007-11-01

    Full Text Available Abstract Background The wild gaur (Bos gaurus is an endangered wild cattle species. In Vietnam, the total number of wild gaurs is estimated at a maximum of 500 individuals. Inbreeding and genetic drift are current relevant threats to this small population size. Therefore, information about the genetic status of the Vietnamese wild gaur population is essential to develop strategies for conservation and effective long-term management for this species. In the present study, we performed cross-species amplification of 130 bovine microsatellite markers, in order to evaluate the applicability and conservation of cattle microsatellite loci in the wild gaur genome. The genetic diversity of Vietnamese wild gaur was also investigated, based on data collected from the 117 successfully amplified loci. Results One hundred-thirty cattle microsatellite markers were tested on a panel of 11 animals. Efficient amplifications were observed for 117 markers (90% with a total of 264 alleles, and of these, 68 (58.1% gave polymorphic band patterns. The number of alleles per locus among the polymorphic markers ranged from two to six. Thirteen loci (BM1314, BM2304, BM6017, BMC2228, BMS332, BMS911, CSSM023, ETH123, HAUT14, HEL11, HEL5, ILSTS005 and INRA189 distributed on nine different cattle chromosomes failed to amplify wild gaur genomic DNA. Three cattle Y-chromosome specific microsatellite markers (INRA124, INRA126 and BM861 were also highly specific in wild gaur, only displaying an amplification product in the males. Genotype data collected from the 117 successfully amplified microsatellites were used to assess the genetic diversity of this species in Vietnam. Polymorphic Information Content (PIC values varied between 0.083 and 0.767 with a mean of 0.252 while observed heterozygosities (Ho ranged from 0.091 to 0.909 (mean of 0.269. Nei's unbiased mean heterozygosity and the mean allele number across loci were 0.298 and 2.2, respectively. Conclusion Extensive

  18. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

    DEFF Research Database (Denmark)

    Pham, Lan Doan; Do, Duy Ngoc; Binh, Nguyen Trong;

    2013-01-01

    geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels...

  19. Multiple trait genetic evaluation of clinical mastitis in three dairy cattle breeds.

    Science.gov (United States)

    Govignon-Gion, A; Dassonneville, R; Baloche, G; Ducrocq, V

    2016-04-01

    In 2010, a routine genetic evaluation on occurrence of clinical mastitis in three main dairy cattle breeds-- Montbéliarde (MO), Normande (NO) and Holstein (HO)--was implemented in France. Records were clinical mastitis events reported by farmers to milk recording technicians and the analyzed trait was the binary variable describing the occurrence of a mastitis case within the first 150 days of the first three lactations. Genetic parameters of clinical mastitis were estimated for the three breeds. Low heritability estimates were found: between 2% and 4% depending on the breed. Despite its low heritability, the trait exhibits genetic variation so efficient genetic improvement is possible. Genetic correlations with other traits were estimated, showing large correlations (often>0.50, in absolute value) between clinical mastitis and somatic cell score (SCS), longevity and some udder traits. Correlation with milk yield was moderate and unfavorable (ρ=0.26 to 0.30). High milking speed was genetically associated with less mastitis in MO (ρ=-0.14) but with more mastitis in HO (ρ=0.18). A two-step approach was implemented for routine evaluation: first, a univariate evaluation based on a linear animal model with permanent environment effect led to pre-adjusted records (defined as records corrected for all non-genetic effects) and associated weights. These data were then combined with similar pre-adjusted records for others traits in a multiple trait BLUP animal model. The combined breeding values for clinical mastitis obtained are the official (published) ones. Mastitis estimated breeding values (EBV) were then combined with SCSs EBV into an udder health index, which receives a weight of 14.5% to 18.5% in the French total merit index (ISU) of the three breeds. Interbull genetic correlations for mastitis occurrence were very high (ρ=0.94) with Nordic countries, where much stricter recording systems exist reflecting a satisfactory quality of phenotypes as reported by the

  20. Multiple trait genetic evaluation of clinical mastitis in three dairy cattle breeds.

    Science.gov (United States)

    Govignon-Gion, A; Dassonneville, R; Baloche, G; Ducrocq, V

    2016-04-01

    In 2010, a routine genetic evaluation on occurrence of clinical mastitis in three main dairy cattle breeds-- Montbéliarde (MO), Normande (NO) and Holstein (HO)--was implemented in France. Records were clinical mastitis events reported by farmers to milk recording technicians and the analyzed trait was the binary variable describing the occurrence of a mastitis case within the first 150 days of the first three lactations. Genetic parameters of clinical mastitis were estimated for the three breeds. Low heritability estimates were found: between 2% and 4% depending on the breed. Despite its low heritability, the trait exhibits genetic variation so efficient genetic improvement is possible. Genetic correlations with other traits were estimated, showing large correlations (often>0.50, in absolute value) between clinical mastitis and somatic cell score (SCS), longevity and some udder traits. Correlation with milk yield was moderate and unfavorable (ρ=0.26 to 0.30). High milking speed was genetically associated with less mastitis in MO (ρ=-0.14) but with more mastitis in HO (ρ=0.18). A two-step approach was implemented for routine evaluation: first, a univariate evaluation based on a linear animal model with permanent environment effect led to pre-adjusted records (defined as records corrected for all non-genetic effects) and associated weights. These data were then combined with similar pre-adjusted records for others traits in a multiple trait BLUP animal model. The combined breeding values for clinical mastitis obtained are the official (published) ones. Mastitis estimated breeding values (EBV) were then combined with SCSs EBV into an udder health index, which receives a weight of 14.5% to 18.5% in the French total merit index (ISU) of the three breeds. Interbull genetic correlations for mastitis occurrence were very high (ρ=0.94) with Nordic countries, where much stricter recording systems exist reflecting a satisfactory quality of phenotypes as reported by the

  1. Genetic polymorphisms of the FATP1 gene and their associations with meat quality traits in Chinese Qinchuan cattle.

    Science.gov (United States)

    Zhao, Z D; Li, A N; Wei, S J; Wang, M M; Li, S J; Zan, L S

    2015-12-21

    Fatty acid transport protein 1 (FATP1), an integral membrane protein that facilitates long-chain fatty acid influx, is involved in the genetic network for oleic acid synthesis. The aim of this study was to examine the association of FATP1 polymorphisms with live animal meat quality traits in Chinese Qinchuan cattle. Quantitative real-time PCR analysis demonstrated that FATP1 has a broad tissue distribution in Qinchuan cattle and is highly expressed in longissimus dorsi muscle and back fat. Using direct DNA sequencing of the FATP1 gene in 458 Qinchuan cattle, four single nucleotide polymorphisms (SNPs; g.28265 G>C, g.28381 G>A, g.28470 T>C, and g.28672 G>A) were identified for genotyping within a 671-bp region, including exon 3, intron 3, exon 4, intron 4, and part of exon 5 of the FATP1 gene. Positive effects of genotypes CC (g.28470 T>C locus) and AA (g.28672 G>A locus) on meat quality traits were obtained by association analysis. These results indicate the associations of g.28470 T>C and g.28672 G>A with meat quality traits in Qinchuan cattle. Thus, the FATP1 gene may be used in marker-assisted selection of beef cattle in breeding programs.

  2. Genetic parameters for female fertility, locomotion, body condition score, and linear type traits in Czech Holstein cattle

    DEFF Research Database (Denmark)

    Zink, Vojtech; Stipkova, M; Lassen, Jan

    2011-01-01

    The aim of this study was to estimate genetic parameters for fertility traits and linear type traits in the Czech Holstein dairy cattle population. Phenotypic data regarding 12 linear type traits, measured in first lactation, and 3 fertility traits, measured in each of first and second lactation......, with the greatest correlation between BCS and CF2 (−0.51). Genetic correlations with locomotion were greatest for CF1 and CF2 (−0.34 for both). Results of this study show that cows that are genetically extreme for angularity, stature, and body depth tend to perform poorly for fertility traits. At the same time...

  3. Conservation Genetics of Crested Newt Species Triturus cristatus and T. carnifex within a Contact Zone in Central Europe: Impact of Interspecific Introgression and Gene Flow

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    Peter Mikulíček

    2009-12-01

    Full Text Available We have studied the population genetic structure of slightly admixed populations of crested newts (Triturus cristatus and T. carnifex in a continuously fragmented landscape, located in northern Salzburg (Austria and neighbouring Bavaria (Germany. Crested newts are listed as Critically Endangered in the provincial Red List of Salzburg and strictly protected by the EU Habitats Directive. We used seven polymorphic microsatellite loci to evaluate genetic diversity and processes that may determine the genetic architecture of populations. Genetic diversity was moderate, pairwise FST-values were comparatively high showing significant genetic differentiation and limited gene flow. Isolation by distance was significant for the whole data set, but not significant when calculated for T. cristatus- and T. carnifex-like populations separately. Bayesian analyses of population structure, using three different programs showed similar results. Spatial statistics reveal that the geographical isolation of populations is very high.

  4. Genetic parameters for body condition score, locomotion, angularity, and production traits in Italian Holstein cattle.

    Science.gov (United States)

    Battagin, M; Sartori, C; Biffani, S; Penasa, M; Cassandro, M

    2013-08-01

    The objectives of this research were to estimate genetic parameters for body condition score (BCS) and locomotion (LOC), and to assess their relationships with angularity (ANG), milk yield, fat and protein content, and fat to protein content ratio (F:P) in the Italian Holstein Friesian breed. The Italian Holstein Friesian Cattle Breeders Association collects type trait data once on all registered first lactation cows. Body condition score and LOC were introduced in the conformation scoring system in 2007 and 2009, respectively. Variance (and covariance) components among traits were estimated with a Bayesian approach via a Gibbs sampling algorithm and an animal model. Heritability estimates were 0.114 and 0.049 for BCS and LOC, respectively. The genetic correlation between BCS and LOC was weak (-0.084) and not different from zero; therefore, the traits seem to be genetically independent, but further investigation on possible departures from linearity of this relationship is needed. Angularity was strongly negatively correlated with BCS (-0.612), and strongly positively correlated with LOC (0.650). The genetic relationship of milk yield with BCS was moderately negative (-0.386), and was moderately positive (0.238) with LOC. These results indicate that high-producing cows tend to be thinner and tend to have better locomotion than low-producing cows. The genetic correlation of BCS with fat content (0.094) and F:P (-0.014) was very weak and not different from zero, and with protein content (0.173) was weak but different from zero. Locomotion was weakly correlated with fat content (0.071), protein content (0.028), and F:P (0.074), and correlations were not different from zero. Phenotypic correlations were generally weaker than their genetic counterparts, ranging from -0.241 (BCS with ANG) to 0.245 (LOC with ANG). Before including BCS and LOC in the selection index of the Italian Holstein breed, the correlations with other traits currently used to improve type and

  5. Population genetics of the native caribou (Rangifer tarandus groenlandicus) and the semi-domestic reindeer (Rangifer tarandus tarandus) in Southwestern Greenland: evidence of introgression

    DEFF Research Database (Denmark)

    Jepsen, B.I.; Siegismund, Hans Redlef; Fredholm, Merete

    2002-01-01

    samples were collected, which included samples from caribou of four different regions and samples from two different reindeer herds. Based on the genetic variation of the five markers, our results shows that the caribou and the reindeer populations in the six regions sampled are genetically differentiated...... within each group and the two subspecies are differentiated from each other. A likely explanation for the genetic isolation of the populations investigated is that natural barriers (glaciers and wide fjords) exists in the area. Furthermore we found that introduced Norwegian domestic reindeer hybridized...

  6. ESTIMATION OF GENETIC PARAMETERS FOR CARCASS TRAITS FOR SIMMENTAL CATTLE IN CROATIA

    Directory of Open Access Journals (Sweden)

    Marija Špehar

    2007-06-01

    Full Text Available The objective of this paper was an estimation of genetic parameters for carcass weight, conformation, fatness class and net gain for Simmental cattle in Croatia. Data of young bulls slaughtered in years 2005 and 2006 with 12 to 24 months of age was taken from the central database of the Croatian Livestock Centre. Three data sets were constructed as follows: 1 data set 1 (DS1 included 80462 records of bulls with known and unknown parents; 2 data set 2 (DS2 had 26245 records of bulls with at least one known parents; 3 data set 3 (DS3 with 6272 records of bulls slaughtered between 12 and 14 months of age. Pedigree for DS1 included a total of 118595 animals, 70415 animals and 19319 animals in pedigree for DS2 and DS3, respectively. Variance components were estimated by REML method as implemented in the VCE-5 program package. Statistical model included region, calving season, abattoir-supervisor interaction as fixed class effects and slaughter age as quadratic regression. Direct additive genetic effect was included in the model as random effect. For carcass weight heritability estimates were 0.10 ± 0.006, 0.13 ± 0.02 and 0.11 ± 0.03 for DS1, DS2 and DS3, respectively. Heritability estimates for net gain were 0.09 ± 0.006, 0.16 ± 0.03 and 0.13 ± 0.03, and for carcass conformation were 0.05 ± 0.006, 0.03 ± 0.01 and 0.05 ± 0.006 for DS1, DS2 and DS3, respectively. Results attained indicate that DS2 can be used for genetic evaluation of the Simmental carcass traits in Croatia. However, in the future more improvement should be done, concerning the constitution of contemporary groups, and special attention should be given to data collection.

  7. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil

    OpenAIRE

    Almeida Leonardo D; Mariante Arthur S; Albuquerque Maria do Socorro M; Paiva Samuel R.; Egito Andréa A; Castro Silvia R; Grattapaglia Dario

    2007-01-01

    Abstract Background Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists...

  8. The genetics of adaptation of cattle to high altitude environment: The case of brisket disease in northwestern Ethiopia

    International Nuclear Information System (INIS)

    populations. All PAP scores (21- 47 mm Hg) fall within the range of low to moderate risks. Differences in means were not significant for any pair of populations. Some of the readings (values <28 mm HG) for the Semien cattle group measured at 3500 m are out of the range of readings of approx. 100,000 cattle that the veterinarian has taken in the Rocky mountains in the course of 20 years. Crosses of the local cattle with Holstein Friesian and Jersey were not more prone to brisket disease than local cattle measured at the same altitudes. In a study comparing PAP readings in yak, cattle and their crosses, the crosses had equally low PAP readings as the yaks. Yaks are known to be resistant to high altitude disease due to an adaptation of vascular system, indicated by thin-walled small pulmonary arteries. The authors speculated about an autosomal dominant gene transmitting genetic attenuation of the hypoxic vasoconstrictor response. We conclude that cattle breeds of North Western Ethiopia are genetically adapted to high altitude. To get an insight on the mechanism of adaptation an in depth histological study on the internal anatomy of cardiovascular and respiratory systems of these genotypes is currently being undertaken. (author)

  9. Genetic and morphological characterisation of the Ankole Longhorn cattle in the African Great Lakes region

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    Okeyo Mwai A

    2008-09-01

    Full Text Available Abstract The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size, genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were genotyped using 15 DNA microsatellites. Femoral length, horn length, horn circumference, rump height, body length and fore-limb circumference showed the largest differences between regions. An overall FST index indicated that 2.7% of the total genetic variation was present among sub-populations. The least differentiation was observed between the two sub-populations of Mbarara south and Luwero in Uganda, while the highest level of differentiation was observed between the Mugamba in Burundi and Malagarasi in Tanzania. An estimated membership of four for the inferred clusters from a model-based Bayesian approach was obtained. Both analyses on distance-based and model-based methods consistently isolated the Mugamba sub-population in Burundi from the others.

  10. Mitochondrial control region genetic diversity and maternal ancestry of a Brangus-Ibage cattle populations

    Directory of Open Access Journals (Sweden)

    Luiz Ernani Henkes

    2005-03-01

    Full Text Available The genetic diversity of 277 nucleotides in the mitochondrial DNA control region (nt 15,964 to 16,240 in reference sequence was analyzed in crossbreed beef cattle (Brangus-Ibage, 5/8 Bos primigenius taurus x 3/8 Bos primigenius indicus as well as in some Nellore samples (B. p. indicus. Fifty-seven mutations were found in Brangus-Ibage comprising 18 haplotypes (haplotype diversity, h = 0.851 ± 0.041 and nucleotide diversity, ntd = 0.009 ± 0.006 and 66 in Nellore (h = 1.00 ± 0.27, ntd = 0.014 ± 0.012. These data indicated sequence identities of 99.6 and 92.1% between the B. p. taurus' reference sequence and Brangus-Ibage and Nellore, respectively. The comparison of our data with sequence data for 612 individuals recovered from GenBank showed a total of 205 haplotypes defined by 99 polymorphic sites. Most of the variability (53% was due to differentiation within breeds. The phylogenetic tree constructed using the neighbor-joining method showed clearly the well-known dichotomy between B. p. taurus and B. p. indicus. The Brangus-Ibage clustered with B. p. taurus lineages; however, the displacement of Nellore from B. p. indicus branch probably indicates a substantial B. p. taurus maternal ancestry in some Nellore samples (obtained from GenBank and reflects the primarily male-driven introduction of this breed in Brazil.

  11. Genetic Association Analysis of Paratuberculosis Forms in Holstein-Friesian Cattle

    Directory of Open Access Journals (Sweden)

    Patricia Vázquez

    2014-01-01

    Full Text Available A genetic susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP infections in ruminants has been longtime suspected to exist. Recently, natural infections in cattle have been reclassified into latent and patent forms based on histopathological findings and their associations with immunological and microbiological variables. This study aims to explore whether these newly defined phenotypes are associated with twenty-four single-nucleotide polymorphisms (SNPs in six bovine candidate genes: nucleotide-binding oligomerization domain 2 (NOD2, solute carrier family 11 member A1 (SLC11A1, nuclear body protein SP110 (SP110, toll-like receptors (TLRs 2 and 4, and CD209 (also known as DC-SIGN, dendritic cell-specific ICAM3-grabbing nonintegrin. SNPs were genotyped for 772 Holstein-Friesian animals (52.6% apparently free; 38.1% latent; 9.3% patent by TaqMan OpenArray technology. Genotypic-phenotypic associations were assessed by logistic regression analysis adjusted for age at slaughter, under five models (codominant, dominant, recessive, overdominant, and log-additive, and corrected for multiple testing. The rs208222804 C allele (CD209 gene was found to be associated with latent paratuberculosis (log-additive model: P<0.0034 after permutation procedure; OR = 0.64, 95% CI = 0.48–0.86. No significant association was detected between any SNP and the patent phenotype. Consequently, CD209 gene may play a key role in the pathogenesis of bovine paratuberculosis.

  12. Behavioural linear standardized scoring system of the Lidia cattle breed by testing in herd: estimation of genetic parameters.

    Science.gov (United States)

    Pelayo, R; Solé, M; Sánchez, M J; Molina, A; Valera, M

    2016-10-01

    Docility is very important for cattle production, and many behavioural tests to measure this trait have been developed. However, very few objective behavioural tests to measure the opposite approach 'aggressive behaviour' have been described. Therefore, the aim of this work was to validate in the Lidia cattle breed a behavioural linear standardized scoring system that measure the aggressiveness and enable genetic analysis of behavioural traits expressing fearless and fighting ability. Reproducibility and repeatability measures were calculated for the 12 linear traits of this scoring system to assess its accuracy, and ranged from 85.3 and 94.2%, and from 66.7 to 97.9%, respectively. Genetic parameters were estimated using an animal model with a Bayesian approach. A total of 1202 behavioural records were used. The pedigree matrix contained 5001 individuals. Heritability values (with standard deviations) ranged between 0.13 (0.04) (Falls of the bull) and 0.41 (0.08) (Speed of approach to horse). Genetic correlations varied from 0.01 (0.07) to 0.90 (0.13). Finally, an exploratory factor analysis using the genetic correlation matrix was calculated. Three main factors were retained to describe the traditional genetic indexes aggressiveness, strength and mobility.

  13. Genetic diversity and frequency of bovine viral diarrhea virus (BVDV) detected in cattle in Turkey

    Science.gov (United States)

    Rapid detection and culling of persistently infected animals and efficacious vaccination are key factors to control bovine viral diarrhea virus (BVDV) infections in cattle. The aim of this study was to investigate frequency of detection of persistently infected cattle and examine the diversity of bo...

  14. Genetic diversity of bovine viral diarrhea virus in cattle from Mexico

    Science.gov (United States)

    Bovine viral diarrhea virus (BVDV) infects cattle populations worldwide causing significant economic losses though its impact in animal health. Previous studies have reported the prevalence of BVDV species and subgenotypes in cattle from the United States and Canada. In this study, we investigated t...

  15. Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle.

    Science.gov (United States)

    DeAtley, K L; Rincon, G; Farber, C R; Medrano, J F; Luna-Nevarez, P; Enns, R M; VanLeeuwen, D M; Silver, G A; Thomas, M G

    2011-07-01

    ETH10 is a dinucleotide microsatellite within the promoter of signal transducer and activator of transcription 6 (STAT6) gene on bovine chromosome 5. ETH10 is included in the panel of genetic markers used in parentage testing procedures of cattle breed associations. Allelic sizes of ETH10 PCR amplicons range from 199 to 225 bp. Objectives of this study were to use microsatellite data from beef cattle breed associations to investigate genetic distance and population stratification among Angus- and Brahman-influenced cattle and to use ETH10 genotypes and growth and ultrasound carcass data to investigate their statistical relationships. Three series of genotype to phenotype association analyses were conducted with 1) Angus data (n=5,094), 2) Brangus data (3/8 Brahman × 5/8 Angus; n=2,296), and 3) multibreed data (n=4,426) of Angus and Brangus cattle. Thirteen alleles and 38 genotypes were observed, but frequencies varied among breed groups. Tests of genetic identity and distance among 6 breed composition groups increasing in Brahman influence from 0 to 75% revealed that as Brahman-influence increased to ≥50%, genetic distance from Angus ranged from 18.3 to 43.5%. This was accomplished with 10 microsatellite loci. A mixed effects model involving genotype as a fixed effect and sire as a random source of variation suggested that Angus cattle with the 217/219 genotype tended to have 2.1% heavier (P=0.07) 205-d BW than other genotypes. In Brangus cattle, allele combinations were classified as small (≤215 bp) or large (≥217 bp). Brangus cattle with the small/large genotype had 2.0% heavier (Pcarcass traits in Angus and Brangus cattle. Results from this study provide support for STAT6 as one of the candidate genes underlying cattle growth QTL on chromosome 5.

  16. Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle.

    Science.gov (United States)

    DeAtley, K L; Rincon, G; Farber, C R; Medrano, J F; Luna-Nevarez, P; Enns, R M; VanLeeuwen, D M; Silver, G A; Thomas, M G

    2011-07-01

    ETH10 is a dinucleotide microsatellite within the promoter of signal transducer and activator of transcription 6 (STAT6) gene on bovine chromosome 5. ETH10 is included in the panel of genetic markers used in parentage testing procedures of cattle breed associations. Allelic sizes of ETH10 PCR amplicons range from 199 to 225 bp. Objectives of this study were to use microsatellite data from beef cattle breed associations to investigate genetic distance and population stratification among Angus- and Brahman-influenced cattle and to use ETH10 genotypes and growth and ultrasound carcass data to investigate their statistical relationships. Three series of genotype to phenotype association analyses were conducted with 1) Angus data (n=5,094), 2) Brangus data (3/8 Brahman × 5/8 Angus; n=2,296), and 3) multibreed data (n=4,426) of Angus and Brangus cattle. Thirteen alleles and 38 genotypes were observed, but frequencies varied among breed groups. Tests of genetic identity and distance among 6 breed composition groups increasing in Brahman influence from 0 to 75% revealed that as Brahman-influence increased to ≥50%, genetic distance from Angus ranged from 18.3 to 43.5%. This was accomplished with 10 microsatellite loci. A mixed effects model involving genotype as a fixed effect and sire as a random source of variation suggested that Angus cattle with the 217/219 genotype tended to have 2.1% heavier (P=0.07) 205-d BW than other genotypes. In Brangus cattle, allele combinations were classified as small (≤215 bp) or large (≥217 bp). Brangus cattle with the small/large genotype had 2.0% heavier (PBrangus cattle. Results from this study provide support for STAT6 as one of the candidate genes underlying cattle growth QTL on chromosome 5. PMID:21357449

  17. Estimation of Genetic Parameters, and Genetic and Environmental Effects on Progeny Carcass Traits of a Nucleus Breeding Population in Japanese Black Cattle

    OpenAIRE

    SAKATA, Ken; Hoque, Azharul; Hirai, Tomokazu; TSUKAGUCHI, Daisuke; TOMARU, Mayuko; Suzuki, Keiichi; Oikawa, Takuro

    2004-01-01

    Genetic parameters of body weight at the start of fattening (BSF), carcass weight (CWT), subcutaneous fat thickness (SFT), rib thickness (RBT), meat quality grade (MQG), beef marbling score (BMS) and rib eye area (REA) in Japanese Black cattle were estimated. The effects of genetic and environmental factors on fattening performance and carcass quality traits of the progeny were also analyzed. The averages of BSF, CWT, SFT, RBT and REA were 189 kg, 408 kg, 24.9 mm, 69.3 mm and 47.5 cm^2, respe...

  18. Development of a genetic sexing strain in Bactrocera carambolae (Diptera: Tephritidae) by introgression of sex sorting components from B. dorsalis, Salaya1 strain

    OpenAIRE

    Isasawin,Siriwan; Aketarawong, Nidchaya; Lertsiri, Sittiwat; Thanaphum, Sujinda

    2014-01-01

    Background The carambola fruit fly, Bactrocera carambolae Drew & Hancock is a high profile key pest that is widely distributed in the southwestern ASEAN region. In addition, it has trans-continentally invaded Suriname, where it has been expanding east and southward since 1975. This fruit fly belongs to Bactrocera dorsalis species complex. The development and application of a genetic sexing strain (Salaya1) of B. dorsalis sensu stricto (s.s.) (Hendel) for the sterile insect technique (SIT) has...

  19. Comparison of models for the genetic evaluation of reproductive traits with censored data in Nellore cattle.

    Science.gov (United States)

    Garcia, D A; Rosa, G J M; Valente, B D; Carvalheiro, R; Albuquerque, L G

    2016-06-01

    In typical genetic evaluation, often some females have missing records due to reproductive failure and due to voluntary and involuntary culling before the breeding season. These partially or unobserved phenotypes are known as censored records and their inclusion into genetic evaluations might lead to better inferences and breeding value predictions. Then, the objective was to compare prediction ability of models in which the phenotypic expression of age at the first calving (AFC) and days to calving (DC) were considered to be censored and uncensored in a Nellore cattle population. Age at first calving and days to calving were analyzed as following: uncensored animals (LM); penalization of 21 d (PLM); censored records simulated from truncated normal distributions (CLM); threshold-linear model in which censored records were handled as missing (TLM) or coded as the upper AFC/DC value within contemporary group (PTLM); and Weibull frailty hazard model (WM). Pearson correlations (PC), the percentage of the 10% best bulls in common (pTOP10%), accuracy of estimated breeding values (), and a cross-validation scheme were performed. Heritability estimates for AFC were 0.18, 0.12, 0.12, 0.17, 0.14, and 0.07 for LM, PLM, CLM, TLM, PTLM, and WM, respectively. PC and pTOP10% were higher among linear models and smaller between these models and WM. The models provided similar r of sire breeding values. Heritability estimates for DC were 0.03, 0.08, 0.06, 0.02, 0.07, and 0.10 for LM, PLM, CLM, TLM, PTLM, and WM, respectively. Strongly associated predictions were observed in CLM, PLM, PTLM, and WM. The highest coincidence levels of sires in the TOP10% were between CLM, PLM, and PTLM. The r of sire breeding values obtained applying CLM, PLM, PTLM, and WM were similar and higher than those obtained with LM and TLM. In terms of prediction ability, WM, PLM, TLM, and PTLM showed similar prediction performance for AFC. On the other hand, CLM, PLM, PTLM, and WM showed the similar prediction

  20. Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information.

    Science.gov (United States)

    Hagger, C

    2005-12-01

    The study investigates the genetic diversity present as well as its development in the Brown Cattle population of Switzerland from pedigree information. The population consisted of three subpopulations, the Braunvieh (BV), the original Braunvieh (OB) and the US-Brown Swiss (BS). The BV is a cross of OB with BS where crossing still continues. The OB is without any genetic influence of BS. The diversity measures effective population size, effective number of ancestors (explaining 99% of reference genome) and founder genome equivalents were calculated for 11 reference populations of animals born in a single year from 1992 onwards. The BS-subpopulation consisted of animals and their known ancestors which were used in the crossing scheme and was, therefore, quite small. The youngest animals were born in 2002, the oldest ones in the 1920s. Average inbreeding was by far the highest in BS, in spite of the lowest quality of pedigrees, and lowest in OB. Effective population size obtained from the difference between average inbreeding of offspring and their parents was, mostly due to the heavy use of few highly inbred BS-sires, strongly overestimated in some BV-reference populations. If this parameter was calculated from the yearly rate of inbreeding and a generation interval of 5 years, no bias was observed and ranking of populations from high to low was OB-BV-BS, i.e. equal to the other diversity parameters. The high genetic diversity found in OB was a consequence of the use of many natural service sires. Rate of decrease of effective number of ancestors was steeper in BV than OB was, however, equal for founder genome equivalents. Founder genome equivalents were more stable than effective population sizes calculated from the difference between average inbreeding of offspring and parents. The five most important ancestors contributed one-third of the 2002-reference genomes of BV and OB, in BV all were BS-sires. The relative amount of BS-genes in the BV-genome increased from

  1. Comparison of models for the genetic evaluation of reproductive traits with censored data in Nellore cattle.

    Science.gov (United States)

    Garcia, D A; Rosa, G J M; Valente, B D; Carvalheiro, R; Albuquerque, L G

    2016-06-01

    In typical genetic evaluation, often some females have missing records due to reproductive failure and due to voluntary and involuntary culling before the breeding season. These partially or unobserved phenotypes are known as censored records and their inclusion into genetic evaluations might lead to better inferences and breeding value predictions. Then, the objective was to compare prediction ability of models in which the phenotypic expression of age at the first calving (AFC) and days to calving (DC) were considered to be censored and uncensored in a Nellore cattle population. Age at first calving and days to calving were analyzed as following: uncensored animals (LM); penalization of 21 d (PLM); censored records simulated from truncated normal distributions (CLM); threshold-linear model in which censored records were handled as missing (TLM) or coded as the upper AFC/DC value within contemporary group (PTLM); and Weibull frailty hazard model (WM). Pearson correlations (PC), the percentage of the 10% best bulls in common (pTOP10%), accuracy of estimated breeding values (), and a cross-validation scheme were performed. Heritability estimates for AFC were 0.18, 0.12, 0.12, 0.17, 0.14, and 0.07 for LM, PLM, CLM, TLM, PTLM, and WM, respectively. PC and pTOP10% were higher among linear models and smaller between these models and WM. The models provided similar r of sire breeding values. Heritability estimates for DC were 0.03, 0.08, 0.06, 0.02, 0.07, and 0.10 for LM, PLM, CLM, TLM, PTLM, and WM, respectively. Strongly associated predictions were observed in CLM, PLM, PTLM, and WM. The highest coincidence levels of sires in the TOP10% were between CLM, PLM, and PTLM. The r of sire breeding values obtained applying CLM, PLM, PTLM, and WM were similar and higher than those obtained with LM and TLM. In terms of prediction ability, WM, PLM, TLM, and PTLM showed similar prediction performance for AFC. On the other hand, CLM, PLM, PTLM, and WM showed the similar prediction

  2. The Agersoe cattle

    DEFF Research Database (Denmark)

    Withen, K.B.; Brüniche-Olsen, A.; Pedersen, Bo Vest;

    2011-01-01

    A phenotypically interesting strain of cattle existed on the small island of Agersoe, on the west coast of Zealand, Denmark, in the beginning of the last decade. The cattle share a great resemblance to the extinct Danish breed, the Island cattle. The objective of this study was to genetically...

  3. Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fish Herichtys minckleyi.

    Science.gov (United States)

    Magalhaes, Isabel S; Ornelas-Garcıa, Claudia Patricia; Leal-Cardin, Mariana; Ramírez, Tania; Barluenga, Marta

    2015-09-01

    Understanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, as well as on the processes constraining it. Intraspecific polymorphisms can provide insight into the mechanisms that generate and maintain phenotypic, behavioural and life history diversification, and can help us understand not only the processes that lead to speciation but also the processes that prevent local fixation of morphs. The 'desert cichlid' Herichtys minckleyi is a highly polymorphic species endemic to a biodiversity hotspot in northern Mexico, the Cuatro Ciénegas valley. This species is polymorphic in body shape and trophic apparatus, and eco-morphotypes coexist in small spring-fed lagoons across the valley. We investigated the genetic structure of these polymorphisms and their phylogeographic history by analysing the entire control region of the mitochondrial DNA and 10 nuclear microsatellite markers in several populations from different sites and morphs. We found two very divergent mitochondrial lineages that most likely predate the closing of the valley and are not associated with morphotypes or sites. One of these lineages is also found in the sister species Herichthys cyanoguttatus. Data from neutral microsatellite markers suggest that most lagoons or drainages constitute their own genetic cluster with sympatric eco-morphotypes forming panmictic populations. Alternative mechanisms such as phenotypic plasticity and a few loci controlled traits provide possible explanations for the sympatric coexistence of discrete nonoverlapping eco-morphotypes with apparent lack of barriers to gene flow within multiple lagoons and drainages. PMID:26175313

  4. An HMM-based comparative genomic framework for detecting introgression in eukaryotes.

    Directory of Open Access Journals (Sweden)

    Kevin J Liu

    2014-06-01

    Full Text Available One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM-a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs to simultaneously capture the (potentially reticulate evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes. Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.

  5. Introgression of tomato chromosomes into the potato genome: an analysis through molecular marker and in situ hybridisation techniques.

    NARCIS (Netherlands)

    Calderé, F.G.

    1998-01-01

    Transfer of alien chromosomes and genes across intergeneric boundaries can be useful not only for the introgression of desirable characters but also for fundamental genetic studies. The successful demonstration of hybridisation of potato ( Solanum tuberosum ) and tomato ( Lycopersicon esculentum ) t

  6. Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds

    OpenAIRE

    Mathieu Gautier; Denis Laloë; Katayoun Moazami-Goudarzi

    2010-01-01

    Background: Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time.[br/] Methodology...

  7. Polymorphism of molecular-genetic systems in the Polish red cattle.

    Science.gov (United States)

    Klauzińska, M; Siadkowska, E; Grochowska, R; Zwierzchowski, L; Zurkowski, M

    2001-01-01

    The object of this study was to investigate gene polymorphism in the Polish Red (PR) cattle, a local Polish breed included in the FAO conservation programme. Milk protein genes and other genes with possible effect on production traits were analysed. Frequencies of different gene variants were compared with those in the Polish Friesian cattle. The following gene polymorphisms were analysed with PCR/RFLP technique: milk protein genes--kappa-casein and beta-lactoglobulin, growth hormone (GH), PitI (a transcription factor) and leptin. Moreover, SSCP analysis was performed of myostatin (MSTN) gene at the site previously shown to cause muscle overgrowth in Belgian Blue double-muscled cattle. A significant difference was found in this study between kappa-casein A and B allele frequency in PR and Friesian cattle. No such differences were found in the frequency of A and B alleles of beta-lactoglobulin, L and V alleles of GH, A and B alleles of PitI, and A, B and C alleles of leptin gene. In the analysed group of the Polish Red cattle three animals were found with the rare AI genotype of -lactoglobulin. No such genotype was identified in analysed Friesians. Moreover, 8 PR animals were identified carrying a mutation in MSTN gene, possibly identical to that causing the double-muscled phenotype in some breeds of meat cattle.

  8. Linear and Poisson models for genetic evaluation of tick resistance in cross-bred Hereford x Nellore cattle.

    Science.gov (United States)

    Ayres, D R; Pereira, R J; Boligon, A A; Silva, F F; Schenkel, F S; Roso, V M; Albuquerque, L G

    2013-12-01

    Cattle resistance to ticks is measured by the number of ticks infesting the animal. The model used for the genetic analysis of cattle resistance to ticks frequently requires logarithmic transformation of the observations. The objective of this study was to evaluate the predictive ability and goodness of fit of different models for the analysis of this trait in cross-bred Hereford x Nellore cattle. Three models were tested: a linear model using logarithmic transformation of the observations (MLOG); a linear model without transformation of the observations (MLIN); and a generalized linear Poisson model with residual term (MPOI). All models included the classificatory effects of contemporary group and genetic group and the covariates age of animal at the time of recording and individual heterozygosis, as well as additive genetic effects as random effects. Heritability estimates were 0.08 ± 0.02, 0.10 ± 0.02 and 0.14 ± 0.04 for MLIN, MLOG and MPOI models, respectively. The model fit quality, verified by deviance information criterion (DIC) and residual mean square, indicated fit superiority of MPOI model. The predictive ability of the models was compared by validation test in independent sample. The MPOI model was slightly superior in terms of goodness of fit and predictive ability, whereas the correlations between observed and predicted tick counts were practically the same for all models. A higher rank correlation between breeding values was observed between models MLOG and MPOI. Poisson model can be used for the selection of tick-resistant animals. PMID:24236604

  9. Genetic diversity, structure and individual assignment of Casta Navarra cattle: a well-differentiated fighting bull population.

    Science.gov (United States)

    Sanz, A; Martin-Burriel, I; Cons, C; Reta, M; Poblador, A; Rodellar, C; Zaragoza, P

    2014-02-01

    The Casta Navarra lineage was one of the populations used to establish the fighting bull (FB) breed, and it has also been reproductively isolated from the others FBs. A total of 1284 individuals from two generations of 16 Casta Navarra herds were sampled to analyse their diversity, their genetic structure and the ability of 28 microsatellite markers to assign individuals to closely related populations. These animals were compared with closely related phylogenetic (FB) or geographical (Pirenaica and Monchina) populations. Hardy-Weinberg equilibrium analysis showed that 82% of the loci had a significant heterozygote deficit as a consequence of the Wahlund effect. The average proportion of genetic variation explained by farm differences was 9% by Wright's FST index. A phylogenetic tree constructed with a neighbour-joining method based on Reynolds genetic distances and a Bayesian Markov chain Monte Carlo clustering approach revealed clear differences between farm groups that generally corresponded to historical information and could unambiguously differentiate Casta Navarra cattle from the other populations. The percentage of animals correctly assigned to the Casta Navarra population was 91.78% for a q threshold of >0.9. Admixture was only detected in 4.45% (q < 0.8) of the cattle. These results are relevant for the maintenance and development of diversity and conservation in the Casta Navarra population.

  10. Evaluating alternate models to estimate genetic parameters of calving traits in United Kingdom Holstein-Friesian dairy cattle

    Directory of Open Access Journals (Sweden)

    Eaglen Sophie A E

    2012-07-01

    Full Text Available Abstract Background The focus in dairy cattle breeding is gradually shifting from production to functional traits and genetic parameters of calving traits are estimated more frequently. However, across countries, various statistical models are used to estimate these parameters. This study evaluates different models for calving ease and stillbirth in United Kingdom Holstein-Friesian cattle. Methods Data from first and later parity records were used. Genetic parameters for calving ease, stillbirth and gestation length were estimated using the restricted maximum likelihood method, considering different models i.e. sire (−maternal grandsire, animal, univariate and bivariate models. Gestation length was fitted as a correlated indicator trait and, for all three traits, genetic correlations between first and later parities were estimated. Potential bias in estimates was avoided by acknowledging a possible environmental direct-maternal covariance. The total heritable variance was estimated for each trait to discuss its theoretical importance and practical value. Prediction error variances and accuracies were calculated to compare the models. Results and discussion On average, direct and maternal heritabilities for calving traits were low, except for direct gestation length. Calving ease in first parity had a significant and negative direct-maternal genetic correlation. Gestation length was maternally correlated to stillbirth in first parity and directly correlated to calving ease in later parities. Multi-trait models had a slightly greater predictive ability than univariate models, especially for the lowly heritable traits. The computation time needed for sire (−maternal grandsire models was much smaller than for animal models with only small differences in accuracy. The sire (−maternal grandsire model was robust when additional genetic components were estimated, while the equivalent animal model had difficulties reaching convergence. Conclusions

  11. Detrimental effect of selection for milk yield on genetic tolerance to heat stress in purebred Zebu cattle: Genetic parameters and trends.

    Science.gov (United States)

    Santana, M L; Pereira, R J; Bignardi, A B; Filho, A E Vercesi; Menéndez-Buxadera, A; El Faro, L

    2015-12-01

    In an attempt to determine the possible detrimental effects of continuous selection for milk yield on the genetic tolerance of Zebu cattle to heat stress, genetic parameters and trends of the response to heat stress for 86,950 test-day (TD) milk yield records from 14,670 first lactations of purebred dairy Gir cows were estimated. A random regression model with regression on days in milk (DIM) and temperature-humidity index (THI) values was applied to the data. The most detrimental effect of THI on milk yield was observed in the stage of lactation with higher milk production, DIM 61 to 120 (-0.099kg/d per THI). Although modest variations were observed for the THI scale, a reduction in additive genetic variance as well as in permanent environmental and residual variance was observed with increasing THI values. The heritability estimates showed a slight increase with increasing THI values for any DIM. The correlations between additive genetic effects across the THI scale showed that, for most of the THI values, genotype by environment interactions due to heat stress were less important for the ranking of bulls. However, for extreme THI values, this type of genotype by environment interaction may lead to an important error in selection. As a result of the selection for milk yield practiced in the dairy Gir population for 3 decades, the genetic trend of cumulative milk yield was significantly positive for production in both high (51.81kg/yr) and low THI values (78.48kg/yr). However, the difference between the breeding values of animals at high and low THI may be considered alarming (355kg in 2011). The genetic trends observed for the regression coefficients related to general production level (intercept of the reaction norm) and specific ability to respond to heat stress (slope of the reaction norm) indicate that the dairy Gir population is heading toward a higher production level at the expense of lower tolerance to heat stress. These trends reflect the genetic

  12. Bovine respiratory disease in feedlot cattle: environmental, genetic, and economic factors.

    Science.gov (United States)

    Snowder, G D; Van Vleck, L D; Cundiff, L V; Bennett, G L

    2006-08-01

    The objective of this study was to characterize genetic, environmental, and economic factors related to the incidence of bovine respiratory disease (BRD) in feedlot calves. Records from 18,112 calves representing 9 breeds (Angus, Braunvieh, Charolais, Gelbvieh, Hereford, Limousin, Pinzgauer, Red Poll, and Simmental) and 3 composite types (MARC I, MARC II, and MARC III) over a 15-yr period (1987 to 2001) were evaluated. Disease incidence was observed and recorded by station veterinary and technical staff. The incidence of BRD varied across years, with the annual observed incidence ranging from 5 to 44%. From 1987 to 1992, the annual average incidence generally exceeded 20%. However, in later years the annual incidence did not exceed 14%. The epidemiological pattern indicated that BRD infection increased dramatically after 5 d on feed and remained high until approximately 80 d on feed. Previous BRD infection during the preweaning period did not influence subsequent BRD infection in the feedlot. Steers were more likely to become sick with BRD than heifers; castration before entry in the feedlot may be a predisposing cause. Few significant differences among breeds were detected for BRD incidence. Adjusted solutions from mixed model analyses indicated that Herefords were generally more susceptible to BRD infection (P < 0.05) than MARC I and III composite types. Composite breed types had similar susceptibility compared with other purebred breeds. Mortality associated with BRD was greatest in Red Poll calves (9%) compared with the average over all breeds (4%). Estimates of heritability for resistance to BRD ranged from 0.04 to 0.08 +/- 0.01. When the observed heritability was transformed to an underlying continuous scale, the estimate increased to 0.18. Selection for resistance to BRD could be effective if phenotypes for BRD resistance were known. Thus, development of an inexpensive and humane method of challenging animals with BRD to determine resistance would be an

  13. Genetic characterization of bovine viral diarrhea virus strains in Beijing, China and innate immune responses of peripheral blood mononuclear cells in persistently infected dairy cattle.

    Science.gov (United States)

    Weng, Xiao Gang; Song, Quan Jiang; Wu, Qiong; Liu, Ming Chao; Wang, Meng Ling; Wang, Jiu Feng

    2015-01-01

    To acquire epidemiological data on the bovine viral diarrhea virus (BVDV) and identify cattle persistently infected (PI) with this virus, 4,327 samples from Holstein dairy cows were screened over a four-year period in Beijing, China. Eighteen BVD viruses were isolated, 12 from PI cattle. Based on genetic analysis of their 5'-untranslated region (5'-UTR), the 18 isolates were assigned to subgenotype BVDV-1m, 1a, 1d, 1q, and 1b. To investigate the innate immune responses in the peripheral-blood mononuclear cells of PI cattle, the expression of Toll-like receptors (TLRs), RIG-I-like receptors, interferon-α (IFN-α), IFN-β, myxovirus (influenza virus) resistance 1 (MX1), and interferon stimulatory gene 15 (ISG15) was assessed by qPCR. When compared with healthy cattle, the expression of TLR-7, IFN-α, and IFN-β mRNA was downregulated, but the expression of MX1 and ISG-15 mRNA was upregulated in PI cattle. Immunoblotting analysis revealed that the expression of interferon regulatory factor 3 (IRF-3) and IRF-7 was lower in PI cattle than in healthy cattle. Thus, BVDV-1m and 1a are the predominant subgenotypes in the Beijing region, and the strains are highly divergent. Our findings also suggest that the TLR-7/IRF-7 signaling pathway plays a role in evasion of host restriction by BVDV.

  14. Development and Identification of Introgression Lines from Cross of Oryza sativa and Oryza minuta

    Institute of Scientific and Technical Information of China (English)

    GUO Si-bin; WEI Yu; LI Xiao-qiong; LIU Kai-qiang; HUANG Feng-kuan; CHEN Cai-hong; GAO Guo-qing

    2013-01-01

    Introgression line population is effectively used in mapping quantitative trait loci (QTLs),identifying favorable genes,discovering hidden genetic variation,evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research.In this study,an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs),which derived from an accession of Oryza minuta (accession No.101133) with BBCC genome,as the donor,and an elite indica cultivar IR24 (O.sativa),as the recipient.Introgression segments from O.minuta were screened using 164 polymorphic simple sequence repeat (SSR) markers in the genome of each IL.Introgressed segments carried by 131 ILs covered the whole O.sativa genome.The average number of homozygous O.minuta segments per introgression line was about 9.99.The average length of introgressed segments was approximate 14.78 cM,and about 79.64%of these segments had sizes less than 20 cM.In the genome of each introgression line,the O.minuta chromosomal segments harbored chromosomal fragments of O.sativa ranging from 1.15% to 27.6%,with an overall average of 8.57%.At each locus,the ratio of substitution of O.minuta alleles had a range of 1.5%-25.2%,with an average of 8.3% Based on the evaluation of the phenotype of these ILs,a wide range of alterations in morphological and yield-related traits were found.After inoculation,ILs 41,11 and 7 showed high resistance to bacterial blight,brown planthopper and whitebacked planthopper,respectively.These O.minuta-O.sativa ILs will serve as genetic materials for identifying and using favorable genes from O.minuta.

  15. Identification of Genetic Associations and Functional Polymorphisms of SAA1 Gene Affecting Milk Production Traits in Dairy Cattle.

    Science.gov (United States)

    Yang, Shaohua; Gao, Yahui; Zhang, Shengli; Zhang, Qin; Sun, Dongxiao

    2016-01-01

    Our initial RNA sequencing (RNA-seq) revealed that the Serum amyloid A1 (SAA1) gene was differentially expressed in the mammary glands of lactating Holstein cows with extremely high versus low phenotypic values of milk protein and fat percentage. To further validate the genetic effect and potential molecular mechanisms of SAA1 gene involved in regulating milk production traits in dairy cattle, we herein performed a study through genotype-phenotype associations. Six identified SNPs were significantly associated with one or more milk production traits (0.00002milk production traits in dairy cows. Subsequently, both luciferase assay and electrophoretic mobility shift assay (EMSA) clearly demonstrated that the allele A of g.-963C>A increased the promoter activity by binding the PARP factor while allele C did not. Bioinformatics analysis indicated that the secondary structure of SAA protein changed by the substitution A/G in the locus c. +2510A>G. Our findings were the first to reveal the significant associations of the SAA1 gene with milk production traits, providing basis for further biological function validation, and two identified SNPs, g.-963C>A and c. +2510A>G, may be considered as genetic markers for breeding in dairy cattle. PMID:27610623

  16. Identification of Genetic Associations and Functional Polymorphisms of SAA1 Gene Affecting Milk Production Traits in Dairy Cattle

    Science.gov (United States)

    Zhang, Shengli; Zhang, Qin; Sun, Dongxiao

    2016-01-01

    Our initial RNA sequencing (RNA-seq) revealed that the Serum amyloid A1 (SAA1) gene was differentially expressed in the mammary glands of lactating Holstein cows with extremely high versus low phenotypic values of milk protein and fat percentage. To further validate the genetic effect and potential molecular mechanisms of SAA1 gene involved in regulating milk production traits in dairy cattle, we herein performed a study through genotype-phenotype associations. Six identified SNPs were significantly associated with one or more milk production traits (0.00002milk production traits in dairy cows. Subsequently, both luciferase assay and electrophoretic mobility shift assay (EMSA) clearly demonstrated that the allele A of g.-963C>A increased the promoter activity by binding the PARP factor while allele C did not. Bioinformatics analysis indicated that the secondary structure of SAA protein changed by the substitution A/G in the locus c. +2510A>G. Our findings were the first to reveal the significant associations of the SAA1 gene with milk production traits, providing basis for further biological function validation, and two identified SNPs, g.-963C>A and c. +2510A>G, may be considered as genetic markers for breeding in dairy cattle. PMID:27610623

  17. Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield-related Quantitative Trait Loci

    Institute of Scientific and Technical Information of China (English)

    Lubin Tan; Fengxia Liu; Wei Xue; Guijuan Wang; Sheng Ye; Zuofeng Zhu; Yongcai Fu; Xiangkun Wang; Chuanqing Sun

    2007-01-01

    Introgression lines population was effectively used in mapping quantitative trait loci (QTLs), identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs), which derived from an accession of Oryza rufipogon Griff, collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing (O. sativa L.), as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats (SSR) markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs (51.4%) were detected at both sites, and the alleles from O. rufipogon at fifteen loci (40.5%) improved the yield and yield components in the Teqing background. These O. rufipogon-O. sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.

  18. Estimation of Genetic Parameters and Breeding Values of Milk Traits for Simmental Cattle in Croatia Using a Lactation Animal Model

    Directory of Open Access Journals (Sweden)

    Miroslav Kapš

    2004-12-01

    Full Text Available The objective of this study was to estimate genetic parameters and to predict breeding values for dairy traits in Simmental cattle in Croatia by developing an animal lactation model. Data consisted of 30761 first lactation records of cows born between 1985 and 2001. By including the pedigree there was a total of 48748 animals. The following effects were analyzed: age, season and year at first calving, days open, breeding organization, farm, animal, and genetic group. Adequacy of the models was tested by using F tests for fixed effects, and REML functions and ‘Mendelian sampling’ for the whole models. The best fit model was determined to have the following effects: age at first calving, days open, year x season interaction and breeding organization x year interaction as fixed, and animal and farm x year as random effects. By including genetic group the model was further improved. From this model, the following heritabilites were estimated: 0.34 ± 0.02, 0.30 ± 0.02, 0.29 ± 0.03 for milk, milk fat and protein yield, respectively. Further, phenotypic and genetic trends were analyzed. The genetic gain in milk traits has been low so far, but by using an appropriate animal model, the breeding value prediction is expected to be improved in terms of accuracy and precision.

  19. Validation and Estimation of Additive Genetic Variation Associated with DNA Tests for Quantitative Beef Cattle Traits

    Science.gov (United States)

    The U.S. National Beef Cattle Evaluation Consortium (NBCEC) has been involved in the validation of commercial DNA tests for quantitative beef quality traits since their first appearance on the U.S. market in the early 2000s. The NBCEC Advisory Council initially requested that the NBCEC set up a syst...

  20. Studies on genetic diversity of bovine viral diarrhea viruses in Danish cattle herds

    DEFF Research Database (Denmark)

    Nagy, Abdou; Fahnøe, Ulrik; Rasmussen, Thomas Bruun;

    2014-01-01

    Scandinavian countries have successfully pursued bovine viral diarrhea virus (BVDV) eradication without the use of vaccines. In Denmark, control and eradication of BVDV were achieved during the last two decades, but occasionally new BVDV infections are detected in some Danish cattle herds. The aim...

  1. Introgression from domestic goat generated variation at the major histocompatibility complex of Alpine ibex.

    Directory of Open Access Journals (Sweden)

    Christine Grossen

    2014-06-01

    Full Text Available The major histocompatibility complex (MHC is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex. At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2, Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus. We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8% to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection.

  2. Expression of genes controlling fat deposition in two genetically diverse beef cattle breeds fed high or low silage diets

    Science.gov (United States)

    2013-01-01

    Background Both genetic background and finishing system can alter fat deposition, thus indicating their influence on adipogenic and lipogenic factors. However, the molecular mechanisms underlying fat deposition and fatty acid composition in beef cattle are not fully understood. This study aimed to assess the effect of breed and dietary silage level on the expression patterns of key genes controlling lipid metabolism in subcutaneous adipose tissue (SAT) and longissimus lumborum (LL) muscle of cattle. To that purpose, forty bulls from two genetically diverse Portuguese bovine breeds with distinct maturity rates, Alentejana and Barrosã, were selected and fed either low (30% maize silage/70% concentrate) or high silage (70% maize silage/30% concentrate) diets. Results The results suggested that enhanced deposition of fatty acids in the SAT from Barrosã bulls, when compared to Alentejana, could be due to higher expression levels of lipogenesis (SCD and LPL) and β-oxidation (CRAT) related genes. Our results also indicated that SREBF1 expression in the SAT is increased by feeding the low silage diet. Together, these results point out to a higher lipid turnover in the SAT of Barrosã bulls when compared to Alentejana. In turn, lipid deposition in the LL muscle is related to the expression of adipogenic (PPARG and FABP4) and lipogenic (ACACA and SCD) genes. The positive correlation between ACACA expression levels and total lipids, as well trans fatty acids, points to ACACA as a major player in intramuscular deposition in ruminants. Moreover, results reinforce the role of FABP4 in intramuscular fat development and the SAT as the major site for lipid metabolism in ruminants. Conclusions Overall, the results showed that SAT and LL muscle fatty acid composition are mostly dependent on the genetic background. In addition, dietary silage level impacted on muscle lipid metabolism to a greater extent than on that of SAT, as evaluated by gene expression levels of adipogenic and

  3. Admixture mapping identifies introgressed genomic regions in North American canids.

    Science.gov (United States)

    vonHoldt, Bridgett M; Kays, Roland; Pollinger, John P; Wayne, Robert K

    2016-06-01

    Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years as coyotes expanded their range into eastern North America. Concomitant with expansion, coyotes hybridized with wolves and some populations became more wolflike, such that coyotes in the northeast have the largest body size of any coyote population. Using a set of 3102 ancestry informative markers, we identified 60 differentially introgressed regions in 44 canines across this admixture zone. These regions are characterized by an excess of exogenous ancestry and, in northeastern coyotes, are enriched for genes affecting body size and skeletal proportions. Further, introgressed wolf-derived alleles have penetrated into Southern US coyote populations. Because no wolves currently exist in this area, these alleles are unlikely to have originated from recent hybridization. Instead, they probably originated from intraspecific gene flow or ancient admixture. We show that grey wolf and coyote admixture has far-reaching effects and, in addition to phenotypically transforming admixed populations, allows for the differential movement of alleles from different parental species to be tested in new genomic backgrounds. PMID:27106273

  4. Introgression and rapid species turnover in sympatric damselflies

    Directory of Open Access Journals (Sweden)

    Cordero-Rivera Adolfo

    2011-07-01

    Full Text Available Abstract Background Studying contemporary hybridization increases our understanding of introgression, adaptation and, ultimately, speciation. The sister species Ischnura elegans and I. graellsii (Odonata: Coenagrionidae are ecologically, morphologically and genetically similar and hybridize. Recently, I. elegans has colonized northern Spain, creating a broad sympatric region with I. graellsii. Here, we review the distribution of both species in Iberia and evaluate the degree of introgression of I. graellsii into I. elegans using six microsatellite markers (442 individuals from 26 populations and five mitochondrial genes in sympatric and allopatric localities. Furthermore, we quantify the effect of hybridization on the frequencies of the genetically controlled colour polymorphism in females of both species. Results In a principal component analysis of the microsatellite data, the first two principal components summarised almost half (41% of the total genetic variation. The first axis revealed a clear separation of I. graellsii and I. elegans populations, while the second axis separated I. elegans populations. Admixture analyses showed extensive hybridization and introgression in I. elegans populations, consistent with I. elegans backcrosses and occasional F1-hybrids, suggesting hybridization is on-going. More specifically, approximately 58% of the 166 Spanish I. elegans individuals were assigned to the I. elegans backcross category, whereas not a single of those individuals was assigned to the backcross with I. graellsii. The mitochondrial genes held little genetic variation, and the most common haplotype was shared by the two species. Conclusions The results suggest rapid species turnover in sympatric regions in favour of I. elegans, corroborating previous findings that I. graellsii suffers a mating disadvantage in sympatry with I. elegans. Examination of morph frequency dynamics indicates that hybridization is likely to have important

  5. Estimates of genetic parameters for visual scores and their correlation with production and reproductive traits in Brahman cattle

    Directory of Open Access Journals (Sweden)

    Tássia Souza Bertipaglia

    2012-06-01

    Full Text Available The objective of this study was to evaluate the association of visual scores of body structure, precocity and muscularity with production (body weight at 18 months and average daily gain and reproductive (scrotal circumference traits in Brahman cattle in order to determine the possible use of these scores as selection criteria to improve carcass quality. Covariance components were estimated by the restricted maximum likelihood method using an animal model that included contemporary group as fixed effect. A total of 1,116 observations of body structure, precocity and muscularity were used. Heritability was 0.39, 043 and 0.40 for body structure, precocity and muscularity, respectively. The genetic correlations were 0.79 between body structure and precocity, 0.87 between body structure and muscularity, and 0.91 between precocity and muscularity. The genetic correlations between visual scores and body weight at 18 months were positive (0.77, 0.57 and 0.59 for body structure, precocity and muscularity, respectively. Similar genetic correlations were observed between average daily gain and visual scores (0.60, 0.57 and 0.48, respectively, whereas the genetic correlations between scrotal circumference and these scores were low (0.13, 0.02, and 0.13. The results indicate that visual scores can be used as selection criteria in Brahman breeding programs. Favorable correlated responses should be seen in average daily gain and body weight at 18 months. However, no correlated response is expected for scrotal circumference.

  6. Molecular Characterization of Bovine SMO Gene and Effects of Its Genetic Variations on Body Size Traits in Qinchuan Cattle (Bos taurus).

    Science.gov (United States)

    Zhang, Ya-Ran; Gui, Lin-Sheng; Li, Yao-Kun; Jiang, Bi-Jie; Wang, Hong-Cheng; Zhang, Ying-Ying; Zan, Lin-Sen

    2015-07-27

    Smoothened (Smo)-mediated Hedgehog (Hh) signaling pathway governs the patterning, morphogenesis and growth of many different regions within animal body plans. This study evaluated the effects of genetic variations of the bovine SMO gene on economically important body size traits in Chinese Qinchuan cattle. Altogether, eight single nucleotide polymorphisms (SNPs: 1-8) were identified and genotyped via direct sequencing covering most of the coding region and 3'UTR of the bovine SMO gene. Both the p.698Ser.>Ser. synonymous mutation resulted from SNP1 and the p.700Ser.>Pro. non-synonymous mutation caused by SNP2 mapped to the intracellular C-terminal tail of bovine Smo protein; the other six SNPs were non-coding variants located in the 3'UTR. The linkage disequilibrium was analyzed, and five haplotypes were discovered in 520 Qinchuan cattle. Association analyses showed that SNP2, SNP3/5, SNP4 and SNP6/7 were significantly associated with some body size traits (p 0.05). Meanwhile, cattle with wild-type combined haplotype Hap1/Hap1 had significantly (p cattle, and the wild-type haplotype Hap1 together with the wild-type alleles of these detected SNPs in the SMO gene could be used to breed cattle with superior body size traits. Therefore, our results could be helpful for marker-assisted selection in beef cattle breeding programs.

  7. Introgression of tomato chromosomes into the potato genome: an analysis through molecular marker and in situ hybridisation techniques.

    OpenAIRE

    Calderé, F.G.

    1998-01-01

    Transfer of alien chromosomes and genes across intergeneric boundaries can be useful not only for the introgression of desirable characters but also for fundamental genetic studies. The successful demonstration of hybridisation of potato ( Solanum tuberosum ) and tomato ( Lycopersicon esculentum ) through protoplast fusion in 1978, created the potential for introgressing chromosomes and genes from one genus into the other. However, real prospects of adding tomato chromosomes into the potato g...

  8. Genetic and morphological characterisation of the Ankole Longhorn cattle in the African Great Lakes region

    OpenAIRE

    Okeyo Mwai A; Wurzinger Maria; Hanotte Olivier; Baumung Roswitha; Ndumu Deo B; Jianlin Han; Kibogo Harrison; Sölkner Johann

    2008-01-01

    Abstract The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size), genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were gen...

  9. Genetic Diversity and Sequence Variations at Growth Hormone Loci among Composite and Hereford Populations of Beef Cattle

    Directory of Open Access Journals (Sweden)

    ALAN J. LYMBERY

    2000-07-01

    Full Text Available A total of 194 Hereford and 235 composite breed cattle from Wokalup Research Station were used in this study. The aims of the study were to: Investigate polymorphisms in the growth hormone gene in the composite and purebred Hereford herds from the Wokalup selection experiment, compare genetic diversity in the growth hormone gene of the breeds, sequencing and compare the sequences of growth hormone loci between composite and purebred Hereford herds with published sequence from Genebank. The genomic DNA was extracted using Wizard genomic DNA purification system from Promega. Two fragments of growth hormone gene were amplified using PCR and continued with RFLP. Each genotype in both loci was sequenced. PCR products of each genotypes were cloned into PCR II, transformed, colonies selection, plasmid DNA extraction continued with cycle sequencing. Polymorphisms were found in both breeds of cattle in both loci of GH-L1 and GH-L2 of the growth hormone gene by PCR-RFLP analysis. Sequencing analysis confirmed the RFLPs data, polymorphism detected using AluI at GH-L1 is due to substitution between leusin/ valine at position 127, while polymorphism at the MspI restriction site was caused by transition of C to T at +837 position.

  10. Genetic dissection of milk yield traits and mastitis resistance quantitative trait loci on chromosome 20 in dairy cattle.

    Science.gov (United States)

    Kadri, Naveen K; Guldbrandtsen, Bernt; Lund, Mogens S; Sahana, Goutam

    2015-12-01

    Intense selection to increase milk yield has had negative consequences for mastitis incidence in dairy cattle. Due to low heritability of mastitis resistance and an unfavorable genetic correlation with milk yield, a reduction in mastitis through traditional breeding has been difficult to achieve. Here, we examined quantitative trait loci (QTL) that segregate for clinical mastitis and milk yield on Bos taurus autosome 20 (BTA20) to determine whether both traits are affected by a single polymorphism (pleiotropy) or by multiple closely linked polymorphisms. In the latter but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle (RDC) and Danish Jersey cattle (JER) with the goal of determining whether these QTL identified in Holsteins were segregating across breeds. Genotypes for 12,566 animals (5,966 HOL, 5,458 RDC, and 1,142 JER) were determined by using the Illumina Bovine SNP50 BeadChip (50K; Illumina, San Diego, CA), which identifies 1,568 single nucleotide polymorphisms on BTA20. Data were combined, phased, and clustered into haplotype states, followed by within- and across-breed haplotype-based association analyses using a linear mixed model. Association signals for both clinical mastitis and milk yield peaked in the 26- to 40-Mb region on BTA20 in HOL. Single-variant association analyses were carried out in the QTL region using whole sequence level variants imputed from references of 2,036 HD genotypes (BovineHD BeadChip; Illumina) and 242 whole-genome sequences. The milk QTL were also segregating in RDC and JER on the BTA20-targeted region; however, an indication of differences in the causal factor(s) was observed across breeds. A previously reported F279Y mutation (rs385640152) within the growth hormone

  11. Genetic dissection of milk yield traits and mastitis resistance quantitative trait loci on chromosome 20 in dairy cattle.

    Science.gov (United States)

    Kadri, Naveen K; Guldbrandtsen, Bernt; Lund, Mogens S; Sahana, Goutam

    2015-12-01

    Intense selection to increase milk yield has had negative consequences for mastitis incidence in dairy cattle. Due to low heritability of mastitis resistance and an unfavorable genetic correlation with milk yield, a reduction in mastitis through traditional breeding has been difficult to achieve. Here, we examined quantitative trait loci (QTL) that segregate for clinical mastitis and milk yield on Bos taurus autosome 20 (BTA20) to determine whether both traits are affected by a single polymorphism (pleiotropy) or by multiple closely linked polymorphisms. In the latter but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle (RDC) and Danish Jersey cattle (JER) with the goal of determining whether these QTL identified in Holsteins were segregating across breeds. Genotypes for 12,566 animals (5,966 HOL, 5,458 RDC, and 1,142 JER) were determined by using the Illumina Bovine SNP50 BeadChip (50K; Illumina, San Diego, CA), which identifies 1,568 single nucleotide polymorphisms on BTA20. Data were combined, phased, and clustered into haplotype states, followed by within- and across-breed haplotype-based association analyses using a linear mixed model. Association signals for both clinical mastitis and milk yield peaked in the 26- to 40-Mb region on BTA20 in HOL. Single-variant association analyses were carried out in the QTL region using whole sequence level variants imputed from references of 2,036 HD genotypes (BovineHD BeadChip; Illumina) and 242 whole-genome sequences. The milk QTL were also segregating in RDC and JER on the BTA20-targeted region; however, an indication of differences in the causal factor(s) was observed across breeds. A previously reported F279Y mutation (rs385640152) within the growth hormone

  12. Models for Estimating Genetic Parameters of Milk Production Traits Using Random Regression Models in Korean Holstein Cattle.

    Science.gov (United States)

    Cho, C I; Alam, M; Choi, T J; Choy, Y H; Choi, J G; Lee, S S; Cho, K H

    2016-05-01

    The objectives of the study were to estimate genetic parameters for milk production traits of Holstein cattle using random regression models (RRMs), and to compare the goodness of fit of various RRMs with homogeneous and heterogeneous residual variances. A total of 126,980 test-day milk production records of the first parity Holstein cows between 2007 and 2014 from the Dairy Cattle Improvement Center of National Agricultural Cooperative Federation in South Korea were used. These records included milk yield (MILK), fat yield (FAT), protein yield (PROT), and solids-not-fat yield (SNF). The statistical models included random effects of genetic and permanent environments using Legendre polynomials (LP) of the third to fifth order (L3-L5), fixed effects of herd-test day, year-season at calving, and a fixed regression for the test-day record (third to fifth order). The residual variances in the models were either homogeneous (HOM) or heterogeneous (15 classes, HET15; 60 classes, HET60). A total of nine models (3 orders of polynomials×3 types of residual variance) including L3-HOM, L3-HET15, L3-HET60, L4-HOM, L4-HET15, L4-HET60, L5-HOM, L5-HET15, and L5-HET60 were compared using Akaike information criteria (AIC) and/or Schwarz Bayesian information criteria (BIC) statistics to identify the model(s) of best fit for their respective traits. The lowest BIC value was observed for the models L5-HET15 (MILK; PROT; SNF) and L4-HET15 (FAT), which fit the best. In general, the BIC values of HET15 models for a particular polynomial order was lower than that of the HET60 model in most cases. This implies that the orders of LP and types of residual variances affect the goodness of models. Also, the heterogeneity of residual variances should be considered for the test-day analysis. The heritability estimates of from the best fitted models ranged from 0.08 to 0.15 for MILK, 0.06 to 0.14 for FAT, 0.08 to 0.12 for PROT, and 0.07 to 0.13 for SNF according to days in milk of first

  13. Models for Estimating Genetic Parameters of Milk Production Traits Using Random Regression Models in Korean Holstein Cattle.

    Science.gov (United States)

    Cho, C I; Alam, M; Choi, T J; Choy, Y H; Choi, J G; Lee, S S; Cho, K H

    2016-05-01

    The objectives of the study were to estimate genetic parameters for milk production traits of Holstein cattle using random regression models (RRMs), and to compare the goodness of fit of various RRMs with homogeneous and heterogeneous residual variances. A total of 126,980 test-day milk production records of the first parity Holstein cows between 2007 and 2014 from the Dairy Cattle Improvement Center of National Agricultural Cooperative Federation in South Korea were used. These records included milk yield (MILK), fat yield (FAT), protein yield (PROT), and solids-not-fat yield (SNF). The statistical models included random effects of genetic and permanent environments using Legendre polynomials (LP) of the third to fifth order (L3-L5), fixed effects of herd-test day, year-season at calving, and a fixed regression for the test-day record (third to fifth order). The residual variances in the models were either homogeneous (HOM) or heterogeneous (15 classes, HET15; 60 classes, HET60). A total of nine models (3 orders of polynomials×3 types of residual variance) including L3-HOM, L3-HET15, L3-HET60, L4-HOM, L4-HET15, L4-HET60, L5-HOM, L5-HET15, and L5-HET60 were compared using Akaike information criteria (AIC) and/or Schwarz Bayesian information criteria (BIC) statistics to identify the model(s) of best fit for their respective traits. The lowest BIC value was observed for the models L5-HET15 (MILK; PROT; SNF) and L4-HET15 (FAT), which fit the best. In general, the BIC values of HET15 models for a particular polynomial order was lower than that of the HET60 model in most cases. This implies that the orders of LP and types of residual variances affect the goodness of models. Also, the heterogeneity of residual variances should be considered for the test-day analysis. The heritability estimates of from the best fitted models ranged from 0.08 to 0.15 for MILK, 0.06 to 0.14 for FAT, 0.08 to 0.12 for PROT, and 0.07 to 0.13 for SNF according to days in milk of first

  14. Introgression of Gossypium klotzschianum Genome into Cultivated Cotton,G.hirsutum

    Institute of Scientific and Technical Information of China (English)

    SHEN Xin-lian; ZHANG Xiang-gui; YANG Yu-wen; CAO Zhi-bin; NI Wan-chao

    2008-01-01

    @@ Exotic Gossypium germplasm is a rich source of useful agronomic traits for improvement programs of cultivated cotton.Efficient use of genetic variation available in the wild relatives depends on the ability to identify and introgress desirable DNA segments from wild species into cultivated cotton.

  15. Genetic variability and population structure in loci related to milk production traits in native Argentine Creole and commercial Argentine Holstein cattle

    Directory of Open Access Journals (Sweden)

    Golijow C.D.

    1999-01-01

    Full Text Available Many cattle breeds have been subjected to high selection pressure for production traits. Consequently, population genetic structure and allelic distribution could differ in breeds under high selection pressure compared to unselected breeds. Analysis of k-casein, aS1-casein and prolactin gene frequencies was made for Argentine Creole (AC and Argentine Holstein (AH cattle herds. The calculated FST values measured the degree of genetic differentiation of subpopulations, depending on the variances of gene frequencies.The AC breed had considerably more variation among herds at the aS1-casein and k-casein loci. Conservation strategies should consider the entire AC population in order to maintain the genetic variability found in this native breed.

  16. Genetic diversity of tyrosine hydroxylase (TH and dopamine b-hydroxylase (DBH genes in cattle breeds

    Directory of Open Access Journals (Sweden)

    Diana Lelidett Lourenco-Jaramillo

    2012-01-01

    Full Text Available DNA from four cattle breeds was used to re-sequence all of the exons and 56% of the introns of the bovine tyrosine hydroxylase (TH gene and 97% and 13% of the bovine dopamine b-hydroxylase (DBH coding and non-coding sequences, respectively. Two novel single nucleotide polymorphisms (SNPs and a microsatellite motif were found in the TH sequences. The DBH sequences contained 62 nucleotide changes, including eight non-synonymous SNPs (nsSNPs that are of particular interest because they may alter protein function and therefore affect the phenotype. These DBH nsSNPs resulted in amino acid substitutions that were predicted to destabilize the protein structure. Six SNPs (one from TH and five from DBH non-synonymous SNPs were genotyped in 140 animals; all of them were polymorphic and had a minor allele frequency of > 9%. There were significant differences in the intra- and inter-population haplotype distributions. The haplotype differences between Brahman cattle and the three B. t. taurus breeds (Charolais, Holstein and Lidia were interesting from a behavioural point of view because of the differences in temperament between these breeds.

  17. Genetic diversity of tyrosine hydroxylase (TH) and dopamine β-hydroxylase (DBH) genes in cattle breeds.

    Science.gov (United States)

    Lourenco-Jaramillo, Diana Lelidett; Sifuentes-Rincón, Ana María; Parra-Bracamonte, Gaspar Manuel; de la Rosa-Reyna, Xochitl Fabiola; Segura-Cabrera, Aldo; Arellano-Vera, Williams

    2012-04-01

    DNA from four cattle breeds was used to re-sequence all of the exons and 56% of the introns of the bovine tyrosine hydroxylase (TH) gene and 97% and 13% of the bovine dopamine β-hydroxylase (DBH) coding and non-coding sequences, respectively. Two novel single nucleotide polymorphisms (SNPs) and a microsatellite motif were found in the TH sequences. The DBH sequences contained 62 nucleotide changes, including eight non-synonymous SNPs (nsSNPs) that are of particular interest because they may alter protein function and therefore affect the phenotype. These DBH nsSNPs resulted in amino acid substitutions that were predicted to destabilize the protein structure. Six SNPs (one from TH and five from DBH non-synonymous SNPs) were genotyped in 140 animals; all of them were polymorphic and had a minor allele frequency of > 9%. There were significant differences in the intra- and inter-population haplotype distributions. The haplotype differences between Brahman cattle and the three B. t. taurus breeds (Charolais, Holstein and Lidia) were interesting from a behavioural point of view because of the differences in temperament between these breeds. PMID:22888292

  18. Genetic diversity of native Turkish cattle breeds: Mantel, AMOVA and bottleneck analysis

    Directory of Open Access Journals (Sweden)

    Yusuf Özşensoy

    2014-09-01

    Full Text Available This study was conducted to evaluate potential extinction risk of Turkish native cattle breeds using Mantel and AMOVA tests and Bottleneck analysis. A total of 271 DNA samples were isolated from Anatolian Black, Anatolian Grey, South Anatolian Red, Native Southern Anatolian Yellow, East Anatolian Red, and Zavot cattle. In this study, genotypes of 20 microsatellites were determined by capillary electrophoresis and fragment analysis. A total of 269 different alleles were detected. The maximum and minimum numbers of total alleles were observed in TGLA122 (n=26 and INRA005 (n=7 loci, respectively. The highest average observed and expected heterozygosity values were determined as 0.619–0.852 and 0.669–0.877, respectively. The average FIS value was 0.068. Results of AMOVA and Mantel tests illustrated statistically significant differences in populations (p<0.001 and correlation (p<0.01. Bottleneck analysis revealed a normal distribution of L–shaped curve indicating that there was no recent risk of extinction for these breeds.

  19. Introgression of a leaf rust resistance gene from Aegilops caudata to bread wheat

    Indian Academy of Sciences (India)

    Amandeep Kaur Riar; Satinder Kaur; H. S. Dhaliwal; Kuldeep Singh; Parveen Chhuneja

    2012-08-01

    Rusts are the most important biotic constraints limiting wheat productivity worldwide. Deployment of cultivars with broad spectrum rust resistance is the only environmentally viable option to combat these diseases. Identification and introgression of novel sources of resistance is a continuous process to combat the ever evolving pathogens. The germplasm of nonprogenitor Aegilops species with substantial amount of variability has been exploited to a limited extent. In the present investigation introgression, inheritance and molecular mapping of a leaf rust resistance gene of Ae. caudata (CC) acc. pau3556 in cultivated wheat were undertaken. An F2 population derived from the cross of Triticum aestivum cv.WL711 – Ae. caudata introgression line T291-2 with wheat cultivar PBW343 segregated for a single dominant leaf rust resistance gene at the seedling and adult plant stages. Progeny testing in F3 confirmed the introgression of a single gene for leaf rust resistance. Bulked segregant analysis using polymorphic D-genome-specific SSR markers and the cosegregation of the 5DS anchored markers (Xcfd18, Xcfd78, Xfd81 and Xcfd189) with the rust resistance in the F2 population mapped the leaf rust resistance gene (LrAC) on the short arm of wheat chromosome 5D. Genetic complementation and the linked molecular markers revealed that LrAC is a novel homoeoallele of an orthologue Lr57 already introgressed from the 5M chromosome of Ae. geniculata on 5DS of wheat.

  20. Short communication: genetic parameters for feed intake, production, and extent of negative energy balance in Nordic Red dairy cattle.

    Science.gov (United States)

    Liinamo, A-E; Mäntysaari, P; Mäntysaari, E A

    2012-11-01

    The aim of this paper was to study the genetic parameters for feed intake, milk production, and energy balance in Nordic Red dairy cattle from an experimental data set. The data were collected at the MTT Agrifood Research Finland Rehtijärvi experimental farm in 4 feeding trials between 1998 and 2008, and included lactation wk 2 to 30 for 291 Nordic Red nucleus heifers descending from 72 different sires. The studied traits included weekly averages for energy-corrected milk yield (ECM, kg/d), dry matter intake (kg/d), body weight (BW, kg), body condition score (BCS, score 1 to 5), and energy balance (EB, MJ of metabolizable energy/d). The data were analyzed with both fixed and random regression models. The heritabilities of ECM and BCS were moderate to high and remained fairly constant over the entire lactation period, whereas the heritabilities of BW and EB were the highest in early lactation (0.47 and 0.37, respectively) and declined later on. The heritabilities of DMI were highest (0.33) around lactation wk 5 and again at lactation wk 30, and were somewhat lower at the beginning of the lactation and in the middle period. The genetic correlations between the traits differed considerably between early and later lactation periods, especially for the trait pairs ECM-dry matter intake, ECM-EB, BW-EB, and BCS-EB, being negative or close to zero in lactation wk 2 to 5 but turning moderate to strong and positive by lactation wk 10. The results suggest that the lactating cows express their genetic potential for feed intake and energy utilization most clearly between lactation wk 2 to 10. The best candidate trait for selection might be EB in lactation wk 2 to 5 because it has a moderate heritability and is not genetically correlated with BW or BCS in that period.

  1. Detection of genetic variants affecting cattle behaviour and their impact on milk production: a genome-wide association study.

    Science.gov (United States)

    Friedrich, Juliane; Brand, Bodo; Ponsuksili, Siriluck; Graunke, Katharina L; Langbein, Jan; Knaust, Jacqueline; Kühn, Christa; Schwerin, Manfred

    2016-02-01

    Behaviour traits of cattle have been reported to affect important production traits, such as meat quality and milk performance as well as reproduction and health. Genetic predisposition is, together with environmental stimuli, undoubtedly involved in the development of behaviour phenotypes. Underlying molecular mechanisms affecting behaviour in general and behaviour and productions traits in particular still have to be studied in detail. Therefore, we performed a genome-wide association study in an F2 Charolais × German Holstein cross-breed population to identify genetic variants that affect behaviour-related traits assessed in an open-field and novel-object test and analysed their putative impact on milk performance. Of 37,201 tested single nucleotide polymorphism (SNPs), four showed a genome-wide and 37 a chromosome-wide significant association with behaviour traits assessed in both tests. Nine of the SNPs that were associated with behaviour traits likewise showed a nominal significant association with milk performance traits. On chromosomes 14 and 29, six SNPs were identified to be associated with exploratory behaviour and inactivity during the novel-object test as well as with milk yield traits. Least squares means for behaviour and milk performance traits for these SNPs revealed that genotypes associated with higher inactivity and less exploratory behaviour promote higher milk yields. Whether these results are due to molecular mechanisms simultaneously affecting behaviour and milk performance or due to a behaviour predisposition, which causes indirect effects on milk performance by influencing individual reactivity, needs further investigation. PMID:26515756

  2. Genetic analyses of days to calving and their relationships with other traits in a Canchim cattle herd

    Directory of Open Access Journals (Sweden)

    Talita Buttarello Mucari

    2007-01-01

    Full Text Available Heritabilities and genetic correlations in a Canchim beef cattle herd were estimated using data on the following traits: male scrotal circumference at twelve months (SC12; days to first calving (DFC for heifers; days to calving (DC for cows; male and female weight (W at twelve months (W12; heifer weight at the start of the first breeding season (WFBS and at first calving (WFC; and cow weight at the start of the breeding season (WBS and at calving (WC. Analyses of the DFC and DC traits were carried out excluding and including penalized (DFC P and DC P non-calving females. The restricted maximum likelihood method was used, applying one-trait models for the DFC and DC analyses and two-trait models for analyses of DFC and DC combined with the other traits studied. Statistical models included fixed and additive direct random effects for all traits, maternal permanent environmental random effect for SC12 and W12, and the animal permanent environmental random effect for DC P, WBS and WC. We found that DFC and DC values can be improved by selecting for an increase in the SC12. Genetic correlations between DFC and W12 and between DC and W12 indicated that selection for increased W12 may increase DFC but does not produce significantly correlated responses in DC. Associations of the other body weight traits with DC and DFC suggest that heavier females experience lower reproductive performance.

  3. Genetic diversity and frequency of bovine viral diarrhea virus (BVDV) detected in cattle in Turkey.

    Science.gov (United States)

    Yilmaz, Huseyin; Altan, Eda; Ridpath, Julia; Turan, Nuri

    2012-09-01

    The aim of this study was to investigate the frequency and diversity of bovine viral diarrhea viruses (BVDV) infecting cattle in Turkey. A total of 1124 bovine blood samples from 19 farms in 4 different Turkish regions were tested by antigen capture ELISA (ACE). BVDV antigen was found in 26 samples from 13 farms. Only 20 of the 26 initial test positive cattle were available for retesting. Of these, 6 of 20 tested positive for BVDV, by ACE and real-time RT-PCR, one month after initial testing. Phylogenetic analysis, based on comparison of the E2 or the 5'UTR coding regions, from 19 of the 26 initial positive samples, indicated that 17 belonged to the BVDV-1 genotype and 2 to the BVDV-2 genotype. Comparison of 5'UTR sequences segregated 8 BVDV-1 strains (strains 5, 6, 10, 11, 12, 13, 17, and 19) to the BVDV1f, 1 strain (strain 8) to the BVDV1i and 1 strain (strain 14) to the BVDV1d subgenotypes. One strain (strain 4) did not group with other subgenotypes but was closer to the BVDV1f. The remaining 6 BVDV-1 strains (strains 1, 2, 3, 7, 9, and 18) segregated to a novel subgenotype. The E2 sequence comparison results were similar, with the exception that strain 5 grouped with the novel subgenotype rather than BVDV1f subgenotype. It appears that among the diverse BVDV strains in circulation there may be a subgenotype that is unique to Turkey. This should be considered in the design of diagnostics and vaccines to be used in Turkey.

  4. Genetic gain in dairy cattle populations is increased using sexed semen in commercial herds

    DEFF Research Database (Denmark)

    Sørensen, Morten Kargo; Andersen, Jakob Voergaard; Pedersen, Louise Dybdahl;

    2011-01-01

    100 cows each. Each year 50 young bulls (YB), 10 active sires and 215 BD were selected on best linear unbiased prediction estimated breeding values by truncation selection across the simulated population, and the YB were tested within the population. Use of sexed semen alone gave a positive increase...... annual genetic gain by 1.8–2.5% compared with schemes without sexed semen and MOET on all BD. Performing MOET on all BD enables selection of offspring with high Mendelian deviations, which increase the annual genetic gain. Use of sexed semen decreased the genetic lag between the sires and the CD by 12...

  5. Genetic and phenotypic relationships of serum leptin concentration with performance, efficiency of gain, and carcass merit of feedlot cattle.

    Science.gov (United States)

    Nkrumah, J D; Keisler, D H; Crews, D H; Basarab, J A; Wang, Z; Li, C; Price, M A; Okine, E K; Moore, S S

    2007-09-01

    Leptin is the hormone product of the obese gene that is synthesized and predominantly expressed by adipocytes. This study estimated the genetic variation in serum leptin concentration and evaluated the genetic and phenotypic relationships of serum leptin concentration with performance, efficiency of gain, and carcass merit. There were 464 steers with records for serum leptin concentration, performance, and efficiency of gain and 381 steers with records for carcass traits. The analyses included a total of 813 steers, including those without phenotypic records. Phenotypic and genetic parameter estimates were obtained using SAS and ASREML, respectively. Serum leptin concentration was moderately heritable (h2 = 0.34 +/- 0.13) and averaged 13.91 (SD = 5.74) ng/mL. Sire breed differences in serum leptin concentration correlated well with breed differences in body composition. Specifically, the serum leptin concentration was 20% greater in Angus-sired steers compared with Charolais-sired steers (P Charolais- than Angus-sired steers (P yield (P Charolais- compared with Angus-sired steers. Steers with greater serum leptin concentration also had greater DMI (P 0.10). Serum leptin concentration was correlated phenotypically with ultrasound backfat (r = 0.41; P yield (r = -0.38; P yield grade (r = 0.32; P yield (r = -0.59 +/- 0.22), and yield grade (r = 0.39 +/- 0.26). Serum leptin concentration can be a valuable tool that can be incorporated into appropriate selection programs to favorably improve the carcass merit of cattle. PMID:17468416

  6. Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection.

    Science.gov (United States)

    García-Ruiz, Adriana; Cole, John B; VanRaden, Paul M; Wiggans, George R; Ruiz-López, Felipe J; Van Tassell, Curtis P

    2016-07-12

    Seven years after the introduction of genomic selection in the United States, it is now possible to evaluate the impact of this technology on the population. Selection differential(s) (SD) and generation interval(s) (GI) were characterized in a four-path selection model that included sire(s) of bulls (SB), sire(s) of cows (SC), dam(s) of bulls (DB), and dam(s) of cows (DC). Changes in SD over time were estimated for milk, fat, and protein yield; somatic cell score (SCS); productive life (PL); and daughter pregnancy rate (DPR) for the Holstein breed. In the period following implementation of genomic selection, dramatic reductions were seen in GI, especially the SB and SC paths. The SB GI reduced from ∼7 y to less than 2.5 y, and the DB GI fell from about 4 y to nearly 2.5 y. SD were relatively stable for yield traits, although modest gains were noted in recent years. The most dramatic response to genomic selection was observed for the lowly heritable traits DPR, PL, and SCS. Genetic trends changed from close to zero to large and favorable, resulting in rapid genetic improvement in fertility, lifespan, and health in a breed where these traits eroded over time. These results clearly demonstrate the positive impact of genomic selection in US dairy cattle, even though this technology has only been in use for a short time. Based on the four-path selection model, rates of genetic gain per year increased from ∼50-100% for yield traits and from threefold to fourfold for lowly heritable traits. PMID:27354521

  7. Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes

    OpenAIRE

    Wheeldon, Tyler J; Rutledge, Linda Y; Patterson, Brent R; White, Bradley N; Wilson, Paul J.

    2013-01-01

    Hybridization has played an important role in the evolutionary history of Canis species in eastern North America. Genetic evidence of coyote–dog hybridization based on mitochondrial DNA (mtDNA) is lacking compared to that based on autosomal markers. This discordance suggests dog introgression into coyotes has potentially been male biased, but this hypothesis has not been formally tested. Therefore, we investigated biparentally, maternally, and paternally inherited genetic markers in a sample ...

  8. Investigation of three strategies for an international genetic evaluation of beef cattle weaning weight

    Directory of Open Access Journals (Sweden)

    Donoghue Kath

    2005-07-01

    Full Text Available Abstract Weaning weights from 83 389 Limousin calves born between 1993 and 2002 in France and the Trans-Tasman block (Australia/New Zealand were analysed to compare different strategies for running an international genetic evaluation for the breed. These records were a subset of the complete data for both countries and comprised a sample of herds that had recorded progeny of sires used across both countries. Genetic and phenotypic parameters for weaning weight were estimated within the countries. The estimates of direct genetic heritabilities were higher in France than in the Trans-Tasman block (0.31 vs. 0.22, while direct-maternal genetic correlations were less negative in the Trans-Tasman block (-0.10 than in France (-0.21. Different strategies for an international evaluation were studied, and the correlations between the estimated breeding values (EBV of national evaluations and these strategies were derived. The international evaluation strategies were a an animal model on raw performance data with non unity genetic correlations and heterogeneous residual and genetic variances across countries; b the same animal model applied to pre-corrected (for fixed effects performance data; and c a sire model on de-regressed proofs (MACE. Estimates of the genetic correlations between weaning weight in both countries were 0.86 (0.80 for direct (maternal genetic effects for the first strategy. Estimation of variance components by MACE appeared to be very sensitive to the sample of bulls and their reliability approximations. Variance component estimates obtained using pre-corrected data were inconsistent with estimates on raw data. However, the EBV predicted using pre-corrected data and parameters estimated from the raw data were similar to those predicted from raw data. Correlations between national and international EBV were always high (> 0.90 for sires, whichever genetic effect (direct or maternal or international evaluation model was considered. The

  9. Introgression of mitochondrial DNA among lineages in a hybridogenetic ant.

    Science.gov (United States)

    Darras, Hugo; Aron, Serge

    2015-02-01

    We report a remarkable pattern of incongruence between nuclear and mitochondrial variations in a social insect, the desert ant Cataglyphis hispanica. This species reproduces by social hybridogenesis. In all populations, two distinct genetic lineages coexist; non-reproductive workers develop from hybrid crosses between the lineages, whereas reproductive offspring (males and new queens) are typically produced asexually by parthenogenesis. Genetic analyses based on nuclear markers revealed that the two lineages remain highly differentiated despite constant hybridization for worker production. Here, we show that, in contrast with nuclear DNA, mitochondrial DNA (mtDNA) does not recover the two lineages as monophyletic. Rather, mitochondrial haplotypes cluster according to their geographical origin. We argue that this cytonuclear incongruence stems from introgression of mtDNA among lineages, and review the mechanisms likely to explain this pattern under social hybridogenesis.

  10. Genetic types of milk proteins prevalence and their relation with production traits in Lithuanian dairy cattle breeds

    OpenAIRE

    Peciulaitienė, Nijolė

    2005-01-01

    First time was investigated distribution of genes coding for milk protein diversity in Lithuanian dairy cattle population and milk protein genes influencing milk yield and composition. According to research results, offer take into account to specific genes loci in cattle genome, influencing expression of desirable milk protein types. Select animals, owning Kapa-casein B and Beta-lactoglobulin B alleles and create specific cattle herds be able to produce qualitative milk suitable for curd and...

  11. Genetic parameters for pathogen-specific mastitis resistance in Danish Holstein cattle

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Madsen, P.; Mark, Thomas;

    2009-01-01

    . uberis, respectively. The heritabilities of groups of pathogen ranged from 0.053 to 0.087. Genetic correlations among the pathogen-specific mastitis traits ranged from 0.45 to 0.77. These estimates tended to be lowest for bacteria eliciting very different immune responses, which can be considered...... as the overall pleiotropic effect of genes affecting resistance to a specific pathogen, and highest for bacteria sharing characteritics regarding immune response. The genetic correlations between the groups of pathogens were high, 0.73 and 0.83. Results showed that the pathogen-specific traits used in this study......The objective of this study was to estimate heritabilities for and genetic correlations among different pathogen-specific mastitis traits. The traits were unspecific mastitis, which is all mastitis treatments regardless of the causative pathogen as well as mastitis caused by Streptococcus...

  12. Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats.

    Science.gov (United States)

    Senerchia, Natacha; Felber, François; North, Béatrice; Sarr, Anouk; Guadagnuolo, Roberto; Parisod, Christian

    2016-06-01

    The maintenance of species integrity despite pervasive hybridization is ruled by the interplay between reproductive barriers. Endogenous postzygotic isolation will shape the patterns of introgression in hybrid zones, leading to variable outcomes depending on the genetic mechanism involved. Here, we analysed experimental and natural hybrid populations of Aegilops geniculata and Aegilops triuncialis to examine the genetics of species boundaries in the face of gene flow. Because long-terminal repeat retrotransposons (LTR-RTs) showing differential evolutionary trajectories are probably to affect hybrid dysgenesis and reproductive isolation between these wild wheat species, we addressed the impact of LTR-RTs in shaping introgression between them. Experimental settings involving artificial sympatry and enforced crossings quantified strong, but incomplete reproductive isolation, and highlighted asymmetrical endogenous postzygotic isolation between the two species. Natural hybrid zones located in the northern Golan Heights were analysed using plastid DNA, amplified fragment length polymorphisms (AFLP) marking random sequences, and sequence-specific amplified polymorphisms (SSAP) tracking insertions from six LTR-RT families. This analysis demonstrated asymmetrical introgression and genome reorganization. In comparison with random sequences and quiescent LTR-RTs, those LTR-RTs predicted to be activated following conflicting interactions in hybrids revealed differential introgression across the hybrid zones. As also reported for synthetic F1 hybrids, such LTR-RTs were specifically reorganized in the genomes of viable hybrids, confirming that conflicts between selfish LTR-RTs may represent key incompatibilities shaping species boundaries and fostering long-term species integrity in the face of gene flow. PMID:26678573

  13. Genetic parameters for EUROP carcass traits within different groups of cattle in Ireland

    NARCIS (Netherlands)

    Hickey, J.M.; Keane, M.G.; Kenny, D.A.; Cromie, A.R.; Veerkamp, R.F.

    2007-01-01

    The first objective of this study was to test the ability of systems of weighing and classifying bovine carcasses used in commercial abattoirs in Ireland to provide information that can be used for the purposes of genetic evaluation of carcass weight, carcass fatness class, and carcass conformation

  14. Genetic evaluation of Angus cattle for carcass marbling using ultrasound and genomic indicators

    Science.gov (United States)

    Objectives were to estimate genetic parameters needed to elucidate the relationships of a molecular breeding value for marbling (MBV), intramuscular fat of yearling bulls measured with ultrasound (IMF) and marbling score of harvested steers (MRB), and to assess the utility of MBV and IMF in predicti...

  15. Genetics of body condition score as an indicator of dairy cattle fertility. A review

    Directory of Open Access Journals (Sweden)

    Bastin, C.

    2013-01-01

    Full Text Available Body condition score (BCS is a subjective measure of the amount of metabolizable energy stored in a live animal. Change in BCS of dairy cows is considered to be an indicator of the extent and the duration of postpartum negative energy balance. Although change in BCS over lactation is lowly heritable, heritability estimates of level of BCS range from 0.20 to 0.50. Also, BCS tends to be more heritable in mid-lactation indicating that genetic differences are more related to how well cows recover from the negative energy balance state. BCS measurements are generally highly correlated within and between lactations. Genetic correlations with BCS are unfavorable for milk, fat, and protein yield, suggesting that genetically superior producers tend to have lower BCS, especially during the lactation. Genetic correlations are generally moderate and favorable with fertility indicating that cows with higher levels of BCS would have a greater chance to conceive after insemination and fewer number of days when not pregnant. Because direct selection to improve fertility might be complicated by several factors, selection for higher levels of BCS, especially in mid-lactation, appears to be a good option to indirectly improve fertility in dairy cows.

  16. Heritable and non-heritable genetic effects on retained placenta in Meuse-Rhine-Yssel cattle

    NARCIS (Netherlands)

    Benedictus, L.; Koets, A.P.; Kuijpers, F.H.J.; Joosten, I.; Eldik, van P.; Heuven, H.C.M.

    2013-01-01

    Failure of the timely expulsion of the fetal membranes, called retained placenta, leads to reduced fertility, increased veterinary costs and reduced milk yields. The objectives of this study were to concurrently look at the heritable and non-heritable genetic effects on retained placenta and test th

  17. Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds.

    Science.gov (United States)

    A deep draft sequence assembly derived from shotgun reads from a single Hereford female and comparative sampling sequences from cows representing six additional bovine breeds has enabled the development of genetic probes to interrogate single nucleotide polymorphisms for population and breed analyse...

  18. Genetic parameters for carcass traits and their live animal indicators in Simmental cattle.

    Science.gov (United States)

    Crews, D H; Pollak, E J; Weaber, R L; Quaas, R L; Lipsey, R J

    2003-06-01

    The objective of this study was to estimate parameters required for genetic evaluation of Simmental carcass merit using carcass and live animal data. Carcass weight, fat thickness, longissimus muscle area, and marbling score were available from 5,750 steers and 1,504 heifers sired by Simmental bulls. Additionally, yearling ultrasound measurements of fat thickness, longissimus muscle area, and estimated percentage of intramuscular fat were available on Simmental bulls (n = 3,409) and heifers (n = 1,503). An extended pedigree was used to construct the relationship matrix (n = 23,968) linking bulls and heifers with ultrasound data to steers and heifers with carcass data. All data were obtained from the American Simmental Association. No animal had both ultrasound and carcass data. Using an animal model and treating corresponding ultrasound and carcass traits separately, genetic parameters were estimated using restricted maximum likelihood. Heritability estimates for carcass traits were 0.48 +/- 0.06, 0.35 +/- 0.05, 0.46 +/- 0.05, and 0.54 +/- 0.05 for carcass weight, fat thickness, longissimus muscle area, and marbling score, respectively. Heritability estimates for bull (heifer) ultrasound traits were 0.53 +/- 0.07 (0.69 +/- 0.09), 0.37 +/- 0.06 (0.51 +/- 0.09), and 0.47 +/- 0.06 (0.52 +/- 0.09) for fat thickness, longissimus muscle area, and intramuscular fat percentage, respectively. Heritability of weight at scan was 0.47 +/- 0.05. Using a bivariate weight model including scan weight of bulls and heifers with carcass weight of slaughter animals, a genetic correlation of 0.77 +/- 0.10 was obtained. Models for fat thickness, longissimus muscle area, and marbling score were each trivariate, including ultrasound measurements on yearling bulls and heifers, and corresponding carcass traits of slaughter animals. Genetic correlations of carcass fat thickness with bull and heifer ultrasound fat were 0.79 +/- 0.13 and 0.83 +/- 0.12, respectively. Genetic correlations of

  19. Genetic Parameter Estimates of Carcass Traits under National Scale Breeding Scheme for Beef Cattle.

    Science.gov (United States)

    Do, ChangHee; Park, ByungHo; Kim, SiDong; Choi, TaeJung; Yang, BohSuk; Park, SuBong; Song, HyungJun

    2016-08-01

    Carcass and price traits of 72,969 Hanwoo cows, bulls and steers aged 16 to 80 months at slaughter collected from 2002 to 2013 at 75 beef packing plants in Korea were analyzed to determine heritability, correlation and breeding value using the Multi-Trait restricted maximum likelihood (REML) animal model procedure. The traits included carcass measurements, scores and grades at 24 h postmortem and bid prices at auction. Relatively high heritability was found for maturity (0.41±0.031), while moderate heritability estimates were obtained for backfat thickness (0.20±0.018), longissimus muscle (LM) area (0.23±0.020), carcass weight (0.28±0.019), yield index (0.20±0.018), yield grade (0.16±0.017), marbling (0.28±0.021), texture (0.14±0.016), quality grade (0.26±0.016) and price/kg (0.24±0.025). Relatively low heritability estimates were observed for meat color (0.06±0.013) and fat color (0.06±0.012). Heritability estimates for most traits were lower than those in the literature. Genetic correlations of carcass measurements with characteristic scores or quality grade of carcass ranged from -0.27 to +0.21. Genetic correlations of yield grade with backfat thickness, LM area and carcass weight were 0.91, -0.43, and -0.09, respectively. Genetic correlations of quality grade with scores of marbling, meat color, fat color and texture were -0.99, 0.48, 0.47, and 0.98, respectively. Genetic correlations of price/kg with LM area, carcass weight, marbling, meat color, texture and maturity were 0.57, 0.64, 0.76, -0.41, -0.79, and -0.42, respectively. Genetic correlations of carcass price with LM area, carcass weight, marbling and texture were 0.61, 0.57, 0.64, and -0.73, respectively, with standard errors ranging from ±0.047 to ±0.058. The mean carcass weight breeding values increased by more than 8 kg, whereas the mean marbling scores decreased by approximately 0.2 from 2000 through 2009. Overall, the results suggest that genetic improvement of productivity and

  20. Genetic parameters for energy balance, feed efficiency, and related traits in Holstein cattle.

    Science.gov (United States)

    Spurlock, D M; Dekkers, J C M; Fernando, R; Koltes, D A; Wolc, A

    2012-09-01

    Objectives of the current study were to estimate genetic parameters in Holstein cows for energy balance (EB) and related traits including dry matter intake (DMI), body weight (BW), body condition score (BCS), energy-corrected milk (ECM) production, and gross feed efficiency (GFE), defined as the ratio of total ECM yield to total DMI over the first 150 d of lactation. Data were recorded for the first half of lactation on 227 and 175 cows in their first or later lactation, respectively. Random regression models were fitted to longitudinal data. Also, each trait was averaged over monthly intervals and analyzed by single and multivariate animal models. Heritability estimates ranged from 0.27 to 0.63, 0.12 to 0.62, 0.12 to 0.49, 0.63 to 0.72, and 0.49 to 0.53 for DMI, ECM yield, EB, BW, and BCS, respectively, averaged over monthly intervals. Daily heritability estimates ranged from 0.18 to 0.30, 0.10 to 0.26, 0.07 to 0.22, 0.43 to 0.67, and 0.25 to 0.38 for DMI, ECM yield, EB, BW, and BCS, respectively. Estimated heritability for GFE was 0.32. The genetic correlation of EB at 10d in milk (DIM) with EB at 150 DIM was -0.19, suggesting the genetic regulation of this trait differs by stage of lactation. Positive genetic correlations were found among DMI, ECM yield, and BW averaged over monthly intervals, whereas correlations of these traits with BCS depended upon stage of lactation. Total ECM yield for the lactation was positively correlated with DMI, but a negative genetic correlation between total ECM yield and EB was found. However, the genetic correlation between total ECM yield and EB in the first month of lactation was -0.02, indicating that total production is not genetically correlated with EB during the first month of lactation, when negative EB is most closely associated with diminished fitness. The genetic correlation between GFE and EB ranged from -0.73 to -0.99, indicating that selection for more efficient cows would favor a lower energy status. However, the

  1. Comparison between sire-maternal grandsire and animal models for genetic evaluation of longevity in dairy cattle populations with small herds

    OpenAIRE

    Gorjanc, G.; Kovac, M.; Ducrocq, Vincent

    2013-01-01

    Survival analysis techniques for sire-maternal grand- sire (MGS) and animal models were used to test the genetic evaluation of longevity in a Slovenian Brown cattle population characterized by small herds. Three genetic models were compared: a sire-MGS model for bulls and an approximate animal model based on estimated breeding values (EBV) from the sire-MGS model for cows, an animal model, and an animal model based on the estimated variance components from the sire-MGS model. In addit...

  2. Implementation of a routine genetic evaluation for longevity based on survival analysis techniques in dairy cattle populations in Switzerland.

    Science.gov (United States)

    Vukasinovic, N; Moll, J; Casanova, L

    2001-09-01

    Genetic evaluation of sires for functional longevity of their daughters based on survival analysis has been implemented in the populations of Braunvieh, Simmental, and Holstein cattle in Switzerland. A Weibull mixed sire-maternal grandsire survival model was used to estimate breeding values of sires with data on cows that calved since April 1, 1980. Data on Braunvieh and Simmental cows included about 1.1 million records, data on Holstein cows comprised about 220,000 records. Data contained approximately 20 to 24% right-censored records and 6 to 9% left-truncated records. Besides the random sire and maternal grandsire effects, the model included effects of herd-year-season, age at first calving, parity, stage of lactation, alpine pasturing (Braunvieh and Simmental), and relative milk yield and relative fat and protein percentage within herd to account for culling for production. Heritability of functional longevity, estimated on a subset of data including approximately 150,000 animals, were 0.181, 0.198, and 0.184 for Braunvieh, Simmental, and Holstein, respectively. Breeding values were estimated for all sires with at least six daughters or three granddaughters in the data. Breeding values of sires are expressed in months of functional productive life and published in sire catalogs along with breeding values for production traits.

  3. Evaluation of biochemical parameters and genetic markers for association with meat tenderness in South African feedlot cattle.

    Science.gov (United States)

    Frylinck, L; van Wyk, G L; Smith, T P L; Strydom, P E; van Marle-Köster, E; Webb, E C; Koohmaraie, M; Smith, M F

    2009-12-01

    A large proportion of South African feedlot cattle are crossbreds of Brahman (BrX, Bos indicus), and Simmental (SiX, Bos taurus). A sample of 20 grain fed bulls from each of these crossbreeds was used to compare meat quality with that of the small frame indigenous Nguni (NgX, Sanga) by evaluating a variety of biochemical and genetic parameters previously shown to be associated with meat tenderness. Shear force values were generally high (5.6kg average at 14days post mortem), with SiX animals higher than BrX or NgX (P=0.051) despite higher calpastatin:calpain ratio in BrX (P<0.05). Calpain activity and cold shortening were both correlated with tenderness for all classes. The sample size was too small to accurately estimate genotypic effects of previously published markers in the CAST and CAPN1 genes, but the allele frequencies suggest that only modest progress would be possible in these South African crossbreds using these markers. PMID:20416642

  4. Non-genetic Factors Affecting Gestation Lenght and Postpartum Intervals in Gudali Zebu Cattle of the Adamawa Highlands of Cameroon

    Directory of Open Access Journals (Sweden)

    Mbah, DA.

    2007-01-01

    Full Text Available The effects of non-genetic factors (sex of calf, calf birth weight, age of cow, season of calving affecting gestation length (GL and open days period (OP in the Ngaoundere Gudali cattle of the Adamawa (Cameroon was investigated. Mean GL was 293.4 ± 0.4 d. Sex of the calf significantly (P< 0.05 affected GL, with male calves being carried in utero approximately 3 days longer than the females (294.1 ± 1.2 vs 291.1 ± 1.2 d. Calf birth weight tended to increase as gestation lengthened. Parity and age of the cow had no significant (P> 0.05 effect on GL. The mean duration of the OP (from calving to conception was 267.7 ± 7.4 d. Approximately 23.2% of the cows conceived within 90 days of calving and a total of 55.6% had conceived by 360 days. The distribution of the OP was bimodal, and could have been influenced by seasonal availability of feed, or long (6 months mating season allowing cows to calve during the following mating season. Calving to conception interval was significantly (P< 0.001 affected by month of calving and parity. Sex of the calf did not affect significantly the duration of the postpartum period, although this period was 5 days longer following the birth of a male calf.

  5. Typing late prehistoric cows and bulls--osteology and genetics of cattle at the Eketorp ringfort on the Oland island in Sweden.

    Directory of Open Access Journals (Sweden)

    Ylva Telldahl

    Full Text Available Human management of livestock and the presence of different breeds have been discussed in archaeozoology and animal breeding. Traditionally osteometrics has been the main tool in addressing these questions. We combine osteometrics with molecular sex identifications of 104 of 340 morphometrically analysed bones in order to investigate the use of cattle at the Eketorp ringfort on the Öland island in Sweden. The fort is dated to 300-1220/50 A.D., revealing three different building phases. In order to investigate specific patterns and shifts through time in the use of cattle the genetic data is evaluated in relation to osteometric patterns and occurrence of pathologies on cattle metapodia. Males were genotyped for a Y-chromosomal SNP in UTY19 that separates the two major haplogroups, Y1 and Y2, in taurine cattle. A subset of the samples were also genotyped for one SNP involved in coat coloration (MC1R, one SNP putatively involved in resistance to cattle plague (TLR4, and one SNP in intron 5 of the IGF-1 gene that has been associated to size and reproduction.The results of the molecular analyses confirm that the skeletal assemblage from Eketorp is dominated by skeletal elements from females, which implies that dairying was important. Pathological lesions on the metapodia were classified into two groups; those associated with the use as draught animals and those lesions without a similar aetiology. The results show that while bulls both exhibit draught related lesions and other types of lesions, cows exhibit other types of lesions. Interestingly, a few elements from females exhibit draught related lesions. We conclude that this reflects the different use of adult female and male cattle.Although we note some variation in the use of cattle at Eketorp between Iron Age and Medieval time we have found little evidence for the use of different types of animals for specific purposes. The use of specific (genetic breeds seems to be a phenomenon that developed

  6. Variance components and genetic parameters for milk production and lactation pattern in an ethiopian multibreed dairy cattle population.

    Science.gov (United States)

    Gebreyohannes, Gebregziabher; Koonawootrittriron, Skorn; Elzo, Mauricio A; Suwanasopee, Thanathip

    2013-09-01

    The objective of this study was to estimate variance components and genetic parameters for lactation milk yield (LY), lactation length (LL), average milk yield per day (YD), initial milk yield (IY), peak milk yield (PY), days to peak (DP) and parameters (ln(a) and c) of the modified incomplete gamma function (MIG) in an Ethiopian multibreed dairy cattle population. The dataset was composed of 5,507 lactation records collected from 1,639 cows in three locations (Bako, Debre Zeit and Holetta) in Ethiopia from 1977 to 2010. Parameters for MIG were obtained from regression analysis of monthly test-day milk data on days in milk. The cows were purebred (Bos indicus) Boran (B) and Horro (H) and their crosses with different fractions of Friesian (F), Jersey (J) and Simmental (S). There were 23 breed groups (B, H, and their crossbreds with F, J, and S) in the population. Fixed and mixed models were used to analyse the data. The fixed model considered herd-year-season, parity and breed group as fixed effects, and residual as random. The single and two-traits mixed animal repeatability models, considered the fixed effects of herd-year-season and parity subclasses, breed as a function of cow H, F, J, and S breed fractions and general heterosis as a function of heterozygosity, and the random additive animal, permanent environment, and residual effects. For the analysis of LY, LL was added as a fixed covariate to all models. Variance components and genetic parameters were estimated using average information restricted maximum likelihood procedures. The results indicated that all traits were affected (p<0.001) by the considered fixed effects. High grade B×F cows (3/16B 13/16F) had the highest least squares means (LSM) for LY (2,490±178.9 kg), IY (10.5±0.8 kg), PY (12.7±0.9 kg), YD (7.6±0.55 kg) and LL (361.4±31.2 d), while B cows had the lowest LSM values for these traits. The LSM of LY, IY, YD, and PY tended to increase from the first to the fifth parity. Single

  7. Microsatellite DNA typing for assessment of genetic variability in Tharparkar breed of Indian zebu (Bos indicus) cattle, a major breed of Rajasthan

    Indian Academy of Sciences (India)

    M. Sodhi; M. Mukesh; B. Prakash; S. P. S. Ahlawat; R. C. Sobti

    2006-12-01

    The present study estimates genetic variability with a set of 25 microsatellite markers in a random sample of 50 animals of Tharparkar breed of Indian zebu (Bos indicus) cattle. Tharparkar is a dual-purpose breed, valued for its milk as well as draught utility, and is adapted to the inhospitable Thar desert conditions of Rajasthan typified by summer temperature hovering above 50°C, sparse rainfall and vegetation, and scarcity of even drinking water. The observed number of alleles ranged from 4 (ETH3, ILSTS030, INRA5, INRA63 and MM8) to 11 (HEL9 and ILSTS034), with allelic diversity (average number of observed alleles per locus) of 6.20. Observed and expected heterozygosity ranged from 0.25 (INRA63) to 0.77 (ETH10), and from 0.51 (HEL5 and HAUT27) to 0.88 (HEL9) respectively. Wide range of genetic variability supported the utility of these microsatellite loci in measurement of genetic diversity indices in other Indian cattle breeds too. Various average genetic variability measures, namely allele diversity (6.20), observed heterozygosity (0.57), expected heterozygosity (0.67) and mean polymorphism information content (0.60) values showed substantial within-breed genetic variability in this major breed of Rajasthan, despite accumulated inbreeding as reflected by high average inbreeding coefficient $(F_{\\text{IS}} = 0.39)$. The Tharparkar population has not experienced a bottleneck in the recent past.

  8. Discovery of novel genetic networks associated with 19 economically important traits in beef cattle

    Directory of Open Access Journals (Sweden)

    Zhihua Jiang, Jennifer J. Michal, Jie Chen, Tyler F. Daniels, Tanja Kunej, Matthew D. Garcia, Charles T. Gaskins, Jan R. Busboom, Leeson J. Alexander, Raymond W. Wright Jr., Michael D. MacNeil

    2009-01-01

    Full Text Available Quantitative or complex traits are determined by the combined effects of many loci, and are affected by genetic networks or molecular pathways. In the present study, we genotyped a total of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a Wagyu x Limousin reference population. Two hundred forty six F2 animals were measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280 single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW analysis revealed 144 significant associations (P < 0.05, but 50 of them were removed from the analysis due to the small number of animals (≤ 9 in one genotype group or absence of one genotype among three genotypes. The remaining 94 single-trait associations were then placed into three groups of quantitative trait modes (QTMs with additive, dominant and overdominant effects. All significant markers and their QTMs associated with each of these 19 traits were involved in a linear regression model analysis, which confirmed single-gene associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high correlations between predicted and actual values of performance, thus providing evidence that the classical Mendelian principles of inheritance can be applied in understanding genetic complexity of complex phenotypes. Our present study also indicated that carcass, eating quality and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted selection for improvement of one category of these traits would not interfere with improvement of another.

  9. Genetic analysis of fertility traits of Holstein dairy cattle in warm and temperate climate

    Directory of Open Access Journals (Sweden)

    Rabie Rahbar

    2016-08-01

    Full Text Available The edited data set for the estimation of heritability, genetic and phenotypic correlations of fertility traits contained up to 23,402 records from 10,894 cows calved between 2001 and 2015. Heritability estimates for success in first service (FS, gestation length (GL, number of inseminations (NI, insemination outcome (IO, calving interval (CI, calving birth weight (CBW and days open (DO were low and ranged between 0.016 (DO and 0.123 (GL. Repeatability of fertility traits was estimated to vary from 0.021 (FS to 0.411 (IO. The genetic correlations between DO × CI, DO × NI and CI × NI were positive and nearly perfect (0.98, 0.88 and 0.88, respectively, while those between DO × IO and CI × IO were negative (-0.98 and -1, respectively. Further, the phenotypic correlations between DO × CI, DO × NI, CI × NI, CBW × IO and SF × IO were 0.99, 0.83, 0.83, 0.99 and 1, respectively, while those between DO × IO, CI × IO, GL × IO and NI × IO were -0.99, -0.99, -0.99 and -1, respectively. Overall genetic parameters imply a good practical management in heat stress conditions will be essential for improving fertility efficiency.

  10. Direct and maternal genetic effects for carcass traits in beef cattle.

    Science.gov (United States)

    DeRouen, S M; Franke, D E; Bidner, T D; Blouin, D C

    1992-12-01

    Carcass measurements were taken on 1,537 steers produced over four generations in a rotational crossbreeding study. Breed direct and maternal additive and heterotic genetic effects were estimated for hot carcass weight (HCWT), retail yield (RY), longissimus muscle area (LM), fat thickness (FT), marbling score (MS), and Warner-Bratzler shear force (WBS). Angus (A), Brahman (B), Charolais (C), and Hereford (H) breeds were involved in straightbred, first-cross, and two-, three-, and four-breed rotational crossbred matings with each crossbred combination including the B. Breed direct (Ig) and maternal (Mg) additive genetic effects and direct (Ih) and maternal (Mh) heterotic genetic effects were estimated using a multiple-regression model. The Ig and Mg effects were expressed as deviations from the overall mean. The IgC effects (Ig for C breed) were significant for HCWT, RY, and LM and resulted in leaner, heavier carcasses. The IgA and IgH effects were, in general, negative (P carcass traits studied.

  11. Direct and maternal genetic effects for carcass traits in beef cattle.

    Science.gov (United States)

    DeRouen, S M; Franke, D E; Bidner, T D; Blouin, D C

    1992-12-01

    Carcass measurements were taken on 1,537 steers produced over four generations in a rotational crossbreeding study. Breed direct and maternal additive and heterotic genetic effects were estimated for hot carcass weight (HCWT), retail yield (RY), longissimus muscle area (LM), fat thickness (FT), marbling score (MS), and Warner-Bratzler shear force (WBS). Angus (A), Brahman (B), Charolais (C), and Hereford (H) breeds were involved in straightbred, first-cross, and two-, three-, and four-breed rotational crossbred matings with each crossbred combination including the B. Breed direct (Ig) and maternal (Mg) additive genetic effects and direct (Ih) and maternal (Mh) heterotic genetic effects were estimated using a multiple-regression model. The Ig and Mg effects were expressed as deviations from the overall mean. The IgC effects (Ig for C breed) were significant for HCWT, RY, and LM and resulted in leaner, heavier carcasses. The IgA and IgH effects were, in general, negative (P carcass traits studied. PMID:1474007

  12. Genetic evaluation of carcass traits in Simmental-sired cattle at different slaughter end points.

    Science.gov (United States)

    Shanks, B C; Tess, M W; Kress, D D; Cunningham, B E

    2001-03-01

    Our objectives were to estimate genetic parameters for carcass traits and evaluate the influence of slaughter end point on estimated breeding values (BV). Data provided by the American Simmental Association were divided into three sets: 1) 9,604 records of hot carcass weight (CW) and percentage retail cuts (PRC), 2) 6,429 records of CW, PRC, and marbling score (MS), and 3) 1,780 records of CW, PRC, MS, fat thickness (FT), and longissimus muscle area (LMA). Weaning weights (WW) from animals with carcass data and from their weaning contemporaries were used. Data were analyzed with a multiple-trait animal model and REML procedures to estimate genetic parameters and BV on an age-, CW-, MS-, or FT-constant basis. The model for carcass traits included fixed contemporary group and covariates for breed, heterozygosity, and slaughter end point and random additive direct genetic and residual effects. Weaning weight was preadjusted for founder effects, direct and maternal heterosis, age of dam, and age of calf. The model for WW included fixed contemporary group and random additive direct genetic, maternal genetic, maternal permanent environment, and residual effects. Heritabilities from data set 1 were 0.34 for CW and 0.25 for PRC on an age-constant basis and 0.25 for PRC on a CW end point. Heritabilities for data set 2 were 0.35, 0.24, and 0.36 for CW, PRC, and MS, respectively, on an age-constant basis. Data set 2 heritabilities were 0.25 for PRC and 0.34 for MS on a CW-constant basis and 0.33 for CW and 0.25 for PRC at a constant MS end point. Heritabilities on an age-constant basis for data set 3 were as follows: CW, 0.32; PRC, 0.09; MS, 0.12; FT, 0.10; and LMA, 0.26. Heritability estimates for data set 3 on a CW-, MS-, and FT-constant basis were similar to those on an age-constant basis. Heritabilities were 0.12 for PRC, 0.12 for MS, 0.14 for FT, and 0.22 for LMA on a CW-constant basis; 0.30 for CW, 0.09 for PRC, 0.10 for FT, and 0.28 for LMA at a constant MS end point

  13. Genetic and antigenic characterization of bovine viral diarrhea viruses isolated from cattle in Hokkaido, Japan.

    Science.gov (United States)

    Abe, Yuri; Tamura, Tomokazu; Torii, Shiho; Wakamori, Shiho; Nagai, Makoto; Mitsuhashi, Kazuya; Mine, Junki; Fujimoto, Yuri; Nagashima, Naofumi; Yoshino, Fumi; Sugita, Yukihiko; Nomura, Takushi; Okamatsu, Masatoshi; Kida, Hiroshi; Sakoda, Yoshihiro

    2016-01-01

    In our previous study, we genetically analyzed bovine viral diarrhea viruses (BVDVs) isolated from 2000 to 2006 in Japan and reported that subgenotype 1b viruses were predominant. In the present study, 766 BVDVs isolated from 2006 to 2014 in Hokkaido, Japan, were genetically analyzed to understand recent epidemics. Phylogenetic analysis based on nucleotide sequences of the 5'-untranslated region of viral genome revealed that 766 isolates were classified as genotype 1 (BVDV-1; 544 isolates) and genotype 2 (BVDV-2; 222). BVDV-1 isolates were further divided into BVDV-1a (93), 1b (371) and 1c (80) subgenotypes, and all BVDV-2 isolates were grouped into BVDV-2a subgenotype (222). Further comparative analysis was performed with BVDV-1a, 1b and 2a viruses isolated from 2001 to 2014. Phylogenetic analysis based on nucleotide sequences of the viral glycoprotein E2 gene, a major target of neutralizing antibodies, revealed that BVDV-1a, 1b and 2a isolates were further classified into several clusters. Cross-neutralization tests showed that BVDV-1b isolates were antigenically different from BVDV-1a isolates, and almost BVDV-1a, 1b and 2a isolates were antigenically similar among each subgenotype and each E2 cluster. Taken together, BVDV-1b viruses are still predominant, and BVDV-2a viruses have increased recently in Hokkaido, Japan. Field isolates of BVDV-1a, 1b and 2a show genetic diversity on the E2 gene with antigenic conservation among each subgenotype during the last 14 years.

  14. Genetic and antigenic characterization of bovine viral diarrhea viruses isolated from cattle in Hokkaido, Japan.

    Science.gov (United States)

    Abe, Yuri; Tamura, Tomokazu; Torii, Shiho; Wakamori, Shiho; Nagai, Makoto; Mitsuhashi, Kazuya; Mine, Junki; Fujimoto, Yuri; Nagashima, Naofumi; Yoshino, Fumi; Sugita, Yukihiko; Nomura, Takushi; Okamatsu, Masatoshi; Kida, Hiroshi; Sakoda, Yoshihiro

    2016-01-01

    In our previous study, we genetically analyzed bovine viral diarrhea viruses (BVDVs) isolated from 2000 to 2006 in Japan and reported that subgenotype 1b viruses were predominant. In the present study, 766 BVDVs isolated from 2006 to 2014 in Hokkaido, Japan, were genetically analyzed to understand recent epidemics. Phylogenetic analysis based on nucleotide sequences of the 5'-untranslated region of viral genome revealed that 766 isolates were classified as genotype 1 (BVDV-1; 544 isolates) and genotype 2 (BVDV-2; 222). BVDV-1 isolates were further divided into BVDV-1a (93), 1b (371) and 1c (80) subgenotypes, and all BVDV-2 isolates were grouped into BVDV-2a subgenotype (222). Further comparative analysis was performed with BVDV-1a, 1b and 2a viruses isolated from 2001 to 2014. Phylogenetic analysis based on nucleotide sequences of the viral glycoprotein E2 gene, a major target of neutralizing antibodies, revealed that BVDV-1a, 1b and 2a isolates were further classified into several clusters. Cross-neutralization tests showed that BVDV-1b isolates were antigenically different from BVDV-1a isolates, and almost BVDV-1a, 1b and 2a isolates were antigenically similar among each subgenotype and each E2 cluster. Taken together, BVDV-1b viruses are still predominant, and BVDV-2a viruses have increased recently in Hokkaido, Japan. Field isolates of BVDV-1a, 1b and 2a show genetic diversity on the E2 gene with antigenic conservation among each subgenotype during the last 14 years. PMID:26400674

  15. Genetics of body condition score as an indicator of dairy cattle fertility. A review

    OpenAIRE

    Bastin, C.; Gengler, N.

    2013-01-01

    Body condition score (BCS) is a subjective measure of the amount of metabolizable energy stored in a live animal. Change in BCS of dairy cows is considered to be an indicator of the extent and the duration of postpartum negative energy balance. Although change in BCS over lactation is lowly heritable, heritability estimates of level of BCS range from 0.20 to 0.50. Also, BCS tends to be more heritable in mid-lactation indicating that genetic differences are more related to how well cows recove...

  16. Genetic evaluation for body condition score in Italian Brown Swiss cattle

    OpenAIRE

    Nicoletti, C.; Santus, E; Testa, L.; O. Bonetti; A. Rossoni

    2010-01-01

    Body Condition Score (BCS) evaluates the body energy reserve in a cow using a numeric classification. It is possible to use the BCS as an indirect indicator of fertility. The genetic evaluation for BCS in Italian Brown Swiss is performed on 73125 BCS evaluations on the same number of primiparous, daughters of 507 sires. Effect of herd by year goes from -1,02 to +0,94 indicating large differences among herds. The primiparous cows show about 3.2 BCS points at calving, their BCS decreases slight...

  17. Breed effects, retained heterosis, and estimates of genetic and phenotypic parameters for carcass and meat traits of beef cattle.

    Science.gov (United States)

    Gregory, K E; Cundiff, L V; Koch, R M; Dikeman, M E; Koohmaraie, M

    1994-05-01

    Retained heterosis for meat traits was estimated in F3 generation castrate males in three composite populations of beef cattle finished on two levels of dietary energy density (2.82 Mcal of ME and 3.07 Mcal of ME and 11.50% CP) and serially slaughtered at four end points at intervals of 20 to 22 d. Breed effects were evaluated in nine parental breeds (Red Poll [R], Hereford [H], Angus [A], Limousin [L], Braunvieh [B], Pinzgauer [P], Gelbvieh [G], Simmental [S], and Charolais [C]) that contributed to the three composite populations (MARC I = 1/4 B, 1/4 C, 1/4 L, 1/8 H, 1/8 A; MARC II = 1/4 G, 1/4 S, 1/4 H, 1/4 A; and MARC III = 1/4 R, 1/4 P, 1/4 H, and 1/4 A). Breed effects were important (P carcass and meat traits evaluated. Dietary energy density and slaughter group affected (P carcasses. Estimates of heritability were intermediate to high for measures of fatness but were generally low for palatability attributes. The high negative genetic correlation (-.56) between percentage of retail product and marbling score and the relatively low genetic correlations between percentage of retail product and palatability attributes suggests the need for simultaneous attention to percentage of retail product and palatability attributes rather than to marbling score. Correlations among breed group means were generally high for measures of fatness with palatability attributes and were high and negative for percentage of retail product with marbling score and with other measures of fatness. Limited opportunity exists for selecting among breeds to achieve high levels of marbling in the longissimus muscle simultaneously with a high percentage of retail product. These results suggest that the most logical approach to resolution of the genetic antagonism between favorable carcass composition and less favorable palatability attributes is to form composite breeds with breed contributions organized to achieve an optimum balance between favorable carcass composition and desirable

  18. Breed effects, retained heterosis, and estimates of genetic and phenotypic parameters for carcass and meat traits of beef cattle.

    Science.gov (United States)

    Gregory, K E; Cundiff, L V; Koch, R M; Dikeman, M E; Koohmaraie, M

    1994-05-01

    Retained heterosis for meat traits was estimated in F3 generation castrate males in three composite populations of beef cattle finished on two levels of dietary energy density (2.82 Mcal of ME and 3.07 Mcal of ME and 11.50% CP) and serially slaughtered at four end points at intervals of 20 to 22 d. Breed effects were evaluated in nine parental breeds (Red Poll [R], Hereford [H], Angus [A], Limousin [L], Braunvieh [B], Pinzgauer [P], Gelbvieh [G], Simmental [S], and Charolais [C]) that contributed to the three composite populations (MARC I = 1/4 B, 1/4 C, 1/4 L, 1/8 H, 1/8 A; MARC II = 1/4 G, 1/4 S, 1/4 H, 1/4 A; and MARC III = 1/4 R, 1/4 P, 1/4 H, and 1/4 A). Breed effects were important (P < .01) for all carcass and meat traits evaluated. Dietary energy density and slaughter group affected (P < .05) most traits evaluated. The effects of retained heterosis were not consistent among composites. For the mean of the three composites, retained heterosis was significant only for percentage of 9-10-11th rib fat and for percentage of retail product. Phenotypic correlations indicated that marbling score was a poor predictor of palatability attributes of individual carcasses. Estimates of heritability were intermediate to high for measures of fatness but were generally low for palatability attributes. The high negative genetic correlation (-.56) between percentage of retail product and marbling score and the relatively low genetic correlations between percentage of retail product and palatability attributes suggests the need for simultaneous attention to percentage of retail product and palatability attributes rather than to marbling score. Correlations among breed group means were generally high for measures of fatness with palatability attributes and were high and negative for percentage of retail product with marbling score and with other measures of fatness. Limited opportunity exists for selecting among breeds to achieve high levels of marbling in the longissimus

  19. Genetic evaluation for body condition score in Italian Brown Swiss cattle

    Directory of Open Access Journals (Sweden)

    C. Nicoletti

    2010-04-01

    Full Text Available Body Condition Score (BCS evaluates the body energy reserve in a cow using a numeric classification. It is possible to use the BCS as an indirect indicator of fertility. The genetic evaluation for BCS in Italian Brown Swiss is performed on 73125 BCS evaluations on the same number of primiparous, daughters of 507 sires. Effect of herd by year goes from -1,02 to +0,94 indicating large differences among herds. The primiparous cows show about 3.2 BCS points at calving, their BCS decreases slightly during first 90 milking days but, after this period, the BCS increases until 3.5 BCS points at the end of first lactation. Sires with larger EBVs guarantee a slower decrease of BCS during the first part of lactation, which is preferred to the strong decrease exhibited by the daughter of low EBV sires. The pseudo-genetic correlations, correlations values estimated among EBV, confirmed the relationships between BCS and other important traits like milk yield (-0.20, final score, dairyness and udder. The correlations between BCS and functional traits, milking speed and functional longevity, is -0.14 and +0.17 respectively.

  20. Estimated genetic parameters for palatability traits of steaks from Brahman cattle.

    Science.gov (United States)

    Riley, D G; Chase, C C; Hammond, A C; West, R L; Johnson, D D; Olson, T A; Coleman, S W

    2003-01-01

    Heritabilities and genetic and phenotypic correlations were estimated from carcass and beef palatability data collected from Brahman calves (n = 504) born in central Florida from 1996 to 2000. Traits evaluated included Warner-Bratzler shear force (after 7, 14, and 21 d of aging), panel tenderness score, connective tissue amount, juiciness, flavor intensity, and off flavor (after 14 d of aging), percentages of raw and cooked lipids, and milligrams per gram of muscle calpastatin activity. Parameters were estimated using an animal model and derivative-free restricted maximum likelihood procedures. Estimated heritabilities for d 7, 14, and 21 shear force were 0.14,0.14, and 0.06, respectively, indicating that improvement in these traits by selection would be slow. Estimated heritabilities of sensory panel attributes were 0.11, 0.12, 0.05, 0.04, and 0.01 for tenderness, connective tissue amount, juiciness, flavor intensity, and off flavor, respectively. The estimated heritabilities for percentages of raw and cooked lipids, and calpastatin activity were 0.34, 0.17, and 0.07, respectively. Most of the estimated genetic correlations among palatability traits and for palatability traits with fat thickness, marbling score, and loin muscle area were consistent with other estimates from the literature. Results indicated that improvement in tenderness based on selection for favorable shear force, sensory panel tenderness, or calpastatin activity would be slow; therefore, postslaughter intervention programs should also be considered.

  1. Estimated genetic parameters for palatability traits of steaks from Brahman cattle.

    Science.gov (United States)

    Riley, D G; Chase, C C; Hammond, A C; West, R L; Johnson, D D; Olson, T A; Coleman, S W

    2003-01-01

    Heritabilities and genetic and phenotypic correlations were estimated from carcass and beef palatability data collected from Brahman calves (n = 504) born in central Florida from 1996 to 2000. Traits evaluated included Warner-Bratzler shear force (after 7, 14, and 21 d of aging), panel tenderness score, connective tissue amount, juiciness, flavor intensity, and off flavor (after 14 d of aging), percentages of raw and cooked lipids, and milligrams per gram of muscle calpastatin activity. Parameters were estimated using an animal model and derivative-free restricted maximum likelihood procedures. Estimated heritabilities for d 7, 14, and 21 shear force were 0.14,0.14, and 0.06, respectively, indicating that improvement in these traits by selection would be slow. Estimated heritabilities of sensory panel attributes were 0.11, 0.12, 0.05, 0.04, and 0.01 for tenderness, connective tissue amount, juiciness, flavor intensity, and off flavor, respectively. The estimated heritabilities for percentages of raw and cooked lipids, and calpastatin activity were 0.34, 0.17, and 0.07, respectively. Most of the estimated genetic correlations among palatability traits and for palatability traits with fat thickness, marbling score, and loin muscle area were consistent with other estimates from the literature. Results indicated that improvement in tenderness based on selection for favorable shear force, sensory panel tenderness, or calpastatin activity would be slow; therefore, postslaughter intervention programs should also be considered. PMID:12597372

  2. Estimation of genetic effects in the presence of multicollinearity in multibreed beef cattle evaluation.

    Science.gov (United States)

    Roso, V M; Schenkel, F S; Miller, S P; Schaeffer, L R

    2005-08-01

    Breed additive, dominance, and epistatic loss effects are of concern in the genetic evaluation of a multibreed population. Multiple regression equations used for fitting these effects may show a high degree of multicollinearity among predictor variables. Typically, when strong linear relationships exist, the regression coefficients have large SE and are sensitive to changes in the data file and to the addition or deletion of variables in the model. Generalized ridge regression methods were applied to obtain stable estimates of direct and maternal breed additive, dominance, and epistatic loss effects in the presence of multicollinearity among predictor variables. Preweaning weight gains of beef calves in Ontario, Canada, from 1986 to 1999 were analyzed. The genetic model included fixed direct and maternal breed additive, dominance, and epistatic loss effects, fixed environmental effects of age of the calf, contemporary group, and age of the dam x sex of the calf, random additive direct and maternal genetic effects, and random maternal permanent environment effect. The degree and the nature of the multicollinearity were identified and ridge regression methods were used as an alternative to ordinary least squares (LS). Ridge parameters were obtained using two different objective methods: 1) generalized ridge estimator of Hoerl and Kennard (R1); and 2) bootstrap in combination with cross-validation (R2). Both ridge regression methods outperformed the LS estimator with respect to mean squared error of predictions (MSEP) and variance inflation factors (VIF) computed over 100 bootstrap samples. The MSEP of R1 and R2 were similar, and they were 3% less than the MSEP of LS. The average VIF of LS, R1, and R2 were equal to 26.81, 6.10, and 4.18, respectively. Ridge regression methods were particularly effective in decreasing the multicollinearity involving predictor variables of breed additive effects. Because of a high degree of confounding between estimates of maternal

  3. Revisiting a classic case of introgression: hybridization and gene flow in Californian sunflowers.

    Science.gov (United States)

    Owens, Gregory L; Baute, Gregory J; Rieseberg, Loren H

    2016-06-01

    During invasion, colonizing species can hybridize with native species, potentially swamping out native genomes. However, theory predicts that introgression will often be biased into the invading species. Thus, empirical estimates of gene flow between native and invasive species are important to quantify the actual threat of hybridization with invasive species. One classic example of introgression occurs in California, where Helianthus bolanderi was thought to be a hybrid between the serpentine endemic Helianthus exilis and the congeneric invader Helianthus annuus. We used genotyping by sequencing to look for signals of introgression and population structure. We find that H. bolanderi and H. exilis form one genetic clade, with weak population structure that is associated with geographic location rather than soil composition and likely represent a single species, not two. Additionally, while our results confirmed early molecular analysis and failed to support the hybrid origin of H. bolanderi, we did find evidence for introgression mainly into the invader H. annuus, as predicted by theory. PMID:26840428

  4. Identification and annotation of genetic variants (SNP/Indel) in Danish Jutland cattle

    DEFF Research Database (Denmark)

    Das, Ashutosh; Panitz, Frank; Holm, Lars-Erik

    We sequenced the whole-genome of a Danish Jutland bull to identify genetic variants (SNP/indel). Using UnifiedGenotyper from the Genome Analysis Toolkit (GATK), we identified 6,812,198 SNPs and 804,453 indels. There were 2,598,000 (38.1%) novel SNPs and 607,923(75.6%) novel indels while the...... remaining was annotated in dbSNP build 133. In-depth annotation of the variants revealed that 45,776 SNPs affected the coding sequences of 11,538 genes, 221 SNPs predicted to cause a premature stop codon, 17 to cause a gain in coding sequence and 20,828 predicted to be non-synonymous. We identified 1...

  5. Genetic parameters for milk yield and persistency in Carora dairy cattle breed using random regression model

    Directory of Open Access Journals (Sweden)

    Emanuela Tullo

    2014-12-01

    Full Text Available In tropical environments, lactation curves with lower peaks and higher persistency (PS might be desirable from both an economical and a physiological point of view. The objective of this study was to obtain genetic parameters for test day (TD yields, and PS for the tropical breed Carora and to compare these with results from a standard 305-d-milk yield animal model. Four random regression models (RRM were used on a dataset composed of 95,606 TD records collected in Venezuela and tested to find the best fitting the data. Estimated daily heritabilities for milk yields ranged from 0.21 to 0.30, with the lowest values around the peak of lactation. Lactation repeatabilities ranged from 0.50 to 0.56. Correlations between the breeding values obtained with the RRM and the lactation model currently used in Venezuela [single trait Animal Model (stAM] are quite high and positive (Pearson correlation=0.71 and Spearman correlation=0.72. Correlations between PS and 305-d-milk yield estimated breeding values (EBV ranged from -0.18 (PS as the deviation of daily productions in the interval 50-279 days in milk from a point at the end of lactation to 0.52 (PS as EBV difference between the second and the first stage of lactation. The use of PS indexes accounting for milk yield may allow the selection of individuals able to express their potential genetic values in tropical environment, without incurring in excessive heat stress losses.

  6. Genetic parameters and investigation of genotype × environment interactions in Nellore × Hereford crossbred for resistance to cattle ticks in different regions of Brazil.

    Science.gov (United States)

    Ayres, D R; Pereira, R J; Boligon, A A; Baldi, F; Roso, V M; Albuquerque, L G

    2015-02-01

    Data from 6,156 Nellore × Hereford crossbred cattle, distributed in 18 herds located in the Brazilian states of Mato Grosso do Sul (MS), São Paulo (SP), Paraná (PR) and Rio Grande do Sul (RS), were analysed in order to investigate genetic variation for resistance to the cattle tick through the estimation of variance components and genetic parameters for counting ticks (Rhipicephalus (Boophilus) microplus) in natural infestation, and also a possible genotype × environment interaction. The tick count data (CC) were transformed to log10(CC + 1) and grouped into two regions, defined by cluster analysis and analysed using the method of restricted maximum likelihood. The statistical model included the additive genetic effect as random and fixed effects of the contemporary group (CG) and genetic group (GG) as classificatory and the age of the animal at the time of counting (linear effect) and individual heterozygosity (linear effect, ranging from 0 to 1) as covariates. In the studied regions, the effect of heterosis found was inversely proportional; in other words, the count of ticks decreased with the increase of heterozygosity. The observed heritability estimation for resistance to tick infestation were 0.12 ± 0.04 and 0.11 ± 0.04 for groups A (RS and south PR) and B (MS, SP and north PR), respectively. The results of this study suggest that selection for animals resistant to ticks would be possible using the tick count to estimate the genetic value of animals, but with a slow genetic progress. The genetic correlation for tick count between the two groups (A and B) was 0.84 ± 0.27 and genotype × environment interaction for this trait was not observed in the studied population. PMID:25108748

  7. Genetic parameters for calving rate and calf survival from linear, threshold, and logistic models in a multibreed beef cattle population.

    Science.gov (United States)

    Guerra, J L L; Franke, D E; Blouin, D C

    2006-12-01

    Generalized mixed linear, threshold, and logistic sire models and Markov chain, Monte Carlo simulation procedures were used to estimate genetic parameters for calving rate and calf survival in a multibreed beef cattle population. Data were obtained from a 5-generation rotational crossbreeding study involving Angus, Brahman, Charolais, and Hereford (1969 to 1995). Gelbvieh and Simmental bulls sired terminal-cross calves from a sample of generation 5 cows. A total of 1,458 cows sired by 158 bulls had a mean calving rate of 78% based on 4,808 calving records. Ninety-one percent of 5,015 calves sired by 260 bulls survived to weaning. Mean heritability estimates and standard deviations for daughter calving rate from posterior distributions were 0.063 +/- 0.024, 0.150 +/- 0.049, and 0.130 +/- 0.047 for linear, threshold, and logistic models, respectively. For calf survival, mean heritability estimates and standard deviations from posterior distributions were 0.049 +/- 0.022, 0.160 +/- 0.058, and 0.190 +/- 0.078 from linear, threshold, and logistic models, respectively. When transformed to an underlying normal scale, linear sire, mixed model, heritability estimates were similar to threshold and logistic sire mixed model estimates. Posterior density distributions of estimated heritabilities from all models were normal. Spearman rank correlations between sire EPD across statistical models were greater than 0.97 for daughter calving rate and for calf survival. Sire EPD had similar ranges across statistical models for daughter calving rate and for calf survival. PMID:17093211

  8. Genetic variability in three Italian beef cattle breeds derived from pedigree information

    Directory of Open Access Journals (Sweden)

    Francesco Filippini

    2010-01-01

    Full Text Available The aim of the present work was to estimate genetic variability in Chianina (CH, Marchigiana (MC and Romagnola (RO breeds using pedigree information. Different approaches based on probability of identity-by-descent (effective population size through an increase in inbreeding Ne or probability of gene origin (total number of founders f, effective number of founders fe, ancestors fa and founder genomes fg were used. Reference populations were defined using female animals born between 1996 and 2000 where both parents are known. Generation intervals were 5.35, 4.93 and 5.15 years for CH, MC and RO, respectively. The total number of founders were 7092, 11947, 3928, for CH, MC and RO, respectively. Complete generation equivalent showed the relative high quality of pedigree information: 5.66 for CH, 4.54 for MC and 4.95 for RO. For CH, MC and RO, respectively, a fe value of 152.1, 70.9 and 89.8, a fa value of 73.6, 48.0 and 59.5 and a fg value of 39.5, 25.0 and 38.5, were calculated. When inbreeding was used effective population sizes were 138, 122 and 124 for CH, MC and RO, respectively. Parameters derived from the probabilities of gene origin were variable among the investigated breeds and the results for MC demonstrate the need to pay specific attention to breeding strategies.

  9. Phenotypic and Genetic Correlations of Feed Efficiency Traits with Growth and Carcass Traits in Nellore Cattle Selected for Postweaning Weight.

    Science.gov (United States)

    Ceacero, Thais Matos; Mercadante, Maria Eugênia Zerlotti; Cyrillo, Joslaine Noely Dos Santos Gonçalves; Canesin, Roberta Carrilho; Bonilha, Sarah Figueiredo Martins; de Albuquerque, Lucia Galvão

    2016-01-01

    This study evaluated phenotypic (rph) and genetic correlations (rg) between 8 feed efficiency traits and other traits of economic interest including weight at selection (WS), loin-eye area (LEA), backfat thickness (BF), and rump fat thickness (RF) in Nellore cattle. Feed efficiency traits were gain:feed, residual feed intake (RFI), residual feed intake adjusted for backfat thickness (RFIb) and for backfat and rump fat thickness (RFIsf), residual body weight gain (RG), residual intake and body weight gain (RIG), and residual intake and body weight gain using RFIb (RIGb) and RFIsf (RIGsf). The variance components were estimated by the restricted maximum likelihood method using a two-trait animal model. The heritability estimates (h2) were 0.14, 0.24, 0.20, 0.22, 0.19, 0.15, 0.11 and 0.11 for gain:feed, RFI, RFIb, RFIsf, RG, RIG, RIGb and RIGsf, respectively. All rph values between traits were close to zero, except for the correlation of feed efficiency traits with dry matter intake and average daily gain. High rg values were observed for the correlation of dry matter intake, average daily gain and metabolic weight with WS and hip height (>0.61) and low to medium values (0.15 to 0.48) with the carcass traits (LEA, BF, RF). Among the feed efficiency traits, RG showed the highest rg with WS and hip height (0.34 and 0.25) and the lowest rg with subcutaneous fat thickness (-0.17 to 0.18). The rg values of RFI, RFIb and RFIsf with WS (0.17, 0.23 and 0.22), BF (0.37, 0.33 and 0.33) and RF (0.30, 0.31 and 0.32) were unfavorable. The rg values of gain:feed, RIG, RIGb and RIGsf with WS were low and favorable (0.07 to 0.22), while medium and unfavorable (-0.22 to -0.45) correlations were observed with fat thickness. The inclusion of subcutaneous fat thickness in the models used to calculate RFI did not reduce the rg between these traits. Selecting animals for higher feed efficiency will result in little or no genetic change in growth and will decrease subcutaneous fat thickness

  10. Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system

    OpenAIRE

    Hoffmann Astrid; Maurer Andreas; Pillen Klaus

    2012-01-01

    Abstract Background In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs) under two contrasting hydroponic nitrogen (N) supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent ‘Scarlett’. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims we...

  11. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

    Directory of Open Access Journals (Sweden)

    Keyan Zhao

    Full Text Available BACKGROUND: The domestication of Asian rice (Oryza sativa was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. CONCLUSIONS/SIGNIFICANCE: Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

  12. Selection for genetic markers in beef cattle reveals complex associations of thyroglobulin and casein1-s1 with carcass and meat traits.

    Science.gov (United States)

    Bennett, G L; Shackelford, S D; Wheeler, T L; King, D A; Casas, E; Smith, T P L

    2013-02-01

    Genetic markers in casein (CSN1S1) and thyroglobulin (TG) genes have previously been associated with fat distribution in cattle. Determining the nature of these genetic associations (additive, recessive, or dominant) has been difficult, because both markers have small minor allele frequencies in most beef cattle populations. This results in few animals homozygous for the minor alleles. selection to increase the frequencies of the minor alleles for 2 SNP markers in these genes was undertaken in a composite population. The objective was to obtain better estimates of genetic effects associated with these markers and determine if there were epistatic interactions. Selection increased the frequencies of minor alleles for both SNP from meat tenderness predicted at the abattoir by visible and near-infrared reflectance spectroscopy (P 0.10). Additive, dominance, and epistatic SNP association effects were estimated from genotypic effects for adjusted fat thickness and predicted meat tenderness. Adjusted fat thickness showed a dominance association with TG SNP (P meat tenderness, heterozygous TG meat was more tender than meat from either homozygote (P < 0.002). Dominance and epistatic associations can result in different SNP allele substitution effects in populations where SNP have the same linkage disequilibrium with causal mutations but have different frequencies. Although the complex associations estimated in this study would contribute little to within-population selection response, they could be important for marker-assisted management or reciprocal selection schemes.

  13. Exploring genetic polymorphism in innate immune genes in Indian cattle (Bos indicus) and buffalo (Bubalus bubalis) using next generation sequencing technology.

    Science.gov (United States)

    Patel, Shreya M; Koringa, Prakash G; Nathani, Neelam M; Patel, Namrata V; Shah, Tejash M; Joshi, Chaitanya G

    2015-02-01

    Activation of innate immunity initiates various cascades of reactions that largely contribute to defense against physical, microbial or chemical damage, prompt for damage repair and removal of causative organisms as well as restoration of tissue homeostasis. Genetic polymorphism in innate immune genes plays prominent role in disease resistance capabilities in various breeds of cattle and buffalo. Here we studied single nucleotide variations (SNP/SNV) and haplotype structure in innate immune genes viz CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1, BNBD4, BNBD5, TAP and LAP in Gir cattle and Murrah buffalo. Targeted sequencing of exonic regions of these genes was performed by Ion Torrent PGM sequencing platform. The sequence reads obtained corresponding to coding regions of these genes were mapped to reference genome of cattle BosTau7 by BWA program using genome analysis tool kit (GATK). Further variant analysis by Unified Genotyper revealed 54 and 224 SNPs in Gir and Murrah respectively and also 32 SNVs was identified. Among these SNPs 43, 36, 11,32,81,21 and 22 variations were in CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1 and TAP genes respectively. Among these identified 278 SNPs, 24 were found to be reported in the dbSNP database. Variant analysis was followed by structure formation of haplotypes based on multiple SNPs using SAS software revealed a large number of haplotypes. The SNP discovery in innate immune genes in cattle and buffalo breeds of India would advance our understanding of role of these genes in determining the disease resistance/susceptibility in Indian breeds. The identified SNPs and haplotype data would also provide a wealth of sequence information for conservation studies, selective breeding and designing future strategies for identifying disease associations involving samples from distinct populations.

  14. Exploring genetic polymorphism in innate immune genes in Indian cattle (Bos indicus and buffalo (Bubalus bubalis using next generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Shreya M. Patel

    2015-02-01

    Full Text Available Activation of innate immunity initiates various cascades of reactions that largely contribute to defense against physical, microbial or chemical damage, prompt for damage repair and removal of causative organisms as well as restoration of tissue homeostasis. Genetic polymorphism in innate immune genes plays prominent role in disease resistance capabilities in various breeds of cattle and buffalo. Here we studied single nucleotide variations (SNP/SNV and haplotype structure in innate immune genes viz CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1, BNBD4, BNBD5, TAP and LAP in Gir cattle and Murrah buffalo. Targeted sequencing of exonic regions of these genes was performed by Ion Torrent PGM sequencing platform. The sequence reads obtained corresponding to coding regions of these genes were mapped to reference genome of cattle BosTau7 by BWA program using genome analysis tool kit (GATK. Further variant analysis by Unified Genotyper revealed 54 and 224 SNPs in Gir and Murrah respectively and also 32 SNVs was identified. Among these SNPs 43, 36, 11,32,81,21 and 22 variations were in CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1 and TAP genes respectively. Among these identified 278 SNPs, 24 were found to be reported in the dbSNP database. Variant analysis was followed by structure formation of haplotypes based on multiple SNPs using SAS software revealed a large number of haplotypes. The SNP discovery in innate immune genes in cattle and buffalo breeds of India would advance our understanding of role of these genes in determining the disease resistance/susceptibility in Indian breeds. The identified SNPs and haplotype data would also provide a wealth of sequence information for conservation studies, selective breeding and designing future strategies for identifying disease associations involving samples from distinct populations.

  15. Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica

    Directory of Open Access Journals (Sweden)

    Lulu Xie

    2016-08-01

    Full Text Available Introgression breeding is a widely used method for the genetic improvement of crop plants; however, the mechanism underlying candidate gene flow patterns during hybridization is poorly understood. In this study, we used a powerful pipeline to investigate a Chinese cabbage (Brassica rapa L. ssp. pekinensis introgression line with the anthocyanin overaccumulation phenotype. Our purpose was to analyze the gene flow patterns during hybridization and elucidate the genetic factors responsible for the accumulation of this important pigment compound. We performed RNA-seq analysis by using two pipelines, one with and one without a reference sequence, to obtain transcriptome data. We identified 930 significantly differentially expressed genes (DEGs between the purple-leaf introgression line and B. rapa green cultivar, namely, 389 up-regulated and 541 down-regulated DEGs that mapped to the B. rapa reference genome. Since only one anthocyanin pathway regulatory gene was identified, i.e., Bra037887 (bHLH, we mined unmapped reads, revealing 2,031 de novo assembled unigenes, including c3563g1i2. Phylogenetic analysis suggested that c3563g1i2, which was transferred from the Brassica B genome of the donor parental line Brassica juncea, may represent an R2R3-MYB transcription factor that participates in the ternary transcriptional activation complex responsible for the anthocyanin overaccumulation phenotype of the B. rapa introgression line. We also identified genes involved in cold and light reaction pathways that were highly upregulated in the introgression line, as confirmed using quantitative real-time PCR analysis. The results of this study shed light on the mechanisms underlying the purple leaf trait in Brassica plants and may facilitate the use of introgressive hybridization for many traits of interest.

  16. Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica.

    Science.gov (United States)

    Xie, Lulu; Li, Fei; Zhang, Shifan; Zhang, Hui; Qian, Wei; Li, Peirong; Zhang, Shujiang; Sun, Rifei

    2016-01-01

    Introgression breeding is a widely used method for the genetic improvement of crop plants; however, the mechanism underlying candidate gene flow patterns during hybridization is poorly understood. In this study, we used a powerful pipeline to investigate a Chinese cabbage (Brassica rapa L. ssp. pekinensis) introgression line with the anthocyanin overaccumulation phenotype. Our purpose was to analyze the gene flow patterns during hybridization and elucidate the genetic factors responsible for the accumulation of this important pigment compound. We performed RNA-seq analysis by using two pipelines, one with and one without a reference sequence, to obtain transcriptome data. We identified 930 significantly differentially expressed genes (DEGs) between the purple-leaf introgression line and B. rapa green cultivar, namely, 389 up-regulated and 541 down-regulated DEGs that mapped to the B. rapa reference genome. Since only one anthocyanin pathway regulatory gene was identified, i.e., Bra037887 (bHLH), we mined unmapped reads, revealing 2031 de novo assembled unigenes, including c3563g1i2. Phylogenetic analysis suggested that c3563g1i2, which was transferred from the Brassica B genome of the donor parental line Brassica juncea, may represent an R2R3-MYB transcription factor that participates in the ternary transcriptional activation complex responsible for the anthocyanin overaccumulation phenotype of the B. rapa introgression line. We also identified genes involved in cold and light reaction pathways that were highly upregulated in the introgression line, as confirmed using quantitative real-time PCR analysis. The results of this study shed light on the mechanisms underlying the purple leaf trait in Brassica plants and may facilitate the use of introgressive hybridization for many traits of interest. PMID:27597857

  17. Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones.

    Science.gov (United States)

    Harrison, Richard G; Larson, Erica L

    2016-06-01

    Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genomewide scale, and recent genome scans have focused on the presence of 'islands' of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the 'same' species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations.

  18. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing.

    Science.gov (United States)

    Ai, Huashui; Fang, Xiaodong; Yang, Bin; Huang, Zhiyong; Chen, Hao; Mao, Likai; Zhang, Feng; Zhang, Lu; Cui, Leilei; He, Weiming; Yang, Jie; Yao, Xiaoming; Zhou, Lisheng; Han, Lijuan; Li, Jing; Sun, Silong; Xie, Xianhua; Lai, Boxian; Su, Ying; Lu, Yao; Yang, Hui; Huang, Tao; Deng, Wenjiang; Nielsen, Rasmus; Ren, Jun; Huang, Lusheng

    2015-03-01

    Domestic pigs have evolved genetic adaptations to their local environmental conditions, such as cold and hot climates. We sequenced the genomes of 69 pigs from 15 geographically divergent locations in China and detected 41 million variants, of which 21 million were absent from the dbSNP database. In a genome-wide scan, we identified a set of loci that likely have a role in regional adaptations to high- and low-latitude environments within China. Intriguingly, we found an exceptionally large (14-Mb) region with a low recombination rate on the X chromosome that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively. Surprisingly, the adaptive sweep in the high-latitude regions has acted on DNA that might have been introgressed from an extinct Sus species. Our findings provide new insights into the evolutionary history of pigs and the role of introgression in adaptation.

  19. Estimation of Genetic Parameters for First Lactation Monthly Test-day Milk Yields using Random Regression Test Day Model in Karan Fries Cattle

    Science.gov (United States)

    Singh, Ajay; Singh, Avtar; Singh, Manvendra; Prakash, Ved; Ambhore, G. S.; Sahoo, S. K.; Dash, Soumya

    2016-01-01

    A single trait linear mixed random regression test-day model was applied for the first time for analyzing the first lactation monthly test-day milk yield records in Karan Fries cattle. The test-day milk yield data was modeled using a random regression model (RRM) considering different order of Legendre polynomial for the additive genetic effect (4th order) and the permanent environmental effect (5th order). Data pertaining to 1,583 lactation records spread over a period of 30 years were recorded and analyzed in the study. The variance component, heritability and genetic correlations among test-day milk yields were estimated using RRM. RRM heritability estimates of test-day milk yield varied from 0.11 to 0.22 in different test-day records. The estimates of genetic correlations between different test-day milk yields ranged 0.01 (test-day 1 [TD-1] and TD-11) to 0.99 (TD-4 and TD-5). The magnitudes of genetic correlations between test-day milk yields decreased as the interval between test-days increased and adjacent test-day had higher correlations. Additive genetic and permanent environment variances were higher for test-day milk yields at both ends of lactation. The residual variance was observed to be lower than the permanent environment variance for all the test-day milk yields. PMID:26954137

  20. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

    NARCIS (Netherlands)

    Utsunomiya, Yuri T.; Bomba, Lorenzo; Lucente, Giordana; Colli, Licia; Negrini, Riccardo; Lenstra, Johannes A.; Erhardt, Georg; Garcia, José F.; Ajmone-Marsan, Paolo; Moazami-Goudarzi, K.; Williams, J.; Wiener, P.; Olsaker, I.; Kantanen, J.; Dunner, S.; Cañón, J.; Rodellar, C.; Martín-Burriel, I.; Valentini, A.; Zanotti, M.; Holm, L. E.; Eythorsdottir, E.; Mommens, G.; Polygen, Van Haeringen; Nijman, I. J.; Dolf, G.; Bradley, D. G.

    2014-01-01

    Background: Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in

  1. Identification and genetic effect of a variable duplication in the promoter region of the cattle ADIPOQ gene

    Science.gov (United States)

    The ADIPOQ gene of cattle, is located in the vicinity of the quantitative trait locus (QTL) wich effects marbling, the rib eye muscle area and fat thickness on BTA1. In our study, a novel variable duplication (NW_003103812.1:g.9232067_9232133 dup) in the bovine ADIPOQ promoter region was identified ...

  2. Genetic variance and covariance components for feed intake, average daily gain, and postweaning gain in growing beef cattle

    Science.gov (United States)

    Feed is the single most expensive cost related to a beef cattle production enterprise. Data collection to determine feed efficient animals is also costly. Currently a 70 d performance test is recommended for accurate calculation of efficiency. Previous research has suggested intake tests can be l...

  3. Characterization of bovine MHC class II DRB3 diversity in South American Holstein cattle populations.

    Science.gov (United States)

    Takeshima, S-N; Giovambattista, G; Okimoto, N; Matsumoto, Y; Rogberg-Muñoz, A; Acosta, T J; Onuma, M; Aida, Y

    2015-12-01

    Holstein cattle dominate the global milk production industry because of their outstanding milk production, however, this breed is susceptible to tropical endemic pathogens and suffers from heat stress and thus fewer Holstein populations are raised in tropical areas. The bovine major histocompatibility complex (BoLA)-DRB3 class II gene is used as a marker for disease and immunological traits, and its polymorphism has been studied extensively in Holstein cattle from temperate and cold regions. We studied the genetic diversity of the BoLA-DRB3 gene in South American Holstein populations to determine whether tropical populations have diverged from those bred in temperate and cold regions by selection and/or crossbreeding with local native breeds. We specifically studied Exon 2 of this gene from 855 South American Holstein individuals by a polymerase chain reaction (PCR) sequence-based typing method. We found a high degree of gene diversity at the allelic (Na > 20 and He > 0.87) and molecular (π > 0.080) levels, but a low degree of population structure (FST = 0.009215). A principal components analysis and tree showed that the Bolivian subtropical population had the largest genetic divergence compared with Holsteins bred in temperate or cold regions, and that this population was closely related to Bolivian Creole cattle. Our results suggest that Holstein genetic divergence can be explained by selection and/or gene introgression from local germplasms. This is the first examination of BoLA-DRB3 in Holsteins adapted to tropical environments, and contributes to an ongoing effort to catalog bovine MHC allele frequencies by breed and location.

  4. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle.

    Directory of Open Access Journals (Sweden)

    Jared E Decker

    2014-03-01

    Full Text Available The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

  5. Broken barriers: human-induced changes to gene flow and introgression in animals: an examination of the ways in which humans increase genetic exchange among populations and species and the consequences for biodiversity.

    Science.gov (United States)

    Crispo, Erika; Moore, Jean-Sébastien; Lee-Yaw, Julie A; Gray, Suzanne M; Haller, Benjamin C

    2011-07-01

    We identify two processes by which humans increase genetic exchange among groups of individuals: by affecting the distribution of groups and dispersal patterns across a landscape, and by affecting interbreeding among sympatric or parapatric groups. Each of these processes might then have two different effects on biodiversity: changes in the number of taxa through merging or splitting of groups, and the extinction/extirpation of taxa through effects on fitness. We review the various ways in which humans are affecting genetic exchange, and highlight the difficulties in predicting the impacts on biodiversity. Gene flow and hybridization are crucially important evolutionary forces influencing biodiversity. Humans alter natural patterns of genetic exchange in myriad ways, and these anthropogenic effects are likely to influence the genetic integrity of populations and species. We argue that taking a gene-centric view towards conservation will help resolve issues pertaining to conservation and management. Editor's suggested further reading in BioEssays A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture Abstract.

  6. Interspecific hybridization and mitochondrial introgression in invasive carcinus shore crabs.

    Directory of Open Access Journals (Sweden)

    John A Darling

    Full Text Available Interspecific hybridization plays an important role in facilitating adaptive evolutionary change. More specifically, recent studies have demonstrated that hybridization may dramatically influence the establishment, spread, and impact of invasive populations. In Japan, previous genetic evidence for the presence of two non-native congeners, the European green crab Carcinus maenas and the Mediterranean green crab C. aestuarii, has raised questions regarding the possibility of hybridization between these sister species. Here I present analysis based on both nuclear microsatellites and the mitochondrial cytochrome C oxidase subunit I (COI gene which unambiguously argues for a hybrid origin of Japanese Carcinus. Despite the presence of mitochondrial lineages derived from both C. maenas and C. aestuarii, the Japanese population is panmictic at nuclear loci and has achieved cytonuclear equilibrium throughout the sampled range in Japan. Furthermore, analysis of admixture at nuclear loci indicates dramatic introgression of the C. maenas mitochondrial genome into a predominantly C. aestuarii nuclear background. These patterns, along with inferences drawn from the observational record, argue for a hybridization event pre-dating the arrival of Carcinus in Japan. The clarification of both invasion history and evolutionary history afforded by genetic analysis provides information that may be critically important to future studies aimed at assessing risks posed by invasive Carcinus populations to Japan and the surrounding region.

  7. Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective.

    Science.gov (United States)

    Jiménez, Rosa Alicia; Ornelas, Juan Francisco

    2016-01-01

    The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence

  8. Genetic relationship of lactation persistency with milk yield, somatic cell score, reproductive traits, and longevity in Slovak Holstein cattle

    OpenAIRE

    Strapáková, Eva; Candrák, Juraj; Strapák, Peter

    2016-01-01

    The objective of this study was to estimate the breeding values (BVs) of lactation persistency, the test day of milk yield, the somatic cell score, reproductive traits (calving interval, days open), longevity in Slovak Holstein dairy cattle. BVs were used for the detection of relationships among the persistency of lactation and other selected traits. Data for the estimation of BVs of milk production and somatic cell score were collected from 855 240 cows. BVs for reproductive t...

  9. Estimates of genetic parameters for visual scores and their correlation with production and reproductive traits in Brahman cattle

    OpenAIRE

    Tássia Souza Bertipaglia; Luis Orlando Duitama Carreño; Carlos Henrique Cavallini Machado; Cristiana Andrighetto; Ricardo da Fonseca

    2012-01-01

    The objective of this study was to evaluate the association of visual scores of body structure, precocity and muscularity with production (body weight at 18 months and average daily gain) and reproductive (scrotal circumference) traits in Brahman cattle in order to determine the possible use of these scores as selection criteria to improve carcass quality. Covariance components were estimated by the restricted maximum likelihood method using an animal model that included contemporary group as...

  10. Genetically similar strains of Escherichia coli O157:H7 isolated from sheep, cattle and human patients

    Directory of Open Access Journals (Sweden)

    Söderlund Robert

    2012-10-01

    Full Text Available Abstract Background Comparatively little is known about the prevalence or the molecular characteristics of the zoonotic pathogen E. coli O157:H7 in the sheep reservoir. To investigate this and determine the host specificity of subclones of the bacterium, we have conducted a slaughterhouse prevalence study in sheep and compared the collected isolates to O157:H7 previously isolated from cattle and human patients. Results Verotoxin-producing O157:H7 was found in 11/597 (1.8% of samples from sheep in Swedish slaughterhouses, 9/492 faecal (1.8% and 2/105 ear samples (1.9%. All positive sheep were eaeA, hlyA, cdtV-B, vtx1, and partial sequencing of vtx2. The observed profiles were similar to those of cattle strains investigated previously. Conclusions The same pathogenic subtypes of VTEC O157:H7, including the highly virulent clade 8, appear to be present in both sheep and cattle in Sweden, suggesting strains can circulate freely between ruminant reservoirs.

  11. Epidemiology and genetic characterization of BVDV, BHV-1, BHV-4, BHV-5 and Brucella spp. infections in cattle in Turkey.

    Science.gov (United States)

    Aslan, Muhammet Eren; Azkur, Ahmet Kursat; Gazyagci, Serkal

    2015-11-01

    The aim of the study was to determine the epidemiological data of bovine viral diarrhea virus (BVDV), bovine herpesvirus-1 (BHV-1), bovine herpesvirus-4 (BHV-4), bovine herpesvirus-5 (BHV-5) and Brucella-associated cattle that were previously reported to have abortion and infertility problems in Ankara, Corum, Kirikkale and Yozgat provinces, Turkey. Whole blood and sera samples were obtained from 656 cattle, and antibodies against Brucella spp. were detected in 45 (6.86%) and 41 (6.25%) animals by Rose Bengal plate and serum tube agglutination tests, respectively. The seropositivity rates against BVDV, BHV-1 and BHV-4 were 70.89%, 41.3% and 28.78%, respectively. RT-PCR and PCR were performed to detect RNA and DNA viruses in blood samples, respectively. The BVDV 5'-untranslated region and BHV-1 gB gene detected in this study were phylogenetically analyzed. The BVDV strains analyzed in this study were closely related to those previously reported from Turkey. The nucleotide sequence from the BHV-1 strain detected in this study is the first nucleotide sequence of BHV-1 circulating in this area of Turkey deposited in the GenBank. The presence of Brucella spp. and prevalence of BHV-1, BHV-4 and BVDV in cattle should be further investigated throughout these regions.

  12. Effect of Genetic Variations within the I-mfa Gene on the Growth Traits of Chinese Cattle.

    Science.gov (United States)

    Huang, Yong-Zhen; Li, Jing-Jing; Zhang, Chun-Lei; Fang, Xing-Tang; Lan, Xian-Yong; Qi, Xing-Lei; Chen, Hong

    2016-10-01

    I-mfa (inhibitor of the MyoD family a) is a transcription modulator that binds to MyoD family members and inhibits their transcriptional activities. It is highly expressed in the sclerotome and plays an important role in the patterning of the somite early in development. In this study, the polymorphisms of the bovine I-mfa gene were detected by polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) and DNA pool sequencing methods in 541 individuals from three Chinese cattle breeds. The results showed that P3 locus had two novel complete linked single nucleotide polymorphisms (NC_007324.4:g.12284A>G and g.12331T>C), resulting in a missense mutation p.S(AGC)113G(GGC) and a synonymous mutation p.H(CAT)128H(CAC), respectively. P4 locus had a novel SNP (NC_007324.4: g.16432C>A), which resulted in a nonsense mutation p.C(TGC)241X(TGA). The statistical analyses indicated that the three SNPs, are associated with the phenotypic traits in Luxi (LX), Qinchuan (QC), and Jiaxian (JX) cattle population (P superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. Our results provide evidence that polymorphisms in the I-mfa gene are associated with growth traits and may be used for marker-assisted selection in beef cattle breeding program.

  13. Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melanophilin gene accountable for a distinctive coat color in Belgian Blue cattle.

    Science.gov (United States)

    Li, Wanbo; Sartelet, Arnaud; Tamma, Nico; Coppieters, Wouter; Georges, Michel; Charlier, Carole

    2016-02-01

    In the course of a reverse genetic screen in the Belgian Blue cattle breed, we uncovered a 10-bp deletion (c.87_96del) in the first coding exon of the melanophilin gene (MLPH), which introduces a premature stop codon (p.Glu32Aspfs*1) in the same exon, truncating 94% of the protein. Recessive damaging mutations in the MLPH gene are well known to cause skin, hair, coat or plumage color dilution phenotypes in numerous species, including human, mice, dog, cat, mink, rabbit, chicken and quail. Large-scale array genotyping undertaken to identify p.Glu32Aspfs*1 homozygous mutant animals revealed a mutation frequency of 5% in the breed and allowed for the identification of 10 homozygous mutants. As expression of a colored coat requires at least one wild-type allele at the co-dominant Roan locus encoded by the KIT ligand gene (KITLG), homozygous mutants for p.Ala227Asp corresponding with the missense mutation were excluded. The six remaining colored calves displayed a distinctive dilution phenotype as anticipated. This new coat color was named 'cool gray'. It is the first damaging mutation in the MLPH gene described in cattle and extends the already long list of species with diluted color due to recessive mutations in MLPH and broadens the color palette of gray in this breed. PMID:26582259

  14. The Genetic Variability of Prolactin and Signal Transducers and Activators of Transcription 5A (STAT5A Genes in Bali Cattle

    Directory of Open Access Journals (Sweden)

    K. A. Paramitasari

    2015-04-01

    Full Text Available The aim of this study was to identify the genetic variability of PRL and STAT5A genes in Bali cattle from Bali, West Nusa Tenggara (NTB, and South Sulawesi (SS using PCR-RFLP method. A total of 262 Bali cattle were identified using RsaI (PRL and AvaI (STAT5A restriction enzymes. PRL gene exon 3, PRL gene exon 4, and STAT5A gene exon 7 amplifications resulted fragments with the lengths of 156 bp, 294 bp, 215 bp, respectively. Genotyping of PRL gene both at exon 3 and 4 produced three genotypes in Bali population and two genotypes in NTB and SS population. For the PRL gene, frequencies of A allele (exon 3 and G allele (exon 4 were dominant to the B allele (exon 3 and A allele (exon 4 across all populations. The results showed that STAT5A|AvaI loci had monomorphic C allele. Heterozygosity values were found low at both exons 3 and 4 of PRL gene in all population. Sequence analysis results of PRL gene both for exons 3 and 4 showed that there was a mutation between adenine (A and guanine (G bases in the RsaI recognized site, whereas in STAT5A gene we can confirm the existence of AvaI restriction site (C|CCGAG.

  15. Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melanophilin gene accountable for a distinctive coat color in Belgian Blue cattle.

    Science.gov (United States)

    Li, Wanbo; Sartelet, Arnaud; Tamma, Nico; Coppieters, Wouter; Georges, Michel; Charlier, Carole

    2016-02-01

    In the course of a reverse genetic screen in the Belgian Blue cattle breed, we uncovered a 10-bp deletion (c.87_96del) in the first coding exon of the melanophilin gene (MLPH), which introduces a premature stop codon (p.Glu32Aspfs*1) in the same exon, truncating 94% of the protein. Recessive damaging mutations in the MLPH gene are well known to cause skin, hair, coat or plumage color dilution phenotypes in numerous species, including human, mice, dog, cat, mink, rabbit, chicken and quail. Large-scale array genotyping undertaken to identify p.Glu32Aspfs*1 homozygous mutant animals revealed a mutation frequency of 5% in the breed and allowed for the identification of 10 homozygous mutants. As expression of a colored coat requires at least one wild-type allele at the co-dominant Roan locus encoded by the KIT ligand gene (KITLG), homozygous mutants for p.Ala227Asp corresponding with the missense mutation were excluded. The six remaining colored calves displayed a distinctive dilution phenotype as anticipated. This new coat color was named 'cool gray'. It is the first damaging mutation in the MLPH gene described in cattle and extends the already long list of species with diluted color due to recessive mutations in MLPH and broadens the color palette of gray in this breed.

  16. High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines.

    Directory of Open Access Journals (Sweden)

    Nora Honsdorf

    Full Text Available Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform "The Plant Accelerator", Adelaide, Australia, was used to screen a set of 47 juvenile (six week old wild barley introgression lines (S42ILs for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r=0.98 between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars.

  17. High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines

    KAUST Repository

    Honsdorf, Nora

    2014-05-13

    Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform "The Plant Accelerator", Adelaide, Australia, was used to screen a set of 47 juvenile (six week old) wild barley introgression lines (S42ILs) for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r = 0.98) between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL) were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars. © 2014 Honsdorf et al.

  18. The Effect of Genetic Variation of the Retinoic Acid Receptor-Related Orphan Receptor C Gene on Fatness in Cattle

    OpenAIRE

    Barendse, W.; Bunch, R. J.; Kijas, J. W.; M. B. Thomas

    2007-01-01

    Genotypes at the retinoic acid receptor-related orphan receptor C (RORC) gene were associated with fatness in 1750 cattle. Ten SNPs were genotyped in RORC and the adjacent gene leucine-rich repeat neuronal 6D (LRRN6D) to map the QTL, 7 of which are in a 4.2-kb sequence around the ligand-binding domain of the RORC gene. Of the 29 inferred haplotypes for these SNPs, 2 have a combined frequency of 54.6% while the top 5 haplotypes have a combined frequency of 85.3%. The average D′ value of linkag...

  19. 牛Dmrt7基因的cDNA克隆及遗传变异%Molecular Cloning and Genetic Variant of the Dmrt 7 gene in Cattle

    Institute of Scientific and Technical Information of China (English)

    淮亚红; 许尚忠

    2009-01-01

    [目的]探讨牛Dmrt7基因的生物学功能及群体遗传变异情况,为进一步研究谊基因对牛精液品质的影响奠定基础.[方法]以牛睾丸组织为材料,根据GenBank上发表的小鼠的Dmrt7基因序列设计并合成2对引物,通过RT-PCR分别进行了扩增并运用DNA-MAN软件及在线工具对所得到的序列进行了生物信息学分析;同时,以牛肾脏、肝脏、睾丸、肺、脾脏、瘤胃、子宫、小肠、心脏、卵巢和肌肉共11个组织为材料,另外设计2对引物用于组织表达谱分析.利用PCR-SSCP技术和DNA测序对Dma7基因的多态性进行检测.[结果]获得了一个长为1 616 bp的cDNA片段(GenBank登录号为EF 534775),谊cDNA包含由1 113个碱基组成的开放读码框(ORF),该ORF蝙码370个氨基酸;发现在第四内含子上有一个C/G突变,随后在277头本地牛品种和国外牛品种中进行群体多态性检测,发现G等位基因频率分布范围从0~0.413 8;基因杂合度,有效等住基因数和多态信息含量分别为0~0.485 1、1.000 0~1.942 3和0~0.367 5.[结论]克隆了牛Dmrt7基18的cDNA序列并进行组织表达谱分析,该G等位基因在本地牛品种和外国牛品种中没有差异.%[Objective] The paper aimed to study the biological function and group genetic variation situation of cattle Dmrt7 gene, which laid a foundation for the future study on the effects of this gene to the quality of cattle sperm . [Method] Cattle testis tissues as materials, 2 pairs primers were designed and combined according to Dmrt7 gene sequence of mice published by GenBank, amplified through RT-PCR and sequence obtained from DNAMAN software and online tool were used for bioinformatics analysis; Meanwhile, 11 tissues of cattle kidney, liver, testis,lung, spleen, rumen, uterus, small intestine, heart, ovary, muscle as materials, besides, 2 pairs primers were designed for tissue expression profile analysis. Dmrfl gene polymorphism were determined by PCR

  20. Genetic (co)variances among birth weight, 200-day weight, and postweaning gain in composites and parental breeds of beef cattle.

    Science.gov (United States)

    Bennett, G L; Gregory, K E

    1996-11-01

    Genetic and environmental (co)variances for birth weight, adjusted 200-d weight, and postweaning gain were estimated in nine parental and three composite populations of beef cattle. The parental breeds were Angus (A), Braunvieh (B), Charolais (C), Gelbvieh (G), Hereford (H), Limousin (L), Pinzgauer (P), Red Poll (R), and Simmental (S). The composites were MARC I (1/4 B, 1/4 C, 1/4 L, 1/8 H, 1/8 A), MARC II (1/4 G, 1/4 S, 1/4 H, 1/4 A), and MARC III (1/4 R, 1/4 P, 1/4 H, 1/4 A). Heritabilities of additive direct genetic effects for birth weight (.50) and postweaning gain (.49) were greater than for 200-d weight (.32). Heritabilities of additive maternal effects of .09 for birth weight and .10 for 200-d weight were much smaller than direct effect heritabilities. Heritabilities were larger in composites than in parental breeds for additive direct effects of all three traits but smaller for maternal 200-d weight. Correlations were high and positive for direct genetic effects of the three weight traits and higher in composites than in the parental breeds. Correlations between direct and maternal genetic effects for both birth weight and 200-d weight were near zero. Some differences in variances among populations were correlated with differences in weight and milk yield. Heavier populations had larger variances, supporting the use of logarithmic transformation of weights to stabilize variances among genetic groups. Increased average milk yield was correlated with decreased phenotypic variance of 200-d weight. Average milk yield was also implicated in the expression of direct and maternal genetic effects for 200-d weight and their covariance. Comparison of univariate and multivariate estimates of genetic variances suggested that it is important to include birth weight in multivariate analyses of all weight traits to account for increased preweaning mortality of calves with extremely heavy or light birth weights. Based on heritability estimates, within-herd selection in

  1. A molecular cytogenetic analysis of introgression in Alstroemeria

    OpenAIRE

    Kamstra, S.A.

    1999-01-01

    This thesis describes the results of a molecular cytogenetic investigation of the process of introgression in Alstroemeria . The aim of this study was to transfer chromosomes or genes from one Alstroemeria species into another. For this, two distantly related species, A. aurea and A. inodora , were hybridized and the resulting hybrids were further backcrossed with the species A. inodora . To monitor the process of introgression accurately it was necessary to identify the individual chromosome...

  2. Introgression evidence and phylogenetic relationships among three (ParaMisgurnus species as revealed by mitochondrial and nuclear DNA markers

    Directory of Open Access Journals (Sweden)

    Jakovlić I.

    2013-01-01

    Full Text Available The taxonomy of (ParaMisgurnus genera is still debated. We therefore used mitochondrial and nuclear DNA markers to analyze the phylogenetic relationships among Misgurnus anguillicaudatus, Paramisgurnus dabryanus and Misgurnus fossilis. Differing phylogenetic signals from mitochondrial and nuclear marker data suggest an introgression event in the history of M. anguillicaudatus and M. mohoity. No substantial genetic evidence was found that Paramisgurnus dabryanus should be classified as a separate genus.

  3. Screening for JH1 genetic defect carriers in Jersey cattle by a polymerase chain reaction and restriction fragment length polymorphism assay.

    Science.gov (United States)

    Zhang, Yi; Guo, Gang; Huang, Hetian; Lu, Lu; Wang, Lijie; Fang, Lingzhao; Liu, Lin; Wang, Yachun; Zhang, Shengli

    2015-09-01

    An autosomal recessive genetic defect termed JH1 has been associated with early embryonic loss in the Jersey cattle breed. The genetic basis has been identified as a cytosine to thymine mutation in the CWC15 gene that changes an amino acid from arginine to a stop code. To screen for JH1 carriers in an imported Jersey population in China, a method based on a polymerase chain reaction amplification followed by a restriction fragment length polymorphism assay (PCR-RFLP) was developed for the accurate diagnosis of the JH1 allele. A total of 449 randomly chosen cows were examined with the PCR-RFLP assay, and 31 were identified as JH1 carriers, corresponding to a carrier frequency of 6.9%. The PCR-RFLP method was validated by DNA sequencing of 8 positive and 13 negative samples, with all 21 samples giving the expected DNA sequence. In addition, 3 negative and 3 positive samples were confirmed by a commercial microarray-based single nucleotide polymorphism assay. Finally, samples from 9 bulls in the United States of known status were correctly identified as carriers (5 bulls) or noncarriers (4 bulls). As the JH1 defect has most likely spread worldwide, implementing routine screening is necessary to avoid the risk of carrier-to-carrier matings and to gradually eradicate the deleterious gene.

  4. Genetic variants in glucocorticoid and mineralocorticoid receptors are associated with concentrations of plasma cortisol, muscle glycogen content, and meat quality traits in male Nellore cattle.

    Science.gov (United States)

    Poleti, M D; DeRijk, R H; Rosa, A F; Moncau, C T; Oliveira, P S; Coutinho, L L; Eler, J P; Balieiro, J C C

    2015-04-01

    The glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) are key components in the regulation of the hypothalamic-pituitary-adrenal neuroendocrine axis and coordinate the physiological response to stress agents to reestablish homeostasis. Genetic variations of GR (NR3C1) and MR (NR3C2) genes could explain the alterations in animals to adapt to challenges, and therefore, their influence on production traits. The present study aimed to identify single-nucleotide polymorphisms (SNPs) in the bovine NR3C1 and NR3C2 genes and explore their associations to relevant traits of beef cattle production. Genotypes and phenotypes were collected from 241 male Nellore cattle (119 noncastrated and 122 castrated surgically) with an average of 24 ± 1.2 mo of age and live weight of 508 ± 39 kg. The traits evaluated were concentrations of plasma adrenocorticotropic hormone (ACTH) and cortisol, muscle glycogen and lactate content, and pH, color, cooking loss, and shear force of longissimus thoracis measured on the 1st, 7th, and 14th days postmortem. Five SNPs were identified, 2 in the NR3C1 gene and 3 in the NR3C2 gene. There was an associative relationship between the SNP NR3C1_1 g.3293A>G and postmortem plasma concentration of cortisol (P = 0.0008). The SNPs NR3C2_1 g.115T>C and NR3C2_2 g.570T>C were associated with muscle glycogen content (P = 0.0306 and P = 0.0158), postmortem plasma concentration of ACTH (P = 0.0118 and P = 0.0095), and cooking loss of the steak aged 1 d (P = 0.0398 and P = 0.0423). Haplotype analysis showed associations of GR haplotypes with postmortem plasma concentrations of cortisol and MR haplotypes with meat color, cooking losses, muscle glycogen content, and plasma concentrations of ACTH. The associations observed in the present study show that SNPs in GR and MR genes are related with changes of hypothalamic-pituitary-adrenal axis activity and metabolic profile in cattle, leading to individual variation in meat quality traits.

  5. Characterization of new allele influencing flowering time in bread wheat introgressed from Triticum militinae.

    Science.gov (United States)

    Ivaničová, Zuzana; Jakobson, Irena; Reis, Diana; Šafář, Jan; Milec, Zbyněk; Abrouk, Michael; Doležel, Jaroslav; Järve, Kadri; Valárik, Miroslav

    2016-09-25

    Flowering time variation was identified within a mapping population of doubled haploid lines developed from a cross between the introgressive line 8.1 and spring bread wheat cv. Tähti. The line 8.1 carried introgressions from tetraploid Triticum militinae in the cv. Tähti genetic background on chromosomes 1A, 2A, 4A, 5A, 7A, 1B and 5B. The most significant QTL for the flowering time variation was identified within the introgressed region on chromosome 5A and its largest effect was associated with the VRN-A1 locus, accounting for up to 70% of phenotypic variance. The allele of T. militinae origin was designated as VRN-A1f-like. The effect of the VRN-A1f-like allele was verified in two other mapping populations. QTL analysis identified that in cv. Tähti and cv. Mooni genetic background, VRN-A1f-like allele incurred a delay of 1.9-18.6 days in flowering time, depending on growing conditions. Sequence comparison of the VRN-A1f-like and VRN-A1a alleles from the parental lines of the mapping populations revealed major mutations in the promoter region as well as in the first intron, including insertion of a MITE element and a large deletion. The sequence variation allowed construction of specific diagnostic PCR markers for VRN-A1f-like allele determination. Identification and quantification of the effect of the VRN-A1f-like allele offers a useful tool for wheat breeding and for studying fine-scale regulation of flowering pathways in wheat. PMID:26899284

  6. Genetic differences based on a beef terminal index are reflected in future phenotypic performance differences in commercial beef cattle.

    Science.gov (United States)

    Connolly, S M; Cromie, A R; Berry, D P

    2016-05-01

    The increased demand for animal-derived protein and energy for human consumption will have to be achieved through a combination of improved animal genetic merit and better management strategies. The objective of the present study was to quantify whether differences in genetic merit among animals materialised into phenotypic differences in commercial herds. Carcass phenotypes on 156 864 animals from 7301 finishing herds were used, which included carcass weight (kg), carcass conformation score (scale 1 to 15), carcass fat score (scale 1 to 15) at slaughter as well as carcass price. The price per kilogram and the total carcass value that the producer received for the animal at slaughter was also used. A terminal index, calculated in the national genetic evaluations, was obtained for each animal. The index was based on pedigree index for calving performance, feed intake and carcass traits from the national genetic evaluations. Animals were categorised into four terminal index groups on the basis of genetic merit estimates that were derived before the expression of the phenotypic information by the validation animals. The association between terminal index and phenotypic performance at slaughter was undertaken using mixed models; whether the association differed by gender (i.e. young bulls, steers and heifers) or by early life experiences (animals born in a dairy herd or beef herd) was also investigated. The regression coefficient of phenotypic carcass weight, carcass conformation and carcass fat on their respective estimated breeding values (EBVs) was 0.92 kg, 1.08 units and 0.79 units, respectively, which is close to the expectation of one. Relative to animals in the lowest genetic merit group, animals in the highest genetic merit group had, on average, a 38.7 kg heavier carcass, with 2.21 units greater carcass conformation, and 0.82 units less fat. The superior genetic merit animals were, on average, slaughtered 6 days younger than their inferior genetic merit

  7. Genetic parameters for methane indicator traits based on milk fatty acids in Dual Purpose Belgian Blue cattle

    OpenAIRE

    Kandel, Purna Bhadra; Gengler, Nicolas; Soyeurt, Hélène

    2012-01-01

    Dairy production is pointed out for its large methane emission. Therefore, specific nutritional strategies are applying to abate methane emission but very less information is available about the animal genetic variability of methane emission. Methane indicators using traits indirectly related to methane and easily recorded like the mid-infrared (MIR) prediction of fatty acid could be used to conduct genetic studies. MIR methane indicators used in this study were derived from published fatty a...

  8. Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression

    DEFF Research Database (Denmark)

    Lorenzen, Eline D; Simonsen, Bo T; Kat, Pieter W;

    2006-01-01

    disequilibrium and maximum-likelihood estimates of genetic drift suggested that admixture between subspecies is a recent event. The fact that introgression is limited between subspecies could be caused by chromosomal differences, hindering gene flow between common and defassa waterbuck....... of range overlap in East Africa, where phenotypically intermediate populations occur. Variation in 478 bp of the mitochondrial DNA control region and 14 polymorphic microsatellite loci were used to describe the genetic structure and phylogeographical pattern of the species, and to assess...... if the intermediate populations are the results of hybridization. In total, 186 individuals from 11 localities were analysed. A high degree of genetic differentiation was found between subspecies, although this was most evident from the microsatellite data. Hybridization was suggested in the phenotypically...

  9. Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits.

    Directory of Open Access Journals (Sweden)

    Ben J Hayes

    2010-09-01

    Full Text Available Prediction of genetic merit using dense SNP genotypes can be used for estimation of breeding values for selection of livestock, crops, and forage species; for prediction of disease risk; and for forensics. The accuracy of these genomic predictions depends in part on the genetic architecture of the trait, in particular number of loci affecting the trait and distribution of their effects. Here we investigate the difference among three traits in distribution of effects and the consequences for the accuracy of genomic predictions. Proportion of black coat colour in Holstein cattle was used as one model complex trait. Three loci, KIT, MITF, and a locus on chromosome 8, together explain 24% of the variation of proportion of black. However, a surprisingly large number of loci of small effect are necessary to capture the remaining variation. A second trait, fat concentration in milk, had one locus of large effect and a host of loci with very small effects. Both these distributions of effects were in contrast to that for a third trait, an index of scores for a number of aspects of cow confirmation ("overall type", which had only loci of small effect. The differences in distribution of effects among the three traits were quantified by estimating the distribution of variance explained by chromosome segments containing 50 SNPs. This approach was taken to account for the imperfect linkage disequilibrium between the SNPs and the QTL affecting the traits. We also show that the accuracy of predicting genetic values is higher for traits with a proportion of large effects (proportion black and fat percentage than for a trait with no loci of large effect (overall type, provided the method of analysis takes advantage of the distribution of loci effects.

  10. Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle

    OpenAIRE

    Ogawa, Shinichiro; Matsuda, Hirokazu; Taniguchi, Yukio; Watanabe, Toshio; Nishimura, Shota; Sugimoto, Yoshikazu; Iwaisaki, Hiroaki

    2014-01-01

    [Background]Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poorly studied. For carcass weight and marbling score in the breed, as well as the extent of whole genome linkage disequilibrium (LD), the effects of equally-spaced single nucleoti...

  11. Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle

    OpenAIRE

    Ogawa, Shinichiro; Matsuda, Hirokazu; Taniguchi, Yukio; Watanabe, Toshio; Nishimura, Shota; Sugimoto, Yoshikazu; Iwaisaki, Hiroaki

    2014-01-01

    Background Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poorly studied. For carcass weight and marbling score in the breed, as well as the extent of whole genome linkage disequilibrium (LD), the effects of equally-spaced single nucleotid...

  12. Powerful methods for detecting introgressed regions from population genomic data.

    Science.gov (United States)

    Rosenzweig, Benjamin K; Pease, James B; Besansky, Nora J; Hahn, Matthew W

    2016-06-01

    Understanding the types and functions of genes that are able to cross species boundaries-and those that are not-is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary statistic that can be used to test for introgression, RNDmin , that makes use of the minimum pairwise sequence distance between two population samples relative to divergence to an outgroup. We find that our method offers a modest increase in power over other, related tests, but that all such tests have high power to detect introgressed loci when migration is recent and strong. RNDmin is robust to variation in the mutation rate, and remains reliable even when estimates of the divergence time between sister species are inaccurate. We apply RNDmin to population genomic data from the African mosquitoes Anopheles quadriannulatus and A. arabiensis, identifying three novel candidate regions for introgression. Interestingly, one of the introgressed loci is on the X chromosome, but outside of an inversion separating these two species. Our results suggest that significant, but rare, sharing of alleles is occurring between species that diverged more than 1 million years ago, and that application of these methods to additional systems are likely to reveal similar results. PMID:26945783

  13. Alien DNA introgression and wheat DNA rearrangements in a stable wheat line derived from the early generation of distant hybridization

    Institute of Scientific and Technical Information of China (English)

    ZHANG Lianquan; LIU Dengcai; YAN Zehong; ZHENG Youliang

    2005-01-01

    Polyploidy has been found to be common in plants. Bread or common wheat (Triticum aestivum L., 2n = 42) is a good example of allopolyploid made up of three diploid genomes A, B and D. In recent years, by the study of mimicking the origination of common wheat, it was found that changes of DNA sequence and gene expression occurred at the early stages of artificial allohexaploid between tetraploid wheat and Aegilops tauschii, which was probably favorable to genetic diploidization of new synthetic hexaploid wheat. Common wheat 99L2 is a new line stable in genetic, which was derived from the early self-pollinated generation of wide hybrids between common wheat and rye. In this study, it was found that at least two rye DNA segments had been introgressed into 99L2. This result suggested that a mechanism of alien DNA introgression may exist, which was different from the traditional mechanism of chromosome pairing and DNA recombination between wheat and alien species. Meanwhile, during the introgression process of alien rye DNA segments, the changes in DNA sequences of wheat itself occurred.

  14. Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle

    Science.gov (United States)

    The previous fifteen years have produced numerous QTL mapping experiments aimed at the identification of causal or linked polymorphisms for use in marker assisted selection programs to increase the rate of genetic gain in livestock species. To date, very few causal mutations for QTL have been ident...

  15. 焦磷酸测序法分析中国荷斯坦牛、娟姗牛及水牛的乳蛋白基因多态性%Genetic polymorphisms of milk protein in Chinese Holstein cattle, Jersey cattle and water buffalo analyzed by pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    任大喜; 陈有亮; 刘建新; 李玲; 林波; 曾庆坤

    2014-01-01

    ObjectiveTo analyze and compare the genetic polymorphisms of milk protein in Chinese Holstein cattle, Jersey cattle and water buffalo.MethodsThe primers were designed according to the milk protein polymorphic sites of Holstein, and the genetic polymorphisms were analyzed by pyrosequencing and confirmed by RP-HPLC.ResultsGenetic polymorphisms of milk protein genes (β-casein,κ-casein andβ-lactoglobulin) were detected in Chinese Holstein cattle and Jersey cattle. However, no polymorphism was found in water buffalo exceptκ-casein, and the polymorphic site was different with Holstein and Jersey. ConclusionMilk protein polymorphism was found in Chinese Holstein, Jersey and buffalo, and pyrose-quencing was a high-throughput and fast method for milk protein genotyping.%目的:本研究旨在分析和比较中国荷斯坦牛、娟姗牛和水牛的乳蛋白基因多态性。方法根据奶牛多态位点设计引物,采用焦磷酸测序法分析乳蛋白基因多态性,并采用高效液相色谱法进行验证。结果荷斯坦牛和娟姗牛的乳蛋白(β-casein,κ-casein和β-lactoglobulin)均存在基因多态性,而水牛仅在κ-casein上存在多态性且多态位点与另两种奶牛不同。结论中国荷斯坦牛、娟姗牛和水牛的乳蛋白基因均存在多态性,焦磷酸测序法能高通量、快速测定乳蛋白基因多态性。

  16. Genetic Polymorphisms of Mc4R and IGF2 Gene Association with Feed Conversion Efficiency Traits in Beef Cattle

    Directory of Open Access Journals (Sweden)

    Xin-hua Du§, Cui Chen§, Zheng-rong Yuan, Li-min Zhang, Xiao-jie Chen, Yan-hui Wang, Xue Gao, Lu-pei Zhang, Hui-jiang Gao, Jun-ya Li and Shang-zhong Xu*

    2013-11-01

    Full Text Available Melanocortin-4 receptor (MC4R gene is part of the central melanocortin pathway located in the hypothalamus, an area of the brain in which appetite is regulated. Insulin-like growth factor 2 (IGF2 gene plays a role in muscle growth, myoblast proliferation and differentiation. Thus, they are candidate genes for feed conversion efficiency (FCE. The study was to investigate the effects of variants in cattle MC4R and IGF2 gene on FCE traits including residual feed intake (RFI, feed conversion ratio (FCR and average daily gain (ADG. We screened single nucleotide polymorphisms (SNPs of the two genes in 118 Simmental bulls by DNA-pool sequencing and genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS analysis. C1069G locus of MC4R and four SNPs (C2209T, G18587C, A22950T and G26920T of IGF2 were identified in the population. The χ2 test showed that only MC4R-C1069G, IGF2-C2209T and IGF2-G18587C loci fitted with Hardy-Weinberg equilibrium (P>0.05. General linear model (GLM was used to analyze differences between genotypes. The results showed that only IGF2-G18587C locus has a significant effect on ADG (P0.05. CC and GG genotypes were the dominant genotypes; individual with CC or GG genotype had a larger ADG than GC (P<0.05.

  17. Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

    Science.gov (United States)

    Yin, T; Wensch-Dorendorf, M; Simianer, H; Swalve, H H; König, S

    2014-06-01

    The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

  18. Hybridization but no evidence for backcrossing and introgression in a sympatric population of great reed warblers and clamorous reed warblers.

    Directory of Open Access Journals (Sweden)

    Bengt Hansson

    Full Text Available Hybridization is observed frequently in birds, but often it is not known whether the hybrids are fertile and if backcrossing occurs. The breeding ranges of the great reed warbler (Acrocephalus arundinaceus and the clamorous reed warbler (A. stentoreus overlap in southern Kazakhstan and a previous study has documented hybridization in a sympatric population. In the present study, we first present a large set of novel microsatellite loci isolated and characterised in great reed warblers. Secondly, we evaluate whether hybridization in the sympatric breeding population has been followed by backcrossing and introgression.We isolated 181 unique microsatellite loci in great reed warblers. Of 41 loci evaluated, 40 amplified and 30 were polymorphic. Bayesian clustering analyses based on genotype data from 23 autosomal loci recognised two well-defined genetic clusters corresponding to the two species. Individuals clustered to a very high extent to either of these clusters (admixture proportions ≥ 0.984 with the exception of four previously suggested arundinaceus-stentoreus hybrid birds that showed mixed ancestry (admixture proportions 0.495-0.619. Analyses of simulated hybrids and backcrossed individuals showed that the sampled birds do not correspond to first-fourth-generation backcrosses, and that fifth or higher generation backcrosses to a high extent resemble 'pure' birds at this set of markers.We conclude that these novel microsatellite loci provide a useful molecular resource for Acrocephalus warblers. The time to reach reproductive isolation is believed to be very long in birds, approximately 5 Myrs, and with an estimated divergence time of 2 Myrs between these warblers, some backcrossing and introgression could have been expected. However, there was no evidence for backcrossing and introgression suggesting that hybrids are either infertile or their progeny inviable. Very low levels of introgression cannot be excluded, which still may be an

  19. Direct and maternal genetic effects on growth, reproduction, and ultrasound traits in zebu Brahman cattle in Colombia.

    Science.gov (United States)

    Martínez, R A; Dassonneville, R; Bejarano, D; Jimenez, A; Even, G; Mészáros, G; Sölkner, J

    2016-07-01

    Covariance components and genetic parameters were estimated for birth weight (BiW); adjusted weights at 4, 7, 12, and 18 mo; and ADG between 0 and 4 mo, between 4 and 7 mo, between 7 and 12 mo, and between 12 and 18 mo. Additionally, reproductive traits, calving interval, and age at first calving were analyzed, together with traits measured by ultrasound: loin eye area, deep fat mean, back fat, and rump fat. Analyses were performed using an animal model, considering the fixed effects of the farm ( = 37), year and month of birth, sex, calving number (1 to 7), season (dry and rainy seasons), region (North Coast, Andean Region, and Oriental Savannas), and conception (natural mating or AI), whereas the age of the cows at calving was considered a polynomial covariate with linear and quadratic effects. Three different models were used to find the one with the best fit for each trait: a single-trait model with an additive direct genetic effect, a single-trait model with additive direct and maternal genetic effects, and finally, a multitrait model with an additive direct genetic effect. For the growth traits, the heritability was between 0.24 and 0.47, with the lowest value for weight at 7 mo and the greatest value for BiW, and the maternal heritability was found to be between 0.15 and 0.21 but did not decrease later on. The correlation between direct and maternal effects was high and negative (-0.59 to -0.76). With ultrasound traits, a model with only direct effects was used. The heritability was between 0.13 and 0.28 for back fat and loin eye area, respectively. The heritabilities for deep fat mean and rump fat were similar, being 0.19 and 0.21, respectively. The reproductive traits showed high residual variance. In particular, the heritability of calving interval was low (0.06). The results showed that the growth traits have an important genetic component, which is a favorable indicator for obtaining improvement progress in the zebu Brahman breed for beef production in

  20. Genetic analysis of somatic cell score in Danish dairy cattle using ramdom regression test-day model

    DEFF Research Database (Denmark)

    Elsaid, Reda; Sabry, Ayman; Lund, Mogens Sandø;

    2011-01-01

    had the lowest − 2ln(L). Furthermore, based on a likelihood ratio test, this model was not significantly better than a model with fifth order LP for PE effect and a fourth order LP for genetic effects. The last two models were applied to the other data sets (set 3 to set 10). In all ten data sets, the...... and correlations are taking into account....

  1. Introgression of mitochondrial DNA among Myodes voles: consequences for energetics?

    Directory of Open Access Journals (Sweden)

    Boratyński Zbyszek

    2011-12-01

    Full Text Available Abstract Background Introgression of mitochondrial DNA (mtDNA is among the most frequently described cases of reticulate evolution. The tendency of mtDNA to cross interspecific barriers is somewhat counter-intuitive considering the key function of enzymes that it encodes in the oxidative-phosphorylation process, which could give rise to hybrid dysfunction. How mtDNA reticulation affects the evolution of metabolic functions is, however, uncertain. Here we investigated how morpho-physiological traits vary in natural populations of a common rodent (the bank vole, Myodes glareolus and whether this variation could be associated with mtDNA introgression. First, we confirmed that M. glareolus harbour mtDNA introgressed from M. rutilus by analyzing mtDNA (cytochrome b, 954 bp and nuclear DNA (four markers; 2333 bp in total sequence variation and reconstructing loci phylogenies among six natural populations in Finland. We then studied geographic variation in body size and basal metabolic rate (BMR among the populations of M. glareolus and tested its relationship with mtDNA type. Results Myodes glareolus and its arctic neighbour, M. rutilus, are reciprocally monophyletic at the analyzed nuclear DNA loci. In contrast, the two northernmost populations of M. glareolus have a fixed mitotype that is shared with M. rutilus, likely due to introgressive hybridization. The analyses of phenotypic traits revealed that the body mass and whole-body, but not mass corrected, BMR are significantly reduced in M. glareolus females from northern Finland that also have the introgressed mitotype. Restricting the analysis to the single population where the mitotypes coexist, the association of mtDNA type with whole-body BMR remained but those with mass corrected BMR and body mass did not. Mitochondrial sequence variation in the introgressed haplotypes is compatible with demographic growth of the populations, but may also be a result of positive selection. Conclusion Our

  2. Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact.

    Science.gov (United States)

    Pons, J-M; Sonsthagen, S; Dove, C; Crochet, P-A

    2014-03-01

    Recent genetic studies have shown that introgression rates among loci may greatly vary according to their location in the genome. In particular, several cases of mito-nuclear discordances have been reported for a wide range of organisms. In the present study, we examine the causes of discordance between mitochondrial (mtDNA) and nuclear DNA introgression detected in North American populations of the Great Black-backed Gull (Larus marinus), a Holarctic species, from the Nearctic North American Herring Gull (Larus smithsonianus). Our results show that extensive unidirectional mtDNA introgression from Larus smithsonianus into Larus marinus in North America cannot be explained by ancestral polymorphism but most likely results from ancient hybridization events occurring when Larus marinus invaded the North America. Conversely, our nuclear DNA results based on 12 microsatellites detected very little introgression from Larus smithsonianus into North American Larus marinus. We discuss these results in the framework of demographic and selective mechanisms that have been postulated to explain mito-nuclear discrepancies. We were unable to demonstrate selection as the main cause of mito-nuclear introgression discordance but cannot dismiss the possible role of selection in the observed pattern. Among demographic explanations, only drift in small populations and bias in mate choice in an invasive context may explain our results. As it is often difficult to demonstrate that selection may be the main factor driving the introgression of mitochondrial DNA in natural populations, we advocate that evaluating alternative demographic neutral hypotheses may help to indirectly support or reject hypotheses invoking selective processes.

  3. Genome engineering in cattle: recent technological advancements.

    Science.gov (United States)

    Wang, Zhongde

    2015-02-01

    Great strides in technological advancements have been made in the past decade in cattle genome engineering. First, the success of cloning cattle by somatic cell nuclear transfer (SCNT) or chromatin transfer (CT) is a significant advancement that has made obsolete the need for using embryonic stem (ES) cells to conduct cell-mediated genome engineering, whereby site-specific genetic modifications can be conducted in bovine somatic cells via DNA homologous recombination (HR) and whereby genetically engineered cattle can subsequently be produced by animal cloning from the genetically modified cells. With this approach, a chosen bovine genomic locus can be precisely modified in somatic cells, such as to knock out (KO) or knock in (KI) a gene via HR, a gene-targeting strategy that had almost exclusively been used in mouse ES cells. Furthermore, by the creative application of embryonic cloning to rejuvenate somatic cells, cattle genome can be sequentially modified in the same line of somatic cells and complex genetic modifications have been achieved in cattle. Very recently, the development of designer nucleases-such as zinc finger nucleases (ZFNs) and transcription activator-like effector nuclease (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-has enabled highly efficient and more facile genome engineering in cattle. Most notably, by employing such designer nucleases, genomes can be engineered at single-nucleotide precision; this process is now often referred to as genome or gene editing. The above achievements are a drastic departure from the traditional methods of creating genetically modified cattle, where foreign DNAs are randomly integrated into the animal genome, most often along with the integrations of bacterial or viral DNAs. Here, I review the most recent technological developments in cattle genome engineering by highlighting some of the major achievements in creating genetically engineered

  4. Perennial aneuploidy as a potential material for gene introgression between maize and Zea perennis

    Institute of Scientific and Technical Information of China (English)

    FU Jie; TANG Qi-lin; YANG Xiu-yan; CHENG Ming-jun; LÜ Gui-hua; WANG Pei; WU Yuan-qi; ZHENG Ming-min; ZHOU Shu-feng; RONG Ting-zhao

    2015-01-01

    Hybridization, which al ows for gene lfow between crops, is dififcult between maize and Zea perennis. In this study, we aim to initiate and study gene lfow between maize and Z. perennis via a special aneuploid plant (MDT) derived from an interspeciifc hybrid of the two species. The chromosome constitution and morphological characters of MDT as wel as certain backcross progenies were examined. Results from genomic in situ hybridization (GISH) indicate that aneuploid MDT consisted of nine maize chromosomes and 30 Z. perennis chromosomes. The backcross progenies of MDT×maize displayed signiifcant diversity of vegetative and ear morphology;several unusual plants with speciifc chromosome constitution were founded in its progenies. Some special perennial progeny with several maize chromosomes were obtained by backcrossing MDT with Z. perennis, and the ifrst whole chromosome introgression from maize to Z. perennis was detected in this study. With this novel material and method, a number of maize-tetraploid teosinte addition or substitution lines can be generated for further study, which has great signiifcance to maize and Z. perennis genetic research, especial y for promoting introgression and transferring desirable traits.

  5. Improvement in genetic evaluation of female fertility in dairy cattle using multiple-trait models including milk production traits

    DEFF Research Database (Denmark)

    Sun, C; Madsen, P; Lund, M S;

    2010-01-01

    This study investigated the improvement in genetic evaluation of fertility traits by using production traits as secondary traits (MILK = 305-d milk yield, FAT = 305-d fat yield, and PROT = 305-d protein yield). Data including 471,742 records from first lactations of Denmark Holstein cows, covering...... (DATAC1, which only contained the first crop daughters) for proven bulls. In addition, the superiority of the models was evaluated by expected reliability of EBV, calculated from the prediction error variance of EBV. Based on these criteria, the models combining milk production traits showed better model...... stability and predictive ability than single-trait models for all the fertility traits, except for nonreturn rate within 56 d after first service. The stability and predictive ability for the model including MILK or PROT were similar to the model including all 3 milk production traits and better than...

  6. Alien Introgression for FHB Resistance in Wheat - Challenges and Strategies

    Science.gov (United States)

    Over one thousand accessions of wheat relatives at different ploidy levels and wheat-alien species derivatives with varied chromosome constitutions were evaluated for Fusarium head blight (FHB) resistance. FHB resistance identified from the relatives and derivatives were introgressed into adapted br...

  7. A molecular cytogenetic analysis of introgression in Alstroemeria

    NARCIS (Netherlands)

    Kamstra, S.A.

    1999-01-01

    This thesis describes the results of a molecular cytogenetic investigation of the process of introgression in Alstroemeria . The aim of this study was to transfer chromosomes or genes from one Alstroemeria species into another. For this, two distantly related species, A. aurea and A. inodora , were

  8. Resistance of beef cattle of two genetic groups to ectoparasites and gastrointestinal nematodes in the state of São Paulo, Brazil.

    Science.gov (United States)

    Oliveira, M C S; Alencar, M M; Giglioti, R; Beraldo, M C D; Aníbal, F F; Correia, R O; Boschini, L; Chagas, A C S; Bilhassi, T B; Oliveira, H N

    2013-10-18

    The resistance to infestations by ectoparasites and infections by gastrointestinal nematodes was studied in 45 animals (males and females) of two genetic groups: purebred Nelore (NI, n=28) and Three-Cross (1/2 Angus+1/4 Canchim+1/4 Nelore - TC, n=17). The animals were monitored for 24 months, during which they were left to graze in tropical pastures without receiving treatment for parasites. Each month the animals were examined for infestations by external parasites, to count the numbers of cattle ticks Rhipicephalus microplus with diameter greater than 4.5mm present on the left side, horn flies (Haematobia irritans) present in the lumbar region and botfly larvae (Dermatobia hominis) present on the entire body. The H. irritans counts were performed with the aid of digital photographs. At the time of examination, fecal samples were collected to count the eggs per gram (EPG) and to perform coprocultures, and peripheral blood samples were drawn to determine the packed cell volume (PCV) and to count the eosinophils. For statistical analysis, the count data were transformed into log₁₀ (n+1), where n is the number of parasites. For PCV, significant effects (Pticks, the transformed means followed by standard errors for the NI and TC animals were 0.06 ± 0.01 and 0.34 ± 0.02, while for horn flies these were 0.92 ± 0.05 and 1.36 ± 0.06 and for botfly larvae they were 0.05 ± 0.03 and 0.45 ± 0.05, respectively. The average EPG values were only influenced by CO (Presistance to ectoparasites. PMID:23916059

  9. Genetic diversity, acaricide resistance status and evolutionary potential of a Rhipicephalus microplus population from a disease-controlled cattle farming area in South Africa.

    Science.gov (United States)

    Robbertse, Luïse; Baron, Samantha; van der Merwe, Nicolaas A; Madder, Maxime; Stoltsz, Wilhelm H; Maritz-Olivier, Christine

    2016-06-01

    The Southern cattle tick, Rhipicephalus microplus is a hematophagous ectoparasite of great veterinary and economic importance. Along with its adaptability, reproductive success and vectoring capacity, R. microplus has been reported to develop resistance to the major chemical classes of acaricides currently in use. In South Africa, the Mnisi community in the Mpumalanga region offers a unique opportunity to study the adaptive potential of R. microplus. The aims of this study therefore included characterising acaricide resistance and determining the level and pattern of genetic diversity for R. microplus in this region from one primary population consisting of 12 communal dip-stations. The level of acaricide resistance was evaluated using single nucleotide polymorphisms (SNPs) in genes that contribute to acaricide insensitivity. Additionally, the ribosomal internal transcribed spacer 2 (ITS2) gene fragments of collected individuals were sequenced and a haplotype network was constructed. A high prevalence of alleles attributed to resistance against formamidines (amitraz) in the octopamine/tyramine (OCT/Tyr) receptor (frequency of 0.55) and pyrethroids in the carboxylesterase (frequency of 0.81) genes were observed. Overall, the sampled tick population was homozygous resistant to pyrethroid-based acaricides in the voltage-gated sodium channel (VGS) gene. A total of 11 haplotypes were identified in the Mnisi R. microplus population from ITS2 analysis with no clear population structure. From these allele frequencies it appears that formamidine resistance in the Mnisi community is on the rise, as the R. microplus populations is acquiring or generating these resistance alleles. Apart from rearing multi-resistant ticks to commonly used acaricides in this community these ticks may pose future problems to its surrounding areas. PMID:26965787

  10. Genetic diversity, acaricide resistance status and evolutionary potential of a Rhipicephalus microplus population from a disease-controlled cattle farming area in South Africa.

    Science.gov (United States)

    Robbertse, Luïse; Baron, Samantha; van der Merwe, Nicolaas A; Madder, Maxime; Stoltsz, Wilhelm H; Maritz-Olivier, Christine

    2016-06-01

    The Southern cattle tick, Rhipicephalus microplus is a hematophagous ectoparasite of great veterinary and economic importance. Along with its adaptability, reproductive success and vectoring capacity, R. microplus has been reported to develop resistance to the major chemical classes of acaricides currently in use. In South Africa, the Mnisi community in the Mpumalanga region offers a unique opportunity to study the adaptive potential of R. microplus. The aims of this study therefore included characterising acaricide resistance and determining the level and pattern of genetic diversity for R. microplus in this region from one primary population consisting of 12 communal dip-stations. The level of acaricide resistance was evaluated using single nucleotide polymorphisms (SNPs) in genes that contribute to acaricide insensitivity. Additionally, the ribosomal internal transcribed spacer 2 (ITS2) gene fragments of collected individuals were sequenced and a haplotype network was constructed. A high prevalence of alleles attributed to resistance against formamidines (amitraz) in the octopamine/tyramine (OCT/Tyr) receptor (frequency of 0.55) and pyrethroids in the carboxylesterase (frequency of 0.81) genes were observed. Overall, the sampled tick population was homozygous resistant to pyrethroid-based acaricides in the voltage-gated sodium channel (VGS) gene. A total of 11 haplotypes were identified in the Mnisi R. microplus population from ITS2 analysis with no clear population structure. From these allele frequencies it appears that formamidine resistance in the Mnisi community is on the rise, as the R. microplus populations is acquiring or generating these resistance alleles. Apart from rearing multi-resistant ticks to commonly used acaricides in this community these ticks may pose future problems to its surrounding areas.

  11. Large-scale asymmetric introgression of cytoplasmic DNA reveals Holocene range displacement in a North American boreal pine complex.

    Science.gov (United States)

    Godbout, Julie; Yeh, Francis C; Bousquet, Jean

    2012-08-01

    Jack pine (Pinus banksiana) and lodgepole pine (Pinus contorta var. latifolia) are two North American boreal hard pines that hybridize in their zone of contact in western Canada. The main objective of this study was to characterize their patterns of introgression resulting from past and recent gene flow, using cytoplasmic markers having maternal or paternal inheritance. Mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) diversity was assessed in allopatric populations of each species and in stands from the current zone of contact containing morphological hybrids. Cluster analyses were used to identify genetic discontinuities among groups of populations. A canonical analysis was also conducted to detect putative associations among cytoplasmic DNA variation, tree morphology, and site ecological features. MtDNA introgression was extensive and asymmetric: it was detected in P. banksiana populations from the hybrid zone and from allopatric areas, but not in P. contorta populations. Very weak cpDNA introgression was observed, and only in P. banksiana populations. The mtDNA introgression pattern indicated that central Canada was first colonized by migrants from a P. contorta glacial population located west of the Rocky Mountains, before being replaced by P. banksiana migrating westward during the Holocene. In contrast, extensive pollen gene flow would have erased the cpDNA traces of this ancient presence of P. contorta. Additional evidence for this process was provided by the results of canonical analysis, which indicated that the current cpDNA background of trees reflected recent pollen gene flow from the surrounding dominant species rather than historical events that took place during the postglacial colonization. PMID:22957188

  12. Introgressive hybridization as a promoter of genome reshuffling in natural homoploid fish hybrids (Cyprinidae, Leuciscinae).

    Science.gov (United States)

    Pereira, C S A; Aboim, M A; Ráb, P; Collares-Pereira, M J

    2014-03-01

    Understanding the mechanisms underlying diversification and speciation by introgressive hybridization is currently one of the major challenges in evolutionary biology. Here, the analysis of hybridization between two pairs of Iberian Leuciscinae provided new data on independent hybrid zones involving Achondrostoma oligolepis (AOL) and Pseudochondrostoma duriense (PDU), and confirmed the occurrence of hybrids between AOL and Pseudochondrostoma polylepis (PPO). A multilevel survey combining morphological, genetic and cytogenomic markers on a vast population screening successfully sorted the selected fishes as admixed. Results were similar in both AOL × PDU and AOL × PPO systems. Overall, hybrid morphotypes, cytogenomic data and genetic profiling indicated preferential backcrossing and suggested AOL as a major genomic contributor. Moreover, results implied AOL as more permissive to introgression than PDU or PPO. Although PDU- and PPO-like individuals appeared more resilient to genome modifications, AOL appeared to be more involved and affected by the ongoing hybridization events, as chromosomal translocations were only found in AOL-like individuals. All hybrids analysed evidenced extensive ribosomal DNA (rDNA) polymorphism that was not found in parental species, but usually seen falling within the range of possible parental combinations. Yet, transgressive phenotypes that cannot be explained by normal recombination, including more rDNA clusters than expected or the occurrence of syntenic rDNAs, were also detected. Present results proved rapid genomic evolution providing the genetic novelty for species to persist. In addition, although the ultimate consequences of such apparently extensive and recurrent events remain unknown, modern genome-wide methodologies are of great promise towards answering questions concerning the causes, dynamics and impacts of hybridization.

  13. Introgressive hybridization: brown bears as vectors for polar bear alleles.

    Science.gov (United States)

    Hailer, Frank

    2015-03-01

    The dynamics and consequences of introgression can inform about numerous evolutionary processes. Biologists have therefore long been interested in hybridization. One challenge, however, lies in the identification of nonadmixed genotypes that can serve as a baseline for accurate quantification of admixture. In this issue of Molecular Ecology, Cahill et al. (2015) analyse a genomic data set of 28 polar bears, eight brown bears and one American black bear. Polar bear alleles are found to be introgressed into brown bears not only near a previously identified admixture zone on the Alaskan Admiralty, Baranof and Chichagof (ABC) Islands, but also far into the North American mainland. Elegantly contrasting admixture levels at autosomal and X chromosomal markers, Cahill and colleagues infer that male-biased dispersal has spread these introgressed alleles away from the Late Pleistocene contact zone. Compared to a previous study on the ABC Island population in which an Alaskan brown bear served as a putatively admixture-free reference, Cahill et al. (2015) utilize a newly sequenced Swedish brown bear as admixture baseline. This approach reveals that brown bears have been impacted by introgression from polar bears to a larger extent (up to 8.8% of their genome), than previously known, including the bear that had previously served as admixture baseline. No evidence for introgression of brown bear into polar bear is found, which the authors argue could be a consequence of selection. Besides adding new exciting pieces to the puzzle of polar/brown bear evolutionary history, the study by Cahill and colleagues highlights that wildlife genomics is moving from analysing single genomes towards a landscape genomics approach. PMID:25775930

  14. Polymorphisms of two Y chromosome microsatellites in Chinese cattle

    Directory of Open Access Journals (Sweden)

    Xue Kai

    2006-09-01

    Full Text Available Abstract Two Y chromosome specific microsatellites UMN2404 and UMN0103 were genotyped and assessed for polymorphisms in a total of 423 unrelated males from 25 indigenous Chinese cattle breeds. Consistently, both microsatellites displayed specific indicine and taurine alleles in each bull examined. The indicine and taurine alleles were detected in 248 males (58.6%, and 175 males (41.4%, respectively, although these frequencies varied amongst different breeds examined. The indicine alleles dominated in the southern group (92.4%, while the taurine alleles dominated in the northern group (95.5%. Hainan Island was possibly the site for the origin of Chinese zebu, and Tibetan cattle were probably independently domesticated from another strain of Bos primigenius. The geographical distribution of these frequencies reveals a pattern of male indicine introgression and a hybrid zone of indicine and taurine cattle in China. The declining south-to-north and east-to-west gradient of male indicine introgression in China could be explained by historical data, geographical segregation and temperature and weather conditions.

  15. Potential chromosomal introgression barriers revealed by linkage analysis in a hybrid of Pinus massoniana and P. hwangshanensis

    Directory of Open Access Journals (Sweden)

    Yin Tongming

    2010-02-01

    Full Text Available Abstract Background Exploring the genetic mechanisms underlying speciation is a hot topic in modern genetics and evolutionary studies. Distortion of marker transmission ratio is frequently ascribed to selection against alleles that cause hybrid incompatibility. The natural introgression between P. massoniana and P. hwangshanensis and their distribution ranges lead to the emergence of the two species as desirable organisms to study the genetic mechanisms for speciation. Results Using seeds sampled from trees at different elevations, we consistently detected sharp decreases in seed germination rates of trees in the hybrid zone, which might be due largely to the hybrid incompatibility. A genetic map was established using 192 megagametophytes from a single tree in the hybrid zone of the two species. Segregation distortion analysis revealed that the percentage of significant-segregation-distortion (SSD markers was extremely high, accounting for more than 25% of the segregating markers. The extension range, the distortion direction, and the distortion intensity of SSD markers also varied dramatically on different linkage groups. Conclusions In this study, we display the potential chromosomal introgression barriers between P. massoniana and P. hwangshanensis. Our study provides a valuable platform for conducting genome-wide association of hybrid incompatible QTLs and/or candidate genes with marker transmission ratio distortion in the hybrid.

  16. New World cattle show ancestry from multiple independent domestication events.

    Science.gov (United States)

    McTavish, Emily Jane; Decker, Jared E; Schnabel, Robert D; Taylor, Jeremy F; Hillis, David M

    2013-04-01

    Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment. PMID:23530234

  17. Genetic associations between daily BW gain and live fleshiness of station-tested young bulls and carcass and meat quality traits of commercial intact males in Piemontese cattle.

    Science.gov (United States)

    Bonfatti, V; Albera, A; Carnier, P

    2013-05-01

    The aim of this study was to investigate genetic relationships between beef traits of station-tested young bulls and carcass and meat quality traits (MQ) of commercial intact males in Piemontese cattle. Phenotypes for daily gain (DG) and live fleshiness traits (width at withers: WW; shoulder muscularity: SM; loin width: LW; loin thickness: LT; thigh muscularity: TM; thigh profile: TP) and thinness of the shin bone (BT) were available for 3,109 and 2,183 performance-tested young bulls, respectively. Carcass daily gain (CDG), carcass conformation (SEUS), pH at 24 h (pH24h) and 8 d after slaughter (pH8d), lightness (L*), redness (a*), yellowness (b*), hue angle (HA), saturation index (SI), drip loss (DL), cooking loss (CL), and shear force (SF) were assessed for 1,208 commercial intact males. (Co) variance components were estimated in a set of twelve 9-traits analyses using REML and linear animal models including all performance-test traits and 1 carcass or MQ trait at a time. Heritabilities ± SE of beef traits ranged from 0.26 ± 0.03 (LW) to 0.47 ± 0.01 (DG), whereas those of carcass traits and MQ from 0.06 ± 0.03 (CL) to 0.63 ± 0.04 (HA). The genetic correlation (rg) between DG and CDG was 0.75 ± 0.10, indicating that DG, as measured at the test station, is a good indicator of the carcass gain achieved by commercial animals under farms conditions. Daily BW gain of station-tested bulls correlated positively with color traits (from 0.11 ± 0.12 to 0.54 ± 0.09), ph8d (rg ± SE = 0.31 ± 0.11), DL (rg ± SE = 0.29 ± 0.17), and CL (rg ± SE = 0.27 ± 0.18). Live fleshiness of station-tested bulls exhibited genetic correlations with MQ of commercial animals that were positive for L* and b* (from 0.13 ± 0.08 to 0.65 ± 0.14) and negative for pH (from -0.27 ± 0.15 to -0.57 ± 0.11), CL (from -0.16 ± 0.23 to -0.43 ± 0.22), and SF (TM: rg ± SE = -0.31 ± 0.15; TP: rg ± SE = -0.41 ± 0.17). The thinness of the shin bone correlated unfavorably with CDG (rg ± SE

  18. Interspecific introgression in cetaceans: DNA markers reveal post-F1 status of a pilot whale.

    Directory of Open Access Journals (Sweden)

    Laura Miralles

    Full Text Available Visual species identification of cetacean strandings is difficult, especially when dead specimens are degraded and/or species are morphologically similar. The two recognised pilot whale species (Globicephala melas and Globicephala macrorhynchus are sympatric in the North Atlantic Ocean. These species are very similar in external appearance and their morphometric characteristics partially overlap; thus visual identification is not always reliable. Genetic species identification ensures correct identification of specimens. Here we have employed one mitochondrial (D-Loop region and eight nuclear loci (microsatellites as genetic markers to identify six stranded pilot whales found in Galicia (Northwest Spain, one of them of ambiguous phenotype. DNA analyses yielded positive amplification of all loci and enabled species identification. Nuclear microsatellite DNA genotypes revealed mixed ancestry for one individual, identified as a post-F1 interspecific hybrid employing two different Bayesian methods. From the mitochondrial sequence the maternal species was Globicephala melas. This is the first hybrid documented between Globicephala melas and G. macrorhynchus, and the first post-F1 hybrid genetically identified between cetaceans, revealing interspecific genetic introgression in marine mammals. We propose to add nuclear loci to genetic databases for cetacean species identification in order to detect hybrid individuals.

  19. A review of introgressive hybridization in amphibians%渐渗杂交在两栖动物中的研究进展

    Institute of Scientific and Technical Information of China (English)

    叶书培; 陈雯; 闵金金; 郑荣泉

    2013-01-01

    There is no doubt that introgressive hybridization plays a major role in evolution. In recent years, a large number of cases about introgressive hybridization in amphibians have been reported constantly. This article summarized the research status at home and abroad and the methods of introgressive hybridization in amphibians. We also discussed the various ways in which humans are affecting genetic exchange and the impacts on amphibians in the past hundreds of years. Finally, the research prospects of introgressive hybridization in amphibians are also proposed.%渐渗杂交在进化过程中拥有极其重要的地位.近些年,两栖类的渐渗杂交例子不断被报道.文章归纳了国内外两栖动物渐渗杂交的研究进展和研究方法,并且总结了过去几百年间人类活动对两栖动物渐渗杂交的影响,最后提出了两栖类渐渗杂交的研究展望.

  20. A genome-wide survey of hybrid incompatibility factors by the introgression of marked segments of Drosophila mauritiana chromosomes into Drosophila simulans

    Energy Technology Data Exchange (ETDEWEB)

    True, J.R.; Laurie, C.C. [Duke Univ., Durham, NC (United States); Weir, B.S. [North Carolina State Univ., Raleigh, NC (United States)

    1996-03-01

    In hybrids between Drosophila simulans and D. mauritiana, males are sterile and females are fertile, in compliance with HALDANE`s rule. The genetic basis of this phenomenon was investigated by introgression of segments of the mauritiana genome into a simulans background. A total of 87 positions throughout the mauritiana genome were marked with P-element insertions and replicate introgressions were made by repeated backcrossing to simulans for 15 generations. The fraction of hemizygous X chromosomal introgressions that are male sterile is {approximately}50% greater than the fraction of homozygous autosomal segments. This result suggests that male sterility factors have evolved at a higher rate on the X, but chromosomal differences in segment length cannot be ruled out. The fraction of homozygous autosomal introgressions that are male sterile is several times greater than the fraction that are either female sterile or inviable. This observation strongly indicates that male sterility factors have evolved more rapidly than either female sterility or inviability factors. These results, combined with previous work on these and other species, suggest that HALDANE`s rule has at least two causes: recessivity of incompatibility factors and differential accumulation of sterility factors affecting males and females. 50 refs., 4 figs., 3 tabs.

  1. The geography of introgression in a patchy environment and the thorn in the side of ecological speciation

    Institute of Scientific and Technical Information of China (English)

    Nicolas BIERNE; Pierre-Alexandre GAGNAIRE; Patrice DAVID

    2013-01-01

    When incompletely isolated taxa coexist in a patchy environment (e.g.mosaic hybrid zones,host-race complexes),patterns of variation may differ between selected traits/genes and neutral markers.While the genetic structure of selected traits/loci tends to coincide with habitat variables (producing Genetic-Environment Association or GEA),genetic differentiation at neutral loci unlinked to any selected locus rather depends on geographic connectivity at a large scale (e.g.IsolationBy-Distance or IBD),although these loci often display GEA at a small scale.This discrepancy has been repeatedly taken as evidence for parallel primary divergence driven by local adaptation.We argue that this interpretation needs to be addressed more thoroughly by considering the altemative hypothesis that speciation was initiated in allopatry and secondary introgression has subsequently erased the signal of past differentiation at neutral loci.We present a model of neutral introgression after secondary contact in a mosaic hybrid zone,which describes how GEAs dissipate with time and how neutral variation self-organizes according to the environmental and geographic structures.We show that although neutral loci can be affected by environmental selection,they are often more affected by history and connectivity:the neutral structure retains the initial geographic separation more than it correlates with the environment during the colonization and introgression phases,and then converges to a migration-drift balance,the most frequent outcome of which is GEA at a local scale but IBD at a large scale.This is the exact pattern usually attributed to parallel ecological speciation.Introgression is heterogeneous in space and depends on the landscape structure (e.g.it is faster in small patches,which are more impacted by immigration).Furthermore,there is no directionality in the association and it is possible to observe reversed GEAs between distant regions.We argue that the history of differentiation should

  2. The geography of introgression in a patchy environment and the thorn in the side of ecological speciation

    Directory of Open Access Journals (Sweden)

    Nicolas BIERNE, Pierre-Alexandre GAGNAIRE, Patrice DAVID

    2013-02-01

    Full Text Available When incompletely isolated taxa coexist in a patchy environment (e.g. mosaic hybrid zones, host-race complexes, patterns of variation may differ between selected traits/genes and neutral markers. While the genetic structure of selected traits/loci tends to coincide with habitat variables (producing Genetic-Environment Association or GEA, genetic differentiation at neutral loci unlinked to any selected locus rather depends on geographic connectivity at a large scale (e.g. Isolation- By-Distance or IBD, although these loci often display GEA at a small scale. This discrepancy has been repeatedly taken as evidence for parallel primary divergence driven by local adaptation. We argue that this interpretation needs to be addressed more thoroughly by considering the alternative hypothesis that speciation was initiated in allopatry and secondary introgression has subsequently erased the signal of past differentiation at neutral loci. We present a model of neutral introgression after secondary contact in a mosaic hybrid zone, which describes how GEAs dissipate with time and how neutral variation self-organizes according to the environmental and geographic structures. We show that although neutral loci can be affected by environmental selection, they are often more affected by history and connectivity: the neutral structure retains the initial geographic separation more than it correlates with the environment during the colonization and introgression phases, and then converges to a migration-drift balance, the most frequent outcome of which is GEA at a local scale but IBD at a large scale. This is the exact pattern usually attributed to parallel ecological speciation. Introgression is heterogeneous in space and depends on the landscape structure (e.g. it is faster in small patches, which are more impacted by immigration. Furthermore, there is no directionality in the association and it is possible to observe reversed GEAs between distant regions. We argue

  3. An introgressed wing pattern acts as a mating cue.

    Science.gov (United States)

    Sánchez, Angela P; Pardo-Diaz, Carolina; Enciso-Romero, Juan; Muñoz, Astrid; Jiggins, Chris D; Salazar, Camilo; Linares, Mauricio

    2015-06-01

    Heliconius butterflies provide good examples of both homoploid hybrid speciation and ecological speciation. In particular, examples of adaptive introgression have been detected among the subspecies of Heliconius timareta, which acquired red color pattern elements from H. melpomene. We tested whether the introgression of red wing pattern elements into H. timareta florencia might also be associated with incipient reproductive isolation (RI) from its close relative, H. timareta subsp. nov., found in the eastern Andes. No choice experiments show a 50% reduction in mating between females of H. t. subsp. nov. and males of H .t. florencia, but not in the reciprocal direction. In choice experiments using wing models, males of H. timareta subsp. nov. approach and court red phenotypes less than their own, whereas males of H. t. florencia prefer models with a red phenotype. Intrinsic postzygotic isolation was not detected in crosses between these H. timareta races. These results suggest that a color pattern trait gained by introgression is triggering RI between H. timareta subsp. nov. and H. t. florencia.

  4. Environmental sensitivity in dairy cattle with focus on fertility traits

    DEFF Research Database (Denmark)

    Ismael, Ahmed; Løvendahl, Peter; Strandberg, Erling

    2012-01-01

    Dairy cattle differ in production, fertility, health, and other important traits in the different environment as both the phenopypic and genetic level (Winding et la., 2005 and Calus et al., 2005). Fertility of Nordic dairy cattle breeds (Holstein, Red, Jersey) is a complex trait and the heritabi......Dairy cattle differ in production, fertility, health, and other important traits in the different environment as both the phenopypic and genetic level (Winding et la., 2005 and Calus et al., 2005). Fertility of Nordic dairy cattle breeds (Holstein, Red, Jersey) is a complex trait...

  5. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana × P. rubens).

    Science.gov (United States)

    de Lafontaine, Guillaume; Prunier, Julien; Gérardi, Sébastien; Bousquet, Jean

    2015-10-01

    The genic species concept implies that while most of the genome can be exchanged somewhat freely between species through introgression, some genomic regions remain impermeable to interspecific gene flow. Hence, interspecific differences can be maintained despite ongoing gene exchange within contact zones. This study assessed the heterogeneous patterns of introgression at gene loci across the hybrid zone of an incipient progenitor-derivative species pair, Picea mariana (black spruce) and Picea rubens (red spruce). The spruce taxa likely diverged in geographic isolation during the Pleistocene and came into secondary contact during late Holocene. A total of 300 SNPs distributed across the 12 linkage groups (LG) of black spruce were genotyped for 385 individual trees from 33 populations distributed across the allopatric zone of each species and within the zone of sympatry. An integrative framework combining three population genomic approaches was used to scan the genomes, revealing heterogeneous patterns of introgression. A total of 23 SNPs scattered over 10 LG were considered impermeable to introgression and putatively under diverging selection. These loci revealed the existence of impermeable genomic regions forming the species boundary and are thus indicative of ongoing speciation between these two genetic lineages. Another 238 SNPs reflected selectively neutral diffusion across the porous species barrier. Finally, 39 highly permeable SNPs suggested ancestral polymorphism along with balancing selection. The heterogeneous patterns of introgression across the genome indicated that the speciation process between black spruce and red spruce is young and incomplete, albeit some interspecific differences are maintained, allowing ongoing species divergence even in sympatry. The approach developed in this study can be used to track the progression of ongoing speciation processes. PMID:26346701

  6. Whole genome linkage disequilibrium maps in cattle

    Directory of Open Access Journals (Sweden)

    Mannen Hideyuki

    2007-10-01

    Full Text Available Abstract Background Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle. Results Linkage disequilibrium was assessed using r2 among all pairs of syntenic markers within eight breeds of cattle from the Bos taurus and Bos indicus subspecies. Bos taurus breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while Bos indicus breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r2 values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle. Conclusion Linkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger sample of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000–50,000 loci will be needed to conduct whole genome association studies in cattle.

  7. Enterocytozoon bieneusi in Dairy Cattle in the Northeast of China: Genetic Diversity of ITS Gene and Evaluation of Zoonotic Transmission Potential.

    Science.gov (United States)

    Zhao, Wei; Zhang, Weizhe; Yang, Fengkun; Zhang, Longxian; Wang, Rongjun; Cao, Jianping; Shen, Yujuan; Liu, Aiqin

    2015-01-01

    Enterocytozoon bieneusi is the most frequently diagnosed microsporidian species in humans. It has been found in a wide range of animals and is considered an important zoonotic pathogen. To date, little information is available on the role that cattle play in the epidemiology of human microsporidiosis caused by E. bieneusi in China. In this study, 133 fecal specimens from dairy cattle were collected in Heilongjiang Province, China. Enterocytozoon bieneusi was identified and genotyped by nested PCR analysis of the internal transcribed spacer (ITS) region of the rRNA gene, with 30.1% positive. Nine ITS genotypes were identified: six known genotypes-O (n = 26), EbpA (n = 2), I (n = 2), J (n = 2), D (n = 1) and BEB4 (n = 1)-and three novel genotypes named as CC-I to CC-III (two each). Genotype O was identified in cattle for the first time. The observation of all the six known genotypes here reported previously in humans, and also the fact of all the three novel genotypes (CHN-DC1 to CHN-DC3) falling into zoonotic group 1, indicate the possibility of cattle in the transmission of E. bieneusi to humans. PMID:25712195

  8. Levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations

    Science.gov (United States)

    A high density panel of more than 777000 genome-wide single nucleotide polymorphisms (SNPs) were used to investigate the population structure of Nelore and Gir, compared to seven other populations worldwide. Principal Component Analysis and model-based ancestry estimation clearly separate the indici...

  9. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  10. Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species.

    Science.gov (United States)

    Muirhead, Christina A; Presgraves, Daven C

    2016-02-01

    Under allopatric speciation, geographic barriers eliminate gene flow between eventual species at all loci in the genome simultaneously. There is increasing evidence, however, that speciation can be complex, with some loci experiencing gene flow during speciation or during bouts of secondary contact. In taxa with heteromorphic sex chromosomes-birds, butterflies, mammals, and Drosophila-the X (or Z) chromosome generally shows reduced levels of gene flow compared to autosomes. To investigate why, we develop population genetic models of secondary contact and gene flow at a neutral locus that is genetically linked to selected loci involved in hybrid incompatibilities and/or local adaptation. Using models that assume weak migration and strong selection, we compare gene flow at X-linked versus autosomal neutral loci as a function of linkage, dominance, sex-specific selection, and sex-specific recombination. For most cases, gene flow at neutral loci on the X is reduced relative to autosomes, as the greater efficacy of hemizygous selection in XY hybrids reduces the opportunity for neutral migrant alleles to escape their genetically linked, locally disfavored alleles via recombination. There are some circumstances, however, involving sex-limited selection and sex-limited recombination that allow neutral loci on the X to introgress more readily than those on autosomes. PMID:26807751

  11. Linked vs unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression.

    Science.gov (United States)

    Koopman, Wim J M; Li, Yinghui; Coart, Els; van de Weg, W Eric; Vosman, Ben; Roldán-Ruiz, Isabel; Smulders, Marinus J M

    2007-01-01

    We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, F(ST) based on unlinked loci indicated small (0.032-0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch

  12. Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes

    Institute of Scientific and Technical Information of China (English)

    Junzhou Li; Deping Wang; Yan Xie a; Hongliang Zhang; Guanglong Hu; Jinjie Li; Anyong Dai; Lifeng Liu; Zichao Li

    2011-01-01

    Introgression lines (ILs) are valuable materials for identifying quantitative trait loci (QTLs),evaluating genetic interactions,and marker assisted breeding.A set of 430 ILs (BC5F3) containing segments from upland tropical japonica cultivar IRAT109 in a lowland temperate japonica cultivar Yuefu background were developed.One hundred and seventy-six polymorphic markers were used to identify introgressed segments.No segment from IRAT 109 was found in 160 lines.Introgressed segments of the other 270 lines covered 99.1% of the donor genome.The mean number of introgressed donor segments per individual was 3.3 with an average length of 14.4 cM.QTL analysis was conducted on basal root thickness (BRT) of the 270 ILs grown under irrigated lowland,upland and hydroponic conditions.A total of 22 QTLs affecting BRT were identified,six QTLs (qBRT3.1,qBRT3.2,qBRT6.1,qBRT8.2,qBRT9.1,and qBRT9.2) were consistently expressed under at least two environments (location and water regime),and qBRT7.2 was a new BRT QTL identified under lowland conditions.IL255 containing qBRT9.1 showed an increase of 10.09% and 7.07% BRT over cultivar Yuefu when grown under upland and lowland conditions,respectively.Using a population of 304 F2:3 lines derived from the cross IL255 × Yuefu,qBRT9.1 was validated and mapped to a 1.2 cM interval between RM24271 and RM566.The presence of qBRT9.1 explained 12% of BRT variation.The results provide upland rice ILs and BRT QTLs for analyzing the genetic basis of drought resistance,detecting favorable genes from upland rice,and rice drought resistance breeding.

  13. Livestock-Associated Methicillin Resistant and Methicillin Susceptible Staphylococcus aureus Sequence Type (CC1 in European Farmed Animals: High Genetic Relatedness of Isolates from Italian Cattle Herds and Humans.

    Directory of Open Access Journals (Sweden)

    Patricia Alba

    Full Text Available Methicillin-resistant Staphylococcus aureus (MRSA Sequence Type (ST1, Clonal Complex(CC1, SCCmec V is one of the major Livestock-Associated (LA- lineages in pig farming industry in Italy and is associated with pigs in other European countries. Recently, it has been increasingly detected in Italian dairy cattle herds. The aim of this study was to analyse the differences between ST1 MRSA and methicillin-susceptible S. aureus (MSSA from cattle and pig herds in Italy and Europe and human isolates. Sixty-tree animal isolates from different holdings and 20 human isolates were characterized by pulsed-field gel electrophoresis (PFGE, spa-typing, SCCmec typing, and by micro-array analysis for several virulence, antimicrobial resistance, and strain/host-specific marker genes. Three major PFGE clusters were detected. The bovine isolates shared a high (≥90% to 100% similarity with human isolates and carried the same SCCmec type IVa. They often showed genetic features typical of human adaptation or present in human-associated CC1: Immune evasion cluster (IEC genes sak and scn, or sea; sat and aphA3-mediated aminoglycoside resistance. Contrary, typical markers of porcine origin in Italy and Spain, like erm(A mediated macrolide-lincosamide-streptograminB, and of vga(A-mediated pleuromutilin resistance were always absent in human and bovine isolates. Most of ST(CC1 MRSA from dairy cattle were multidrug-resistant and contained virulence and immunomodulatory genes associated with full capability of colonizing humans. As such, these strains may represent a greater human hazard than the porcine strains. The zoonotic capacity of CC1 LA-MRSA from livestock must be taken seriously and measures should be implemented at farm-level to prevent spill-over.

  14. Livestock-Associated Methicillin Resistant and Methicillin Susceptible Staphylococcus aureus Sequence Type (CC)1 in European Farmed Animals: High Genetic Relatedness of Isolates from Italian Cattle Herds and Humans.

    Science.gov (United States)

    Alba, Patricia; Feltrin, Fabiola; Cordaro, Gessica; Porrero, María Concepción; Kraushaar, Britta; Argudín, María Angeles; Nykäsenoja, Suvi; Monaco, Monica; Stegger, Marc; Aarestrup, Frank M; Butaye, Patrick; Franco, Alessia; Battisti, Antonio

    2015-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) Sequence Type (ST)1, Clonal Complex(CC)1, SCCmec V is one of the major Livestock-Associated (LA-) lineages in pig farming industry in Italy and is associated with pigs in other European countries. Recently, it has been increasingly detected in Italian dairy cattle herds. The aim of this study was to analyse the differences between ST1 MRSA and methicillin-susceptible S. aureus (MSSA) from cattle and pig herds in Italy and Europe and human isolates. Sixty-tree animal isolates from different holdings and 20 human isolates were characterized by pulsed-field gel electrophoresis (PFGE), spa-typing, SCCmec typing, and by micro-array analysis for several virulence, antimicrobial resistance, and strain/host-specific marker genes. Three major PFGE clusters were detected. The bovine isolates shared a high (≥90% to 100%) similarity with human isolates and carried the same SCCmec type IVa. They often showed genetic features typical of human adaptation or present in human-associated CC1: Immune evasion cluster (IEC) genes sak and scn, or sea; sat and aphA3-mediated aminoglycoside resistance. Contrary, typical markers of porcine origin in Italy and Spain, like erm(A) mediated macrolide-lincosamide-streptograminB, and of vga(A)-mediated pleuromutilin resistance were always absent in human and bovine isolates. Most of ST(CC)1 MRSA from dairy cattle were multidrug-resistant and contained virulence and immunomodulatory genes associated with full capability of colonizing humans. As such, these strains may represent a greater human hazard than the porcine strains. The zoonotic capacity of CC1 LA-MRSA from livestock must be taken seriously and measures should be implemented at farm-level to prevent spill-over.

  15. Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin.

    Science.gov (United States)

    Lamer, James T; Ruebush, Blake C; Arbieva, Zarema H; McClelland, Michael A; Epifanio, John M; Sass, Greg G

    2015-08-01

    Hybridization among conspecifics in native and introduced habitats has important implications for biological invasions in new ecosystems. Bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are genetically isolated and occur in sympatry within their native range. Following their introduction to North America, however, introgressant hybrids have been reported throughout their expanded range within the Mississippi River Basin (MRB). The extent of introgression, both spatially and generationally, is largely unknown. Therefore, we examined mixed-species populations from across the MRB to characterize the extent of interspecific gene flow. We assayed 2798 individuals from nine locations with a suite of species-diagnostic SNPs (57 nuclear and one mitochondrial). Forty-four per cent (n = 1244) of individuals displayed hybrid genotypes. Moreover, the composition of hybrid genotypes varied among locations and represented complex hybrid swarms with multiple generations of gene flow. Introgressive hybrids were identified from all locations, were bidirectional and followed a bimodal distribution consisting primarily of parental or parental-like genotypes and phenotypes. All described hybrid categories were present among individuals from 1999 to 2008, with parents and later-generation backcrosses representing the largest proportion of individuals among years. Our mitochondrial SNP (COII), tested on a subset of 730 individuals, revealed a silver carp maternal bias in 13 of 21 (62%) F1 hybrids, in all silver carp backcrosses, and maintained throughout many of the bighead carp backcrosses. The application of this suite of diagnostic markers and the spatial coverage permits a deeper examination of the complexity in hybrid swarms between two invasive, introduced species. PMID:26096550

  16. Factors influencing the efficiency of a marker-assisted introgression programme in Merino sheep

    Directory of Open Access Journals (Sweden)

    Henshall John

    2007-09-01

    Full Text Available Abstract This study investigated a marker-assisted introgression programme in Australian Merino sheep. The goal was to introgress an allele with a large negative effect on fibre diameter into a Merino flock possessing medium average fibre diameter. The influence of two factors was explored: the strategy used to select animals from the purebred and backcross line for backcrossing purposes and the use of selection on background markers to accelerate the return to the purebred line's genome. The results were compared to introgression based on EBVs only. Introgression using EBVs only produced almost the same response in the dollar index as marker-based introgression methods. However, this study did not account for some of the costs associated with implementing the programmes, including the costs of phenotyping and genotyping. Given that the cost of measuring fibre diameter is low, it was concluded that introgression on EBVs only would be the preferred method since the marginal profit of marker-assisted introgression would not be large enough to cover the additional cost of genotyping. In marker-assisted introgression, reciprocal crossing of male and female selection candidates from the backcross and the purebred line was the most advantageous strategy from a practical and profit point of view. Selection for background markers was less profitable in this study than recovering the donor genome by selection on phenotype.

  17. Proliferation rates of bovine primary muscle cells relate to liveweight and carcase weight in cattle.

    Science.gov (United States)

    Coles, Chantal A; Wadeson, Jenny; Leyton, Carolina P; Siddell, Jason P; Greenwood, Paul L; White, Jason D; McDonagh, Matthew B

    2015-01-01

    Muscling in cattle is largely influenced by genetic background, ultimately affecting beef yield and is of major interest to the beef industry. This investigation aimed to determine whether primary skeletal muscle cells isolated from different breeds of cattle with a varying genetic potential for muscling differ in their myogenic proliferative capacity. Primary skeletal muscle cells were isolated and cultured from the Longissimus muscle (LM) of 6 month old Angus, Hereford and Wagyu X Angus cattle. Cells were assessed for rate of proliferation and gene expression of PAX7, MYOD, MYF5, and MYOG. Proliferation rates were found to differ between breeds of cattle whereby myoblasts from Angus cattle were found to proliferate at a greater rate than those of Hereford and Wagyu X Angus during early stages of growth (5-20 hours in culture) in vitro (P cattle (P cattle (P cattle.

  18. Genetic divergence in cellular resistance to heat shock in cattle: differences between breeds developed in temperate versus hot climates in responses of preimplantation embryos, reproductive tract tissues and lymphocytes to increased culture temperatures.

    Science.gov (United States)

    Paula-Lopes, F F; Chase, C C; Al-Katanani, Y M; Krininger, C E; Rivera, R M; Tekin, S; Majewski, A C; Ocon, O M; Olson, T A; Hansen, P J

    2003-02-01

    The detrimental effects of heat stress on fertility in cattle are less pronounced in heat-tolerant breeds. Although these genetic differences reflect differences in thermoregulation, cells from heat-tolerant breeds are less adversely compromised by increased temperature (that is, heat shock) than cells from heat-sensitive breeds. Experiments were performed to test the hypothesis that cells and tissues from two thermotolerant breeds (Brahman and Senepol) are better able to survive and function after exposure to increased temperature than cells and tissues from two thermosensitive breeds (Holstein and Angus). Exposure of embryos at>eight-cell stage at day 5 after insemination to heat shock of 41.0 degrees C for 6 h decreased development to the blastocyst stage and the number of cells per embryo. However, the deleterious effect of heat shock on blastocyst formation and the number of cells per embryo was less pronounced for Brahman than for Holstein and Angus breeds. Embryos from Senepol cows had very low development and it was not possible to determine heat shock effects in this breed. In contrast to the sensitivity of embryos to heat shock, there was no effect of a 41.0 degrees C heat shock on [(3)H]leucine incorporation into proteins secreted by oviductal or endometrial explants. Lymphocytes from Brahman and Senepol cows were more resistant to heat-induced apoptosis than lymphocytes from other breeds. Heat shock reduced lymphocyte glutathione content but the magnitude of the decrease was not affected by breed. In conclusion, embryos from Brahman cows are more resistant to heat shock than embryos from Holstein or Angus cows. Genetic differences are also present in thermotolerance for apoptosis response in lymphocytes, with Brahman and Senepol cattle being more resistant to heat shock than Angus and Holstein breeds. It is likely that the evolutionary forces that led to the Brahman and Senepol breeds being adapted to hot climates resulted in the selection of genes

  19. Feasible introgression of an anti-pathogen transgene into an urban mosquito population without using gene-drive.

    Directory of Open Access Journals (Sweden)

    Kenichi W Okamoto

    2014-07-01

    Full Text Available Introgressing anti-pathogen constructs into wild vector populations could reduce disease transmission. It is generally assumed that such introgression would require linking an anti-pathogen gene with a selfish genetic element or similar technologies. Yet none of the proposed transgenic anti-pathogen gene-drive mechanisms are likely to be implemented as public health measures in the near future. Thus, much attention now focuses instead on transgenic strategies aimed at mosquito population suppression, an approach generally perceived to be practical. By contrast, aiming to replace vector competent mosquito populations with vector incompetent populations by releasing mosquitoes carrying a single anti-pathogen gene without a gene-drive mechanism is widely considered impractical.Here we use Skeeter Buster, a previously published stochastic, spatially explicit model of Aedes aegypti to investigate whether a number of approaches for releasing mosquitoes with only an anti-pathogen construct would be efficient and effective in the tropical city of Iquitos, Peru. To assess the performance of such releases using realistic release numbers, we compare the transient and long-term effects of this strategy with two other genetic control strategies that have been developed in Ae. aegypti: release of a strain with female-specific lethality, and a strain with both female-specific lethality and an anti-pathogen gene. We find that releasing mosquitoes carrying only an anti-pathogen construct can substantially decrease vector competence of a natural population, even at release ratios well below that required for the two currently feasible alternatives that rely on population reduction. Finally, although current genetic control strategies based on population reduction are compromised by immigration of wild-type mosquitoes, releasing mosquitoes carrying only an anti-pathogen gene is considerably more robust to such immigration.Contrary to the widely held view that

  20. Genetic and ecological aspects of gene flow from wheat (Triticum aestivum L.) to Aegilops L. species

    OpenAIRE

    Schoenenberger, Nicola; Küpfer, Philippe

    2006-01-01

    Genetic and ecological aspects of gene flow from wheat (Triticum aestivum L.) to Aegilops L. species Hybridisation and introgression from crops to wild relatives is a key issue in risk assessment. In the present study, hybridisation and introgression dynamics from hexaploid wheat (2n=42) to tetraploid Aegilops species (2n=28) were investigated by experiments in natural conditions or in the greenhouse, and by genetic analyses. In order to study crop-weed hybridisation as a function of distance...

  1. Influence of Introgression and Geological Processes on Phylogenetic Relationships of Western North American Mountain Suckers (Pantosteus, Catostomidae)

    Science.gov (United States)

    Unmack, Peter J.; Dowling, Thomas E.; Laitinen, Nina J.; Secor, Carol L.; Mayden, Richard L.; Shiozawa, Dennis K.; Smith, Gerald R.

    2014-01-01

    Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression. PMID:24619087

  2. Exploring New Alleles Involved in Tomato Fruit Quality in an Introgression Line Library of Solanum pimpinellifolium.

    Science.gov (United States)

    Barrantes, Walter; López-Casado, Gloria; García-Martínez, Santiago; Alonso, Aranzazu; Rubio, Fernando; Ruiz, Juan J; Fernández-Muñoz, Rafael; Granell, Antonio; Monforte, Antonio J

    2016-01-01

    We have studied a genomic library of introgression lines from the Solanum pimpinellifolium accession TO-937 into the genetic background of the "Moneymaker" cultivar in order to evaluate the accession's breeding potential. Overall, no deleterious phenotypes were observed, and the plants and fruits were phenotypically very similar to those of "Moneymaker," which confirms the feasibility of translating the current results into elite breeding programs. We identified chromosomal regions associated with traits that were both vegetative (plant vigor, trichome density) and fruit-related (morphology, organoleptic quality, color). A trichome-density locus was mapped on chromosome 10 that had not previously been associated with insect resistance, which indicates that the increment of trichomes by itself does not confer resistance. A large number of quantitative trait loci (QTLs) have been identified for fruit weight. Interestingly, fruit weight QTLs on chromosomes 1 and 10 showed a magnitude effect similar to that of QTLs previously defined as important in domestication and diversification. Low variability was observed for fruit-shape-related traits. We were, however, able to identify a QTL for shoulder height, although the effects were quite low, thus demonstrating the suitability of the current population for QTL detection. Regarding organoleptic traits, consistent QTLs were detected for soluble solid content (SSC). Interestingly, QTLs on chromosomes 2 and 9 increased SSC but did not affect fruit weight, making them quite promising for introduction in modern cultivars. Three ILs with introgressions on chromosomes 1, 2, and 10 increased the internal fruit color, making them candidates for increasing the color of modern cultivars. Comparing the QTL detection between this IL population and a recombinant inbred line population from the same cross, we found that QTL stability across generations depended on the trait, as it was very high for fruit weight but low for organoleptic

  3. Toward Understanding the Genetic Basis of Yak Ovary Reproduction: A Characterization and Comparative Analyses of Estrus Ovary Transcriptiome in Yak and Cattle.

    Directory of Open Access Journals (Sweden)

    Daoliang Lan

    Full Text Available Yaks (Bos grunniens are endemic species that can adapt well to thin air, cold temperatures, and high altitude. These species can survive in harsh plateau environments and are major source of animal production for local residents, being an important breed in the Qinghai-Tibet Plateau. However, compared with ordinary cattle that live in the plains, yaks generally have lower fertility. Investigating the basic physiological molecular features of yak ovary and identifying the biological events underlying the differences between the ovaries of yak and plain cattle is necessary to understand the specificity of yak reproduction. Therefore, RNA-seq technology was applied to analyze transcriptome data comparatively between the yak and plain cattle estrous ovaries.After deep sequencing, 3,653,032 clean reads with a total of 4,828,772,880 base pairs were obtained from yak ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome, among which, 12,731 and 14,631 genes were assigned to Gene Ontology (GO categories and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. Furthermore, comparison of yak and cattle ovary transcriptome data revealed that 1307 genes were significantly and differentially expressed between the two libraries, wherein 661 genes were upregulated and 646 genes were downregulated in yak ovary. Functional analysis showed that the differentially expressed genes were involved in various Gene Ontology (GO categories and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. GO annotations indicated that the genes related to "cell adhesion," "hormonal" biological processes, and "calcium ion binding," "cation transmembrane transport" molecular events were significantly active. KEGG pathway analysis showed that the "complement and coagulation cascade" pathway was the most enriched in yak ovary transcriptome data, followed by the "cytochrome P450" related and "ECM-receptor interaction" pathways. Moreover, several

  4. Carbon Footprint of Beef Cattle

    Directory of Open Access Journals (Sweden)

    Jim Dyer

    2012-12-01

    Full Text Available The carbon footprint of beef cattle is presented for Canada, The United States, The European Union, Australia and Brazil. The values ranged between 8 and 22 kg CO2e per kg of live weight (LW depending on the type of farming system, the location, the year, the type of management practices, the allocation, as well as the boundaries of the study. Substantial reductions have been observed for most of these countries in the last thirty years. For instance, in Canada the mean carbon footprint of beef cattle at the exit gate of the farm decreased from 18.2 kg CO2e per kg LW in 1981 to 9.5 kg CO2e per kg LW in 2006 mainly because of improved genetics, better diets, and more sustainable land management practices. Cattle production results in products other than meat, such as hides, offal and products for rendering plants; hence the environmental burden must be distributed between these useful products. In order to do this, the cattle carbon footprint needs to be reported in kg of CO2e per kg of product. For example, in Canada in 2006, on a mass basis, the carbon footprint of cattle by-products at the exit gate of the slaughterhouse was 12.9 kg CO2e per kg of product. Based on an economic allocation, the carbon footprints of meat (primal cuts, hide, offal and fat, bones and other products for rendering were 19.6, 12.3, 7 and 2 kg CO2e per kg of product, respectively.

  5. Molecular, physicochemical and rheological characteristics of introgressive Triticale/Triticum monococcum ssp. monococcum lines with wheat 1D/1A chromosome substitution.

    Science.gov (United States)

    Salmanowicz, Bolesław P; Langner, Monika; Wiśniewska, Halina; Apolinarska, Barbara; Kwiatek, Michał; Błaszczyk, Lidia

    2013-01-01

    Three sets of hexaploid introgressive triticale lines, with Triticum monococcum ssp. monococcum (cultivated einkorn wheat) genes and a bread wheat chromosome 1D substituted for chromosome 1A, and one set of secondary triticale lines were evaluated for grain and flour physicochemical and dough rheological characteristics in two generations (F7 and F8). Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) confirmed the 1D/1A chromosome substitution. The presence or absence of einkorn high-molecular-weight (HMW) glutenin subunits and the wheat Glu-D1d locus encoding the 5 + 10 subunits was assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), capillary zone electrophoresis, and allele-specific molecular markers. Significant differences were found among physicochemical properties (with the exception of the Hagberg falling number) of all introgressive Triticale/T. monococcum lines and the secondary triticale lines. The wheat 1D/1A chromosome substitution also affected these properties. The results showed that in all introgressive triticale lines, the protein and gluten content, Zeleny sedimentation value, and water absorption capacity, were increased. The rheological parameters estimated using micro-farinograph, reomixer, and Kieffer dough extensibility systems also showed an appreciable increase in dough-mixing properties, maximum resistance to extension (Rmax), and dough extensibility. Introgressive Triticale/T. monococcum lines with 5 + 10 subunits have particularly favorable rheological parameters. The results obtained in this study suggest that the cultivated einkorn genome Am, in the context of hexaploid secondary triticale lines and with a wheat 1D/1A substitution, has the potential to improve gluten polymer interactions and be a valuable genetic resource for triticale quality improvement. PMID:23896593

  6. Molecular, Physicochemical and Rheological Characteristics of Introgressive Triticale/Triticum monococcum ssp. monococcum Lines with Wheat 1D/1A Chromosome Substitution

    Directory of Open Access Journals (Sweden)

    Lidia Błaszczyk

    2013-07-01

    Full Text Available Three sets of hexaploid introgressive triticale lines, with Triticum monococcum ssp. monococcum (cultivated einkorn wheat genes and a bread wheat chromosome 1D substituted for chromosome 1A, and one set of secondary triticale lines were evaluated for grain and flour physicochemical and dough rheological characteristics in two generations (F7 and F8. Genomic in situ hybridization (GISH and fluorescence in situ hybridization (FISH confirmed the 1D/1A chromosome substitution. The presence or absence of einkorn high-molecular-weight (HMW glutenin subunits and the wheat Glu-D1d locus encoding the 5 + 10 subunits was assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE, capillary zone electrophoresis, and allele-specific molecular markers. Significant differences were found among physicochemical properties (with the exception of the Hagberg falling number of all introgressive Triticale/T. monococcum lines and the secondary triticale lines. The wheat 1D/1A chromosome substitution also affected these properties. The results showed that in all introgressive triticale lines, the protein and gluten content, Zeleny sedimentation value, and water absorption capacity, were increased. The rheological parameters estimated using micro-farinograph, reomixer, and Kieffer dough extensibility systems also showed an appreciable increase in dough-mixing properties, maximum resistance to extension (Rmax, and dough extensibility. Introgressive Triticale/T. monococcum lines with 5 + 10 subunits have particularly favorable rheological parameters. The results obtained in this study suggest that the cultivated einkorn genome Am, in the context of hexaploid secondary triticale lines and with a wheat 1D/1A substitution, has the potential to improve gluten polymer interactions and be a valuable genetic resource for triticale quality improvement.

  7. The use of clones in dairy cattle breeding.

    NARCIS (Netherlands)

    Boer, de I.J.M.

    1994-01-01

    The aim of this thesis was to determine a breeding scheme that optimally uses large scale production of genetically identical individuals (clones) in dairy cattle. Such a breeding scheme should optimize the continuous genetic improvement of the breeding population (genetic response), and the selecti

  8. [Allelic polymorphism of kappa-casein gene (CSN3) in Russian cattle breeds and its informative value as a genetic marker].

    Science.gov (United States)

    Sulimova, G E; Abani Azari, M; Rostamzadeh, J; Mohammad Abani, M R; Lazebnyĭ, O E

    2007-01-01

    The frequencies of the kappa-casein gene (CSN3) alleles and genotypes have been determined in five Russian cattle breeds (Bestuzhev, Kalmyk, Russian Black Pied, Yaroslavl, and Yakut breeds) by means of PCR-RFLP analysis using two independent restriction nucleases (HinfI and TaqI) and by allele-specific PCR. Typing alleles A and B of CSN3 is of practical importance, because allele B is correlated with commercially valuable parameters of milk productivity (protein content and milk yield) and improves the cheese yielding capacity. The frequencies of the B allele of CSN3 in the breeds studied vary from 0.16 to 0.50; and those of the AB and BB genotypes, from 0.27 to 0.60 and from 0.02 to 0.23, respectively. The Yaroslavl breed had the highest frequencies of CSN3 allele B and genotype BB (0.50 and 0.23, respectively). The frequencies of the B allele and BB genotype in other breeds studied varied from 0.25 to 0.32 and from 0.03 to 0.09, respectively. In none of the breeds studied have the observed and expected heterozygosities been found to differ from each other significantly. However, the observed genotype distributions significantly differ from the expected one in some herds (in most such cases, an excess of heterozygotes is observed). Two herds of the Yaroslavl breed dramatically differ from each other in the heterozygosity level: a deficit (D = -0.14) and an excess (D = 0.20) of heterozygotes have been observed at the Mikhailovskoe and Gorshikha farms, respectively. In general, however, the heterozygosity of the Yaroslavl breed corresponds to the expected level (D = 0.04). Analysis of breeds for homogeneity with the use of Kulback's test has shown that all cattle breeds studied are heterogeneous, the CSN3 diversity within breeds being higher than that among different breeds, which is confirmed by low Fst values (0.0025-0.0431). Thus, a DNA marker based on CSN3 gene polymorphism is extremely important for breeding practice as a marker of milk quality; however, it is

  9. Weak population structure in European roe deer (Capreolus capreolus and evidence of introgressive hybridization with Siberian roe deer (C. pygargus in northeastern Poland.

    Directory of Open Access Journals (Sweden)

    Juanita Olano-Marin

    Full Text Available We investigated contemporary and historical influences on the pattern of genetic diversity of European roe deer (Capreolus capreolus. The study was conducted in northeastern Poland, a zone where vast areas of primeval forests are conserved and where the European roe deer was never driven to extinction. A total of 319 unique samples collected in three sampling areas were genotyped at 16 microsatellites and one fragment (610 bp of mitochondrial DNA (mtDNA control region. Genetic diversity was high, and a low degree of genetic differentiation among sampling areas was observed with both microsatellites and mtDNA. No evidence of genetic differentiation between roe deer inhabiting open fields and forested areas was found, indicating that the ability of the species to exploit these contrasting environments might be the result of its phenotypic plasticity. Half of the studied individuals carried an mtDNA haplotype that did not belong to C. capreolus, but to a related species that does not occur naturally in the area, the Siberian roe deer (C. pygargus. No differentiation between individuals with Siberian and European mtDNA haplotypes was detected at microsatellite loci. Introgression of mtDNA of Siberian roe deer into the genome of European roe deer has recently been detected in eastern Europe. Such introgression might be caused by human-mediated translocations of Siberian roe deer within the range of European roe deer or by natural hybridization between these species in the past.

  10. Estimation of Genetic Gain on Growth and Carcass Traits over Direct and Index Selection for Growth and Feed Efficiency of Japanese Black Cattle by computer simulation(Animal Production Science Animal Breeding and Genetics)

    OpenAIRE

    HOQUE,Md. Azharul / SUZUKI,Keiichi / OIKAWA,Takuro

    2007-01-01

    A simulation study was performed for performance traits on 740 bulls and carcass traits on 1,774 progeny in Japanese Black cattle to compare the efficiency of direct and index selection. Performance traits included average daily gain (ADG), final body weight (BWF), metabolic body weight (MWT), feed intake (FI), feed conversion ratio (FCR) and residual feed intake (RFI). Progeny traits were carcass weight (CWT), rib eye area (REA), rib thickness (RBT), subcutaneous fat thickness (SFT), marblin...

  11. Genomic selection in small dairy cattle populations

    DEFF Research Database (Denmark)

    Thomasen, Jørn Rind

    on optimization of genomc selction for a small dairy cattle breed such as Danish Jersey. Implementing genetic superior breeding schemes thus requires more accurate genomc predictions. Besides international collaboration, genotyping of cows is an efficient way to obtain more accurate genomic predictions...

  12. Breeding for longevity in Italian Chianina cattle

    NARCIS (Netherlands)

    Forabosco, F.

    2005-01-01

    The objective of this thesis was to evaluate genetic aspects of longevity (LPL) in the Chianina beef cattle population in order to define how to include this trait in selection criteria. The Chianina breed has been raised for over twenty-two centuries inItaly

  13. Cattle breeding goals and production circumstances.

    NARCIS (Netherlands)

    Groen, A.F.

    1989-01-01

    This thesis gives the results of a study on the relationship between cattle breeding goals and production circumstances. The relationship between breeding goals and production circumstances mostly arises from the influences of production circumstances on the economic values of geneticim

  14. Whole genome linkage disequilibrium maps in cattle

    Science.gov (United States)

    Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides bac...

  15. Selection efficiencies for improving drought/salt tolerances and yield using introgression breeding in rice(Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    Ying; Wang; Lubiao; Zhang; Afif; Nafisah; Linghua; Zhu; Jianlong; Xu; Zhikang; Li

    2013-01-01

    The backcross(BC) breeding strategy has been increasingly used for developing high yielding varieties with improved abiotic stress tolerances in rice. In this study, 189Huang-Hua-Zhan(HHZ) introgression lines(ILs) developed from three different selection schemes were evaluated for yield related traits under drought stress and non-stress conditions in the target and off-season winter nursery environments to assess the selection efficiency of BC breeding for improving different complex traits, and led us to five important results. The first result indicated that the primary target traits should be selected first in the target environments(TEs) in order to achieve the maximum genetic gain. Secondly, BC breeding for drought tolerance(DT) in rice was almost equally effective by strong phenotypic selection in the main target environments and in the winter-season of Hainan.Thirdly, exploiting genetic diversity in the subspecific gene pools is of great importance for future genetic improvement of complex traits in rice. Fourthly, considerable genetic gain can be effectively achieved by selection for secondary target traits among the ILs with the primary traits. Finally, the developed ILs provide useful materials for future genetic/genomic dissection and molecular breeding of complex traits.

  16. Targeted introgression of cotton fibre quality quantitative trait loci using molecular markers

    International Nuclear Information System (INIS)

    Within the framework of a cotton breeding programme, molecular markers are used to improve the efficiency of the introgression of fibre quality traits of Gossypium barbadense into G. hirsutum. A saturated genetic map was developed based on genotyping data obtained from the BC1 (75 plants) and BC2 (200 plants) generations. Phenotypic measurements conducted over three generations (BC1, BC2 and BC2S1) allowed 80 quantitative trait loci (QTL) to be detected for fibre length, uniformity, strength, elongation, fineness and colour. Positive QTL, i.e. those for which favourable alleles came from the G. barbadense parent, were harboured by 19 QTL-rich regions on 15 'carrier' chromosomes. In subsequent generations (BC3 and BC4), markers framing the QTL-rich regions were used to select about 10 percent of over 400 plants analysed in each generation. Although BC plants selected through the marker-assisted selection (MAS) process show promising fibre quality, only their full field evaluation will allow validation of the procedure. (author)

  17. Heritabilities and genetic correlations of body condition score and muscularity with productive traits and their trend functions in Italian Simmental cattle

    OpenAIRE

    Erika Frigo; Antonia B. Samorè; Daniele Vicario; Alessandro Bagnato; Ottavia Pedron

    2013-01-01

    With the aim to study the genetics of energy and muscle balance in the Italian Simmental breed, the objectives of this study were: i) the estimation of the genetic parameters for body condition score (BCS) and muscularity (MU) score; ii) the estimation of genetic correlations of BCS and MU with productive traits; iii) the estimation of the expected pattern of BCS and MU over lactation. A total of 47,839 records of first-parity lactating cows, collected from 1999 to 2007 in 2794 herds, were us...

  18. SNPs to Chips: Changing the paradigm of mapping and selection in cattle

    Science.gov (United States)

    The past 25 years of research on the cattle genome has focused on DNA marker based tools that can be applied to genetic improvement in cattle. However, the paradigm of marker assisted selection for complex traits has recently shifted from focusing on genetic variation contained in specific quantita...

  19. REPRODUCTIVE TRAITS SELECTION IN NELORE BEEF CATTLE

    Directory of Open Access Journals (Sweden)

    Heverton Luis Moreira

    2015-08-01

    Full Text Available Genetic breeding programs of beef cattle in Brazil are including new features, mainly related to reproductive efficiency.Thus, it is necessary to study the effectiveness of selection and quantify genetic gain for these traits in herds. This study estimated genetic and phenotypic parameters and genetic trends for reproductive traits used in breeding programs for Nelore beef cattle. The traits studied were the scrotal circumference (SC at 365 and 450 days of age (SC365 and SC450, age at first calving (AFC and gestation length, as a cow trait (GLcow and a calf trait (GLcalf. The (covariance components were obtained with the Restricted Maximum Likelihood Methodology in a single and double-trait analysis of the animal model. For scrotal circumference (SC365 and SC450, positive and favorable genetic gains were observed. For AFC, GLcow and GLcalf, the trends were favorable for selection, but without significant genetic gain. Selection for large SC may reduce AFC and improve female reproductive efficiency. The selection for reproductive traits (SC365, SC450, AFC and GL may improve reproductive and productive efficiency of Nelore cattle, if used as a selection criterion.

  20. Genetically modified soybean plants and their ecosystem

    OpenAIRE

    Milošević Mirjana B.; Zlokolica Marija Ž.; Sekulić Petar Ð.; Jarak Mirjana N.; Taški Ksenija J.

    2004-01-01

    Transgenic plants are developed by introgressing new genes using methods of molecular genetics and genetic engineering. The presence of these genes in plant genome is identified on the basis of specific oligonucleotides primers, and the use of PCR (Polymerase Chain Reaction) and DNA fragments multiplication. Genetically modified plants such as soybean constitute a newly created bioenergetic potential whose gene expression can cause disturbance of the biological balance ecosystem, soil structu...

  1. Extended Genetic Diversity of Bovine Viral Diarrhea Virus and Frequency of Genotypes and Subtypes in Cattle in Italy between 1995 and 2013

    OpenAIRE

    Camilla Luzzago; Stefania Lauzi; Erika Ebranati; Monica Giammarioli; Ana Moreno; Vincenza Cannella; Loretta Masoero; Elena Canelli; Annalisa Guercio; Claudio Caruso; Massimo Ciccozzi; Gian Mario De Mia; Pier Luigi Acutis; Gianguglielmo Zehender; Simone Peletto

    2014-01-01

    Genetic typing of bovine viral diarrhea virus (BVDV) has distinguished BVDV-1 and BVDV-2 species and an emerging putative third species (HoBi-like virus), recently detected in southern Italy, signaling the occurrence of natural infection in Europe. Recognizing the need to update the data on BVDV genetic variability in Italy for mounting local and European alerts, a wide collection of 5′ UTR sequences (n = 371) was selected to identify the frequency of genotypes and subtypes at the herd level....

  2. Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower.

    Science.gov (United States)

    Whitney, Kenneth D; Broman, Karl W; Kane, Nolan C; Hovick, Stephen M; Randell, Rebecca A; Rieseberg, Loren H

    2015-05-01

    The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 single nucleotide polymorphism (SNP) markers and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favoured in the wild. QTL for a number of other ecophysiological, phenological and architectural traits colocalized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence. PMID:25522096

  3. Propagule pressure and stream characteristics influence introgression: Cutthroat and rainbow trout in British Columbia

    Science.gov (United States)

    Bennett, S.N.; Olson, J.R.; Kershner, J.L.; Corbett, P.

    2010-01-01

    Hybridization and introgression between introduced and native salmonids threaten the continued persistence of many inland cutthroat trout species. Environmental models have been developed to predict the spread of introgression, but few studies have assessed the role of propagule pressure. We used an extensive set of fish stocking records and geographic information system (GIS) data to produce a spatially explicit index of potential propagule pressure exerted by introduced rainbow trout in the Upper Kootenay River, British Columbia, Canada. We then used logistic regression and the information-theoretic approach to test the ability of a set of environmental and spatial variables to predict the level of introgression between native westslope cutthroat trout and introduced rainbow trout. Introgression was assessed using between four and seven co-dominant, diagnostic nuclear markers at 45 sites in 31 different streams. The best model for predicting introgression included our GIS propagule pressure index and an environmental variable that accounted for the biogeoclimatic zone of the site (r2 = 0.62). This model was 1.4 times more likely to explain introgression than the next-best model, which consisted of only the propagule pressure index variable. We created a composite model based on the model-averaged results of the seven top models that included environmental, spatial, and propagule pressure variables. The propagule pressure index had the highest importance weight (0.995) of all variables tested and was negatively related to sites with no introgression. This study used an index of propagule pressure and demonstrated that propagule pressure had the greatest influence on the level of introgression between a native and introduced trout in a human-induced hybrid zone. ?? 2010 by the Ecological Society of America.

  4. Assessing Introgression betweenEuropean Wildcats (Felis silvestris silvestris) and Domestic Cats (Felis silvestris catus)

    OpenAIRE

    Nussberger, Beatrice

    2013-01-01

    Introgression is an important issue in evolutionarybiology. It is defined as the flow of genes between taxa through hybridization beyond the first generation. Introduced genes of a closely related taxon may serve as raw material for rapid adaptive evolutionary change. On the other hand, introgression could lead to reduced fitness in hybrids, i.e. outbreeding depression, if the newly mixed traits are maladapted to the environment or if, on the genomiclevel, co-adapted gene complexes are di...

  5. 西北农区奶牛遗传改良与DHI测定分析%The Genetic Improvement and DHI Analysis of the Dairy Cattle in the Northwest District

    Institute of Scientific and Technical Information of China (English)

    高建斌; 昝林森; 辛亚平

    2011-01-01

    The author researched the present agricultural areas in the five northwest provinces on the present situation of Chinese dairy industry development, and collected related data of genetic improvement and production performance measurement, which were statisticed and analyzed. Discussing the existing problems of genetic improvement in the five northwest provinces, so people could conclude that DHI measurement system were significant to the cattle breeding production and management, and propose several advices to improve and perfect the genetic improvement and DHI measurement system, and also provide some value information for further speeding up of the dairy improvement in the farming areas of five northwest provinces.%通过调研西北5省农区的奶牛养殖现状,收集有关遗传改良和生产性能数据资料,并加以统计分析,讨论了西北农区奶牛遗传改良工作中现存问题,认为奶牛DHI测定体系对奶牛养殖的生产与管理具有重要意义,提出了今后发展与完善奶牛遗传改良工作和DHI测定体系的建议和措施,为进一步加快西北5省农区奶牛遗传改良工作和提高奶牛生产性能水平,提供了一定的参考价值.

  6. Genetic Variation in CAPN1 Gene and Its Association with Carcass Traits in Chinese Cattle%CAPN1基因遗传变异及其对牛肉质性状的效应分析

    Institute of Scientific and Technical Information of China (English)

    武秀香; 施雪奎; 吴海涛; 毛永江; 杨章平; 李俊雅; 高会江

    2011-01-01

    shearing force and marbling score than others (P<0.05), while the cattle with TT in site C4684T had lower shearing force than that of CT (P<0.05) and individuals with TT had lower former PH after rowing of acid than that of CC (P<0.05).Combined-genotype analysis indicated that the cattle with GGTT had lower shearing force than that of AACC, AGCT and AACT (P<0.05) and lower score of marbling than that of the rest (P<0.05), while the score of fat color of these cattle were higher than others.But there were no significant associations between two sites and other straits.[Conclusion]Site C4684T and A4558G of CAPN1 gene could be used as genetic marks for beef tenderness and marbling score traits.

  7. Genetic Polymorphisms in Exon 4 of IGF2 Gene of Red Cattle and Its Genetic Effects%草原红牛IGF2基因外显子4的遗传多态性及遗传效应分析

    Institute of Scientific and Technical Information of China (English)

    牛伟萍; 刘晶; 张金玉; 张明军; 杨润军; 赵志辉

    2011-01-01

    The method of PCR - SSCP was used to study the genetic polymorphism of IGF2 gene exon 4 in Red Cattle. Using the linear model, the correlations of different genotypes of mutation points with the naked body and meat quality traits was analyzed. The results showed that there is a SNP site (C250G) in exon 4. The gene has two genotypes, AA and AB. In rid fat weight, genotype AB is 3.1% higher than genotype AA( P < 0.05). Meanwhile, in bone weight and eye muscle area, genotype AB is 15.7% and 46.05 % lower than genotype AA, respectively ( P < O. 01). The genetic polymorphism of the IGF2 gene Exon4 probably has direct genetic effects on meat quality traits in Red Cattle.%运用PCR-SSCP方法检测草原红牛IGF2基因第4外显子的多态性,采用最小二乘法拟合线性模型将突变位点的不同基因型与牛胴体和肉质性状进行关联分析.结果表明:在外显子4上有1个SNP位点(C250G),该基因具有AA和AB 2种基因型,草原红牛AB基因型个体肋脂质量比AA基因型个体高3.1%(P<0.05),骨质量和眼肌面积较AA基因型个体分别低15.7%和46.05%(P<0.01).IGF2基因的遗传多态性可能直接影响草原红牛的肉质性状.

  8. Diet and fertility in cattle

    Directory of Open Access Journals (Sweden)

    Petrujkić Tihomir

    2003-01-01

    Full Text Available The diet of high-yield dairy cows process a very complex and acute problem. Much new knowledge in the area of production and preparation of feedstuffs, diet technology, and the interactions that occur between the components of the nutritive feed ration are required in order to resolve this problem. It is necessary constantly to coordinate feed norms with genetic potential which is ever changing and advanced. The observed problems must be resolved using multidisciplinary methods so that a diet can yield good health, and that health contribute to better reproduction and possibilities for more successful breeding and improved performance in cattle farming. In certain countries, thanks to their geographic position and climatic conditions which allow rainfall throughout the year, a natural green diet can be applied, which provides large numbers of green mass components, and with additives which can be supplemented relatively easily. This type of diet is not possible in our farms. It is very important to know which feedstuff components are laking for certain categories of cattle. The used ration must be constant and administered to animals of certain age or production characteristics in order to improve production results at cattle farms. A great problem occurs when diet is reduced due to dried grass and the resulting stress in animals. A 50% diet reduction in young cattle often results in the occurrence of respiratory diseases. Following 10-14 days of treatment, the disease disappears in young animals, but the energy deficit leads to the weakening (depression of the immune system. Even a so-called high-energy diet often causes respiratory diseases. A diet deficient in proteins also affects cows after lactation, as opposed to a normative diet, and a reduced protein diet disturbs the microbial activity in the rumen and the synthesis of compounds which are important for both the cow and the calf, making room for the incidence of metabolic diseases, most

  9. Heritabilities and genetic correlations of body condition score and muscularity with productive traits and their trend functions in Italian Simmental cattle

    Directory of Open Access Journals (Sweden)

    Erika Frigo

    2013-05-01

    Full Text Available With the aim to study the genetics of energy and muscle balance in the Italian Simmental breed, the objectives of this study were: i the estimation of the genetic parameters for body condition score (BCS and muscularity (MU score; ii the estimation of genetic correlations of BCS and MU with productive traits; iii the estimation of the expected pattern of BCS and MU over lactation. A total of 47,839 records of first-parity lactating cows, collected from 1999 to 2007 in 2794 herds, were used. Two-trait animal models were analyzed using restricted maximum likelihood (REML procedures to estimate (covariance components. The expected patterns of BCS and MU along the lactation of first parity cows were estimated from the solutions of DIM fixed effect obtained from an univariate mixed model for both the traits. The heritability estimated was 0.18 for BCS, 0.38 for MU, and ranged from 0.13 to 0.18 for yield traits. The genetic correlations between BCS, MU and yield traits were negative (-0.17 to -0.63. The genetic correlation between BCS and MU was strongly positive (0.88, indicating that cows that genetically tend to have high BCS are more likely to have high values of MU. The genetic parameters estimated suggested that selection for BCS and MU in dual purpose breeds may be possible, and BCS may indirectly improve MU. The expected patterns for BCS and MU showed the trend of these two traits along the lactation and can help farmers in planning the best management of the lactating cows.

  10. Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing.

    Science.gov (United States)

    Ma, Xin; Fu, Yongcai; Zhao, Xinhui; Jiang, Liyun; Zhu, Zuofeng; Gu, Ping; Xu, Wenying; Su, Zhen; Sun, Chuanqing; Tan, Lubin

    2016-01-01

    Oryza nivara, an annual wild AA-genome species of rice, is an important gene pool for broadening the genetic diversity of cultivated rice (O. sativa L.). Towards identifying and utilizing favourable alleles from O. nivara, we developed a set of introgression lines (ILs) by introducing O. nivara segments into the elite indica rice variety 93-11 background through advanced backcrossing and repeated selfing. Using whole-genome resequencing, a high-density genetic map containing 1,070 bin-markers was constructed for the 131 ILs, with an average length of 349 kb per bin. The 131 ILs cover 95% of O. nivara genome, providing a relatively complete genomic library for introgressing O. nivara alleles for trait improvement. Using this high-density bin-map, QTL mapping for 13 yield-related traits was performed and a total of 65 QTLs were detected across two environments. At ~36.9% of detected QTLs, the alleles from O. nivara conferred improving effects on yield-associated traits. Six cloned genes, Sh4/SHA1, Bh4, Sd1, TE/TAD1, GS3 and FZP, colocalised in the peak intervals of 9 QTLs. In conclusion, we developed new genetic materials for exploration and use of beneficial alleles from wild rice and provided a basis for future fine mapping and cloning of the favourable O. nivara-derived QTLs. PMID:27251022

  11. Assessment of diversity in Harpagophytum with RAPD and ISSR markers provides evidence of introgression.

    Science.gov (United States)

    Muzila, Mbaki; Werlemark, Gun; Ortiz, Rodomiro; Sehic, Jasna; Fatih, Moneim; Setshogo, Moffat; Mpoloka, Wata; Nybom, Hilde

    2014-10-01

    The genus Harpagophytum has two species: H. procumbens which is an important medicinal plant in southern Africa, and H. zeyheri. Genetic diversity in 96 samples, obtained by germinating seeds collected from Botswana, was assessed using six inter-simple sequence repeat (ISSR) and 10 random amplified polymorphic DNA (RAPD) primers. These DNA markers yielded a total of 138 polymorphic bands. Polymorphism information content (PIC) ranged from 0.06 to 0.39 for ISSR primers, and from 0.09 to 0.43 for RAPD primers. Jaccard's similarity coefficients were highest when seedlings derived from the same fruit capsule were compared, while seedlings from different fruits on the same plant had intermediate values. The lowest values were recorded among seedlings from different plants. These results were consistent with an outcrossing breeding system in Harpagophytum. Analysis of molecular variance revealed significant differentiation (PHarpagophytum. About 39% of the variability occurred between the two species, H. procumbens and H. zeyheri. Plants with an intermediate morphology, i.e. putative hybrids (PH), showed 21% differentiation when compared with H. procumbens ssp. procumbens (PP), and 19% when compared with H. procumbens ssp. transvaalense (PT) or with H. zeyheri (ZZ). In addition, a deviating variant of PT was identified, here termed 'procumbens new variety' (PN). PN showed only 9% differentiation when compared with PT, 22% when compared with PP or with PH, and 41% when compared with ZZ. Considerable differentiation between the two Harpagophytum species was revealed also by a cluster analysis. Introgression was, however, suggested by the intermediate position of the putative hybrid plants in a principal component analysis while inter-specific gene flow was shown by a Bayesian genetic structure analysis. PMID:25363276

  12. Mapping Heterotic Loci for Yield and Agronomic Traits Using Chromosome Segment Introgression Lines in Cotton

    Institute of Scientific and Technical Information of China (English)

    Xian Guo; Yuping Guo; Jun Ma; Fang Wang; Mizhen Sun; Lijuan Gui; Jiajia Zhou

    2013-01-01

    In the present study,a set of chromosome segment introgression lines (CSILs) using Gossypium hirsutum L.TM-1 as the recipient parent and G.barbadense Hai7124 as the donor parent were used to explore the genetic basis of heterosis for interspecific hybrids.Two sets of F1 populations individually derived from CSlLs crossing with both parents were configured to investigate heterotic loci (HL) and substitution effect loci (SL).A total of 58 HL and 39 SL were identified in 3 years.One stable HL,hLP-A4-3,could be detected in all 3 years.Three HLs,hBS-A8-1,hLP-D6-1,and hSI-D7-11,could be detected in 2 years.Four SLs,sBS-D7-1,sLP-A8-1,sLP-D7-1,and sLP-D12-1,could be detected in 2 years.HL and SL tended to be distributed in some HL-rich chromosome segments with close positions.Compared with QTL detected in a former study,HL showed little overlap with QTL,indicating that trait phenotype and heterosis might be controlled by different sets of loci.All three forms of genetic effects (partial-,full-,over-dominant) were identified,while the over-dominant effect made the main contribution to heterosis.These results may help lay the foundation for clarifying the heredity mechanism of heterosis in cotton.

  13. Variability and performance evaluation of introgressed Nigerian dura x Deli dura oil palm progenies.

    Science.gov (United States)

    Noh, A; Rafii, M Y; Mohd Din, A; Kushairi, A; Norziha, A; Rajanaidu, N; Latif, M A; Malek, M A

    2014-01-01

    Twelve introgressed oil palm (Elaeis guineensis) progenies of Nigerian dura x Deli dura were evaluated for bunch yield, yield attributes, bunch quality components and vegetative characters at the Malaysian Palm Oil Board Research Station, in Keratong, Pahang, Malaysia. Analysis of variance revealed significant to highly significant genotypic differences, indicating sufficient genetic variability among the progenies for bunch yield and its attributes, vegetative characters and bunch quality components, except fruit to bunch ratio. Fresh fruit bunch yield ranged from 167 kg·palm(-1)·year(-1) in PK1330 to 212 kg·palm(-1)·year(-1) in PK1351, with a mean yield of 192 kg·palm(-1)·year(-1). Among the progeny, PK1313 had the highest oil to bunch ratio (19.36%), due to its high mesocarp to fruit ratio, fruit to bunch ratio and low shell to fruit ratio. Among the progenies, PK1313 produced the highest oil yield of 31.4 kg·palm(-1)·year(-1), due to a high mesocarp to fruit ratio (61.2%) and a low shell to fruit ratio (30.7%), coupled with high fruit to bunch ratio (65.6%). PK1330 was found promising for selection, as it had desirable vegetative characters, including smaller petiole cross section (27.15 cm2), short rachis length (4.83 m), short palm height (1.85 m), and the lowest leaf number (164.6), as these vegetative characters are prerequisites for selecting palms for high density planting and high yield per hectare. The genetic variability among the progenies was found to be high, indicating ample scope for further breeding, followed by selection. PMID:24781997

  14. Association study of genetic variants at single nucleotide polymorphism rs109231409 of mannose-binding lectins 1 gene with mastitis susceptibility in Vrindavani crossbred cattle

    Directory of Open Access Journals (Sweden)

    V. N. Muhasin Asaf

    2014-10-01

    Full Text Available Aim: The present study was undertaken to identify whether single nucleotide polymorphism (SNP rs109231409 located on mannose-binding lectins 1 (MBL1 gene was associated with mastitis tolerance/susceptibility. Materials and Methods: After grouping 100 Vrindavani crossbred cattle as mastitis positive and negative animals, they were genotyped using polymerase chain reaction (PCR-restriction fragment length polymorphisms method. Gene and genotype frequencies of different patterns were estimated by standard procedure (POPGENE version 1.32, (University of Alberta, Canada and statistical analysis was carried out by logistic regression methods using STATA 12 software (StataCorp LP, USA. Results: The 588 bp fragment of MBL1 gene was amplified using PCR. PCR product was digested with ApaI restriction enzyme showed two distinct genotypes viz., GG (311 bp and 272 bp fragments and GA (588 bp, 311 bp and 277 bp fragments. The gene, genotype frequencies, average heterozygosity, polymorphic information content and χ2 values for the locus rs109231409 was ascertained. Conclusions: No significant association between SNP “rs109231409” with mastitis tolerance was found. Although there is a lack of association, further studies have to be undertaken in a large population in order to validate the impact of rs109231409 (g.855G >A on mastitis tolerance.

  15. Progressive introgression between ¤Brassica napus¤ (oilseed rape) and ¤B-rapa¤

    DEFF Research Database (Denmark)

    Hansen, L.B.; Siegismund, H.R.; Bagger Jørgensen, Rikke

    2003-01-01

    We have earlier shown extensive introgression between oilseed rape (Brassica napus) and B. rapa in a weedy population using AFLP markers specific for the nuclear genomes. In order to describe the progress of this introgression, we examined 117 offspring from 12 maternal plants from the introgressed...... maternal plants. It seemed that B. rapa most often functioned as the maternal plant in the introgression process and that the amount of oilseed rape DNA was highly diminished in the offspring compared to their introgressed maternal plants. However, our analysis of plants from the weedy population indicated...... that introgression can lead to both (1) exchange of chloroplast DNA between species producing B. rapa-like plants with B. napus chloroplasts and (2) incorporation of B. napus C-genome DNA into the B. rapa genome. Therefore, we question whether it can be regarded as containment to position transgenes...

  16. Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression.

    Science.gov (United States)

    Li, Runsheng; Ren, Xiaoliang; Bi, Yu; Ho, Vincy Wing Sze; Hsieh, Chia-Ling; Young, Amanda; Zhang, Zhihong; Lin, Tingting; Zhao, Yanmei; Miao, Long; Sarkies, Peter; Zhao, Zhongying

    2016-09-01

    Hybrid incompatibility (HI) prevents gene flow between species, thus lying at the heart of speciation genetics. One of the most common HIs is male sterility. Two superficially contradictory observations exist for hybrid male sterility. First, an introgression on the X Chromosome is more likely to produce male sterility than on autosome (so-called large-X theory); second, spermatogenesis genes are enriched on the autosomes but depleted on the X Chromosome (demasculinization of X Chromosome). Analysis of gene expression in Drosophila hybrids suggests a genetic interaction between the X Chromosome and autosomes that is essential for male fertility. However, the prevalence of such an interaction and its underlying mechanism remain largely unknown. Here we examine the interaction in nematode species by contrasting the expression of both coding genes and transposable elements (TEs) between hybrid sterile males and its parental nematode males. We use two lines of hybrid sterile males, each carrying an independent introgression fragment from Caenorhabditis briggsae X Chromosome in an otherwise Caenorhabditis nigoni background, which demonstrate similar defects in spermatogenesis. We observe a similar pattern of down-regulated genes that are specific for spermatogenesis between the two hybrids. Importantly, the down-regulated genes caused by the X Chromosome introgressions show a significant enrichment on the autosomes, supporting an epistatic interaction between the X Chromosome and autosomes. We investigate the underlying mechanism of the interaction by measuring small RNAs and find that a subset of 22G RNAs specifically targeting the down-regulated spermatogenesis genes is significantly up-regulated in hybrids, suggesting that perturbation of small RNA-mediated regulation may contribute to the X-autosome interaction.

  17. Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome.

    Science.gov (United States)

    Kim, Woonsu; Park, Hyesun; Seo, Seongwon

    2016-01-01

    The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle.

  18. Economic and Biological Values for Pasture-Based Dairy Cattle Porduction Systems and their Application in Genetic Improvement in the Tropics

    DEFF Research Database (Denmark)

    Wahinya, P K; Otieno, Tobias Okeno; Kosgey, I S;

    2015-01-01

    during the estimation of economic values. Genetic improvements targeting MY and growth traits would be recommended to production system with unlimited feed supply for profit maximization. However, since dairy production systems in the tropics are characterised by feed scarcity, fixing the herd...

  19. Extended Genetic Diversity of Bovine Viral Diarrhea Virus and Frequency of Genotypes and Subtypes in Cattle in Italy between 1995 and 2013

    Directory of Open Access Journals (Sweden)

    Camilla Luzzago

    2014-01-01

    Full Text Available Genetic typing of bovine viral diarrhea virus (BVDV has distinguished BVDV-1 and BVDV-2 species and an emerging putative third species (HoBi-like virus, recently detected in southern Italy, signaling the occurrence of natural infection in Europe. Recognizing the need to update the data on BVDV genetic variability in Italy for mounting local and European alerts, a wide collection of 5′ UTR sequences (n = 371 was selected to identify the frequency of genotypes and subtypes at the herd level. BVDV-1 had the highest frequency, followed by sporadic BVDV-2. No novel HoBi-like viruses were identified. Four distribution patterns of BVDV-1 subtypes were observed: highly prevalent subtypes with a wide temporal-spatial distribution (1b and 1e, low prevalent subtypes with a widespread geographic distribution (1a, 1d, 1g, 1h, and 1k or a restricted geographic distribution (1f, and sporadic subtypes detected only in single herds (1c, 1j, and 1l. BVDV-1c, k, and l are reported for the first time in Italy. A unique genetic variant was detected in the majority of herds, but cocirculation of genetic variants was also observed. Northern Italy ranked first for BVDV introduction, prevalence, and dispersion. Nevertheless, the presence of sporadic variants in other restricted areas suggests the risk of different routes of BVDV introduction.

  20. Extended genetic diversity of bovine viral diarrhea virus and frequency of genotypes and subtypes in cattle in Italy between 1995 and 2013.

    Science.gov (United States)

    Luzzago, Camilla; Lauzi, Stefania; Ebranati, Erika; Giammarioli, Monica; Moreno, Ana; Cannella, Vincenza; Masoero, Loretta; Canelli, Elena; Guercio, Annalisa; Caruso, Claudio; Ciccozzi, Massimo; De Mia, Gian Mario; Acutis, Pier Luigi; Zehender, Gianguglielmo; Peletto, Simone

    2014-01-01

    Genetic typing of bovine viral diarrhea virus (BVDV) has distinguished BVDV-1 and BVDV-2 species and an emerging putative third species (HoBi-like virus), recently detected in southern Italy, signaling the occurrence of natural infection in Europe. Recognizing the need to update the data on BVDV genetic variability in Italy for mounting local and European alerts, a wide collection of 5' UTR sequences (n = 371) was selected to identify the frequency of genotypes and subtypes at the herd level. BVDV-1 had the highest frequency, followed by sporadic BVDV-2. No novel HoBi-like viruses were identified. Four distribution patterns of BVDV-1 subtypes were observed: highly prevalent subtypes with a wide temporal-spatial distribution (1b and 1e), low prevalent subtypes with a widespread geographic distribution (1a, 1d, 1g, 1h, and 1k) or a restricted geographic distribution (1f), and sporadic subtypes detected only in single herds (1c, 1j, and 1l). BVDV-1c, k, and l are reported for the first time in Italy. A unique genetic variant was detected in the majority of herds, but cocirculation of genetic variants was also observed. Northern Italy ranked first for BVDV introduction, prevalence, and dispersion. Nevertheless, the presence of sporadic variants in other restricted areas suggests the risk of different routes of BVDV introduction.

  1. k-Casein, b-lactoglobulin and growth hormone allele frequencies and genetic distances in Nelore, Gyr, Guzerá, Caracu, Charolais, Canchim and Santa Gertrudis cattle

    Directory of Open Access Journals (Sweden)

    Paola Augusta Kemenes

    1999-12-01

    Full Text Available The genotypes for k-casein (k-CN, b-lactoglobulin (b-LG and growth hormone (GH were determined by polymerase chain reaction (PCR and restriction enzyme digestion in seven breeds of cattle (Nelore, Gyr, Guzerá, Caracu, Charolais, Canchim and Santa Gertrudis. k-Casein had two alleles with the A allele occurring at a higher frequency in Bos indicus breeds (0.93, 0.92 and 0.91% for Gyr, Guzerá and Nelore, respectively. The b-lactoglobulin locus had two alleles in all of the breeds. European breeds had a higher frequency of the b-LG A allele than Zebu breeds. The GH locus had two alleles (L and V in Bos taurus and was monomorphic (L allele only in all of the Bos indicus breeds evaluated. The highest frequency for the V allele was observed in Charolais cattle. The markers used revealed a considerable similarity among breeds, with two main groups being discernible. One group consisted of Zebu and Santa Gertrudis breeds and the other consisted of European and Canchim breeds.Os genótipos de k-caseína (k-CN, b-lactoglobulina (b-LG e hormônio de crescimento foram determinados por reação em cadeia de polimerase (PCR e digestão com enzima de restrição em sete raças de bovinos (Nelore, Gir, Guzerá, Caracu, Charolesa, Canchim and Santa Gertrudis. A k-caseína apresentou dois alelos e as freqüências mais elevadas para o alelo A foram observadas em Bos indicus (0,93, 0,92 e 0,91% para as raças Gir, Guzerá e Nelore, respectivamente. A b-lactoglobulina apresentou dois alelos em todas as raças estudadas, sendo a freqüência do alelo A mais elevada nas raças européias. O loco de hormônio de crescimento apresentou dois alelos em Bos taurus e foi monomórfico (alelo L em todas as raças zebuínas. A maior freqüência para o alelo V foi observado na raça Charolesa. Os marcadores investigados revelaram alta similaridade entre as raças, com a formação de dois grupos principais: um composto de raças zebuínas e a raça Santa Gertrudis e outro

  2. Bovine herpesvirus-1: Genetic diversity of field strains from cattle with respiratory disease, genital, fetal disease and systemic neonatal disease and their relationship to vaccine strains.

    Science.gov (United States)

    Fulton, R W; d'Offay, J M; Dubovi, E J; Eberle, R

    2016-09-01

    Bovine herpesvirus-1 (BoHV-1) causes disease in cattle with varied clinical forms. In the U.S. there are two BoHV1 subtypes, BoHV-1.1 and BoHV-1.2b. Control programs in North America incorporate modified live (MLV) or killed (KV) viral vaccines. However, BoHV-1 strains continue to be isolated from diseased animals or fetuses after vaccination. It is possible to differentiate BoHV-1 wild-type from MLV vaccine strains by determining their single nucleotide polymorphism (SNP) patterns through either whole-genome sequencing or PCR sequencing of genomic regions containing vaccine-defining SNPs. To determine the BoHV-1 subtype in clinical isolates and their relationship to MLV strains, 8 isolates from varied clinical disease at three different laboratories in the U.S. were sequenced and phylogenetically analyzed. Five samples were isolated within the past 5 years from New York and 3 were archived samples recovered 35 years prior from Oklahoma and Louisiana. Based on phylogenetic analysis, four of the cases appeared to be due to an MLV vaccine: 3 cases of aborted fetuses and one neonate with systemic BoHV-1 disease. One aborted fetus was from a herd with no reported history of MLV vaccination in two years. The remaining four isolates did not group with any MLV vaccines: two were associated with bovine respiratory disease, one with vulvovaginitis, and a fourth was determined to be a BoHV-1.2b respiratory isolate. Recovery of BoHV-1.1 that is very closely related to an MLV vaccine virus from a herd not receiving vaccines in an extended period prior to its isolation suggests that MLV viruses may remain latent or circulate within herds for long periods. PMID:27374060

  3. Introgression Between Cultivars and Wild Populations of Momordica charantia L. (Cucurbitaceae in Taiwan

    Directory of Open Access Journals (Sweden)

    Yu-Chung Chiang

    2012-05-01

    Full Text Available The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM. Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes.

  4. QTL mapping for production traits in Czech Fleckvieh cattle

    DEFF Research Database (Denmark)

    Matejickova, J; Stipkova, M; Sahana, Goutam;

    2013-01-01

    The objective of this study was to find QTL for milk production traits in Czech Fleckvieh cattle on chromosomes 6, 7, 11, 14, and 23 where QTL were previously identified in other dairy cattle populations. Sixteen grandsire families were genotyped for 38 microsatellite markers on the selected...... of milk production in the Czech Fleckvieh cattle....... associated with milk production traits appeared on other studied chromosomes (BTA6, BTA7, BTA11, and BTA23). This first QTL search on five chromosomes in Czech Fleckvieh population showed several suggestive QTL that can be promising for further studies and contribute to better understanding of genetics...

  5. Genetic and environmental effects on sexual precocity traits in Nellore cattle Efeitos genéticos e ambientais sobre características de precocidade sexual em bovinos Nelore

    Directory of Open Access Journals (Sweden)

    Sarah Laguna Meirelles

    2009-08-01

    Full Text Available The objective of this study was to estimate the heritability of probability of early pregnancy (PEP and scrotal circumference (SC and the genetic correlation between these traits in Nellore cattle. PEP records from 11,696 Nellore females born between 1983 and 2001 were analyzed. PEP was assumed to be one for females that effectively bred in the herd (19.84% and zero for those discarded before first calving (80.16%. The model used to study PEP included the effects of contemporary group, age of dam at calving and heifer weaning age, direct additive genetic effects, and residual effects. For SC, 9335 records were analyzed considering the effect of contemporary group, direct additive genetic effects and residual effects. Covariance components were estimated by Gibbs sampling applied to a two-trait sire model, using a threshold model for PEP and a linear model for SC. Estimated mean heritability was 0.47 ± 0.05 for PEP and 0.27 ± 0.03 for SC, and the genetic correlation between traits was 0.12 ± 0.20. These results indicated the existence of additive genetic variation for PEP and this trait should therefore respond to selection. The estimated genetic correlation between PEP and SC indicated a low, but favorable, association. Thus, SC might be used together with PEP in genetic evaluations of sexual precocity. This procedure would increase the accuracy of predicting expected progeny differences for PEP.O objetivo neste trabalho foi estimar a herdabilidade das características probabilidade de prenhez precoce (PPP e perímetro escrotal (PE de animais da raça Nelore e a correlação genética entre essas características. Foram analisados dados de probabilidade de prenhez precoce de 11.696 fêmeas da raça Nelore nascidas entre 1983 e 2001. A probabilidade de prenhez precoce assumiu o valor 1 para fêmeas que efetivamente reproduziram no rebanho (19,84% e zero para aquelas descartadas antes do primeiro parto (80,16%. O modelo para PPP incluiu os

  6. Genetically modified soybean plants and their ecosystem

    Directory of Open Access Journals (Sweden)

    Milošević Mirjana B.

    2004-01-01

    Full Text Available Transgenic plants are developed by introgressing new genes using methods of molecular genetics and genetic engineering. The presence of these genes in plant genome is identified on the basis of specific oligonucleotides primers, and the use of PCR (Polymerase Chain Reaction and DNA fragments multiplication. Genetically modified plants such as soybean constitute a newly created bioenergetic potential whose gene expression can cause disturbance of the biological balance ecosystem, soil structure and soil microbiological activity. Genetically modified plants may acquire monogenic or polygenic traits causing genetic and physiological changes in these plants, which may elicit a certain reaction of the environment including changes of microbiological composition of soil rhizosphere. The aim of introgressing genes for certain traits into a cultivated plant is to enhance its yield and intensify food production. There are more and more genetically modified plant species such as soybean, corn, potato, rice and others and there is a pressure to use them as human food and animal feed. Genetically modified soybean plants with introgressed gene for resistance to total herbicides, such as Round-up, are more productive than non-modified herbicide-sensitive soybeans.

  7. Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.

    Science.gov (United States)

    Wen, Dingqiao; Yu, Yun; Hahn, Matthew W; Nakhleh, Luay

    2016-06-01

    The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence. PMID:26808290

  8. Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system

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    Hoffmann Astrid

    2012-10-01

    Full Text Available Abstract Background In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs under two contrasting hydroponic nitrogen (N supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent ‘Scarlett’. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1 to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2 to locate quantitative trait loci (QTL that control the examined traits, (3 to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4 to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross. Results The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population. Conclusion Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

  9. Identification of Chromosome Segment Substitution Lines of Gossypium barbadense Introgressed in G. hirsutum and Quantitative Trait Locus Mapping for Fiber Quality and Yield Traits.

    Science.gov (United States)

    Zhai, Huanchen; Gong, Wankui; Tan, Yunna; Liu, Aiying; Song, Weiwu; Li, Junwen; Deng, Zhuying; Kong, Linglei; Gong, Juwu; Shang, Haihong; Chen, Tingting; Ge, Qun; Shi, Yuzhen; Yuan, Youlu

    2016-01-01

    Chromosome segment substitution lines MBI9804, MBI9855, MBI9752, and MBI9134, which were obtained by advanced backcrossing and continuously inbreeding from an interspecific cross between CCRI36, a cultivar of upland cotton (Gossypium hirsutum) as the recurrent parent, and Hai1, a cultivar of sea island cotton (G. barbadense) as the donor parent, were used to construct a multiple parent population of (MBI9804×MBI9855)×(MBI9752×MBI9134). The segregating generations of double-crossed F1 and F2 and F2:3 were used to map the quantitative trait locus (QTL) for fiber quality and yield-related traits. The recovery rate of the recurrent parent CCRI36 in the four parental lines was from 94.3%-96.9%. Each of the parental lines harbored 12-20 introgressed segments from Hai1across 21 chromosomes. The number of introgressed segments ranged from 1 to 27 for the individuals in the three generations, mostly from 9 to 18, which represented a genetic length of between 126 cM and 246 cM. A total of 24 QTLs controlling fiber quality and 11 QTLs controlling yield traits were detected using the three segregating generations. These QTLs were distributed across 11 chromosomes and could collectively explain 1.78%-20.27% of the observed phenotypic variations. Sixteen QTLs were consistently detected in two or more generations, four of them were for fiber yield traits and 12 were for fiber quality traits. One introgressed segment could significantly reduce both lint percentage and fiber micronaire. This study provides useful information for gene cloning and marker-assisted breeding for excellent fiber quality. PMID:27603312

  10. Extensive introgression in a malaria vector species complex revealed by phylogenomics

    Science.gov (United States)

    Fontaine, Michael C.; Pease, James B.; Steele, Aaron; Waterhouse, Robert M.; Neafsey, Daniel E.; Sharakhov, Igor V.; Jiang, Xiaofang; Hall, Andrew B.; Catteruccia, Flaminia; Kakani, Evdoxia; Mitchell, Sara N.; Wu, Yi-Chieh; Smith, Hilary A.; Love, R. Rebecca; Lawniczak, Mara K.; Slotman, Michel A.; Emrich, Scott J.; Hahn, Matthew W.; Besansky, Nora J.

    2015-01-01

    Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny, and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between these malaria vectors means that only a small fraction of the genome, mainly on the X chromosome, has not crossed species boundaries. Our results suggest that traits enhancing vectorial capacity may be gained through interspecific gene flow, including between non-sister species. PMID:25431491

  11. Molecular cytogenetic characterization of alien introgressions with gene Fhb3 for resistance to Fusarium head blight disease of wheat

    Science.gov (United States)

    Fusarium head blight (FHB) resistance was identified in the alien species Leymus racemosus, and wheat-Leymus introgression lines with FHB resistance were reported previously. Detailed molecular cytogenetic analysis of alien introgressions T01, T09, and T14 and the mapping of Fhb3, a new gene for FHB...

  12. Sequencing and Characterization of Divergent Marbling Levels in the Beef Cattle (Longissimus dorsi Muscle) Transcriptome

    OpenAIRE

    Dong CHEN; Li, Wufeng; Du, Min; Wu, Meng; Cao, Binghai

    2015-01-01

    Marbling is an important trait regarding the quality of beef. Analysis of beef cattle transcriptome and its expression profile data are essential to extend the genetic information resources and would support further studies on beef cattle. RNA sequencing was performed in beef cattle using the Illumina High-Seq2000 platform. Approximately 251.58 million clean reads were generated from a high marbling (H) group and low marbling (L) group. Approximately 80.12% of the 19,994 bovine genes (protein...

  13. A single nucleotide polymorphism in CAPN1 associated with marbling score in Korean cattle

    OpenAIRE

    Kim Ji; Han Chang; Lee Hae; Namgoong Sohg; Bae Joon; Kim Lyoung; Park Byung; Yoon Du-Hak; Cheong Hyun; Cheong Il-Cheong; Shin Hyoung

    2008-01-01

    Abstract Background Marbling score (MS) is the major quantitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the micromolar calcium-activated neutral protease gene (micro-calpain, CAPN1) and carcass traits in Korean cattle (also known as Hanwoo). Results By direct DNA sequencing in 24 unrelated Korean cattle, we identified 39 sequence variants within exons and their flanking regions in CAPN1. Among them, 12 co...

  14. Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity

    OpenAIRE

    Lee, Kyung-Tai; Chung, Won-Hyong; Lee, Sung-Yeoun; Choi, Jung-Woo; Kim, Jiwoong; Lim, Dajeong; Lee, Seunghwan; Jang, Gul-Won; Kim, Bumsoo; Choy, Yun Ho; Liao, Xiaoping; Stothard, Paul; Moore, Stephen S; Lee, Sang-Heon; Ahn, Sungmin

    2013-01-01

    Background Hanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred as beef cattle. Genetic variation was analyzed by whole-genome deep resequencing of a Hanwoo bull. The Hanwoo genome was compared to that of two other breeds, Black Angus and Holstein, and genes with...

  15. Origins of cattle on Chirikof Island, Alaska, elucidated from genome-wide SNP genotypes

    OpenAIRE

    Decker, J.E.; Taylor, J. F.; Kantanen, J.; Millbrooke, A; Schnabel, R D; Alexander, L. J.; MacNeil, M. D.

    2016-01-01

    Feral livestock may harbor genetic variation of commercial, scientific, historical or esthetic value. The origins and uniqueness of feral cattle on Chirikof Island, Alaska, are uncertain. The island is now part of the Alaska Maritime Wildlife Refuge and Federal wildlife managers want grazing to cease, presumably leading to demise of the cattle. Here we characterize the cattle of Chirikof Island relative to extant breeds and discern their origins. Our analyses support the inference that Yakut ...

  16. Análise de fatores genéticos e ambientais que afetam a infestação de fêmeas bovinas da raça Caracu por carrapatos (Boophilus microplus Genetic analysis of the infestation of Caracu female cattle breed by cattle tick (Boophilus microplus

    Directory of Open Access Journals (Sweden)

    Angelina Bossi Fraga

    2003-12-01

    cattle tick Boophilus microplus (Canestrini, 1887 and to estimate genetic parameters for the level of this infestation. Countings of the parasite were done on female cattle from two herds, during all four seasons of the year, in two consecutive years (from September 1998 through July 2000. The number of ticks (NC on one side of the animal was counted, and the infestations were also evaluated by scores (EC, according to the estimated number of parasites on the animal. Each animal had from one to eight observations. A total of 4,079 and 3,994 observations were obtained for NC and EC, respectively. The data were analyzed by the least squares method with a model that included the effects of herd (H, color of the animal (C, H x C, animal within H x C as error a, year, season, thickness of the hair, and age of animal as a covariable (linear and quadratic effects. The variance and covariance components were estimated by the restricted maximum likelihood derivative free method, using a model that included the effects of contemporary group (herd - year - season, hair thickness and age of the animal as a covariable (linear and quadratic effects, and the random additive direct and permanent environmental effects. Before the analyses, NC was transformed to log10 (n + 1 and EC was transformed to (x + 0.5 ½, where n is the number of ticks counted on the animal and x is the score for EC (0 to 4. The incidence of ticks was higher during the summer, and the ticker the hair the higher the infestation. The heritability and repeatability estimates were equal to 0.22 and 0.29, and 0.15 and 0.21 for NC and EC, respectively, and the genetic correlation between NC and EC was 1.00. The results indicate that there is enough additive genetic variation on tick numbers to support a selection program to increase resistance.

  17. Inventory analysis of West African cattle breeds

    International Nuclear Information System (INIS)

    The improvement of livestock productivity and the preservation of their genetic diversity to allow breeders to select animals adapted to environmental changes, diseases and social needs, require a detailed inventory and genetic characterization of domesticated animal breeds. Indeed, in developing countries, the notion of breed is not clearly defined, as visual traits are often used and characterization procedures are often subjective. So it is necessary to upgrade the phenotypic approach using genetic information. At CIRDES, a regional centre for subhumid livestock research and development, such studies have been conducted. This paper focuses on cattle breed inventory in seven countries of West Africa as a tool for genetic research on cattle improvement. Data collection was done using a bibliographical study, complemented by in situ investigations. According to phenotypic description and concepts used by indigenous livestock keepers, 13 local cattle breeds were recognized: N'dama, Kouri, the Baoule-Somba group, the Lagoon cattle group, zebu Azawak, zebu Maure, zebu Touareg, zebu Goudali, zebu Bororo, zebu White Fulani, zebu Djelli, zebu Peuhl soudanien and zebu Gobra (Toronke). Nine exotic breeds, (American Brahman, Gir, Girolando, Droughtmaster, Santa Gertrudis, Holstein, Montbeliarde, Jersey and Brown Swiss) and five typical cross-breeds (Holstein x Goudali; Montbeliarde x Goudali; Holstein x Azawak; Brown Swiss x Azawak; and Brown Swiss x zebu peuhl soudanien) were also found. From this initial investigation, the areas of heavy concentration of herds and the most important breeds were described. The review has also indicated the necessity for a balance between improving livestock productivity and the conservation of trypanotolerant breeds at risk of extinction in West Africa. (author)

  18. 苜蓿的遗传标记技术及其利用的研究进展%Progress in Genetic Mark and its utility Research of Alfalfa

    Institute of Scientific and Technical Information of China (English)

    于林清; 王照兰; 萨仁; 卢欣石

    2001-01-01

    Recent progress in genetic mark and its utility were reviewed in this paper. The alfalfa research advances in germplasm analysis, introgression, genefic linkage map and heterosis prediction were highlighted.

  19. Analysis of Introgressed Segments in Near-isogenic Lines for F1 Pollen Sterility in Rice (Oryza sativa)

    Institute of Scientific and Technical Information of China (English)

    LI Wen-tao; ZENG Rui-zhen; ZHANG Ze-min; Akshay TALUKDAR; ZHANG Gui-quan

    2003-01-01

    One hundred and fifty-eight microsatellite markers showing polymorphism among parents were used to survey the introgressed segments in the 50 near-isogenic lines of F1 pollen sterility. Two hundred and sixty introgressed segments were detected in 50 near-isogenic lines, each carrying 5.2 introgressed segments on an average. Among the 260 segments, one hundred carrying F1 pollen sterility loci concentrated on the region of F1 pollen sterility genes, and the remaining one hundred and sixty without F1 pollen sterility loci distributed randomly over 12 chromosomes. Both the average number and length of the introgressed segments decreased along with the increase of backcross generations. The number of introgressed segments was less than four and the length was less than 20 cM in the near-isogenic lines after backcrossing for four or more times.

  20. Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models

    Directory of Open Access Journals (Sweden)

    Wielstra Ben

    2012-08-01

    Full Text Available Abstract Background If the geographical displacement of one species by another is accompanied by hybridization, mitochondrial DNA can introgress asymmetrically, from the outcompeted species into the invading species, over a large area. We explore this phenomenon using the two parapatric crested newt species, Triturus macedonicus and T. karelinii, distributed on the Balkan Peninsula in south-eastern Europe, as a model. Results We first delimit a ca. 54,000 km2 area in which T. macedonicus contains T. karelinii mitochondrial DNA. This introgression zone bisects the range of T. karelinii, cutting off a T. karelinii enclave. The high similarity of introgressed mitochondrial DNA haplotypes with those found in T. karelinii suggests a recent transfer across the species boundary. We then use ecological niche modeling to explore habitat suitability of the location of the present day introgression zone under current, mid-Holocene and Last Glacial Maximum conditions. This area was inhospitable during the Last Glacial Maximum for both species, but would have been habitable at the mid-Holocene. Since the mid-Holocene, habitat suitability generally increased for T. macedonicus, whereas it decreased for T. karelinii. Conclusion The presence of a T. karelinii enclave suggests that T. karelinii was the first to colonize the area where the present day introgression zone is positioned after the Last Glacial Maximum. Subsequently, we propose T. karelinii was outcompeted by T. macedonicus, which captured T. karelinii mitochondrial DNA via introgressive hybridization in the process. Ecological niche modeling suggests that this replacement was likely facilitated by a shift in climate since the mid-Holocene. We suggest that the northwestern part of the current introgression zone was probably never inhabited by T. karelinii itself, and that T. karelinii mitochondrial DNA spread there through T. macedonicus exclusively. Considering the spatial distribution of the

  1. Are cattle, sheep, and goats endangered species?

    Science.gov (United States)

    Taberlet, P; Valentini, A; Rezaei, H R; Naderi, S; Pompanon, F; Negrini, R; Ajmone-Marsan, P

    2008-01-01

    For about 10 000 years, farmers have been managing cattle, sheep, and goats in a sustainable way, leading to animals that are well adapted to the local conditions. About 200 years ago, the situation started to change dramatically, with the rise of the concept of breed. All animals from the same breed began to be selected for the same phenotypic characteristics, and reproduction among breeds was seriously reduced. This corresponded to a strong fragmentation of the initial populations. A few decades ago, the selection pressures were increased again in order to further improve productivity, without enough emphasis on the preservation of the overall genetic diversity. The efficiency of modern selection methods successfully increased the production, but with a dramatic loss of genetic variability. Many industrial breeds now suffer from inbreeding, with effective population sizes falling below 50. With the development of these industrial breeds came economic pressure on farmers to abandon their traditional breeds, and many of these have recently become extinct as a result. This means that genetic resources in cattle, sheep, and goats are highly endangered, particularly in developed countries. It is therefore important to take measures that promote a sustainable management of these genetic resources; first, by in situ preservation of endangered breeds; second, by using selection programmes to restore the genetic diversity of industrial breeds; and finally, by protecting the wild relatives that might provide useful genetic resources. PMID:17927711

  2. Capturing flavors from Capsicum baccatum by introgression in sweet pepper

    NARCIS (Netherlands)

    Eggink, P.M.; Tikunov, Y.M.; Maliepaard, C.A.; Haanstra, J.P.W.; Rooij, de H.; Vogelaar, A.; Gutteling, E.W.; Freymark, G.; Bovy, A.G.; Visser, R.G.F.

    2014-01-01

    The species Capsicum baccatum includes the most common hot peppers of the Andean cuisine, known for their rich variation in flavors and aromas. So far the C. baccatum genetic variation remained merely concealed for Capsicum annuum breeding, due to post-fertilization genetic barriers encountered in i

  3. Genetic Variation at C878T in Bovine SCD1 Gene and Its Association with Some Fat Traits in Chinese Simmetal Cattle%牛SCD1基因C878T位点遗传多态性与中国西门塔尔牛部分脂肪相关性状的效应分析

    Institute of Scientific and Technical Information of China (English)

    武秀香; 施雪奎; 常玲玲; 杨章平; 李俊雅; 毛永江; 高会江

    2011-01-01

    为探索8个中国牛群SCD1基因多态性与屠宰和肉质性状的相关性,选取中国西门塔尔牛、雷琼牛、云南高峰牛、BMY牛、闽南黄牛、鲁西黄牛、渤海黑牛和中国南方荷斯坦牛等8个群体共682头个体为研究对象,采用PCR-SSCP法分析SCD1基因遗传多态性.结果表明,在878 bp处发现1个碱基C→T的突变(C878T),导致蛋白质肽链中丙氨酸(alanine)突变为缬氨酸(valine).C878T位点在所研究群体中表现为CC、CT和TT3种基因型,其中,中国西门塔尔牛中TT基因型频率较高(0.114),鲁西黄牛和渤海黑牛中较低(0.050/0.063),4个热带群体中未发现TT基因型.采用GLM对SCD1基因C878T位点与132头中国西门塔尔屠宰牛的部分脂肪相关性状进行关联分析.结果,CC基因型个体肌间脂肪含量和肠系膜油质量显著高于TT型个体(P<0.05),背膘厚极显著低于TT型个体(P<0.01),其他性状间差异不显著(P>0.05).结果表明,SCD1基因C878T位点突变对中国西门塔尔牛脂肪相关性状有较大的遗传效应,可用于其部分屠宰与肉质性状的分子标记辅助选择.%This experiment was conducted to study the effect of SCD1 gene. To explore the effect of genetic variance in SCD1 gene on carcass and meat traits,682 cattle were selected randomly,including Chinese Simmetal cattle ( Simme) , Leiqiong cattle (LQ) , Yunnan Gaofeng cattle (GF) ,BMY cattle (BMY) , Minnan cattle (MN), Luxi cattle ( LX) , Bohai Black cattle (BH) and Holstein of South Chinese ( Hols. ) ,the polymorphism of specific fragment of SCD1 gene was analyzed by PCR-SSCP technique. A nucleotide mutation had been found at site 878, leading to an amino acid change (Glycine to Valine) at site 293,it was C878T. Three genotypes (CC,CT and TT) had been found at this site,and the frequency of genotype TT was highest in Chinese Simmetal population with the value of 0. 114, and lower in Luxi cattle , Bohai Black cattle and Holstein with the value of 0. 050

  4. Integrative Taxonomy of Southeast Asian Snail-Eating Turtles (Geoemydidae: Malayemys) Reveals a New Species and Mitochondrial Introgression.

    Science.gov (United States)

    Ihlow, Flora; Vamberger, Melita; Flecks, Morris; Hartmann, Timo; Cota, Michael; Makchai, Sunchai; Meewattana, Pratheep; Dawson, Jeffrey E; Kheng, Long; Rödder, Dennis; Fritz, Uwe

    2016-01-01

    Based on an integrative taxonomic approach, we examine the differentiation of Southeast Asian snail-eating turtles using information from 1863 bp of mitochondrial DNA, 12 microsatellite loci, morphology and a correlative species distribution model. Our analyses reveal three genetically distinct groups with limited mitochondrial introgression in one group. All three groups exhibit distinct nuclear gene pools and distinct morphology. Two of these groups correspond to the previously recognized species Malayemys macrocephala (Chao Phraya Basin) and M. subtrijuga (Lower Mekong Basin). The third and genetically most divergent group from the Khorat Basin represents a previously unrecognized species, which is described herein. Although Malayemys are extensively traded and used for religious release, only few studied turtles appear to be translocated by humans. Historic fluctuations in potential distributions were assessed using species distribution models (SDMs). The Last Glacial Maximum (LGM) projection of the predictive SDMs suggests two distinct glacial distribution ranges, implying that the divergence of M. macrocephala and M. subtrijuga occurred in allopatry and was triggered by Pleistocene climate fluctuations. Only the projection derived from the global circulation model MIROC reveals a distinct third glacial distribution range for the newly discovered Malayemys species.

  5. Placentation in cloned cattle

    DEFF Research Database (Denmark)

    Miglino, M A; Pereira, F T V; Visintin, J A;

    2007-01-01

    To elucidate the morphological differences between placentas from normal and cloned cattle pregnancies reaching term, the umbilical cord, placentomes and interplacentomal region of the fetal membranes were examined macroscopically as well as by light and scanning electron microscopy. In pregnancies...

  6. Use of multiple-trait animal models for genetic evaluation of milk, fat and protein lactation yields of dairy cattle in Belgium

    Directory of Open Access Journals (Sweden)

    Pierre Coenraets

    1997-01-01

    Full Text Available Comparison of computation time between single-trait and multiple-trait evaluations showed that with the use of the canonicat transformation associated with multiple diagonalization of (covariance matrices, multiple-trait analysis for milk, fat and protein yields is not more expensive than three single-trait analyzes. Rank correlations between breeding values for 54,820 cows with records (for their 1,406 sires estimated with the single-trait and multiple-trait models were over .98 (.99 in fat yield and over .99 (.99 in milk and protein yields. The relative gain expressed as reduction in mean prediction error variance was 3% (1% in milk yield, 6% (3% in fat yield, and .4% (.2% in protein yield for cows (for sires. Relative genetic gains were 3% (1%, 6% (2% and .5% (.2% respectively in milk, fat and protein yields for cows (for sires. The use of multiple-trait models bas therefore the advantages of improved precision and reduced selection bics. Multiple-trait analysis could be extended for the analyzes of test-day records. Results show that this or similar multiple-trait animal model could be implemented immediately in Belgium at low computing cost, using the proposed algorithme and could be the first step to new, more advanced evaluation methods.

  7. Parâmetros genéticos e nível de endogamia em bovinos da raça Santa Gertrudis no Brasil Genetic parameters and inbreeding levels in Santa Gertrudis cattle in Brazil

    Directory of Open Access Journals (Sweden)

    P.M.T. Ribeiro

    2000-12-01

    Full Text Available O presente trabalho teve o objetivo de estimar os parâmetros genético, fenotípico e de ambiente e do nível de endogamia em bovinos da raça Santa Gertrudis. As características estudadas foram peso ao nascer (PN, peso aos 120 dias de idade (P120, peso à desmama (PD, peso a um ano de idade (PANO e peso ao sobreano (PSANO. Foram utilizados dados de produção de 12.737 animais e dados de pedigree de 17.184 animais de 10 gerações anteriores aos animais com dados de produção, num total de 29.921 animais. As análises genéticas foram feitas por meio de metodologia de modelos mistos sob modelo animal. A média da endogamia observada não foi elevada (0,0395. As estimativas de herdabilidade para essa população podem ser consideradas de média a baixa magnitude, o que sugere que processos seletivos terão eficiência apenas a longo prazo. As estimativas de herdabilidade dos efeitos genéticos direto foram: PN = 0,16; P120 = 0,06; PD = 0,13; PANO = 0,12; PSANO = 0,12.The present study was carried out in order to estimate genetic, phenotypic and environmental parameters, and inbreeding levels of Santa Gertrudis cattle in Brazil. The traits analyzed were birth weight (PN, 120-day weight (P120, weaning weight (PD, one-year weight (PANO and 18-month weight (PSANO. A total of 12,737 weight records and pedigree informations of 17,184 animals from 10 generations prior to animals with records (total of 29,921 animals in pedigree were used. Mixed model methodology under animal model was used in the genetic analyses. Average inbreeding level was not high (0.0395. Heritability estimates for all traits varied from moderate to low (PN = 0.16; P120 = 0.06; PD = 0.13; PANO = 0.12; PSANO = 0.12.

  8. Metanálise bayesiana de parâmetros genéticos para características de crescimento em bovinos de corte Bayesian meta-analysis of genetic parameters for growth traits in beef cattle

    Directory of Open Access Journals (Sweden)

    Juliana Di Giorgio Giannotti

    2006-01-01

    Full Text Available Foi conduzida uma metanálise, sob enfoque bayesiano, em um conjunto de estimativas de herdabilidade, para características de crescimento em bovinos de corte de raças indianas, com 869 estimativas de herdabilidade de efeito direto, 186 estimativas de herdabilidade de efeito materno e 123 estimativas do coeficiente de correlação genética entre os efeitos direto e materno. A construção e o desenvolvimento de um modelo hierárquico possibilitam a obtenção de estimativas combinadas de herdabilidade para as características peso ao nascimento, peso ao desmame, peso aos 365 dias e peso aos 550 dias, cujos valores são, respectivamente: 0,31, 0,24, 0,28 e 0,33 para efeitos diretos; 0,09, 0,13, 0,12 e 0,05 para efeitos maternos; e -0,16, -0,16, -0,20 e -0,16 para as correlações entre esses efeitos. A metanálise conduzida sob enfoque bayesiano mostrou-se bastante adequada, uma vez que um modelo hierárquico considera as variâncias dentro e entre os estudos, e sua implementação e condução são facilitadas em virtude, principalmente, do avanço conseguido na área computacional.Bayesian meta-analysis was performed in a data set of heritability estimates for growth traits of zebu beef cattle with 869 direct heritabilities, 186 maternal heritabilities, and 123 direct-maternal genetic correlation. The fitting and development of a hierarchical model made possible to obtain pooled heritability estimates for birth weight, weaning weight, weight at 365 days of age and weight at 550 days of age, whose values were, respectively: 0.31, 0.24, 0.28 e 0.33 for direct effects; 0.09, 0.13, 0.12 e 0.05 for maternal effects; and -0.16, -0.16, -0.20 e -0.16 for direct-maternal genetic correlation. Meta-analysis conducted under Bayesian framework was adequate, since hierarchical model considers between-study and within-study variances, and its implementation and conduction are facilitated, mainly, due to the advance in computational area.

  9. Prevalence and multilocus genotyping of Cryptosporidium andersoni in dairy cattle and He cattle in Xinjiang, China.

    Science.gov (United States)

    Qi, Meng; Wang, Rongjun; Jing, Bo; Jian, Fuchun; Ning, Changshen; Zhang, Longxian

    2016-10-01

    Cryptosporidium andersoni is the predominant species in post-weaned and adult cattle in China. The aim of this study was to determine the prevalence and understand the transmission of cattle cryptosporidiosis in the Xinjiang Uyghur Autonomous Region, China, a total of 1827 fecal samples (436 from He cattle and 1391 from dairy cattle) were examined for the presence of C. andersoni-like oocysts by microscopy after Sheather's sugar flotation technique. The overall prevalence of C. andersoni-like was 3.8% (70/1827) and all the C. andersoni-like isolates were identified as C. andersoni at the SSU rRNA locus. Among the C. andersoni isolates, a total of 60 isolates were successfully characterized into eight multilocus sequence typing (MLST) subtypes using MLST analysis at the four microsatellite/minisatellite loci (MS1, MS2, MS3 and MS16), and three new subtypes were identified. The MLST subtype A4,A4,A4,A1 showed a predominance and a wide distribution among the eight MLST subtypes obtained in the investigated areas. The MLST subtypes A2,A4,A2,A1 and A4,A5,A2,A1 showed a unique distribution in the investigated areas. A linkage disequilibrium analysis showed the presence of an epidemic population genetic structure of C. andersoni isolated from dairy and He cattle in Xinjiang. These findings provide new insights into the genetic structure of C. andersoni isolates and are also helpful to explore the infection source of C. andersoni in cattle in Xinjiang, China. PMID:27448954

  10. Design of a DNA panel for genomic studies in Russian cattle breeds

    Science.gov (United States)

    A panel of 96 DNA samples (Russian Cattle Genomic Diversity Panel 1.0 or RCGDP 1.0) characterizing the breadth of genetic diversity in popular Russian cattle breeds was designed. The panel contains from four to eight animals from each of 11 dairy and six dairy-meat and meat breeds. The main criterio...

  11. Short communication: Genotyping of cows to speed up availability of genomic estimated breeding values for direct health traits in Austrian Fleckvieh (Simmental) cattle--genetic and economic aspects.

    Science.gov (United States)

    Egger-Danner, C; Schwarzenbacher, H; Willam, A

    2014-07-01

    The aim of this study was to quantify the impact of genotyping cows with reliable phenotypes for direct health traits on annual monetary genetic gain (AMGG) and discounted profit. The calculations were based on a deterministic approach using ZPLAN software (University of Hohenheim, Stuttgart, Germany). It was assumed that increases in reliability of the total merit index (TMI) of 5, 15, and 25 percentage points were achieved through genotyping 5,000, 25,000, and 50,000 cows, respectively. Costs for phenotyping, genotyping, and genomic estimated breeding values vary between €150 and €20 per cow. The gain in genotyping cows for traits with medium to high heritability is more than for direct health traits with low heritability. The AMGG is increased by 1.5% if the reliability of TMI is 5 percentage points higher (i.e., 5,000 cows genotyped) and 6.53% higher AMGG can be expected when the reliability of TMI is increased by 25 percentage points (i.e., 50,000 cows genotyped). The discounted profit depends not only on the costs of genotyping but also on the population size. This study indicates that genotyping cows with reliable phenotypes is feasible to speed up the availability of genomic estimated breeding values for direct health traits. But, because of the huge amount of valid phenotypes and genotypes needed to establish an efficient genomic evaluation, it is likely that financial constraints will be the main limiting factor for implementation into breeding program such as Fleckvieh Austria. PMID:24835973

  12. Diversification of primary gene pool through introgression of resistance to foliar diseases from synthetic amphidiploids to cultivated groundnut(Arachis hypogaea L.)

    Institute of Scientific and Technical Information of China (English)

    Varsha; Kumari; M.V.C.Gowda; Vinod; Tasiwal; Manish; K.Pandey; Ramesh; S.Bhat; Nalini; Mallikarjuna; Hari; D.Upadhyaya; Rajeev; K.Varshney

    2014-01-01

    Groundnut(Arachis hypogaea L.)is widely grown and consumed around the world and is considered to have originated from a single hybridization event between two wild diploids.The utilization of wild germplasm in breeding programs has been restricted by reproductive barriers between wild and cultivated species and technical difficulties in making large numbers of crosses.Efforts to overcome these hurdles have resulted in the development of synthetic amphidiploids,namely ISATGR 278-18(Arachis duranesis×Arachis batizocoi)and ISATGR 5B(Arachis magna×A.batizocoi),which possess several desirable traits,including resistance to foliar diseases that generally cause huge yield losses annually in groundnut growing areas of Asia,America,and Africa.With an objective to improve foliar disease resistance,the primary gene pool was diversified by introgressing foliar disease resistance in five cultivated genotypes(ICGV 91114,ICGS 76,ICGV 91278,JL 24,and DH 86)from synthetic amphidiploids using a backcross breeding approach.Several introgression lines with resistance to two foliar diseases(rust and late leaf spot)were identified with levels of resistance equal to the donors.These backcross derived lines have shown a wide range of variation for several morphological and agronomic traits.These lines,after further evaluation and selection,can serve as donors in future breeding programs aimed atdeveloping improved cultivars with desirable agronomic traits,high resilience to biotic/abiotic stresses and a broadened genetic base.

  13. Tendências genéticas para escores visuais de conformação, precocidade e musculatura à desmama de bovinos Nelore Genetic trends in Nelore cattle selected for visual scores of conformation, precocity and musculature at weaning

    Directory of Open Access Journals (Sweden)

    Selma Forni

    2007-06-01

    Full Text Available Os objetivos neste estudo foram estimar os coeficientes de herdabilidade e a mudança genética nos escores visuais de conformação (C, precocidade (P e musculatura (M à desmama de bovinos Nelore e avaliar as mudanças promovidas pelo programa de seleção ao qual os animais foram submetidos. Foram utilizados dados de 56.076 animais nascidos entre 1990 e 2002. Os componentes de variância foram estimados por máxima verossimilhança restrita e os valores genéticos foram preditos pelo método dos modelos mistos aplicando-se um modelo animal. As tendências genéticas foram estimadas pela regressão dos valores genéticos sobre o ano de nascimento dos animais. Os coeficientes de herdabilidade do efeito direto estimados foram de 0,122±0,012; 0,153±0,012; e 0,124±0,012 e, para o efeito materno, de 0,043±0,010; 0,038±0,009; e 0,056±0,010 para C, P e M, respectivamente. As tendências genéticas diretas estimadas foram de 0,013; 0,022 e 0,018 pontos de escore ao ano para C, P e M, respectivamente, o que representa incremento anual de 0,42; 0,67 e 0,60% ao ano em relação à média fenotípica. As tendências genéticas do efeito materno foram de -0,0020; -0,0010; e -0,0009 pontos de escore ao ano para C, P e M, respectivamente, o que representa uma mudança anual de -0,07; -0,03; e -0,03% na média fenotípica da população.The aims of this study were to estimate heritability coefficients and genetic trends for visual scores of conformation (C, finishing precocity (P and musculature (M in Nelore beef cattle. Variance components and heritability coefficients were estimated by restrict maximum likelihood and breeding values were predicted by an animal mixed model using data from 56,076 animals born between 1990 and 2002. Genetic trends for each trait were estimated by the regression of breeding values on animal birth year. Heritability estimates for direct effect of C, P and M were respectively 0.122±0.012, 0.153±0.012 and 0.124±0.012. In

  14. Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

    Directory of Open Access Journals (Sweden)

    Analiza G. Tagle

    2016-02-01

    Full Text Available To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived line of IR64, YTH288, was developed using a new-plant-type cultivar, IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading (DTH, culm length (CL, flag leaf length (FLL, flag leaf width (FLW, and filled spikelet number per panicle (FSN. Six putative QTL were detected: four on chromosome 4 (for CL, FLL, FLW, and FSN and two on chromosome 2 (for DTH and FLL. All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes 2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic effects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars. Abbreviations NPT, new plant type; QTL, quantitative trait loci (locus; GF, grain fertility; DTH, days to heading; CL, culm length; PL, panicle length; LL, leaf length; FLL, flag leaf length; LW, leaf width; FLW, flag leaf width; FSN, filled spikelet number per panicle; TSN, total spikelet number per panicle; PN, panicle number per plant; IRRI, International Rice Research Institute; NIL, near-isogenic line; IL, introgression line; SSR, simple sequence repeat; PCR, polymerase chain reaction

  15. Desempenho de diferentes grupos genéticos de bovinos de corte em confinamento Performance evaluation of different beef cattle genetic groups under feedlot

    Directory of Open Access Journals (Sweden)

    Kepler Euclides Filho

    2003-10-01

    de MS ingerida/kg de ganho de peso versus 6,66 kg de MS ingerida/kg de ganho de peso.It was utilized data from 188 animals from ten genetic groups. For the statistical analysis, the animals were grouped into three subgroups according to age, sex and diet. Thus, the subgroups analyzed were: 1 intacted yearling males receiving the "a" ration: 39 Nellore (N, 12 Brangus (BR, 8 1/2 Simmental - 1/2 Nellore (SN, 8 1/2 Caracu - 1/2 Nellore (CCN, 21 1/2 Valdostana - 1/2 Nellore (VAN; 2 intacted weaned males receiving the "b" diet: 12 N, 12 1/2 Canchim - 1/2 1/4 Angus - 1/4 Nellore (CAN, 16 1/2 Canchim - 1/4 Simmental - 1/4 Nellore (CSN, 12 Braford - 1/2 Brangus (BRBD, 12 1/2 Braford - 1/4 Angus - 1/4 Nellore (BDAN, 7 Brahman - 1/4 Angus - 1/4 Nellore (BHAN; 3 weaned females receiving the "b" diet under two formulations, one in which the concentrate represented 30% of total dry matter (DM and the other in which the participation of the concentrate was 50% of total DM. For this subgroup the analysis included 29 females, 15 CAN and 14 CSN. Animals in subgroups 1 and 2, were fed a diet contained 50% of concentrate in the DM. Animals in subgroup 1 had similar performances. The average daily gain was 1.60 kg/day and average feed conversion was 6.41 kg of DM intake/kg of weight gain. The statistical analysis revealed that for average daily gain as well as for feed conversion, it were observed differences only among animals on subgroup 2. The greater average daily gain was recorded on CSN animals (1.69 kg/day and the best feed conversion on CSN and BHAN animals (4.76 kg of DM intake/kg of weight gain and 4.67 kg of DM intake/kg of weight gain. The analyses of subgroup 3 allowed the conclusion that in spite of not having any difference between genetic groups, formulation showed an important effect, mainly on feed conversion. The animals receiving the diet formulation in which the concentrate represented 30% of the total DM showed better feed conversion (5.58 kg of DM intake/kg of

  16. Chromosome engineering for alien gene introgression in wheat: Progress and prospective

    Science.gov (United States)

    Chromosome engineering is a useful strategy for introgression of desirable genes from wild relatives into cultivated wheat. However, it has been a challenge to transfer a small amount of alien chromatin containing the gene of interest from one genome to another non-homologous genome through classic...

  17. Polimorfismo genético de beta-lactoglobulina y alphalactoalbúmina en el ganado criollo colombiano, mediante PCR-SSCP Genetic polymorphism of beta-lactoglobulin and alpha-lactoalbumin in Colombian Creole cattle by PCR-SSCP

    Directory of Open Access Journals (Sweden)

    Jaime A Rosero-Alpala

    2011-12-01

    Full Text Available La población de ganado criollo colombiano ha venido presentando una inquietante disminución al pasar de 23.415 ejemplares en 1999 a 20.102 en 2003. A pesar de los esfuerzos por recuperar las razas criollas el panorama para su conservación es incierto, por tanto la búsqueda de caracteres deseables puede contribuir a su valoración y conservación. Los genes relacionados con el mejoramiento de la calidad de la leche producida por estas razas se consideran de gran importancia en la industria láctea, por tal razón y con el objetivo de caracterizar los genes beta-lactoglobulina y alpha-lactoalbúmina se analizaron 30 muestras de sangre de cada una de las razas criollas (Blanco Orejinegro, Caqueteño, Casanareño, Costeño con cuernos, Chino Santandereano, Hartón del Valle, Romosinuano y Sanmartinero, dos razas sintéticas colombianas (Lucerna y Velásquez y dos razas foráneas (Holstein y Brahman. Se amplificaron fragmentos de 262pb para beta-lactoglobulina (b-LG y de 166 pb para alpha-lactoalbúmina (a-LA que se genotipificaron mediante PCR-SSCP. El promedio de la frecuencia para b-LG A y b-LG B fue de 0.46 ± 0.020 y de 0.53 ± 0.020, respectivamente, y de 0.35 ± 0.019 para a-LA A y 0.64 ± 0.019 para a-LA B. El promedio de diversidad genética (He para b-LG fue 0.498 y de 0.455 para a-LA. Los ganados criollos representan una base genética valiosa, como alternativa para mejorar genéticamente los hatos destinados a la producción de leche con mejores características en calidad para la industria láctea.The Colombian Creole Cattle has showed a preoccupant population decreasing, from 23,415 individuals in 1999 to 20,102 in 2003. Despite that many efforts to recover the creole breeds have been done, its future conservation is unclear. Searching for economic desirable genes may contribute to its preservation and utilization as a genetic resource. Genes related with the improvement of milk proteins are considered as an economic important

  18. Growing hairs in shorn cattle

    OpenAIRE

    Cecília José Veríssimo; Selma D'Agostino; Fernanda Pessoa; Luciandra Macedo Toledo; Keila Maria Roncato Duarte

    2013-01-01

    The shearing operation can provide double benefits to the cattle: they can become more heat tolerant and the tick infestation decreases. The cattle tick Rhipicephalus (Boophilus) microplus causes great losses to dairy cattle, especially to the Holstein cattle because they are very susceptible to this tick. Its control is becoming each day more difficult, owing to the increasing resistance to acaricides they are acquiring. The objective of this work was to study the growing of haircoat followi...

  19. Modelo hierárquico bayesiano aplicado na avaliação genética de curvas de crescimento de bovinos de corte Bayesian hierarchical model appllied to genetic evaluation of of beef cattle growth curves

    Directory of Open Access Journals (Sweden)

    N.A.M. Silva

    2010-04-01

    Full Text Available A estimação dos componentes de (covariância dos parâmetros de modelos de crescimento pode ser feita por vários métodos. A metodologia bayesiana se apresenta como uma forma alternativa de estimação. Foi realizado um estudo, por meio de dados simulados e de dados reais de animais Nelore, para a estimação dos componentes de (covariância dos parâmetros do modelo de crescimento de Von Bertalanffy, por meio da metodologia hierárquica bayesiana. Com base nos componentes estimados, foram encontradas as herdabilidades para cada parâmetro do modelo e as correlações genéticas e ambientais entre esses parâmetros. As distribuições marginais a posteriori dos parâmetros a, R, μ, u, G e σ2e foram obtidas por meio do algoritmo Gibbs Sampler e as dos parâmetros b e k por meio do algoritmo Metropolis-Hastings. A metodologia se mostrou eficiente, proporcionando estimativas para os parâmetros próximas aos valores simulados. Os parâmetros a e k dos dados reais apresentaram valores de herdabilidades compatíveis com a realidade, indicando que esses parâmetros poderiam ser usados para fins de seleção.The estimation of the (covariance components for the parameters of the growth models can be evaluated by many methods. The Bayesian approach is an alternative method of the estimation. A study was performed using simulated and real data from Nelore cattle for estimation of the (covariance components for the parameters of Von Bertalanffy growth curve, using a bayesian hierarchical model. From the estimated components, the heritabilities for each parameter and genetic and environmental correlations between these parameters were determined. The samples of posterior marginal distributions for the parameters a, R, μ , u, G, and σ2e were obtained by using Gibbs Sampler algorithm and for the parameters b e k by using the Metropolis-Hastings algorithm. The efficiency of the bayesian inference methodology was verified since estimated parameters were

  20. North African hybrid sparrows (Passer domesticus, P. hispaniolensis) back from oblivion - ecological segregation and asymmetric mitochondrial introgression between parental species.

    Science.gov (United States)

    Ait Belkacem, Abdelkrim; Gast, Oliver; Stuckas, Heiko; Canal, David; LoValvo, Mario; Giacalone, Gabriele; Päckert, Martin

    2016-08-01

    A stabilized hybrid form of the house sparrow (Passer domesticus) and the Spanish sparrow (P. hispaniolensis) is known as Passer italiae from the Italian Peninsula and a few Mediterranean islands. The growing attention for the Italian hybrid sparrow and increasing knowledge on its biology and genetic constitution greatly contrast the complete lack of knowledge of the long-known phenotypical hybrid sparrow populations from North Africa. Our study provides new data on the breeding biology and variation of mitochondrial DNA in three Algerian populations of house sparrows, Spanish sparrows,