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Sample records for based genetic diversity

  1. Genetic diversity of Najdi sheep based on microsatellite analysis

    African Journals Online (AJOL)

    MUNEEB

    2012-10-16

    Oct 16, 2012 ... Handley LJL, Byrne K, Santucci F, Townsend S, Taylor M, Bruford MW,. Hewitt GM (2007). Genetic structure of European sheep breeds. Heredity 99:620-631. Hoda A, Dobi P, Hyka G (2009). Genetic diversity and distances of. Albanian local sheep breeds using microsatellite markers. Livest. res. rural Dev.

  2. Genetic diversity of Shaanxi soybean landraces based on ...

    African Journals Online (AJOL)

    DR TONUKARI NYEROVWO

    2011-06-06

    Jun 6, 2011 ... organized into linkage maps (Cregan et al., 1999). SSR markers have been used to evaluate genetic diversity and domestication of crops (Fu et al., 2007; Yoon et al.,. 2009; Li et al., 2010; Guo et al., 2010), develop genetic map (McCallum et al., 2006) and assistant selection in plant breeding (Kelley et al., ...

  3. Genetic diversity in Chinese natural zoysiagrass based on inter ...

    African Journals Online (AJOL)

    Zoysiagrass (Zoysia sp.) is extensively used in turf establishment and livestock herbage due to its many outstanding characters. Native Zoysia sp. are widely distributed in China. Inter-simple sequence repeat (ISSR) markers were used to investigate the genetic diversity and genetic relationships of 81 Chinese wild ...

  4. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  5. Genetic diversity among four Eucalyptus species (myrtaceae) based ...

    African Journals Online (AJOL)

    The results indicate that 16 positive and 13 negative markers were detected. The marker fragments size ranged between 175 to 630 bp for the negative markers and 235 to 945 bp for the positive markers. Key words: Eucalyptus, random amplified polymorphic DNA (RAPD), genetic diversity, DNA fingerprinting PCR, ...

  6. Molecular based assessment of genetic diversity of xoconostle ...

    African Journals Online (AJOL)

    aghomotsegin

    2014-01-08

    Jan 8, 2014 ... Xoconostle or acidic prickly pear is an important fruit in Mexico; it is produced by a group of Opuntia plants known for their nutritional qualities and adapted to harsh environmental conditions. In this study, we report for the first time the estimation of genetic diversity within a set of 24 xoconostle accessions ...

  7. Genetic diversity studies of Kherigarh cattle based on microsatellite ...

    Indian Academy of Sciences (India)

    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 ...

  8. Molecular based assessment of genetic diversity of xoconostle ...

    African Journals Online (AJOL)

    Xoconostle or acidic prickly pear is an important fruit in Mexico; it is produced by a group of Opuntia plants known for their nutritional qualities and adapted to harsh environmental conditions. In this study, we report for the first time the estimation of genetic diversity within a set of 24 xoconostle accessions using inter simple ...

  9. The genetic diversity among strawberry breeding resources based on SSRs

    Directory of Open Access Journals (Sweden)

    Soohwan Lim

    Full Text Available ABSTRACT: Cultivated strawberry (Fragaria × ananassa Duch. is a high value horticultural crop. In this study, the genetic diversity of 160 strawberry accessions was determined using five highly polymorphic simple sequence repeat (SSR markers. Sixty different alleles were identified, with allele frequencies in the range of 0.006 to1. Similarity scores were in the range of 0.034 to 0.963 (average: 0.507. The accessions were categorized into five groups. Group 1 contained two diploid Fragaria vesca species and one unknown accession. Group 2 contained one accession (F x ananassa. Group 3 contained 20 F × ananassa accessions and six unknown accessions. Group 4 contained 48 F. × ananassa accessions, one octaploid Fragaria chiloensis species, and six unknown accessions while Group 5 contained 69 F. × ananassa accessions and six unknown accessions. Accessions within a pedigree were frequently grouped together. A total of 30 novel accessions were categorized alongside existing accessions. These results will allow breeders to develop strategies which incorporate more genetic diversity into new cultivars.

  10. Genetic diversity of Iranian potato soft rot bacteria based on ...

    African Journals Online (AJOL)

    Based on biochemical and physiological tests, the Iranian strains were identified as either Pectobacterium carotovorum subsp. carotovorum or P. carotovorum subsp. wasabiae. Sequence analysis of recA gene revealed that the strains closely related to Pectobacterium spp. To assess the genomic diversity, polymerase ...

  11. Genetic diversity based on morphological data in Panicum maximum hybrids

    Directory of Open Access Journals (Sweden)

    Janaina Azevedo Martuscello

    2012-09-01

    Full Text Available The objective of this experiment was to evaluate the genetic divergence between hybrids obtained from 10 sexual genitors of the Panicum maximum breeding program at Embrapa Beef Cattle. For this, the following morphological descriptors were used: plant height, growth habit, leaf aspect, leaf waxiness, hair density on the sheath (DePB and blade (DePL, degree of hardiness of the hairs on the leaf sheath (DuPB and blade (DuPL and length of hairs on the sheath and blade. The characteristics growth habit and waxiness were not included in the analysis for being invariant. The phenotypic correlations were low and, therefore, not used to eliminate variables. By the principal component analysis, an 84.3% accumulation of the variation was observed until the fourth component. The last four principal components presented an estimate lower than 0.7 and allowed the identification of the variables DePB, DuPB and DuPL as the least important for diversity studies. The morphological characters used were not efficient to distinguish the progenies, but allowed the formation of morphological groups that converged with the graphic analysis of the principal components. An apparent error rate of 17.04% was observed in the classification of the individuals in the groups and 55.5% in the classification of the individuals in the progenies. The individuals in the P. maximum half-sib progenies are genetically divergent, but may not be grouped with only the descriptors used in this experiment. The pubescence characteristics were the least important in the discrimination of the genotypes.

  12. Genetic diversity studies of Kherigarh cattle based on microsatellite ...

    Indian Academy of Sciences (India)

    for genetic characterization of livestock genetic resources. The population structure, genetic variability and genetic bot- tlenecks in Kherigarh cattle have been evaluated using 21 mi- crosatellite markers from the United Nations Food and Agri- culture Organization (FAO) recommended list for the mea- surement of domestic ...

  13. Genetic diversity based on SSR markers in maize (Zea mays L ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 87; Issue 3. Genetic diversity based on SSR markers in maize (Zea mays L.) landraces from Wuling mountain region in China. Yao Qi-Lun Fang Ping Kang Ke-Cheng Pan Guang-Tang. Research Note Volume 87 Issue 3 December 2008 pp 287-291 ...

  14. Genetic diversity of Ardi goat based on microsatellite analysis ...

    African Journals Online (AJOL)

    The aim of this study was to analyze the genetic variability of Ardi goats found in the central regions of the kingdom of Saudi Arabia using 14 microsatellite markers. Allelic richness was considerably high in this population indicating high genetic polymorphism as expected heterozygozity was 0.675. Furthermore, the ...

  15. Genetic diversity of Najdi sheep based on microsatellite analysis ...

    African Journals Online (AJOL)

    The prime objective of this research was to measure the genetic polymorphism of main sheep breed of Saudi Arabia, Najdi. Randomly selected 49 blood samples were used to extract the DNA followed by polymerase chain reaction (PCR), using 19 microsatellite markers, which were used to investigate the genetic ...

  16. Reconsideration for conservation units of wild Primula sieboldii in Japan based on adaptive diversity and molecular genetic diversity.

    Science.gov (United States)

    Yoshida, Yasuko; Honjo, Masanori; Kitamoto, Naoko; Ohsawa, Ryo

    2009-08-01

    Primula sieboldii E. Morren is a perennial clonal herb that is widely distributed in Japan, but in danger of extinction in the wild. In a previous study, we revealed the genetic diversity of the species using chloroplast and nuclear DNA and used this information to define conservation units. However, we lacked information on adaptive genetic diversity, which is important for long-term survival and, thus, for the definition of conservation units. In order to identify adaptive traits that showed adaptive differentiation among populations, we studied the genetic variation in six quantitative traits within and among populations for 3 years in a common garden using 110 genets from five natural populations from three regions of Japan. The number of days to bud initiation was adaptive quantitative trait for which the degree of genetic differentiation among populations (QST) was considerably larger than that in eight microsatellite markers (FST). The relationship between this trait and environmental factors revealed that the number of days to bud initiation was negatively correlated, with the mean temperature during the growing period at each habitat. This suggests that adaptive differentiation in the delay before bud initiation was caused by selective pressure resulting from temperature differences among habitats. Our results suggest that based on adaptive diversity and neutral genetic diversity, the Saitama population represents a new conservation unit.

  17. Evaluating human genetic diversity

    National Research Council Canada - National Science Library

    This book assesses the scientific value and merit of research on human genetic differences--including a collection of DNA samples that represents the whole of human genetic diversity--and the ethical...

  18. Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia.

    Science.gov (United States)

    Tapio, Miika; Ozerov, Mikhail; Tapio, Ilma; Toro, Miguel A; Marzanov, Nurbiy; Cinkulov, Mirjana; Goncharenko, Galina; Kiselyova, Tatyana; Murawski, Maziek; Kantanen, Juha

    2010-08-10

    Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.

  19. Genetic diversity in wild species of passion fruit (Passiflora trintae) based on molecular markers.

    Science.gov (United States)

    Cerqueira-Silva, C B M; Cardoso-Silva, C B; Santos, E S L; Conceição, L D H C S; Pereira, A S; Oliveira, A C; Corrêa, R X

    2010-10-26

    In spite of the importance of and the considerable variability observed in Passiflora (Passifloraceae), little is known about the genetic diversity of most of the species of this genus. We evaluated the genetic diversity by RAPD markers in 18 genotypes of Passiflora trintae. The 15 primers generated 112 markers, 84% of which were polymorphic. The genetic distance estimated by the complement of the Dice index (average dissimilarity = 0.30) and genotype grouping based on the UPGMA algorithm showed low variability among genotypes. More attention should be given to the study and conservation of the biodiversity of this economically important genus.

  20. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

  1. Genetic diversity studies of Kherigarh cattle based on microsatellite ...

    Indian Academy of Sciences (India)

    startling rate, by use of microsatellite markers recommended by the Food and Agriculture Organization. Microsatellite geno- types were derived, and allelic and genotypic frequencies, heterozygosities and gene diversity were estimated. A total of 131 ..... Bassam B. J., Coetano-Anolles G. and Gresshoff P. M. 1991 Fast.

  2. Genetic Diversity of Rose germplasm based on RAPD analysis

    African Journals Online (AJOL)

    AHSAN IQBAL

    2012-06-12

    Jun 12, 2012 ... Random amplified polymorphic DNA (RAPD) markers have been found to be very useful in studying the genetic variability of ... produced by primer GLD-20, while GLC-02 produced the minimum number of bands (2). Maximum polymorphism in ..... ability and occurrence of pseudo bands. However, it can.

  3. Microsatellite based investigation of genetic diversity in 24 synthetic ...

    African Journals Online (AJOL)

    Muhammad Shakeel

    2012-09-06

    Sep 6, 2012 ... molecular diagnostics have been evolved to the level that alien introgression detection no longer remains too complex a process. For speeding up alien introgression and production/maintenance of genetic stock programs, the use of polyhaploidy, through sexual hybridization of bread wheat, has emerged ...

  4. GENETIC AND MORPHOAGRONOMIC DIVERSITY OF Passiflora spp. BASED ON QUANTITATIVE MEASUREMENTS OF FLOWERS AND FRUITS

    Directory of Open Access Journals (Sweden)

    JAMILE DA SILVA OLIVEIRA

    Full Text Available ABSTRACT The aim of this study was to characterize Passiflora spp. accessions and its genetic diversity based on quantitative morphological descriptors of flowers and fruits. The study was conducted at Embrapa Cerrados, Planaltina-DF. Fifteen Passiflora spp. accessions were characterized using 14 quantitative morphological descriptors. Genetic distances among accessions were estimated based on Mahalanobis’ generalized distance. Cluster analysis via dendrogram and graphic dispersion was analyzed. The relative contribution of characters for accession divergence was also calculated. The morphoagronomic characterization based on quantitative descriptors of flowers and fruits contributed to the differentiation of Passiflora spp. accessions, serving as an important tool for variability quantification. This information is useful to perform Passiflora spp. characterization and genetic diversity studies.

  5. Microsatellite-based genetic diversity among accessions of maize landraces from Sinaloa in México.

    Science.gov (United States)

    Pineda-Hidalgo, Karen V; Méndez-Marroquín, Karla P; Alvarez, Elthon Vega; Chávez-Ontiveros, Jeanett; Sánchez-Peña, Pedro; Garzón-Tiznado, Jose A; Vega-García, Misael O; López-Valenzuela, Jose A

    2013-12-01

    In the state of Sinaloa México, traditional farmers still cultivate maize accessions with a wide diversity of morphological characteristics, but the gene reservoir maintained in these populations has been poorly studied and it is being lost due to changes in land use and the adoption of hybrid commercial varieties. The aim of this study was to evaluate the genetic diversity of some of these maize populations to contribute to their preservation. Twenty eight accessions were used for the analysis. DNA was extracted from 396 individuals and probed with 20 microsatellites distributed across the maize genome. A total of 121 alleles were obtained (average of 6.1 alleles per locus) and a total genetic diversity of 0.72. The UPGMA-cluster analysis, model-based population structure and principal component analysis revealed three major groups, one formed mainly by accessions of races typical of the Northwestern lowlands (Chapalote, Dulcillo del Noroeste, Tabloncillo Perla, Blando de Sonora and Elotero de Sinaloa) and the other two with accessions mainly from Tabloncillo and Tuxpeño. The high number of alleles per locus and total genetic diversity found in this study demonstrate a broad genetic basis of the accessions of maize landraces from Sinaloa, representing a gene reservoir useful in breeding programs. © 2013 The Authors.

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

    Directory of Open Access Journals (Sweden)

    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

  7. Short tandem repeat (STR based genetic diversity and relationship of indigenous Niger cattle

    Directory of Open Access Journals (Sweden)

    M. Grema

    2017-11-01

    Full Text Available The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding estimate within breeds was found to be moderate with 0.024, 0.043 and 0.044 in Zebu Arabe, Zebu Bororo and Kuri cattle respectively. The global F statistics showed low genetic differentiation among Niger cattle with about 2.6 % of total variation being attributed to between-breed differences. Neighbor-joining tree derived from pairwise allele sharing distance revealed Zebu Arabe and Kuri clustering together while Zebu Bororo appeared to be relatively distinct from the other two breeds. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances that showed individuals across populations being more related than individuals within populations. Individuals were assigned to their respective source populations based on STR genotypes, and the percent correct assignment of Zebu Bororo (87.5 to 93.8 % was consistently higher than Zebu Arabe (59.3 to 70.4 % and Kuri (80.0 to 83.3 % cattle. The qualitative and quantitative tests for mutation drift equilibrium revealed absence of genetic bottleneck events in Niger cattle in the recent past. High genetic diversity and poor genetic structure among indigenous cattle breeds of Niger might be due to historic zebu–taurine admixture and ongoing breeding practices in the region. The results of the present study are expected to help in formulating effective strategies for conservation and genetic improvement of indigenous Niger cattle breeds.

  8. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

    Directory of Open Access Journals (Sweden)

    Slobodan Katic

    2011-08-01

    Full Text Available Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  9. Genetic Diversity Analysis of Tagetes Species Using PCR Based Molecular Markers

    International Nuclear Information System (INIS)

    Shahzadi, I.; Ahmad, R.; Waheed, U.; Shah, M. F.

    2016-01-01

    Tagetes is a genus of medicinally important wild and cultivated plants containing several chemical compounds. Lack of information on variation at molecular level present in Tagetes species is paramount to understand the genetic basis of medicinally important compounds. Current study aims at finding genetic variability in Tagetes species using random and specific molecular markers. Two primer systems including 25 RAPD and 3 STS (limonene gene) were used to ascertain genetic diversity of 15 Tagetes genotypes belonging to different species. We found that 20 of the 25 tested RAPD primers generated stable band patterns with 167 loci of amplification products. The proportion of polymorphic bands was 95.21 percent for RAPD primers. Three STS primers generated a total of 29 amplification products, of which 96.55 percent were polymorphic. Homology of genotypes was 53.18 percent and 51.11 percent with RAPD and STS primers respectively. The dendrogram obtained revealed that the range of overall genetic distances estimated was 22 percent to 100 percent through RAPD and 9 percent to 100 percent through STS markers. The findings help to establish that PCR-based assay such as RAPD and STS could be used successfully for estimation of genetic diversity of different genotypes of Tagetes that can be used for selection of parents for improvement of the species. (author)

  10. Imposing genetic diversity.

    Science.gov (United States)

    Sparrow, Robert

    2015-01-01

    The idea that a world in which everyone was born "perfect" would be a world in which something valuable was missing often comes up in debates about the ethics of technologies of prenatal testing and preimplantation genetic diagnosis (PGD). This thought plays an important role in the "disability critique" of prenatal testing. However, the idea that human genetic variation is an important good with significant benefits for society at large is also embraced by a wide range of figures writing in the bioethics literature, including some who are notoriously hostile to the idea that we should not select against disability. By developing a number of thought experiments wherein we are to contemplate increasing genetic diversity from a lower baseline in order to secure this value, I argue that this powerful intuition is more problematic than is generally recognized, especially where the price of diversity is the well-being of particular individuals.

  11. Genetic diversity among coffee tree progenies Big Coffee VL based on growth traits and production.

    Science.gov (United States)

    Silva, J A; Carvalho, S P; Bruzi, A T; Guimarães, R J; Oliveira, L L; Simões, L C

    2016-11-21

    In a coffee plantation of a coffee 'Acaiá' cultivar (Coffea arabica), on the Midwest of Minas Gerais in Capitólio city, a different kind of coffee tree was found (1989), possibly due to a mutation. It presented larger leaves and grains than those of conventional coffee trees and was named as "Big Coffee VL." The aim of this study was to estimate the genetic diversity of Big Coffee VL progenies cultivated at Universidade Federal de Lavras, by evaluating growth and production traits, based on genetic distances and clusters. The experiment was established in a lattice design with 100 progenies of this coffee tree and 23 repetitions. Traits evaluated were vigor, plant height, stem diameter, node number of plagiotropic branches, pair numbers of plagiotropic branches, and productivity. Genetic divergence was evaluated by multivariate procedures: Mahalanobis generalized distance, clustering methods, and principal component analysis. Genetic distances were estimated using Mahalanobis distance and presented variations from 0.04 to 18.70. The most similar progenies were P23 and P29 and the most dissimilar progenies were G8 and P14. The progenies were divided into three groups, with P14 present as an isolated group. Thus, it was possible to observe the existence of genetic variability among the progenies of Big Coffee VL, which can be used in breeding programs to increase grain size. Progenies G8 and P14 presented the highest genetic distance, and were the most suitable for future integration of crossings in plant breeding programs.

  12. 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.

  13. Synthesis and assessment of date palm genetic diversity studies

    Science.gov (United States)

    A thorough assessment of genetic diversity and population differentiation of Phoenix dactylifera are critical for its dynamic conservation and sustainable utilization of its genetic diversity. Estimates of genetic diversity based on phenotypic, biochemical and molecular markers; and fruit quality tr...

  14. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    Directory of Open Access Journals (Sweden)

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

    Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

  15. Microsatellite based genetic diversity study in indigenous chicken ecotypes of Karnataka

    Directory of Open Access Journals (Sweden)

    B. H. Rudresh

    2015-08-01

    Full Text Available Aim: The current study was the first of its kind taken upon indigenous ecotypes of the Karnataka in order to unravel the diversity details at 20 chicken microsatellite regions. Materials and Methods: 210 indigenous chicken belonging to six districts of Bangalore and Mysore division formed the target sample for the present study. The genomic deoxyribonucleic acid was isolated by phenol chloroform isoamyl alcohol method. A panel of 20 microsatellite regions, including 14 recommended by FAO and six identified from published scientific literature became the targeted chicken genomic region. 27-33 samples were successfully genotyped in each of the six ecotypes through simplex or multiplex polymerase chain reactions, polyacrylamide gel electrophoresis and silver staining for the selected microsatellite panel. Results: The chickens of Ramanagara and Chamrajnagara were most distant with a Nei’s genetic distance value of 0.22. The chickens of Bangalore rural and Mysore were least distant with a value of 0.056. The Ramanagara and Chamrajnagara pair had Nei’s genetic identity value of 0.802, which is least among all pairs of ecotypes. There were five main nodes from which the six ecotypes evolved on the basis 20 microsatellite markers used in this study. This study indicates that the four ecotypes Ramnagara, Bangalore Rural, Chickaballapura and Mysore are genetically identical due to their common ancestral evolution while, Mandya and Chamrajnagara ecotypes formed a relatively different cluster due to a separate common ancestral chicken population and less number of generations since drifting from bifurcation node. Conclusion: Twenty microsatellite markers based genetic diversity study on six indigenous ecotypes indicated lower genetic distances as well as lower FST values compared to the distinguished breeds reported. There were two main clusters, which differentiated into six ecotypes. They may differentiate into more distinct varieties if bred in

  16. ASSESSMENT OF GENETIC DIVERSITY OF REHMANNIA GLUTINOSA LIBOSCH BASED ON ISSR MARKERS

    Directory of Open Access Journals (Sweden)

    YANQING ZHOU, WUJUN GAO, HONGYING DUAN, FENGPING GU

    2007-08-01

    Full Text Available In order to assess the genetic diversity of Rehmannia glutinosa Libosch cultivars ( lines in Huai zone, Inter-simple sequence repeat (ISSR was performed. Ten appropriate ISSR primers were selected from a total of 44 ISSR ones for ISSR PCR amplification. The ten primers could amplify one hundred and ten bands. Based on them, A Jaccard’s genetic similarity matrix and a dendrogram for these ten cultivars were established using SPSS 10.0 software. In this dendrogram, they could be divided into two groups : Group1 contained six individuals such as Zupei 85.5, Datian 85.5, Zupei 9302, Jinbai, Jinzhuangyuan and Datian9302; Group2 consisted of four ones such as Beijing No.1, Dahongpao, Dihuang9104 and wild dihuang. Furthermore, Principal coordinate analysis (PCA supported the above cluster analysis; Shannon\\'s Information index (I is 0.3577, effective number of alleles (Ne is 1.4037, the percentage of polymorphic loci is 71.82 % by means of POPGENE32 software; A DNA fingerprint was developed with a single primer, ISSR6, in which each of ten individuals tested had its unique fingerprint pattern and was distinguished from each other. The results revealed that ISSR method is suitable for DNA fingerprinting, identification and genetic diversity analysis of Rehmannia glutinosa in Huai zone.

  17. Genetic Phylogeny and Diversity of some Romanian Silkworms Based on RAPD Technique

    Directory of Open Access Journals (Sweden)

    Emilia Maria Furdui

    2011-05-01

    Full Text Available Randomly amplified polymorphic DNA (RAPD markers were used in the present study to analyze genetic diversity and phylogenetic relationships among some race and hybrids of Romanian Bombyx mori. DNA from 8 hybrids and 1 race was amplified with 35 highly polymorphic RAPD primers, of which 21 markers generated polymorphic bands that were used to analyze genetic phylogeny and diversity. A total of 921 polymorphic bands were detected and UPGMA cluster analysis of Jaccard’s genetic distance grouped silkworm strains on the basis of their origin, obtaining a dendogram reflecting their genetic relationship.

  18. Genetic diversity based on SSR markers in maize (Zea mays L ...

    Indian Academy of Sciences (India)

    Introduction. Genetic diversity of maize (Zea mays L.) plays a key role in maize breeding (William and Michael 2002). Knowledge of the amount and the distribution of genetic variation within and among maize landraces will provide a guide for predict- ing the degree of inheritance, variation, and level of heterosis, that are ...

  19. Genetic diversity of five goat breeds in China based on microsatellite ...

    African Journals Online (AJOL)

    The mean heterozygosity (H) of the populations ranged from 0.7936 to 0.8202. The mean number of effective allele (Ne) of the populations ranged from 5.3373 to 5.8812 and the coefficient of genetic differentiation between breeds was 0.0620. It was suggested that the five goat populations have abundant genetic diversity ...

  20. Mitochondrial DNA-based genetic diversity of genus Lygus (Hemiptera: Miridae) in North America

    Science.gov (United States)

    The genus Lygus is widely distributed in North American and Eurasian continents. It is the most-studied genus in the family Miridae. However, very less information on the genetic diversity of this genus is available. Studying genetic variation among Lygus pest species and thereby constructing a ...

  1. Short tandem repeat (STR) based genetic diversity and relationship of indigenous Niger cattle

    OpenAIRE

    M. Grema; M. Grema; A. Traoré; A. Traoré; M. Issa; M. Hamani; M. Abdou; A. Soudré; M. Sanou; M. Sanou; R. Pichler; H. H. Tamboura; Y. Alhassane; K. Periasamy

    2017-01-01

    The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR) marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding esti...

  2. The first genetic map of pigeon pea based on diversity arrays ...

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... ... genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays ...

  3. Assessment of Genetic Diversity in Seed Plants Based on a Uniform π Criterion

    Directory of Open Access Journals (Sweden)

    Bin Ai

    2014-12-01

    Full Text Available Despite substantial advances in genotyping techniques and massively accumulated data over the past half century, a uniform measurement of neutral genetic diversity derived by different molecular markers across a wide taxonomical range has not yet been formulated. We collected genetic diversity data on seed plants derived by AFLP, allozyme, ISSR, RAPD, SSR and nucleotide sequences, converted expected heterozygosity (He to nucleotide diversity (π, and reassessed the relationship between plant genetic diversity and life history traits or extinction risk. We successfully established a uniform π criterion and developed a comprehensive plant genetic diversity database. The mean population-level and species-level π values across seed plants were 0.00374 (966 taxa, 155 families, 47 orders and 0.00569 (728 taxa, 130 families, 46 orders, respectively. Significant differences were recovered for breeding system (p < 0.001 at the population level and geographic range (p = 0.023 at the species level. Selfing taxa had significantly lower π values than outcrossing and mixed-mating taxa, whereas narrowly distributed taxa had significantly lower π values than widely distributed taxa. Despite significant differences between the two extreme threat categories (critically endangered and least concern, the genetic diversity reduction on the way to extinction was difficult to detect in early stages.

  4. Assessing Genetic Diversity Based on Gliadin Proteins in Aegilops cylindrica Populations from Northwest of Iran

    Directory of Open Access Journals (Sweden)

    Toraj KHABIRI

    2013-02-01

    Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ω type of geliadins. Conversely, the lowest number of bands were pertained to the β type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to β type while, the lowest one was belonged to ω type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

  5. Diversity and population structure of a dominant deciduous tree based on morphological and genetic data.

    Science.gov (United States)

    Zhang, Qin-di; Jia, Rui-Zhi; Meng, Chao; Ti, Chao-Wen; Wang, Yi-Ling

    2015-08-26

    Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon-Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range. Published by Oxford University

  6. Genetic diversity in a Brazilian bovine herd based on four microsatellite loci

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    Almeida Sabrina E. Matos

    2000-01-01

    Full Text Available Microsatellites or short tandem repeats (STRs, DNA markers relatively abundant in the genome, have a high degree of polymorphism and therefore great potential for characterizing populations. The present study estimates genetic variability in a set of four microsatellites (BMS3013, BMS3004, HEL10 and TGLA122 in a Brazilian hybrid bovine breed (5/8 Aberdeen Angus x 3/8 Nelore. The objectives were to determine the effect of crossbreeding and selection in these animals' genetic diversity as well as to discover the herd's genetic relationship with that of other breeds. Low diversity was verified in BMS3013 and high diversity was detected in BMS3004, HEL10 and TGLA122. Two alleles in TGLA122 are described here for the first time (TGLA122*155 and TGLA122*163. These genes are possibly characteristics of Zebu animals since they have not been found in other taurine samples so far investigated. Low interpopulational diversity was observed among taurine cattle populations, and clusters obtained on TGLA122 phylogenetic trees agreed with the bovine herd's geographic origin. Therefore, despite TGLA122's high polymorphism and high levels of intrapopulational diversity, the system engenders consistent bovine phylogenies. We detected an intriguingly high similarity between Brangus Ibagé and Red Angus since the former is a hybrid having 3/8 of Nelore genes. Either these animals' environment or genetic selective practices applied to the breed probably favor the Angus genotype.

  7. Genetic diversity of Gobio gobio populations in the Czech Republic and Slovakia, based on RAPD markers

    Czech Academy of Sciences Publication Activity Database

    Mendel, Jan; Lusková, Věra; Halačka, Karel; Lusk, Stanislav; Vetešník, Lukáš

    2005-01-01

    Roč. 54, Suppl. 1 (2005), s. 13-24 ISSN 0139-7893. [Distribution, taxonomy and genetic status of the European species of the genus Gobio. Brno, 09.09.2003-11.09.2003] R&D Projects: GA AV ČR(CZ) IAA6045005; GA AV ČR IBS5045111 Institutional research plan: CEZ:AV0Z60930519 Keywords : Gobio * diagnostic markers * intraspecific diversity Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.585, year: 2005

  8. Genetic Diversity and Population Structure of Broomcorn Millet (Panicum miliaceum L.) Cultivars and Landraces in China Based on Microsatellite Markers

    Science.gov (United States)

    Liu, Minxuan; Xu, Yue; He, Jihong; Zhang, Shuang; Wang, Yinyue; Lu, Ping

    2016-01-01

    Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, we analyzed the genetic diversity of 88 accessions of broomcorn millet collected from various provinces of China. Amplification with 67 simple sequence repeat (SSR) primers revealed moderate levels of diversity in the investigated accessions. A total of 179 alleles were detected, with an average of 2.7 alleles per locus. Polymorphism information content and expected heterozygosity ranged from 0.043 to 0.729 (mean = 0.376) and 0.045 to 0.771 (mean = 0.445), respectively. Cluster analysis based on the unweighted pair group method of mathematical averages separated the 88 accessions into four groups at a genetic similarity level of 0.633. A genetic structure assay indicated a close correlation between geographical regions and genetic diversity. The uncovered information will be valuable for defining gene pools and developing breeding programs for broomcorn millet. Furthermore, the millet-specific SSR markers developed in this study should serve as useful tools for assessment of genetic diversity and elucidation of population structure in broomcorn millet. PMID:26985894

  9. Identifying predictors of activity based anorexia susceptibility in diverse genetic rodent populations.

    Directory of Open Access Journals (Sweden)

    Eneda Pjetri

    Full Text Available Animal studies are very useful in detection of early disease indicators and in unravelling the pathophysiological processes underlying core psychiatric disorder phenotypes. Early indicators are critical for preventive and efficient treatment of progressive psychiatric disorders like anorexia nervosa. Comparable to physical hyperactivity observed in anorexia nervosa patients, in the activity-based anorexia rodent model, mice and rats express paradoxical high voluntary wheel running activity levels when food restricted. Eleven inbred mouse strains and outbred Wistar WU rats were exposed to the activity-based anorexia model in search of identifying susceptibility predictors. Body weight, food intake and wheel running activity levels of each individual mouse and rat were measured. Mouse strains and rats with high wheel running activity levels during food restriction exhibited accelerated body weight loss. Linear mixed models for repeated measures analysis showed that baseline wheel running activity levels preceding the scheduled food restriction phase strongly predicted activity-based anorexia susceptibility (mice: Beta  =  -0.0158 (±0.003 SE, P<0.0001; rats: Beta  =  -0.0242 (±0.004 SE, P<0.0001 compared to other baseline parameters. These results suggest that physical activity levels play an important role in activity-based anorexia susceptibility in different rodent species with genetically diverse background. These findings support previous retrospective studies on physical activity levels in anorexia nervosa patients and indicate that pre-morbid physical activity levels could reflect an early indicator for disease severity.

  10. Genetic diversity of five goat breeds in China based on microsatellite ...

    African Journals Online (AJOL)

    USER

    2012-07-05

    Jul 5, 2012 ... The genetic diversity of five goat breeds in China was surveyed using 15 microsatellites. The five goat breeds included Tangshan dairy goat (TSD), Liaoning cashmere goat (LNC), Nanjiang yellow goat (NJY),. Chengde polled goat (CDP) and Leizhou black goat (LZB). The mean polymorphism information ...

  11. Genetic diversity of Iranian potato soft rot bacteria based on PCR ...

    African Journals Online (AJOL)

    TENEBRA

    2012-01-19

    Jan 19, 2012 ... Key words: Genetic diversity, polymerase chain reaction-restriction fragment length polymorphism (PCR-. RFLP), recA gene, Pectobacterium spp. .... each restriction enzyme was used for digestions, which were incubated overnight at the .... (2006) with application of the molecular marker of PCR-RFLP, ...

  12. Conservation of eelgrass (Zostera marina genetic diversity in a mesocosm-based restoration experiment.

    Directory of Open Access Journals (Sweden)

    Brian S Ort

    Full Text Available Eelgrass (Zostera marina forms the foundation of an important shallow coastal community in protected estuaries and bays. Widespread population declines have stimulated restoration efforts, but these have often overlooked the importance of maintaining the evolutionary potential of restored populations by minimizing the reduction in genetic diversity that typically accompanies restoration. In an experiment simulating a small-scale restoration, we tested the effectiveness of a buoy-deployed seeding technique to maintain genetic diversity comparable to the seed source populations. Seeds from three extant source populations in San Francisco Bay were introduced into eighteen flow-through baywater mesocosms. Following seedling establishment, we used seven polymorphic microsatellite loci to compare genetic diversity indices from 128 shoots to those found in the source populations. Importantly, allelic richness and expected heterozygosity were not significantly reduced in the mesocosms, which also preserved the strong population differentiation present among source populations. However, the inbreeding coefficient F IS was elevated in two of the three sets of mesocosms when they were grouped according to their source population. This is probably a Wahlund effect from confining all half-siblings within each spathe to a single mesocosm, elevating F IS when the mesocosms were considered together. The conservation of most alleles and preservation of expected heterozygosity suggests that this seeding technique is an improvement over whole-shoot transplantation in the conservation of genetic diversity in eelgrass restoration efforts.

  13. Genetic diversity, inbreeding and cancer.

    Science.gov (United States)

    Ujvari, Beata; Klaassen, Marcel; Raven, Nynke; Russell, Tracey; Vittecoq, Marion; Hamede, Rodrigo; Thomas, Frédéric; Madsen, Thomas

    2018-03-28

    Genetic diversity is essential for adaptive capacities, providing organisms with the potential of successfully responding to intrinsic and extrinsic challenges. Although a clear reciprocal link between genetic diversity and resistance to parasites and pathogens has been established across taxa, the impact of loss of genetic diversity by inbreeding on the emergence and progression of non-communicable diseases, such as cancer, has been overlooked. Here we provide an overview of such associations and show that low genetic diversity and inbreeding associate with an increased risk of cancer in both humans and animals. Cancer being a multifaceted disease, loss of genetic diversity can directly (via accumulation of oncogenic homozygous mutations) and indirectly (via increased susceptibility to oncogenic pathogens) impact abnormal cell emergence and escape of immune surveillance. The observed link between reduced genetic diversity and cancer in wildlife may further imperil the long-term survival of numerous endangered species, highlighting the need to consider the impact of cancer in conservation biology. Finally, the somewhat incongruent data originating from human studies suggest that the association between genetic diversity and cancer development is multifactorial and may be tumour specific. Further studies are therefore crucial in order to elucidate the underpinnings of the interactions between genetic diversity, inbreeding and cancer. © 2018 The Author(s).

  14. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    Science.gov (United States)

    Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

    2013-03-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

  15. Genetic diversity and DNA fingerprinting in jute (Corchorus spp. based on SSR markers

    Directory of Open Access Journals (Sweden)

    Liwu Zhang

    2015-10-01

    Full Text Available Genetic diversity analysis and DNA finger printing are very useful in breeding programs, seed conservation and management. Jute (Corchorus spp. is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties (Huangma 179 and Kuanyechangguo from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with CoSSR305-120 and CoSSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

  16. Genetic Diversity of Iranian and Exotic Sainfoin Accessions (Onobrychis viciifolia Scop Based on Morphological Traits

    Directory of Open Access Journals (Sweden)

    M. Zarabiyan

    2016-12-01

    Full Text Available Sainfoin (Onobrychis viciifolia Scop. is widely grown as forage and pasture legume in Iran and is tolerant to environmental stresses. To investigate the genetic diversity among 56 accessions of sainfoin germplasm (including 46 Iranian and 10 foreign based on morphological and agronomic characteristics, present experiment was conducted as randomized complete block design with three replications in Isfahan University of Technology Research Farm during 2010-2011. The results of analysis of variance indicated considerable variation between studied germplasm for all traits and the better performance for Iranian accessions. The estimation of broad sense heritability for plant height, number of stems per plant, number of stems per meter square and number of nods per stem was high suggesting contribution of the major genes for controlling these traits. On the basis of means comparison, the forage yield was greatest for the first cutting as compared to the second cutting. Also the highest yield obtained from second year. Regarding the palatability (based on leaf to stem ratio the exotic accessions had higher values. Developing of superior cultivars may be possible through combining high yield and palatability in breeding programs.

  17. Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers.

    Science.gov (United States)

    Ndiaye, Ndèye Penda; Sow, Adama; Dayo, Guiguigbaza-Kossigan; Ndiaye, Saliou; Sawadogo, Germain Jerôme; Sembène, Mbacké

    2015-08-01

    In Senegal, uncontrolled cross-breeding of cattle breeds and changes in production systems are assumed to lead to an increase of gene flow between populations. This might constitute a relevant threat to livestock improvement. Therewith, this study was carried out to assess the current genetic diversity and the phylogenetic relationships of the four native Senegalese cattle breeds (Gobra zebu, Maure zebu, Djakoré, and N'Dama). Genomic DNA was isolated from blood samples of 120 unrelated animals collected from three agro-ecological areas of Senegal according to their phenotypic traits. Genotyping was done using 11 specific highly polymorphic microsatellite makers recommended by Food and Agriculture Organization. The basic measures of genetic variation and phylogenetic trees were computed using bioinformatics' software. A total of 115 alleles were identified with a number of alleles (Na) at one locus ranging from 6 to 16. All loci were polymorphic with a mean polymorphic information content of 0.76. The mean allelic richness (Rs) lay within the narrow range of 5.14 in N'Dama taurine to 6.10 in Gobra zebu. While, the expected heterozygosity (HE) per breed was high in general with an overall mean of 0.76±0.04. Generally, the heterozygote deficiency (FIS) of 0.073±0.026 was relatively due to inbreeding among these cattle breeds or the occurrence of population substructure. The high values of allelic and gene diversity showed that Senegalese native cattle breeds represented an important reservoir of genetic variation. The genetic distances and clustering trees concluded that the N'Dama cattle were most distinct among the investigated cattle populations. So, the principal component analyses showed qualitatively that there was an intensive genetic admixture between the Gobra zebu and Maure zebu breeds. The broad genetic diversity in Senegalese cattle breeds will allow for greater opportunities for improvement of productivity and adaptation relative to global changes. For

  18. Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers

    Directory of Open Access Journals (Sweden)

    Ndèye Penda Ndiaye

    2015-08-01

    Full Text Available Aim: In Senegal, uncontrolled cross-breeding of cattle breeds and changes in production systems are assumed to lead to an increase of gene flow between populations. This might constitute a relevant threat to livestock improvement. Therewith, this study was carried out to assess the current genetic diversity and the phylogenetic relationships of the four native Senegalese cattle breeds (Gobra zebu, Maure zebu, Djakoré, and N’Dama. Methods: Genomic DNA was isolated from blood samples of 120 unrelated animals collected from three agro-ecological areas of Senegal according to their phenotypic traits. Genotyping was done using 11 specific highly polymorphic microsatellite makers recommended by Food and Agriculture Organization. The basic measures of genetic variation and phylogenetic trees were computed using bioinformatics’ software. Results: A total of 115 alleles were identified with a number of alleles (Na at one locus ranging from 6 to 16. All loci were polymorphic with a mean polymorphic information content of 0.76. The mean allelic richness (Rs lay within the narrow range of 5.14 in N’Dama taurine to 6.10 in Gobra zebu. While, the expected heterozygosity (HE per breed was high in general with an overall mean of 0.76±0.04. Generally, the heterozygote deficiency (FIS of 0.073±0.026 was relatively due to inbreeding among these cattle breeds or the occurrence of population substructure. The high values of allelic and gene diversity showed that Senegalese native cattle breeds represented an important reservoir of genetic variation. The genetic distances and clustering trees concluded that the N’Dama cattle were most distinct among the investigated cattle populations. So, the principal component analyses showed qualitatively that there was an intensive genetic admixture between the Gobra zebu and Maure zebu breeds. Conclusions: The broad genetic diversity in Senegalese cattle breeds will allow for greater opportunities for improvement of

  19. Genetic diversity of some apple cultivars in the south of Syria based on morphological characters

    Directory of Open Access Journals (Sweden)

    O. Al-Halabi

    2015-12-01

    Full Text Available This work was aimed to evaluate genetic diversity among five local and six introduced apple cultivars in the germplasm which located in the South of Syria based on 29 morphological characters of leaf and fruit. The analysis of variance showed significant differences at P < 0.05 for all measured parameters, however the mean values of Limb length and width, fruit weight, length, and width indicated to a wide range of diversity between local and introduced cultivars, that the introduced cultivars have mostly the highest mean value while the local cultivars have the lowest mean values, that clearly found in the local apple cultivar Ksairi (K which revealed the lowest mean value of fruit weight (FW, fruit length (FL and fruit diameter (FD in the comparison with all studied cultivars. Likewise, principal component analysis (PCA was used and the first 4 principal components accounted for 76.4% of the total variance, with eigen values 29.2%, 18.8%, 16.9% and 11.5% respectively. The main important characters in PC1 are correlated with the high mean value of width of stalk cavity (WP, fruit weight (FW, fruit diameter (FD, fruit length (FL, core length (CL, width of calyx cavity (WC, core width (CW, depth of stalk cavity (DP, stalk diameter (SD, seed width (SeW and leaf margin (LM. PC2 discriminated among cultivars depending on Fruit shape (FS, leaf shape (LS, over color (OC, maturity time (MT, core shape (CS, limp length (LL and leaf base (LB which were able to differentiate between all studied cultivars . PC3 is correlated with the high mean value of Stalk length (SL, titratable acidity (TA, total sugar (TS, and total soluble solids (TSS. PC4 is correlated with the high mean value of depth of calyx cavity (DC, leaf apices (LA and fruit cross section (FCS. Cluster analysis was also used that divided the studied cultivars into two clusters, the first cluster included all local apple cultivars, in addition to Leaz Golden (LG cultivar, however AbouGhabra (AG

  20. Genetic diversity analysis of Capsicum spp germplasm bank accessions based on α/β-esterase polymorphism.

    Science.gov (United States)

    Monteiro, E R; Bronzato, A R; Orasmo, G R; Lopes, A C A; Gomes, R L F; Mangolin, C A; Machado, M F P S

    2013-04-12

    Genetic diversity and structure were analyzed in 10 accessions belonging to Banco Ativo de Germoplasma de Capsicum located at Federal University of Piauí in northwestern Brazil that receives pepper samples grown in community gardens in various regions and Brazilian states. Selections were made from seeds of C. chinense (4 accessions), C. annuum (5 accessions), and C. baccatum (1 accession). Samples consisting of leaves were collected from 4-10 plants of each accession (a total of 85 plants). Native polyacrylamide gel electrophoresis was used to identify α- and β-esterase polymorphisms. Polymorphism was clearly detected in 5 loci. Sixteen alleles were found at 5 α/β-esterase loci of the three Capsicum species. In the C. chinense samples, the highest HO and HE values were 0.3625 and 0.4395, respectively, whereas in C. annuum samples, HO and HE values were 0.2980 and 0.3310, respectively; the estimated HO and HE values in C. chinense samples were higher than those detected in C. annuum samples. A deficit of homozygous individuals was found in C. chinense (FIS = -0.6978) and C. annuum (FIS = 0.7750). Genetic differentiation between C. chinense and C. annuum at these loci was high (FST = 0.1867) indicating that C. chinense and C. annuum are genetically structured species for α/β- esterase isozymes. The esterase analysis showed high genetic diversity among the C. chinense and C. annuum samples and very high genetic differentiation (FST = 0.6321) among the C. chinense and C. annuum samples and the C. baccatum accession.

  1. MULTIVARIATE DIVERSITY, HERITABILITY AND GENETIC ...

    African Journals Online (AJOL)

    sorghum (Sorghum bicolor (L.) Moench germplasm from Ethiopia and Eritrea. Genetic. Resources and Crop Evolution 46:273-284. Ayele, M. 1999. Genetic diversity in tef. (Eragrostis tef (Zucc) Trotter) for osmotic adjustment, root traits, and Amplified. Fragment Length Polymorphism. PhD Thesis,. Texas Tech University, USA.

  2. Genetic diversity of Xanthomonas axonopodis pv. citri based on plasmid profile and pulsed field gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Carvalho Flávia Maria de Souza

    2005-01-01

    Full Text Available Xanthomonas axonopodis pv. citri strains that cause disease in citrus were investigated by pulsed field and plasmid profile analysis. For the first method, genomic DNA was digested by the rare-cutting enzymes Xba I and Vsp I. The strains evaluated were collected in seven different States of Brazil and in Argentina, Bolivia, Paraguay and Uruguay. Genetic variability was found among strains of X. axonopodis pv. citri from different geographical areas Argentina, Bolivia and Uruguay, with similarities varying from 0.62 to 0.83. However, the strains collected in Brazil, despite being from different States, have shown a genetic similarity ranging from 0.83 to 1.00. Cluster analysis showed a relationship between genomic similarity and geographical origin of the strains. Plasmids were observed in all strains, with a total of five different plasmids, with sizes between 57.7 and 83.0 kilobases. The 72.6 kb plasmid was the most frequent, present in 15 out of 22 strains, while the 68.1 kb plasmid was observed in two strains only. Although the plasmid diversity detected in the present study was not very great, the X. axonopodis pv. citri strains evaluated showed a considerable degree of diversity with regard to this extrachromosomal genetic element.

  3. Genetic diversity of European cultivars of common wheat (Triticum aestivum L. based on RAPD and protein markers

    Directory of Open Access Journals (Sweden)

    Tímea KUŤKA HLOZÁKOVÁ

    2016-12-01

    Full Text Available The knowledge of genetic diversity of wheat genotypes based on DNA and protein polymorphism is very important for breeding programs (MAS. The objective of this study was to assess the genetic variability among twenty – four European cultivars of common wheat using SDS – PAGE and RAPD techniques. Protein electrophoreses showed 31 polymorphic bands with 63.2% polymorphism. Genetic similarity based on Jaccard´s coefficient ranged from 0.067 to 0.933. Also twelve different Glu – 1 encoded allelic variants were identified among these 24 genotypes resulting from combination of 3 alleles of Glu – 1A, 7 of Glu – 1B and 2 of Glu – 1D loci. One novel allelic variant 6.5+7.5 at the Glu – 1B locus was identified. RAPD analysis showed that the number of polymorphic amplicons was 56 out of a total of 63 amplicons, thus revealing a level of 37.56% polymorphism. Maximum level of polymorphism (55.8% was observed for the primer OPA – 03 and minimum one for OPD – 08 (13.8%. Genetic similarity based on Jaccard´s coefficient ranged from 0.396 to 0.805. As a result of this investigation, might be expected that the SDS – PAGE using protein markers and RAPD – PCR using DNA markers would be a useful tool for assessment of genetic diversity among wheat genotypes.

  4. DEVELOPMENT OF DNA BASED MICROSATELLITE MARKER TECHNOLOGY FOR STUDIES OF GENETIC DIVERSITY IN CENTRAL STONEROLLER (CAMPOSTOMA ANOMALUM) POPULATIONS

    Science.gov (United States)

    The level of genetic diversity of aquatic species is a critical indicator of stream system condition for which few data exist. There is strong evidence suggesting that environmental stressors affect the genetic diversity of exposed populations. In order to study genetic diversi...

  5. Genetic diversity and population structure analysis in Perilla frutescens from Northern areas of China based on simple sequence repeats.

    Science.gov (United States)

    Ma, S J; Sa, K J; Hong, T K; Lee, J K

    2017-09-21

    In this study, 21 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population structure among 77 Perilla accessions from high-latitude and middle-latitude areas of China. Ninety-five alleles were identified with an average of 4.52 alleles per locus. The average polymorphic information content (PIC) and genetic diversity values were 0.346 and 0.372, respectively. The level of genetic diversity and PIC value for cultivated accessions of Perilla frutescens var. frutescens from middle-latitude areas were higher than accessions from high-latitude areas. Based on the dendrogram of unweighted pair group method with arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 46%. All accessions of the cultivated var. frutescens were discriminated from the cultivated P. frutescens var. crispa. Furthermore, most accessions of the cultivated var. frutescens collected in high-latitude and middle-latitude areas were distinguished depending on their geographical location. However, the geographical locations of several accessions of the cultivated var. frutescens have no relation with their positions in the UPGMA dendrogram and population structure. This result implies that the diffusion of accessions of the cultivated Perilla crop in the northern areas of China might be through multiple routes. On the population structure analysis, 77 Perilla accessions were divided into Group I, Group II, and an admixed group based on a membership probability threshold of 0.8. Finally, the findings in this study can provide useful theoretical knowledge for further study on the population structure and genetic diversity of Perilla and benefit for Perilla crop breeding and germplasm conservation.

  6. Assessment of ISSR based molecular genetic diversity of Hassawi rice in Saudi Arabia.

    Science.gov (United States)

    Al-Turki, T A; Basahi, Mohammed A

    2015-09-01

    Inter simple sequence repeat (ISSR) analysis, using 14 primers was performed to estimate genetic diversity among 27 landraces of Hassawi rice growing in Al-Ahsa region of Saudi Arabia and deposited at King Abdulaziz City for Science and Technology with KACST IDs. The average polymorphism produced by 11 selected primers was more than 75%. The analysis of ISSR polymorphism divided the examined rice landraces into two groups; In one group (A), one accession (KACST 191) was clearly delimited as a distant landrace from other 12 landraces grouped in two clusters; cluster I of seven landraces of close geographic distributions; four of them grow at close geographic locations (KACST IDs 32, 183, 184, 185, 186, 187 and 188) and cluster II is comprised of five landraces KACST IDs (190, 308, 352, 353 and 355). In group B, the landraces were more closely related to each other as compared to the landraces of group A. In this group a small cluster of two landraces (KACST 305 & KACST 333) was clearly distant from a large group of three clusters comprised of landraces having KACST IDs 189 & 192, landraces 302, 306, 307, 308 & 310 and landraces with KACST IDs 334, 351, 354, 356 & 357 respectively. These results indicate that ISSR fingerprints are efficient in the identification and resolution of genetic diversity between the landraces of the Hassawi rice and will be an efficient method in the authentication of the rice germplasm in the gene bank of Saudi Arabia.

  7. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

    Directory of Open Access Journals (Sweden)

    Jurado Juan J

    2009-09-01

    Full Text Available Abstract Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008 consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08 mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will

  8. Genetic Diversity of Some Sweet Cherry Cultivars Based on Molecular Markers

    Directory of Open Access Journals (Sweden)

    Ioana Virginia Berindean

    2016-11-01

    Full Text Available Sweet cherry (Prunus avium L., originated around the Caspian and Black Sea, is an important fruit tree species of economic interest, and hence, breeding and conservation are requested (. Genetic analysis at the molecular level can be used effectively to study molecular polymorphism existing between intraspecific and interspecific tree species and phylogenetic relationships between them and their hybrids. The purpose of this study was to characterize and determine genetic relationships among the sweet cherry native genotypes belonging to Fruit Research & Development Station Bistrita, Romania, using RAPD markers. To eliminate the existence of possible synonyms from national romanian collection, we collect four Van cultivars, from four different national collection. For molecular analysis of the 16 varieties of sweet cherry were considered 13 RAPD primers selected from the literature. They were later used to determine the genetic variability at the molecular level using PAST program, and the dendrogram was generated based on Jaccard’s genetic distance. The dendrogram constructed by PAST software. The quantity and quality of the DNA obtained was suitable to achieve PCR amplification step. Only seven out of the 13 RAPD primers have generate polymorphic bands. The rest of seven were monomorphics. The most polymorphic primer was OPB10 which generated 11 bands from which 100% were polymorphic.Seven RAPD primers generated a high level of polymorphism which allowed to divide these cherry varieties into two groups according to their genetic geographical origin and the pedigree.

  9. Molecular Genetic Diversity of Date (Phoenix dactylifera) Germplasm in Qatar based on Microsatellite Markers

    KAUST Repository

    Ahmed, Talaat

    2016-01-25

    Depending on morphological traits alone, studying the genetic diversity of date palm is a very difficult task since morphological characteristics are highly affected by the environment. DNA markers are excellent option that can help and enhance the discriminatory power of morphological characteristics. To study the genetic diversity among date palm cultivars grown in Qatar, fifteen Date palm samples were collected from Qatar University Experimental Farm. DNAs were extracted from fresh leaves by using commercial DNeasy Plant System Kit (Qiagen, Inc., Valencia, CA). Total of 18 (Inter Simple Sequence Repeat) ISSR single primers were used to amplify DNA fragments using genomic DNA of the 15 samples. First screening was done to test the ability of these primers to amplify clear bands using Date palm genomic DNA. All 18 ISSR primers successfully produced clear bands in the first screening. Then, each primer was used separately to genotype the whole set of 15 Date palm samples. Total of 4794 bands were generated using 18 ISSR primers for the 15 Date palm samples. On average, each primer generated 400 bands. The Number of amplified bands varied from cultivar to cultivar. The highest number of bands was obtained using Primers 2, 5 and 12 for the 15 (470 bands), while the lowest number of bands were obtained by Primers 1, 7 and 8 where they produced only 329 bands. Markers were scored for the presence and absence of the corresponding band among the different cultivars. Data were subjected to cluster analysis. A similarity matrix was constructed and the similarity values were used for cluster analysis.

  10. Genetic diversity among air yam (Dioscorea bulbifera) varieties based on single sequence repeat markers.

    Science.gov (United States)

    Silva, D M; Siqueira, M V B M; Carrasco, N F; Mantello, C C; Nascimento, W F; Veasey, E A

    2016-05-23

    Dioscorea is the largest genus in the Dioscoreaceae family, and includes a number of economically important species including the air yam, D. bulbifera L. This study aimed to develop new single sequence repeat primers and characterize the genetic diversity of local varieties that originated in several municipalities of Brazil. We developed an enriched genomic library for D. bulbifera resulting in seven primers, six of which were polymorphic, and added four polymorphic loci developed for other Dioscorea species. This resulted in 10 polymorphic primers to evaluate 42 air yam accessions. Thirty-three alleles (bands) were found, with an average of 3.3 alleles per locus. The discrimination power ranged from 0.113 to 0.834, with an average of 0.595. Both principal coordinate and cluster analyses (using the Jaccard Index) failed to clearly separate the accessions according to their origins. However, the 13 accessions from Conceição dos Ouros, Minas Gerais State were clustered above zero on the principal coordinate 2 axis, and were also clustered into one subgroup in the cluster analysis. Accessions from Ubatuba, São Paulo State were clustered below zero on the same principal coordinate 2 axis, except for one accession, although they were scattered in several subgroups in the cluster analysis. Therefore, we found little spatial structure in the accessions, although those from Conceição dos Ouros and Ubatuba exhibited some spatial structure, and that there is a considerable level of genetic diversity in D. bulbifera maintained by traditional farmers in Brazil.

  11. Genetic Diversity of Methylotrophic Bacteria from Human Mouth Based on Amplified Ribosomal DNA Restriction Analysis (ARDRA

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    CINDY OKTAVIA SUSANTO

    2011-06-01

    Full Text Available Methylotrophs inhabit the human mouth. In this study, methylotrophic bacteria were isolated from the human mouth microflora of 63 subjects, especially from the tongue, gingival, and subgingival area using minimal agar supplemented with 1% methanol. The obtained isolates were subjected to biochemical assays, continued with antibiotics susceptibility testing using ampicillin (10 g, tetracycline (20 g, kanamycin (30 g, trimethoprim (5 g, and streptomycin (10 g. Genetic diversity was analyzed using ARDRA method. Isolates varying in morphology characteristics were amplified for 16S rRNA gene and continued with DNA sequencing. As many as 21 methylotrophic bacterial isolates were purified and divided into seven groups with different phenotypic profiles. A majority of the isolates were resistant to trimethoprim but sensitive to kanamycin, streptomycin, and tetracycline. Resistance to ampicillin was variable in each isolate. ARDRA showed nine different digestion profiles. DNA sequencing analysis of the 16S rRNA gene showed that six isolates with different phenotypic and digestion profiles were closely related to Methylobacterium radiotoleran (94%, Microbacterium esteraromaticum (99%, Pseudomonas sp. (100%, and three of them were exhibited 99, 99, and 98% sequence similarity with Gordonia sp., respectively. The results of this study revealed diversity among methylotrophic bacteria particularly in human mouth.

  12. Evaluation of Genetic Diversity Using Parameters Based on Probability of Gene Origin in the Slovak Spotted Bulls

    Directory of Open Access Journals (Sweden)

    E. Hazuchová

    2012-05-01

    Full Text Available The aim of this study was to assess the diversity based on probability of gene origin in Slovak Spotted bulls. The pedigree information was available from The Breeding Services of the Slovak Republic, s. e. The pedigree file consisted of 752 individuals. The 62 sires born from 1995 to 2009 and registered in Herd book set up the analyzed reference (RP population. Total number of founders in the RP was 308, effective number of founders was 115 and the effective number of ancestors was 37. The number of ancestors explaining 50 % of the diversity was 15 and founder’s genome equivalent was 20.46. The sire GS Malf and Horwein were with 16 offspring’s the most frequently used bulls in the artificial insemination. We found that the genetic conservation index for RP was 16.34 %. Results will be used in genetic management of breeding work in Slovak Spotted and monitoring of parameters characterizing genetic diversity and their development, as well.

  13. Forensic molecular genetic diversity analysis of Chinese Hui ethnic group based on a novel STR panel.

    Science.gov (United States)

    Fang, Yating; Guo, Yuxin; Xie, Tong; Jin, Xiaoye; Lan, Qiong; Zhou, Yongsong; Zhu, Bofeng

    2018-03-26

    In present study, the genetic polymorphisms of 22 autosomal short tandem repeat (STR) loci were analyzed in 496 unrelated Chinese Xinjiang Hui individuals. These autosomal STR loci were multiplex amplified and genotyped based on a novel STR panel. There were 246 observed alleles with the allele frequencies ranging from 0.0010 to 0.3609. All polymorphic information content values were higher than 0.7. The combined power of discrimination and the combined probability of exclusion were 0.999999999999999999999999999426766 and 0.999999999860491, respectively. Based on analysis of molecular variance method, genetic differentiation analysis between the Xinjiang Hui and other reported groups were conducted at these 22 loci. The results indicated that there were no significant differences in statistics between Hui group and Northern Han group (including Han groups from Hebei, Henan, Shaanxi provinces), and significant deviations with Southern Han group (including those from Guangdong, Guangxi provinces) at 7 loci, and Uygur group at 10 loci. To sum up, these 22 autosomal STR loci were high genetic polymorphic in Xinjiang Hui group.

  14. Genetic diversity of Candidatus Liberibacter asiaticus based on two hypervariable effector genes in Thailand.

    Science.gov (United States)

    Puttamuk, Thamrongjet; Zhou, Lijuan; Thaveechai, Niphone; Zhang, Shouan; Armstrong, Cheryl M; Duan, Yongping

    2014-01-01

    Huanglongbing (HLB), also known as citrus greening, is one of the most destructive diseases of citrus worldwide. HLB is associated with three species of 'Candidatus Liberibacter' with 'Ca. L. asiaticus' (Las) being the most widely distributed around the world, and the only species detected in Thailand. To understand the genetic diversity of Las bacteria in Thailand, we evaluated two closely-related effector genes, lasAI and lasAII, found within the Las prophages from 239 infected citrus and 55 infected psyllid samples collected from different provinces in Thailand. The results indicated that most of the Las-infected samples collected from Thailand contained at least one prophage sequence with 48.29% containing prophage 1 (FP1), 63.26% containing prophage 2 (FP2), and 19.38% containing both prophages. Interestingly, FP2 was found to be the predominant population in Las-infected citrus samples while Las-infected psyllids contained primarily FP1. The multiple banding patterns that resulted from amplification of lasAI imply extensive variation exists within the full and partial repeat sequence while the single band from lasAII indicates a low amount of variation within the repeat sequence. Phylogenetic analysis of Las-infected samples from 22 provinces in Thailand suggested that the bacterial pathogen may have been introduced to Thailand from China and the Philippines. This is the first report evaluating the genetic variation of a large population of Ca. L. asiaticus infected samples in Thailand using the two effector genes from Las prophage regions.

  15. Diversity Outbred Mice Identify Population-Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity

    Science.gov (United States)

    Gatti, Daniel M.; Morgan, Daniel L.; Kissling, Grace E.; Shockley, Keith R.; Knudsen, Gabriel A.; Shepard, Kim G.; Price, Herman C.; King, Deborah; Witt, Kristine L.; Pedersen, Lars C.; Munger, Steven C.; Svenson, Karen L.; Churchill, Gary A.

    2014-01-01

    Background Inhalation of benzene at levels below the current exposure limit values leads to hematotoxicity in occupationally exposed workers. Objective We sought to evaluate Diversity Outbred (DO) mice as a tool for exposure threshold assessment and to identify genetic factors that influence benzene-induced genotoxicity. Methods We exposed male DO mice to benzene (0, 1, 10, or 100 ppm; 75 mice/exposure group) via inhalation for 28 days (6 hr/day for 5 days/week). The study was repeated using two independent cohorts of 300 animals each. We measured micronuclei frequency in reticulocytes from peripheral blood and bone marrow and applied benchmark concentration modeling to estimate exposure thresholds. We genotyped the mice and performed linkage analysis. Results We observed a dose-dependent increase in benzene-induced chromosomal damage and estimated a benchmark concentration limit of 0.205 ppm benzene using DO mice. This estimate is an order of magnitude below the value estimated using B6C3F1 mice. We identified a locus on Chr 10 (31.87 Mb) that contained a pair of overexpressed sulfotransferases that were inversely correlated with genotoxicity. Conclusions The genetically diverse DO mice provided a reproducible response to benzene exposure. The DO mice display interindividual variation in toxicity response and, as such, may more accurately reflect the range of response that is observed in human populations. Studies using DO mice can localize genetic associations with high precision. The identification of sulfotransferases as candidate genes suggests that DO mice may provide additional insight into benzene-induced genotoxicity. Citation French JE, Gatti DM, Morgan DL, Kissling GE, Shockley KR, Knudsen GA, Shepard KG, Price HC, King D, Witt KL, Pedersen LC, Munger SC, Svenson KL, Churchill GA. 2015. Diversity Outbred mice identify population-based exposure thresholds and genetic factors that influence benzene-induced genotoxicity. Environ Health Perspect 123:237

  16. Personalized Medicine and Human Genetic Diversity

    OpenAIRE

    Lu, Yi-Fan; Goldstein, David B.; Angrist, Misha; Cavalleri, Gianpiero

    2014-01-01

    Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more mo...

  17. Genetic Diversity of Foxtail Millet (Setaria italica L.) From Main Asian Habitats Based on the NRDNA ITS Region

    International Nuclear Information System (INIS)

    Sun, Y. L.; Zheng, S. L.; Lee, J. K.

    2016-01-01

    Foxtail millet (Setaria italica (L.) P. Beauv.) is a crop of historical importance in some Asian and European countries. In this study, we selected the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) as the DNA marker to analyze genetic diversity and relationships of 20 foxtail millet strains collected from three representative Asian countries, including China, Korea, and Pakistan. Due to the length limitation of the nrDNA ITS region, 17 typical variable nucleotide sites were only found, of which 4 sites belonged to insertion, 3 sites deletion, and 10 sites substitution. According to the result of sequence alignment, strains were grouped clearly with the relevant of collected geographical region. Based on the sequence similarity and nucleotide variation, one Main China Group (MCG) and one Main Korea Group (MKG) occurred, and the strains from Pakistan were found to be close to MKG, considered to be originally transmitted from Korea and spread to Pakistan. Certain genetic diversity between strains from Pakistan and Korea were recognized as long-time environment evolution and adaptation. Among strains from Korea, K2, K3, K4, and K5 showed nearer phylogenetic relationship to MCG, considered as Chinese populations. All strains from China showed relatively near phylogenetic relationship with each other, supporting the statement that China is one of origin areas. The result also suggested that there was no introduced strain found in the Chinese strains investigated in this study. This work would provide more sequence sources and help clearer strain distinguishing, genetic diversity and phylogenetic relationship of foxtail millet. (author)

  18. Genetic diversity and relatedness of sweet cherry (prunus avium L.) cultivars based on single nucleotide polymorphic markers.

    Science.gov (United States)

    Fernandez I Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font I Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

    2012-01-01

    Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3' untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3' UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, "Stella" was separated from "Compact Stella." This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3' UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry.

  19. Genetic diversity in a crop metapopulation.

    Science.gov (United States)

    van Heerwaarden, J; van Eeuwijk, F A; Ross-Ibarra, J

    2010-01-01

    The need to protect crop genetic resources has sparked a growing interest in the genetic diversity maintained in traditional farming systems worldwide. Although traditional seed management has been proposed as an important determinant of genetic diversity and structure in crops, no models exist that can adequately describe the genetic effects of seed management. We present a metapopulation model that accounts for several features unique to managed crop populations. Using traditional maize agriculture as an example, we develop a coalescence-based model of a crop metapopulation undergoing pollen and seed flow as well as seed replacement. In contrast to metapopulation work on natural systems, we model seed migration as episodic and originating from a single source per population rather than as a constant immigration from the entire metapopulation. We find that the correlated origin of migrants leads to surprising results, including a loss of invariance of within-deme diversity and a parabolic relationship between F(ST) and migration quantity. In contrast, the effects of migration frequency on diversity and structure are more similar to classical predictions, suggesting that seed migration in managed crop populations cannot be described by a single parameter. In addition to migration, we investigate the effects of deme size and extinction rates on genetic structure, and show that high levels of pollen migration may mask the effects of seed management on structure. Our results highlight the importance of analytically evaluating the effects of deviations from classical metapopulation models, especially in systems for which data are available to estimate specific model parameters.

  20. Evolution and genetic diversity of Theileria.

    Science.gov (United States)

    Sivakumar, Thillaiampalam; Hayashida, Kyoko; Sugimoto, Chihiro; Yokoyama, Naoaki

    2014-10-01

    Theileria parasites infect a wide range of domestic and wild ruminants worldwide, causing diseases with varying degrees of severity. A broad classification, based on the parasite's ability to transform the leukocytes of host animals, divides Theileria into two groups, consisting of transforming and non-transforming species. The evolution of transforming Theileria has been accompanied by drastic changes in its genetic makeup, such as acquisition or expansion of gene families, which are thought to play critical roles in the transformation of host cells. Genetic variation among Theileria parasites is sometimes linked with host specificity and virulence in the parasites. Immunity against Theileria parasites primarily involves cell-mediated immune responses in the host. Immunodominance and major histocompatibility complex class I phenotype-specificity result in a host immunity that is tightly focused and strain-specific. Immune escape in Theileria is facilitated by genetic diversity in its antigenic determinants, which potentially results in a loss of T cell receptor recognition in its host. In the recent past, several reviews have focused on genetic diversity in the transforming species, Theileriaparva and Theileriaannulata. In contrast, genetic diversity in Theileriaorientalis, a benign non-transforming parasite, which occasionally causes disease outbreaks in cattle, has not been extensively examined. In this review, therefore, we provide an outline of the evolution of Theileria, which includes T. orientalis, and discuss the possible mechanisms generating genetic diversity among parasite populations. Additionally, we discuss the potential implications of a genetically diverse parasite population in the context of Theileria vaccine development. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems.

    Science.gov (United States)

    Sharma, Vishakha; Nandineni, Madhusudan R

    2014-04-01

    Potato (Solanum tuberosum) is an important non-cereal crop throughout the world and is highly recommended for ensuring global food security. Owing to the complexities in genetics and inheritance pattern of potato, the conventional method of cross breeding for developing improved varieties has been difficult. Identification and tagging of desirable traits with informative molecular markers would aid in the development of improved varieties. Insertional polymorphism of copia-like and gypsy-like long terminal repeat retrotransposons (RTN) were investigated among 47 potato varieties from India using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) marker techniques and were compared with the DNA profiles obtained with simple sequence repeats (SSRs). The genetic polymorphism, efficiency of polymorphism and effectiveness of marker systems were evaluated to assess the extent of genetic diversity among Indian potato varieties. A total of 139 polymorphic SSR alleles, 270 IRAP and 98 REMAP polymorphic bands, showing polymorphism of 100%, 87.9% and 68.5%, respectively, were used for detailed characterization of the genetic relationships among potato varieties by using cluster analysis and principal coordinate analysis (PCoA). IRAP analysis resulted in the highest number of polymorphic bands with an average of 15 polymorphic bands per assay unit when compared to the other two marker systems. Based on pair-wise comparison, the genetic similarity was calculated using Dice similarity coefficient. The SSRs showed a wide range in genetic similarity values (0.485-0.971) as compared to IRAP (0.69-0.911) and REMAP (0.713-0.947). A Mantel's matrix correspondence test showed a high positive correlation (r=0.6) between IRAP and REMAP, an intermediate value (r=0.58) for IRAP and SSR and the lowest value (r=0.17) for SSR and REMAP. Statistically significant cophenetic correlation coefficient values, of 0.961, 0.941 and 0

  2. Microsatellite-based analysis of the genetic structure and diversity of Aleurocanthus spiniferus (Hemiptera: Aleyrodidae) from tea plants in China.

    Science.gov (United States)

    Tang, Xiao-Tian; Tao, Huan-Huan; Du, Yu-Zhou

    2015-04-10

    Although Aleurocanthus spiniferus (Quaintance) (Hemiptera: Aleyrodidae) is a well known insect pest of tea plants, little information is available about its genetic structure and diversity. The present study used microsatellite markers to assess the genetic structure and diversity of this species on tea plants in China. For this purpose, 193 individuals from ten natural populations were analyzed using ten microsatellite markers. Our results indicated that the average number of alleles (A) across populations was 35.6, and all observed heterozygosities (HO) were greater than 0.7, indicating an excess of heterozygosity and a relatively high level of genetic diversity among populations, and the number of private alleles per population ranged from 3 to 26. Pairwise FST analysis suggested that the number of genetic differentiation events was moderate (0.05Bottleneck test indicated that most populations had experienced a population bottleneck. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Genetic Diversity in Insect Metal Tolerance

    Directory of Open Access Journals (Sweden)

    Thomas J. S. Merritt

    2017-11-01

    Full Text Available Insects encounter a variety of metals in their environment, many of which are required at some concentration for normal organismal homeostasis, but essentially all of which are toxic at higher concentrations. Insects have evolved a variety of genetic, and likely epigenetic, mechanisms to deal with metal stress. A recurring theme in all these systems is complexity and diversity; even simple, single gene, cases are complex. Of the known gene families, the metallothioneins are perhaps the best understood and provide good examples of how diverse metal response is. Interestingly, there is considerable diversity across taxa in these metal-responsive systems, including duplications to form small gene families and complex expression of single loci. Strikingly, different species have evolved different mechanisms to cope with the same, or similar, stress suggesting both independent derivation of, and plasticity in, the pathways involved. It is likely that some metal-response systems evolved early in evolutionary time and have been conserved, while others have diverged, and still others evolved more recently and convergently. In addition to conventional genetics, insects likely respond to environmental metal through a variety of epigenetic systems, but direct tests are lacking. Ultimately, it is likely that classical genetic and epigenetic factors interact in regulating insect metal responses. In light of this diversity across species, future studies including a broad-based examination of gene expression in non-model species in complex environments will likely uncover additional genes and genetic and epigenetic mechanisms.

  4. Genetic Diversity in Insect Metal Tolerance.

    Science.gov (United States)

    Merritt, Thomas J S; Bewick, Adam J

    2017-01-01

    Insects encounter a variety of metals in their environment, many of which are required at some concentration for normal organismal homeostasis, but essentially all of which are toxic at higher concentrations. Insects have evolved a variety of genetic, and likely epigenetic, mechanisms to deal with metal stress. A recurring theme in all these systems is complexity and diversity; even simple, single gene, cases are complex. Of the known gene families, the metallothioneins are perhaps the best understood and provide good examples of how diverse metal response is. Interestingly, there is considerable diversity across taxa in these metal-responsive systems, including duplications to form small gene families and complex expression of single loci. Strikingly, different species have evolved different mechanisms to cope with the same, or similar, stress suggesting both independent derivation of, and plasticity in, the pathways involved. It is likely that some metal-response systems evolved early in evolutionary time and have been conserved, while others have diverged, and still others evolved more recently and convergently. In addition to conventional genetics, insects likely respond to environmental metal through a variety of epigenetic systems, but direct tests are lacking. Ultimately, it is likely that classical genetic and epigenetic factors interact in regulating insect metal responses. In light of this diversity across species, future studies including a broad-based examination of gene expression in non-model species in complex environments will likely uncover additional genes and genetic and epigenetic mechanisms.

  5. The genetic diversity and evolution of field pea (Pisum studied by high throughput retrotransposon based insertion polymorphism (RBIP marker analysis

    Directory of Open Access Journals (Sweden)

    Smýkal Petr

    2010-02-01

    Full Text Available Abstract Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP markers by the Tagged Array Marker (TAM method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3 corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture

  6. Genetic diversity and selection of common bean lines based on technological quality and biofortification.

    Science.gov (United States)

    Steckling, S de M; Ribeiro, N D; Arns, F D; Mezzomo, H C; Possobom, M T D F

    2017-03-22

    The development of common bean cultivars with high technological quality that are biofortified with minerals, is required to meet the demand for food with health benefits. The objectives of this study were to evaluate whether common bean genotypes differ in terms of technological and mineral biofortification traits, to study the correlations between these characters, to analyze the genetic dissimilarity of common bean genotypes, and to select superior lines for these traits. For this, 14 common bean genotypes were evaluated in experiments conducted in three growing seasons in the Rio Grande do Sul State, Brazil. A significant genotype x environment interaction was observed for technological quality (mass of 100 grains and cooking time) and biofortification traits (concentration of potassium, phosphorus, calcium, iron, zinc, and copper). Positive correlation estimates were obtained between phosphorus and potassium (r = 0.575), iron and zinc (r = 0.641), copper and iron (r = 0.729), and copper and phosphorus (r = 0.533). In the main component cluster analysis, four groups of genotypes were formed. The following lines are recommended for selection: LP 11-363 for fast-cooking, CNFC 11 948 for high iron concentration, and LEC 03-14 for high potassium, phosphorus, and calcium concentrations in grains. Common bean lines with high phosphorus and iron concentrations in grains can be indirectly selected based on higher potassium, copper, and zinc concentrations. Controlled crossings between LP 11-363 x CNFC 11 948 and LP 11-363 x LEC 03-14 are recommended to obtain segregating lines that are fast-cooking and biofortified with minerals.

  7. Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

    Directory of Open Access Journals (Sweden)

    Rangel Paulo HN

    2010-06-01

    Full Text Available Abstract Background Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size. Results The thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection, with, approximately, 15% of its size. The method was compared with other methodologies based on the M strategy, and also with a core collection generated by random sampling. Higher proportions of retained alleles (in a core collection of equal size or similar proportions of retained alleles (in a core collection of smaller size were detected in the two methods based on the M strategy compared to the proposed methodology. Core sub-collections constructed by different methods were compared regarding the increase or maintenance of phenotypic diversity. No change on phenotypic diversity was detected by measuring the trait "Weight of 100 Seeds", for the tested sampling methods. Effects on linkage disequilibrium between unlinked microsatellite loci, due to sampling, are discussed. Conclusions Building of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest, and then by pairwise genetic distances, estimated by DNA polymorphism analysis at molecular marker loci. The resulting thematic core collection

  8. Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach.

    Science.gov (United States)

    Pessoa-Filho, Marco; Rangel, Paulo H N; Ferreira, Marcio E

    2010-06-24

    Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size. The thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection, with, approximately, 15% of its size. The method was compared with other methodologies based on the M strategy, and also with a core collection generated by random sampling. Higher proportions of retained alleles (in a core collection of equal size) or similar proportions of retained alleles (in a core collection of smaller size) were detected in the two methods based on the M strategy compared to the proposed methodology. Core sub-collections constructed by different methods were compared regarding the increase or maintenance of phenotypic diversity. No change on phenotypic diversity was detected by measuring the trait "Weight of 100 Seeds", for the tested sampling methods. Effects on linkage disequilibrium between unlinked microsatellite loci, due to sampling, are discussed. Building of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest, and then by pairwise genetic distances, estimated by DNA polymorphism analysis at molecular marker loci. The resulting thematic core collection potentially reflects the maximum allele richness with the smallest

  9. Genetic diversity in a crop metapopulation

    NARCIS (Netherlands)

    Heerwaarden, van J.; Eeuwijk, van F.A.; Ross-Ibarra, J.

    2010-01-01

    The need to protect crop genetic resources has sparked a growing interest in the genetic diversity maintained in traditional farming systems worldwide. Although traditional seed management has been proposed as an important determinant of genetic diversity and structure in crops, no models exist that

  10. Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes.

    Science.gov (United States)

    Roy, Subhas Chandra; Moitra, Kaushik; De Sarker, Dilip

    2017-01-01

    Genetic diversity was assessed in the four orchid species using NGS based ddRAD sequencing data. The assembled nucleotide sequences (fastq) were deposited in the SRA archive of NCBI Database with accession number (SRP063543 for Dendrobium , SRP065790 for Geodorum, SRP072201 for Cymbidium and SRP072378 for Rhynchostylis ). Total base pair read was 1.1 Mbp in case of Dendrobium sp., 553.3 Kbp for Geodorum sp., 1.6 Gbp for Cymbidium , and 1.4 Gbp for Rhynchostylis . Average GC% was 43.9 in Geodorum , 43.7% in Dendrobium , 41.2% in Cymbidium and 42.3% in Rhynchostylis . Four partial gene sequences were used in DnaSP5 program for nucleotide diversity and phylogenetic relationship determination ( Ycf2 gene of Dendrobium, matK gene of Geodorum , psbD gene of Cymbidium and Ycf2 gene of Ryhnchostylis ). Nucleotide diversity (per site) Pi (π) was 0.10560 in Dendrobium, 0.03586 in Geodorum, 0.01364 in Cymbidium and 0.011344 in Rhynchostylis . Neutrality test statistics showed the negative value in all the four orchid species (Tajima's D value -2.17959 in Dendrobium , -2.01655 in Geodorum, -2.12362 in Rhynchostylis and -1.54222 in Cymbidium ) indicating the purifying selection. Result for these gene sequences ( mat K and Ycf 2 and psb D) indicate that they were not evolved neutrally, but signifying that selection might have played a role in evolution of these genes in these four groups of orchids. Phylogenetic relationship was analyzed by reconstructing dendrogram based on the matK, psbD and Ycf2 gene sequences using maximum likelihood method in MEGA6 program.

  11. Assessment of Worldwide Genetic Diversity of Siberian Wild Rye (Elymus sibiricus L. Germplasm Based on Gliadin Analysis

    Directory of Open Access Journals (Sweden)

    Changbing Zhang

    2012-04-01

    Full Text Available E. sibiricus L., the type species of the genus Elymus, is a perennial, self-pollinating and allotetraploid grass indigenous to Northern Asia, which in some countries can be cultivated as an important forage grass. In the present study, eighty-six Elymus sibiricus accessions, mostly from different parts of Asia, were assayed by gliadin markers based on Acid Polyacrylamide Gel Electrophoresis to differentiate and explore their genetic relationships. The genetic similarity matrix was calculated by 47 polymorphic bands, which ranged from 0.108 to 0.952 with an average of 0.373. The total Shannon diversity index (Ho and the Simpson index (He was 0.460 and 0.302, respectively. Cluster analysis showed a clear demarcation between accessions from Qinghai-Tibetan Plateau, China and the others as separate groups. The clustering pattern was probably dependent on geographic origin and ecological adaptability of the accessions. The population structure analysis based on Shannon indices showed that the proportion of variance within and among the five geographic regions of the Northern Hemisphere was 55.9 and 44.1%, respectively, or 63.4 and 36.6% within and among six Chinese provinces. This distinct geographical divergence was perhaps depended on ecogeographical conditions such as climate difference and mountain distribution. The results of gladin analysis in this study are useful for the collection and preservation of E. sibiricus germplasm resources.

  12. RAPD and SSR based genetic diversity analysis of elite-2 set of ...

    African Journals Online (AJOL)

    Background: Synthetic hexaploid wheats are artificially reconstituted hexaploid wheats that possess high genetic variation which could be utilized for the development of new improved wheat varieties. One such group of synthetic wheats is called the Elite-II set of synthetic wheats that are derived from crossing durum wheat ...

  13. Genetic diversity and species diversity of stream fishes covary across a land-use gradient

    Science.gov (United States)

    Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

  14. Genetic diversity based on MIRU-VNTR profile of isolates of Mycobacterium bovis from Mexican cattle.

    Science.gov (United States)

    Nava Vargas, Alejandro; Milián Suazo, Feliciano; Cantó Alarcón, Germinal Jorge; Rubio Venegas, Yezenia; Guerrero Solorio, Roberto; Rodríguez Hernández, Elba; Pizano Martìnez, Oscar

    2016-09-01

    Bovine tuberculosis (bTB) is a disease caused by Mycobacterium bovis (M. bovis), which affects cattle, animal species and humans. To determinate the genetic structure of strains of M. bovis in mexican cattle, 467 isolates obtained from 2009 to 2010 from different regions of Mexico with known spoligotype were included in the study. The isolates were genotyped by interspersed repeated mycobacterial units-variable number tandem repeats (MIRU-VNTR) obtaining 13 MIRU-VNTR groups. When combining MIRU-VNTR patterns with its spolygotypes, the Hunter genetic discrimination index (HGDI), we obtained 421 genetic patterns distributed in 17 groups. The HGDI for the total loci was 0.99. The locus that presented the higher HGDI was 2461 (0.857), while the locus with the lowest HGDI was 2686 (0.239). When we analyzed our results, using just 6 or 8 MIRU-VNTR we obtained an discriminatory power of 0.8499 and 0.8875 respectively indicating lower HGDI than 12 MIRU-VNTR locus. Copyright © 2016. Published by Elsevier B.V.

  15. Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis.

    Science.gov (United States)

    Dachapak, Sujinna; Somta, Prakit; Poonchaivilaisak, Supalak; Yimram, Tarika; Srinives, Peerasak

    2017-04-01

    Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei's genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.

  16. Molecular characterization and assessment of genetic diversity of ...

    African Journals Online (AJOL)

    R Madhusudhana

    Selecting parents of diverse genetic base with contrasting phenotype is an important step in developing mapping populations for quantitative trait loci (QTL) detection and marker-assisted selection. We studied genetic diversity in 31 sorghum parents using 413 sorghum simple sequence repeats (SSR) markers.

  17. Identification and genetic diversity analysis of Memecylon species using ISSR, RAPD and Gene-based DNA barcoding tools

    Directory of Open Access Journals (Sweden)

    Bharathi Tumkur Ramasetty

    2016-11-01

    Conclusion: Data from the present study reveals that chloroplast psbA-trnH region could be used as a potential candidate region for identifying Memecylon species, and ISSR marker system could be used for estimating genetic diversity since it has high percent polymorphism compared to RAPD marker.

  18. Personalized medicine and human genetic diversity.

    Science.gov (United States)

    Lu, Yi-Fan; Goldstein, David B; Angrist, Misha; Cavalleri, Gianpiero

    2014-07-24

    Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more modern studies including genome-wide association studies (GWAS) and next-generation sequencing. We introduce several examples, such as sickle cell anemia and Tay-Sachs disease that are caused by rare mutations and are more frequent in certain geographical populations, and common treatment responses that are caused by common variants, such as hepatitis C infection. We conclude with comments about the continued relevance of human genetic diversity in medical genetics and personalized medicine more generally. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  19. Population dynamics of genetically diverse Plasmodium falciparum lineages: community-based prospective study in rural Amazonia

    Science.gov (United States)

    ORJUELA-SÁNCHEZ, P.; SILVA-NUNES, M. DA; DA SILVA, N. S.; SCOPEL, K.K.G.; GONÇALVES, R. M.; MALAFRONTE, R. S.; FERREIRA, M. U.

    2010-01-01

    SUMMARY Temporal changes in the prevalence of antigenic variants in Plasmodium falciparum populations have been interpreted as evidence of immune-mediated frequency-dependent selection, but evolutively neutral processes may generate similar patterns of serotype replacement. Over 4 years, we investigated the population dynamics of P. falciparum polymorphisms at the community level by using 11 putatively neutral microsatellite markers. Plasmodium falciparum populations were less diverse than sympatric P. vivax isolates, with less multiple-clone infections, lower number of alleles per locus and lower virtual heterozygosity, but both species showed significant multilocus linkage disequilibrium. Evolutively neutral P. falciparum polymorphisms showed a high turnover rate, with few lineages persisting for several months in the population. Similar results had previously been obtained, in the same community, for sympatric P. vivax isolates. In contrast, the prevalence of the 2 dimorphic types of a major antigen, MSP-2, remained remarkably stable throughout the study period. We suggest that the relatively fast turnover of parasite lineages represents the typical population dynamics of neutral polymorphisms in small populations, with clear implications for the detection of frequency-dependent selection of polymorphisms. PMID:19631016

  20. Genetic diversity of a brazilian wine grape germplasm collection based on morphoagronomic traits

    Directory of Open Access Journals (Sweden)

    Patrícia Coelho de S. Leão

    2010-12-01

    Full Text Available The objectives of this study were to evaluate the performance of cultivars, to quantify the variability and to estimate the genetic distances of 66 wine grape accessions in the Grape Germplasm Bank of the EMBRAPA Semi-Arid, in Juazeiro, BA, Brazil, through the characterization of discrete and continuous phenotypic variables. Multivariate statistics, such as, principal components, Tocher's optimization procedure, and the graphic of the distance, were efficient in grouping more similar genotypes, according to their phenotypic characteristics. There was no agreement in the formation of groups between continuous and discrete morpho-agronomic traits, when Tocher's optimization procedure was used. Discrete variables allowed the separation of Vitis vinifera and hybrids in different groups. Significant positive correlations were observed between weight, length and width of bunches, and a negative correlation between titratable acidity and TSS/TTA. The major part (84.12% of the total variation present in the original data was explained by the four principal components. The results revealed little variability between wine grape accessions in the Grape Germplasm Bank of Embrapa Semi-Arid.

  1. Genetic diversity of the Mycobacterium tuberculosis Beijing family based on SNP and VNTR typing profiles in Asian countries.

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    Yih-Yuan Chen

    Full Text Available The Mycobacterium tuberculosis (MTB Beijing strain is highly virulent, drug resistant, and endemic over Asia. To explore the genetic diversity of this family in several different regions of eastern Asia, 338 Beijing strains collected in Taiwan (Republic of China were analyzed by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR typing and compared with published MIRU-VNTR profiles and by the Hunter-Gaston diversity index (HGDI of Beijing strains from Japan and South Korea. The results revealed that VNTR2163b (HGDI>0.6 and five other loci (VNTR424, VNTR4052, VNTR1955, VNTR4156 and VNTR 2996; HGDI>0.3 could be used to discriminate the Beijing strains in a given geographic region. Analysis based on the number of VNTR repeats showed three VNTRs (VNTR424, 3192, and 1955 to be phylogenetically informative loci. In addition, to determine the geographic variation of sequence types in MTB populations, we also compared sequence type (ST data of our strains with published ST profiles of Beijing strains from Japan and Thailand. ST10, ST22, and ST19 were found to be prevalent in Taiwan (82% and Thailand (92%. Furthermore, classification of Beijing sublineages as ancient or modern in Taiwan was found to depend on the repeat number of VNTR424. Finally, phylogenetic relationships of MTB isolates in Taiwan, South Korea, and Japan were revealed by a minimum spanning tree based on MIRU-VNTR genotyping. In this topology, the MIRU-VNTR genotypes of the respective clusters were tightly correlated to other genotypic characters. These results are consistent with the hypothesis that clonal evolution of these MTB lineages has occurred.

  2. Genetic Diversity of the Mycobacterium tuberculosis Beijing Family Based on SNP and VNTR Typing Profiles in Asian Countries

    Science.gov (United States)

    Chen, Yih-Yuan; Chang, Jia-Ru; Huang, Wei-Feng; Kuo, Shu-Chen; Su, Ih-Jen; Sun, Jun-Ren; Chiueh, Tzong-Shi; Huang, Tsi-Shu; Chen, Yao-Shen; Dou, Horng-Yunn

    2012-01-01

    The Mycobacterium tuberculosis (MTB) Beijing strain is highly virulent, drug resistant, and endemic over Asia. To explore the genetic diversity of this family in several different regions of eastern Asia, 338 Beijing strains collected in Taiwan (Republic of China) were analyzed by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and compared with published MIRU-VNTR profiles and by the Hunter-Gaston diversity index (HGDI) of Beijing strains from Japan and South Korea. The results revealed that VNTR2163b (HGDI>0.6) and five other loci (VNTR424, VNTR4052, VNTR1955, VNTR4156 and VNTR 2996; HGDI>0.3) could be used to discriminate the Beijing strains in a given geographic region. Analysis based on the number of VNTR repeats showed three VNTRs (VNTR424, 3192, and 1955) to be phylogenetically informative loci. In addition, to determine the geographic variation of sequence types in MTB populations, we also compared sequence type (ST) data of our strains with published ST profiles of Beijing strains from Japan and Thailand. ST10, ST22, and ST19 were found to be prevalent in Taiwan (82%) and Thailand (92%). Furthermore, classification of Beijing sublineages as ancient or modern in Taiwan was found to depend on the repeat number of VNTR424. Finally, phylogenetic relationships of MTB isolates in Taiwan, South Korea, and Japan were revealed by a minimum spanning tree based on MIRU-VNTR genotyping. In this topology, the MIRU-VNTR genotypes of the respective clusters were tightly correlated to other genotypic characters. These results are consistent with the hypothesis that clonal evolution of these MTB lineages has occurred. PMID:22808061

  3. Cameroon native goat populations' genetic diversity and maternal ...

    African Journals Online (AJOL)

    Mitochondrial diversity of native goat populations was high (Hd = 69, with haplotype diversity = 0.9945) indicating a rich genetic diversity with 5 clades. The Cameroon goat populations belong to Haplogroup A, the most abundant in the world. Based on the previous migratory scenarios, the Cameroon native goats may have ...

  4. Genetic diversity evaluation of rapeseed genotypes ( Brassica ...

    African Journals Online (AJOL)

    Oilseed is the most important source of vegetable oil and the basis of breeding strategies is genetic diversity assessment. Genetic diversity of 19 rapeseed genotypes as well as their ancient ancestors Brassica rapa L. and Brassica oleracea L. were assessed using random amplified polymorphic DNA (RAPD) primers and ...

  5. Genetic diversity in European Pisum germplasm collections

    NARCIS (Netherlands)

    Jing, R.; Ambrose, M.A.; Knox, M.R.; Smykal, P.; Hybl, M.; Ramos, A.; Caminero, C.; Burstin, J.; Duc, G.; Soest, van L.J.; Swiecicki, W.K.; Pereira, M.G.; Vishnyakova, M.; Davenport, G.F.; Flavell, A.J.; Ellis, T.

    2012-01-01

    The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European

  6. Genetic diversity in breonadia salicina based on intra-species sequence variation of chloroplast dna spacer sequence

    International Nuclear Information System (INIS)

    Qurainy, F.A.; Gaafar, A.R.Z.

    2014-01-01

    Assessment and knowledge of the genetic diversity and variation within and between populations of rare and endangered plants is very important for effective conservation. Intergenic spacer sequences variation of psbA-trnH locus of chloroplast genome was assessed within Breonadia salicina (Rubiaceae), a critically endangered and endemic plant species to South western part of Kingdom of Saudi Arabia. The obtained sequence data from 19 individuals in three populations revealed nine haplotypes. The aligned sequences obtained from the overall Saudi accessions extended to 355 bp, revealing nine haplotypes. A high level of haplotype diversity (Hd = 0.842) and low level of nucleotide diversity (Pi = 0.0058) were detected. Consistently, both hierarchical analysis of molecular variance (AMOVA) and constructed neighbor-joining tree indicated null genetic differentiation among populations. This level of differentiation between populations or between regions in psbA-trnH sequences may be due to effects of the abundance of ancestral haplotype sharing and the presence of private haplotypes fixed for each population. Furthermore, the results revealed almost the same level of genetic diversity in comparison with Yemeni accessions, in which Saudi accessions were sharing three haplotypes from the four haplotypes found in Yemeni accessions. (author)

  7. Genetic Diversity Analysis of Indian Salmon, Eleutheronema tetradactylum from South Asian Countries Based on Mitochondrial COI Gene Sequences

    Directory of Open Access Journals (Sweden)

    Ramakrishnan THIRUMARAISELVI

    2015-12-01

    Full Text Available Eleutheronema tetradactylum is an important commercial fish species exposed to intense exploitation both in Southeast Asian countries and Northern parts of Australia. Research on the population structure of E. tetradactylum in these coastal waters is substantial in order to ensure sustainable use and appropriate resource management. In this study, genetic variation, diversity and population structure of E. tetradactylum among four FAO fishing areas, along South Asian countries, were evaluated using cytochrome c oxidase subunit I (COI gene. Totally 30 sequences of COI gene were collected from four FAO fishing areas. Among these 30 individuals, 18 distinct haplotypes were defined. High levels of haplotype diversity (hd = 0.952 ± 0.096 and nucleotide diversity (π = 0.01536 ± 0.00312 were observed in the population within the Bay of Bengal. No haplotype and nucleotide diversity were observed in South China Sea population. Hierarchical analysis of molecular variance (AMOVA indicated that 0.81% of the genetic variation occurred within the populations, while 7.09% variation occurred among populations. Significant genealogical branches were recognized in North Australian populations (one clade, South China Sea populations (one clade, Arabian Sea and Bay of Bengal populations (one clade on the neighbor-joining tree. These results suggested that E. tetradactylum populations in FAO fishing areas 51, 57 and 61 have developed different genetic structures. Tests of neutral evolution and mismatch distribution suggest that a population growth of E. tetradactylum may take place in these fishing areas.

  8. Pyrosequencing and genetic diversity of microeukaryotes

    DEFF Research Database (Denmark)

    Harder, Christoffer Bugge

    a well-studied country is an illustration of the limited knowledge of the microbial diversity. Finally, Article I separates a group of closely related fungi that could not be determined by morphology by using a phylogenetic analysis combining three marker genes. Using multiple markers makes it possible...... pathogens themselves. Protozoa is a morphological group which occurs in many different eukaryotic phyla, and many apparently morphologically similar types are very different from each others genetically. This complicates the development of good primers for analysis of their diversity with modern DNA based...... methods. Compared to other microorganisms such as fungi, algae and bacteria, much less is known about protozoa. It has been an essential element of this thesis to to advance our knowledge of protozoa by developing new primers for DNA-based studies of protozoa impact on ecosystems or as indicators...

  9. Inbreeding and genetic diversity analysis in a hatchery release population and clones of Rhopilema esculentum based on microsatellite markers

    Science.gov (United States)

    Tian, Tao; Chen, Zaizhong; Wang, Mosang; Hu, Yulong; Wang, Weiji

    2017-05-01

    Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye (Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed ( H o) and expected ( H e) heterozygosity ranged from 0.152 to 0.839 (mean=0.464) and from 0.235 to 0.821 (mean=0.618), respectively. The polymorphism information content (PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.

  10. Genetic diversity of native chicken based on analysis of D-Loop mtDNA marker

    Directory of Open Access Journals (Sweden)

    Tike Sartika

    2000-06-01

    Full Text Available Production was carried out using control region/D-loop mtDNA marker. The base population of native chicken was selected from subpopulation at Cianjur, Jatiwangi, Depok, Bogor I, and Bogor 2. Samples from each population was 10 heads and 2 samples Green Jungle Fowl (Gallus various from East Java as out Group samples. Two primers binding conserved tRNA Phenylalanine gene and tRNA Glutamine gene were DNA Heavy stranded HI255 (5'-CATCTTGGCATCTTCAGTGCC-3' and DNA Light stranded Ll6750 (5'-AGGACTACGGCTTGAAAAGC-3' was used to amplify D-Ioop mtDNA chicken. PCR-RFLP methods with 6 restriction enzymes 4 cutter such as, Alul (AG↓CT, Hpall (C↓CGG, Mbol (↓GATC, Rsal (GT↓AC, NlaIII (CATG↓ and HaeIII (GG↓CC were used to detect polymorphism within and between subpopulation. Result of experiment show that mtDNA which was amplified by PCR was 1320 bp, consist of 1227 bp control region/D-loop, 45 bp tRNA Glutamine gene and 48 bp tRNA Phenylalananine gene. PCR product which were digested from 6 endonucleases enzyme show that native chicken within and between population was monomorphic and if its compare with Green Jungle Fowl was polymorphic.

  11. Genetic diversity of Plasmodium vivax over time and space: a community-based study in rural Amazonia.

    Science.gov (United States)

    Batista, Camilla L; Barbosa, Susana; Da Silva Bastos, Melissa; Viana, Susana Ariane S; Ferreira, Marcelo U

    2015-02-01

    To examine how community-level genetic diversity of the malaria parasite Plasmodium vivax varies across time and space, we investigated the dynamics of parasite polymorphisms during the early phases of occupation of a frontier settlement in the Amazon Basin of Brazil. Microsatellite characterization of 84 isolates of P. vivax sampled over 3 years revealed a moderate-to-high genetic diversity (mean expected heterozygosity, 0.699), with a large proportion (78.5%) of multiple-clone infections (MCI), but also a strong multilocus linkage disequilibrium (LD) consistent with rare outcrossing. Little temporal and no spatial clustering was observed in the distribution of parasite haplotypes. A single microsatellite haplotype was shared by 3 parasites collected during an outbreak; all other 81 haplotypes were recovered only once. The lowest parasite diversity, with the smallest proportion of MCI and the strongest LD, was observed at the time of the outbreak, providing a clear example of epidemic population structure in a human pathogen. Population genetic parameters returned to pre-outbreak values during last 2 years of study, despite the concomitant decline in malaria incidence. We suggest that parasite genotyping can be useful for tracking the spread of new parasite strains associated with outbreaks in areas approaching malaria elimination.

  12. Genetic Diversity of Cowpea (Vigna unguiculata (L.) Walp.) Accession in Kenya Gene Bank Based on Simple Sequence Repeat Markers.

    Science.gov (United States)

    Wamalwa, Emily N; Muoma, John; Wekesa, Clabe

    2016-01-01

    Increased agricultural production is an urgent issue. Projected global population is 9 million people by mid of this century. Estimation projects death of 1 million people for lack of food quality (micronutrient deficit) and quantity (protein deficit). Majority of these people will be living in developing countries. Other global challenges include shrinking cultivable lands, salinity, and flooding due to climate changes, new emerging pathogens, and pests. These affect crop production. Furthermore, they are major threats to crop genetic resources and food security. Genetic diversity in cultivated crops indicates gene pool richness. It is the greatest resource for plant breeders to select lines that enhance food security. This study was conducted by Masinde Muliro University to evaluate genetic diversity in 19 cowpea accessions from Kenya national gene bank. Accessions clustered into two major groups. High divergence was observed between accessions from Ethiopia and Australia and those from Western Kenya. Upper Volta accessions were closely related to those from Western Kenya. Low variation was observed between accessions from Eastern and Rift Valley than those from Western and Coastal regions of Kenya. Diversity obtained in this study can further be exploited for the improvement of cowpea in Kenya as a measure of food security.

  13. Genetic Diversity of Cowpea (Vigna unguiculata (L. Walp. Accession in Kenya Gene Bank Based on Simple Sequence Repeat Markers

    Directory of Open Access Journals (Sweden)

    Emily N. Wamalwa

    2016-01-01

    Full Text Available Increased agricultural production is an urgent issue. Projected global population is 9 million people by mid of this century. Estimation projects death of 1 million people for lack of food quality (micronutrient deficit and quantity (protein deficit. Majority of these people will be living in developing countries. Other global challenges include shrinking cultivable lands, salinity, and flooding due to climate changes, new emerging pathogens, and pests. These affect crop production. Furthermore, they are major threats to crop genetic resources and food security. Genetic diversity in cultivated crops indicates gene pool richness. It is the greatest resource for plant breeders to select lines that enhance food security. This study was conducted by Masinde Muliro University to evaluate genetic diversity in 19 cowpea accessions from Kenya national gene bank. Accessions clustered into two major groups. High divergence was observed between accessions from Ethiopia and Australia and those from Western Kenya. Upper Volta accessions were closely related to those from Western Kenya. Low variation was observed between accessions from Eastern and Rift Valley than those from Western and Coastal regions of Kenya. Diversity obtained in this study can further be exploited for the improvement of cowpea in Kenya as a measure of food security.

  14. Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences.

    Directory of Open Access Journals (Sweden)

    Jianbin Liu

    Full Text Available The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.

  15. What factors shape genetic diversity in cetaceans?

    Science.gov (United States)

    Vachon, Felicia; Whitehead, Hal; Frasier, Timothy R

    2018-02-01

    Understanding what factors drive patterns of genetic diversity is a central aspect of many biological questions, ranging from the inference of historical demography to assessing the evolutionary potential of a species. However, as a larger number of datasets have become available, it is becoming clear that the relationship between the characteristics of a species and its genetic diversity is more complex than previously assumed. This may be particularly true for cetaceans, due to their relatively long lifespans, long generation times, complex social structures, and extensive ranges. In this study, we used microsatellite and mitochondrial DNA data from a systematic literature review to produce estimates of diversity for both markers across 42 cetacean species. Factors relating to demography, distribution, classification, biology, and behavior were then tested using phylogenetic methods and linear models to assess their relative influence on the genetic diversity of both marker types. The results show that while relative nuclear diversity is correlated with population size, mitochondrial diversity is not. This is particularly relevant given the widespread use of mitochondrial DNA to infer historical demography. Instead, mitochondrial diversity was mostly influenced by the range and social structure of the species. In addition to population size, habitat type (neritic vs. oceanic) had a significant correlation with relative nuclear diversity. Combined, these results show that many often-unconsidered factors are likely influencing patterns of genetic diversity in cetaceans, with implications regarding how to interpret, and what can be inferred from, existing patterns of diversity.

  16. Selection of a seed orchard of Eucalyptus dunnii based on genetic diversity criteria calculated using molecular markers.

    Science.gov (United States)

    Marcucci Poltri, S N; Zelener, N; Rodriguez Traverso, J; Gelid, P; Hopp, H E

    2003-06-01

    A Eucalyptus dunnii Maiden breeding population of 46 accessions originated in Australia and selected for fitness to subtropical and cold environments was screened by Amplified Fragment Length Polymorphism (AFLP) and microsatellite markers to obtain quantitative estimates of genetic diversity. A randomly chosen group of AFLP primers generated 205 AFLP bands that were used to fingerprint the genotypes and to evaluate genetic relationships among accessions. Sixty-eight percent (140) of the bands were polymorphic markers. The mean diversity index (DI) was 0.33 and about 52% of the loci had values greater than 0.4. Cluster analysis derived from similarity indices (SI) revealed no particular grouping among accessions suggesting the absence of closely related genotypes, except for five pairs of genotypes. Bootstrap analysis results confirmed the suitability of AFLP to describe genetic relationships in this breeding population. In addition, four highly informative microsatellites were used to construct an identification matrix that discriminated nearly all of the genotypes. Mean values for the number of alleles per locus, DI and SI among accessions were 13, 0.78 and 0.19, respectively, indicating that the breeding population has high genetic diversity. However, several genotypes showed the presence of single microsatellite bands suggesting a putatively important degree of homozygosity. Molecular data were used to design a clonal seed orchard. To achieve this aim, the nine most divergent pairs of genotypes were chosen, thereby retaining 95.2% of the total number of alleles from the 140 polymorphic AFLP loci and the four microsatellite loci analyzed. Mean DI and SI for AFLP and microsatellites showed no significant differences between the original breeding population and the selected seed orchard, confirming that a seed orchard can be designed with a limited number of individuals, which allows similar accessions to be discarded and avoids inbreeding.

  17. Genetic diversity of pigeon pea (Cajanus cajan (l.) Millsp.) based on molecular characterization using randomly amplified polymorphic DNA (RAPD) markers

    Science.gov (United States)

    Khoiriyah, N.; Yuniastuti, E.; Purnomo, D.

    2018-03-01

    Pigeon pea (Cajanus cajan (L.) Millsp.) is an annual leguminous crop (perennial) which has advantages over other local leguminous crops as drought resistant, hold collapsed and strong pods. The research on drought resistance plant is very important to adapt to climate change adverse impact to support food security. The potential of pigeon pie has not been supported by accurate data. To explore the potential of pigeon pea, it is necessary to record the important properties by characterization, one of which is molecular. Increasing genetic diversity can be done through mutation which widely used gamma ray for the induction. The purpose of this study was to identify the genetic diversity of pigeon pea of black, white and brown seeds type resulted by gamma-ray irradiation with a wavelength of 100, 200 and 300 grays by using RAPD method. The experiment resulted 14 bands, 12 of them are polymorphic bands and 2 of them are monomorphic with size varied from 300 bp to 1.3 kbp. The dendrogram showed from 30 accessions are divided into two main clusters, B shows clear genetical divergence from other clusters and some others split randomly. The range of similarity coefficient is from 0.43 to 1.00

  18. Genetic diversity and relationships among cabbage ( Brassica ...

    African Journals Online (AJOL)

    The integration of our data with historical documents confirmed that traditional cabbage landraces cultivated in North of China were first introduced from Russia. Key words: Amplified fragment length polymorphism (AFLP), genetic diversity, cabbage (Brassica oleracea var. capitata), landraces, population structure.

  19. mycobacterium tuberculosis genetic diversity and drug resistance ...

    African Journals Online (AJOL)

    East African Medical Journal Vol. 88 No. 12 December 2011. MYCOBACTERIUM TUBERCULOSIS GENETIC DIVERSITY AND DRUG RESISTANCE CONFERRING MUTATIONS. IN THE DEMOCRATIC REPUBLIC OF THE CONGO. L. Fenner, Institute of Social and Preventive Medicine, University of Bern, Switzerland, S.

  20. Genetic diversity of grasscutter (Thryonomys swinderianus ...

    African Journals Online (AJOL)

    Saharan Africa. There are very limited ecological studies on the grasscutter despite its importance as a protein resource. The objective of this study was to apply novel microsatellite markers to determine the genetic structure and diversity of ...

  1. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 94; Issue 4. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation ... Keywords. agarwood; conservation; home gardens; genetic diversity; population genetic structure; amplified fragment length polymorphism.

  2. Genetic Diversity and Population Structure of Toona Ciliata Roem. Based on Sequence-Related Amplified Polymorphism (SRAP) Markers

    OpenAIRE

    Li, Pei; Zhan, Xin; Que, Qingmin; Qu, Wenting; Liu, Mingqian; Ouyang, Kunxi; Li, Juncheng; Deng, Xiaomei; Zhang, Junjie; Liao, Boyong; Pian, Ruiqi; Chen, Xiaoyang

    2015-01-01

    Sequence-related amplified polymorphism (SRAP) markers were used to investigate the genetic diversity among 30 populations of Toona ciliata Roem. sampled from the species’ distribution area in China. To analyze the polymorphism in the SRAP profiles, 1505 primer pairs were screened and 24 selected. A total of 656 SRAP bands ranging from 100 to 1500 bp were acquired, of these 505 bands (77%) were polymorphic. The polymorphism information content (PIC) values ranged from 0.32 to 0.45, with an av...

  3. Genetic diversity of 11 European pig breeds

    NARCIS (Netherlands)

    Lavall, G.; Iannuccelli, N.; Legault, C.; Milan, D.; Groenen, M.A.M.; Andersson, L.; Fredholm, M.; Geldermann, H.; Foulley, J.L.; Chevalet, C.; Ollivier, L.

    2000-01-01

    A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed

  4. RAPD markers demonstrate genetic diversity in Pterocarpus ...

    African Journals Online (AJOL)

    RAPD markers demonstrate genetic diversity in Pterocarpus angolensis from Zimbabwe and Zambia. E Chisha-Kasumu, S Woodward, A Price. Abstract. Understanding the availability, extent and apportionment of genetic variability in natural populations of the southern African savanna tree Pterocarpus angolensis can ...

  5. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    Molecular diversity and genetic relationships in Secale. E. Santos, M. Matos, P. Silva, A. M. Figueiras, C. Benito and O. Pinto-Carnide. J. Genet. 95, 273–281. Table 1. RAPD and ISSR primers used in this study. Primer. 5 –3. Primer. 5 –3. RAPDs (Operon). A1. CAGGCCCTTC. C5. CATGACCGCC. A4. AATCGGGCTG. C6.

  6. Genetic diversity of Sclerocarya birrea subspecies birrea ...

    African Journals Online (AJOL)

    Sclerocarya birrea, multipurpose plant is characteristic of the Sahel-Sudanian savanna and is widespread in West Africa. Although this species has a high socio-economic importance, its genetic organization was not well characterized in Burkina Faso. In this study, the intra and interpopulation genetic diversity of S. birrea ...

  7. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    Supplementary data: Molecular diversity and genetic relationships in Secale. E. Santos, M. Matos, P. Silva, A. M. Figueiras, C. Benito and O. Pinto-Carnide. J. Genet. 95, 273–281. Table 1. RAPD and ISSR primers used in this study. Primer. 5 –3. Primer. 5 –3. RAPDs (Operon). A1. CAGGCCCTTC. C5. CATGACCGCC. A4.

  8. Genetic diversity in Cinnamomum zeylanicum Blume. (Lauraceae ...

    African Journals Online (AJOL)

    In this study, unweighed pair group method with arithmetic averages (UPGMA) analysis showed up to 89% genetic variation among these accessions, which is further supported by principle co-ordinate analysis (PCA). Key words: Genetic diversity, Cinnamomum zeylanicum, RAPD markers, DNA polymorphism.

  9. GENETIC DIVERSITY AND ECO-GEOGRAPHICAL DISTRIBUTION ...

    African Journals Online (AJOL)

    ACSS

    GENETIC DIVERSITY AND ECO-GEOGRAPHICAL DISTRIBUTION OF Eleusine ... floccifolia were analysed for genetic variation and inter-relationships using 20 microsatellite markers. All the ..... Key: ND = not done, B = B genome, A = A genome, AB = both A and B genome of Eleusine coracana subsp coracana (Dida et.

  10. Alfalfa domestication history, genetic diversity and genetic resources

    OpenAIRE

    Prosperi, Jean-Marie; Jenczewski, Eric; Muller, Marie-Helene; Fourtier, Stéphane; Sampoux, Jean-Paul; Ronfort, Joelle

    2014-01-01

    AGAP : GE²pop; The domestication history of alfalfa is poorly known. Here, we summarize recent results obtained from the investigation of the genetic diversity available in the Medicago sativa species complex, using different molecular markers and morphological characterization. We conclude that a large genetic diversity is still available in the wild form of the species, but original populations are restricted to a relatively small geographic area and in some instances submitted to gene flow...

  11. Evaluation of microsatellite-based genetic diversity, protein and mineral content in chickpea accessions grown in Kyrgyzstan.

    Science.gov (United States)

    Torutaeva, Elnura; Asanaliev, Abdybek; Prieto-Linde, Maria Luisa; Zborowska, Anna; Ortiz, Rodomiro; Bryngelsson, Tomas; Garkava-Gustavsson, Larisa

    2014-10-01

    The genetic diversity of 23 chickpea accessions representing Kyrgyz landraces and cultivars, ICARDA breeding lines, Spanish and Turkish cultivars was characterized using nine microsatellite (SSR) markers which generated a total of 122 alleles. The number of alleles (Na) per locus varied from 9 to 20. The observed heterozygosity (Ho) ranged between 0.05 and 0.43 (average 0.13) whereas both the expected heterozygosity (He) and polymorphic information content (PIC) ranged from 0.71 to 0.90 (average 0.83). Analysis of molecular variance (AMOVA) showed that 62% of the total genetic variation was found within accessions while the remaining 38% was found among accessions. Principal coordinate analysis (PCoA) indicated the presence of two groups. The two Kyrgyz cultivars were found apart from these groups. Cluster analysis generally confirmed the results of PCoA and also separated the Kyrgyz cultivars from the subcluster formed by Kyrgyz landraces and the subclusters formed by breeding lines from ICARDA along with landraces from Turkey and Spain. In addition, protein content and mineral concentration were determined. Protein content and mineral concentrations for Ca, S, Mg, P, K, Fe, Mn, Cu and Zn varied significantly among accessions. The results show that Kyrgyz germplasm provides a source of diversity for improvement of chickpea. © 2014 The Authors.

  12. Implications of recurrent disturbance for genetic diversity.

    Science.gov (United States)

    Davies, Ian D; Cary, Geoffrey J; Landguth, Erin L; Lindenmayer, David B; Banks, Sam C

    2016-02-01

    Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.

  13. Assessing the genetic diversity of five Tanzanian chicken ecotypes ...

    African Journals Online (AJOL)

    Diversity was assessed based on morphological measurements and 29 microsatellite markers recommended by ISAG/FAO advisory group on animal genetic diversity. A principal component analysis (PCA) of morphological measures distinguished individuals most by body sizes and body weight. Morogoro Medium, Pemba ...

  14. Assessing the genetic diversity of cultivars and wild soybeans using ...

    African Journals Online (AJOL)

    Increasing the diversity of the soybean germplasm base could introduce new genes affecting agronomic traits. In this study, we demonstrated the differences of genetic diversity level among 40 soybean accessions of cultivars, landraces and wild soybeans collected in the Shanxi Agricultural University using 40 simple ...

  15. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    ... organization of genetic diversity. The Andean and Mesoamerican genotypes were present in similar frequencies (51 vs. 49%, respectively). All SSR markers tested were polymorphic with mean polymorphism information content (PIC) of 0.8. The model-based cluster analysis of SSR diversity in the STRUCTURE software ...

  16. Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing.

    Science.gov (United States)

    Su, Wenjin; Wang, Lianjun; Lei, Jian; Chai, Shasha; Liu, Yi; Yang, Yuanyuan; Yang, Xinsun; Jiao, Chunhai

    2017-01-01

    Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.

  17. Genetic diversity of some Saudi barley (Hordeum Vulgare L ...

    African Journals Online (AJOL)

    enoh

    2012-03-13

    Mar 13, 2012 ... Full Length Research Paper. Genetic diversity of some Saudi barley (Hordeum. Vulgare L.) landraces based on microsatellite markers. El-Awady A. M. Mohamed 1,2 and El-Tarras A. E. Adel1,2. 1Biotechnology and Genetic Engineering Research Unit, Scientific Research Center, College of Medicine, Taif.

  18. Evaluation of genetic diversity of Portuguese Pinus sylvestris L ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 92; Online resources. Evaluation of genetic diversity of Portuguese Pinus sylvestris L. populations based on molecular data and inferences about the future use of this germplasm. J. Cipriano A. Carvalho C. Fernandes M. J. Gaspar J. Pires J. Bento L. Roxo J. Louzada J. Lima- ...

  19. Genetic diversity in African nutmeg (Monodora myristica) accessions ...

    African Journals Online (AJOL)

    The mean polymorphic information content (PIC) and genetic diversity (He) were 0.673 and 0.697, respectively, indicating high genetic variation among the accessions. Cluster analysis delineated the accessions into four major groups. The maximum similarity index (0.88) based on Dice coefficient was recorded between ...

  20. Genetic diversity and germplasm resource research on tung tree ...

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... characteristics such as insulation, acid and alkali resis- tance, as well as anticorrosion properties. It has gradually been applied to manufacturing modern paint, ..... genetic base and current situations of cultivars. This is different from earlier studies on genetic diversity at population level of some other plants, ...

  1. An analysis of the genetic diversity and genetic structure of ...

    African Journals Online (AJOL)

    Scientific approaches to conservation of threatened species depend on a good understanding of the genetic information of wild and artificial population. The genetic diversity and structure analysis of 10 Eucommia ulmoides population was analyzed using inter-simple sequence repeat (ISSR) markers in this paper.

  2. Pyrosequencing and genetic diversity of microeukaryotes

    DEFF Research Database (Denmark)

    Harder, Christoffer Bugge

    Free-living, heterotrophic protozoa have an important ecological role in most terrestrial ecosystems by their grazing of bacteria as one of the first links in food chains and webs. Furthermore, some of them serve as reservoirs for disease-causing bacteria and /or as occasional opportunistic...... pathogens themselves. Protozoa is a morphological group which occurs in many different eukaryotic phyla, and many apparently morphologically similar types are very different from each others genetically. This complicates the development of good primers for analysis of their diversity with modern DNA based...... methods. Compared to other microorganisms such as fungi, algae and bacteria, much less is known about protozoa. It has been an essential element of this thesis to to advance our knowledge of protozoa by developing new primers for DNA-based studies of protozoa impact on ecosystems or as indicators...

  3. Effects of complex life cycles on genetic diversity: cyclical parthenogenesis.

    Science.gov (United States)

    Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

    2016-11-01

    Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).

  4. Genetic diversity of cultured and wild populations of the freshwater prawn Macrobrachium rosenbergii based on microsatellite analysis

    Science.gov (United States)

    Freshwater prawn Macrobrachium rosenbergii culture in the Western Hemisphere is primarily, if not entirely, based on thirty-six individual prawn introduced to Hawaii from Malaysia in 1965 and 1966. Little information is available regarding the genetic background or current population status of cult...

  5. An ecologically-based method for selecting ecological indicators for assessing risks to biological diversity from genetically-engineered plants

    DEFF Research Database (Denmark)

    Andow, D. A.; Lövei, Gabor L; Arpaia, Salvatore

    2013-01-01

    The environmental risks associated with genetically-engineered (GE) organisms have been controversial, and so have the models for the assessment of these risks. We propose an ecologically-based environmental risk assessment (ERA) model that follows the 1998 USEPA guidelines, focusing on potential...

  6. Monitoring changes in genetic diversity

    CSIR Research Space (South Africa)

    Bruford, MW

    2018-01-01

    Full Text Available state-of-the-art in genetic monitoring, with an emphasis on new molecular tools and the richness of data they provide to supplement existing approaches. We also briefly consider proxy approaches that may be useful for many-species, global scale...

  7. Population Genetic Diversity in the Australian 'Seascape': A Bioregion Approach.

    Directory of Open Access Journals (Sweden)

    Lisa C Pope

    Full Text Available Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA bioregions, latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4. Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a 'hump' in diversity across the range studied (-9.4 to -43.7°S. Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales.

  8. A call for tiger management using "reserves" of genetic diversity.

    Science.gov (United States)

    Bay, Rachael A; Ramakrishnan, Uma; Hadly, Elizabeth A

    2014-01-01

    Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.

  9. Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters.

    Science.gov (United States)

    Tar'an, B; Zhang, C; Warkentin, T; Tullu, A; Vandenberg, A

    2005-04-01

    Random amplified polymorphic DNA, simple sequence repeat, and inter-simple sequence repeat markers were used to estimate the genetic relations among 65 pea varieties (Pisum sativum L.) and 21 accessions from wild Pisum subspecies (subsp.) abyssinicum, asiaticum, elatius, transcaucasicum, and var. arvense. Fifty-one of these varieties are currently available for growers in western Canada. Nei and Li's genetic similarity (GS) estimates calculated using the marker data showed that pair-wise comparison values among the 65 varieties ranged from 0.34 to 1.00. GS analysis on varieties grouped according to their originating breeding programs demonstrated that different levels of diversity were maintained at different breeding programs. Unweighted pair-group method arithmetic average cluster analysis and principal coordinate analysis on the marker-based GS grouped the cultivated varieties separately from the wild accessions. The majority of the food and feed varieties were grouped separately from the silage and specialty varieties, regardless of the originating breeding programs. The analysis also revealed some genetically distinct varieties such as Croma, CDC Handel, 1096M-8, and CDC Acer. The relations among the cultivated varieties, as revealed by molecular-marker-based GS, were not significantly correlated with those based on the agronomic characters, suggesting that the 2 systems give different estimates of genetic relations among the varieties. However, on a smaller scale, a consistent subcluster of genotypes was identified on the basis of agronomic characters and their marker-based GS. Furthermore, a number of variety-specific markers were identified in the current study, which could be useful for variety identification. Breeding strategies to maintain or enhance the genetic diversity of future varieties are proposed.

  10. Neglect of genetic diversity in implementation of the Convention on Biological Diversity

    Science.gov (United States)

    Linda Laikre; Fred W. Allendorf; Laurel C. Aroner; C. Scott Baker; David P. Gregovich; Michael M. Hansen; Jennifer A. Jackson; Katherine C. Kendall; Kevin Mckelvey; Maile C. Neel; Isabelle Olivieri; Nils Ryman; Michael K. Schwartz; Ruth Short Bull; Jeffrey B. Stetz; David A. Tallmon; Barbara L. Taylor; Christina D. Vojta; Donald M. Waller; Robin S. Waples

    2009-01-01

    Genetic diversity is the foundation for all biological diversity; the persistence and evolutionary potential of species depend on it. World leaders have agreed on the conservation of genetic diversity as an explicit goal of the Convention on Biological Diversity (CBD). Nevertheless, actions to protect genetic diversity are largely lacking. With only months left to the...

  11. Genomic management of animal genetic diversity

    NARCIS (Netherlands)

    Oldenbroek, Kor

    2017-01-01

    Recently developed genomic tools, like SNP-genotyping and whole genome sequencing, and their analysis, offer great opportunities for the conservation and utilisation of animal genetic diversity, both among and within breeds. These genomic tools can be used to detect potentially valuable rare alleles

  12. High genetic diversity of Mycospaherella graminicola ( Zymoseptoria ...

    African Journals Online (AJOL)

    High genetic diversity of Mycospaherella graminicola (Zymoseptoria tritici) from a single wheat field in Tunisia as revealed by SSR markers. Samia Berraies, Mohamed Salah Gharbi, François Belzile, Amor Yahyaoui, Mohamed Rebah Hajlaoui, Mokhtar Trifi, Martine Jean, Salah Rezgui ...

  13. Genetic diversity of Cytospora chrysospermaisolates obtained from ...

    African Journals Online (AJOL)

    Cluster analysis of the data using Centroid method and Jaccard´s similarity coefficient, divided the isolates into six groups, showing a high genetic diversity among populations of C. chrysosperma. Although there was no correlation between geographical origins and the resulting groups of RAPD analysis, but the amount of ...

  14. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    Over the years, there has been much controversy about the taxonomy of the Secale genus. ... have become routine in plant biotechnology, such as genetic diversity studies. ISSR (Zietkiewicz et al. 1994) and ... 1996) were not amplified in the bulk DNA samples. The number of plants used to construct the bulk samples was.

  15. Genetic diversity among sorghum landraces and polymorphism ...

    African Journals Online (AJOL)

    Microsatellites or simple sequence repeats (SSR) are playing an important role in molecular breeding. This investigation was undertaken to study the genetic diversity among local sorghum accessions from two different agro-ecological zones of Burkina Faso and to assess the polymorphism within local improved varieties ...

  16. Analysis of genetic diversity inpigeonpeagermplasm using ...

    Indian Academy of Sciences (India)

    Navya

    2016-11-25

    Nov 25, 2016 ... techniques are useful and could be a better alternative to other marker techniques in analyzing the genetic diversity .... the SSR primer alone in REMAP reactions, in control experiments for REMAP, the retrotransposon ... Molecular marker technology has evolved into a very powerful tool in plant biology for.

  17. Genetic diversity analysis of Tinospora cordifolia germplasm ...

    Indian Academy of Sciences (India)

    2012-04-03

    Apr 3, 2012 ... c Indian Academy of Sciences. RESEARCH NOTE. Genetic diversity analysis of Tinospora cordifolia germplasm collected from northwestern Himalayan region of India. VIJAY RANA1, KALPANA THAKUR1, RITU SOOD1, VARUN SHARMA1 and T. R. SHARMA2∗. 1Rice and Wheat Research Centre, Malan ...

  18. Genetic diversity among endangered rare Dalbergia cochinchinensis

    African Journals Online (AJOL)

    hocvan

    Dalbergia cochinchinensis is a species of legume in the Fabaceae family. This species is popular and valuable in Vietnam and is currently listed on the Vietnam Red List and on the IUCN Red List as endangered. Genetic diversity of the 35 genotypes of D. cochinchinensis species were evaluated by using 52 markers ...

  19. Genetic diversity among endangered rare Dalbergia ...

    African Journals Online (AJOL)

    Genetic diversity among endangered rare Dalbergia cochinchinensis (Fabaceae) genotypes in Vietnam revealed by random amplified polymorphic DNA (RAPD) ... The number of amplified fragments varied from 1 (OPR15, OPB05, RA142, OPR08, UBC348, OPE14 and OPO04) to 8 (OPP19) and their sizes ranged from 250 ...

  20. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    The objective of this study was to quantify the molecular diversity and to determine the genetic relationships amongSecalespp. and among cultivars ofSecale ... Faculty of Sciences, Campo Grande, Lisboa, Portugal; Departamento de Genética, Facultad de Biologia, Universidad Complutense, C/ José Antonio Novais, 12, ...

  1. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers.

    Science.gov (United States)

    Garzón-Martínez, Gina A; Osorio-Guarín, Jaime A; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E; Landsman, David; Mariño-Ramírez, Leonardo; Barrero, Luz Stella

    2015-12-01

    The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation F ST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies.

  2. Does genetic diversity predict health in humans?

    Directory of Open Access Journals (Sweden)

    Hanne C Lie

    2009-07-01

    Full Text Available Genetic diversity, especially at genes important for immune functioning within the Major Histocompatibility Complex (MHC, has been associated with fitness-related traits, including disease resistance, in many species. Recently, genetic diversity has been associated with mate preferences in humans. Here we asked whether these preferences are adaptive in terms of obtaining healthier mates. We investigated whether genetic diversity (heterozygosity and standardized mean d(2 at MHC and nonMHC microsatellite loci, predicted health in 153 individuals. Individuals with greater allelic diversity (d(2 at nonMHC loci and at one MHC locus, linked to HLA-DRB1, reported fewer symptoms over a four-month period than individuals with lower d(2. In contrast, there were no associations between MHC or nonMHC heterozygosity and health. NonMHC-d(2 has previously been found to predict male preferences for female faces. Thus, the current findings suggest that nonMHC diversity may play a role in both natural and sexual selection acting on human populations.

  3. Genetic Diversity and Population Structure of Toona Ciliata Roem. Based on Sequence-Related Amplified Polymorphism (SRAP Markers

    Directory of Open Access Journals (Sweden)

    Pei Li

    2015-04-01

    Full Text Available Sequence-related amplified polymorphism (SRAP markers were used to investigate the genetic diversity among 30 populations of Toona ciliata Roem. sampled from the species’ distribution area in China. To analyze the polymorphism in the SRAP profiles, 1505 primer pairs were screened and 24 selected. A total of 656 SRAP bands ranging from 100 to 1500 bp were acquired, of these 505 bands (77% were polymorphic. The polymorphism information content (PIC values ranged from 0.32 to 0.45, with an average of 0.41. An analysis of molecular variance (AMOVA indicated that the most significant variation was attributable to differences among the populations and that variation within the populations was small. STRUCTURE analysis divided the 30 populations into two parts. The unweighted pair group method of arithmetic averages (UPGMA clustering and principal coordinates analysis (PCoA showed that the 30 populations could be classified into four types. The results demonstrate a clear geographical trend for T. ciliata in China and provide a theoretical basis for future breeding and conservation strategy of T. ciliata.

  4. ISSR-based analysis of genetic diversity among sorghum landraces growing in some parts of Saudi Arabia and Yemen.

    Science.gov (United States)

    Basahi, Mohammed

    2015-11-01

    Inter simple sequence repeats (ISSR) analysis was used to determine the genetic diversity among 15 genotypes of sorghum [Sorghum bicolor (L.) Moench] growing in some parts of Saudi Arabia and Yemen. A total of 92 alleles were amplified, with an average of 13 ISSR alleles per primer. Cluster analysis divided the 15 genotypes into two main groups. Group A consisted of five genotypes with white grains from Jazan and Abha with a similarity coefficient range of 0.527 to 0.818. Group B was comprised of 10 genotypes; two genotypes from Al-Qassim were clearly delimited from the remaining eight samples with a coefficient range from 0.709 to 0.490. The eight genotypes were divided into two clusters; one was comprised of landraces with dark grains from Abha in Saudi Arabia and Ab in Yemen, with a similarity coefficient range between 0.563 and 0.781, and the other cluster was differentiated into three white-colored-grain genotypes and one colored-grain genotype; all samples from North Yemen had a similarity coefficient range from 0.454 to 0.800. The current results encourage further collection and authentication of sorghum landraces in the gene banks of Saudi Arabia. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  5. Genetic diversity in Populus nigra plantations from west of Iran

    Directory of Open Access Journals (Sweden)

    Afrooz Alimohamadi

    2012-11-01

    Full Text Available In order to adopt strategies for forest conservation and development,it is necessary to estimate the amount and distribution of genetic diversity in existing populations of poplar in Iran. In this study, the genetic diversity between eight stands of Populus nigra established in Kermanshah province was evaluated on the basis of molecular and morphological markers. To amplify microsatellite loci (WPMS09, WPMS16 and WPMS18, DNA extraction from young and fresh leaveswas done. Various conditions of the PCR assay were examined and to evaluate the morphological variation of the morphological characters leaves (consist of 19 traits were measured. In addition, height growth was measured, to evaluate the growth function of the stands in homogeneous conditions. Genetic diversity in termof polymorphic loci was 0%, because three investigated microsatellite loci were monomorphic. The total number of alleles for 3 microsatellite loci was 6 (na = 2, ne = 2, heo = 1, hee = 0.51. Genetic identity based on Nei was 100%, so genetic distance was 0%. The whole sampled trees represented the same thus the genotype. No significant differences between the mean values of all morphological characters and height growth were revealed. Observed genetic similarity gave indication that same ramets had been selected to plant in poplar plantation established in Kermanshah province.These results suggest the need for an initial evaluation of the genetic diversity in selected ramets for planting in plantation to avoid repetition.

  6. An analysis of the genetic diversity and genetic structure of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-12-26

    Dec 26, 2011 ... levels of genetic diversity (Hamrick and Godt, 1996). In addition, E. ulmoides is distributed in a wide range of climatic and geographic conditions in China during the cultivation history of more than 2,000 years (Zhang,. 1992) and rich vitality and high adaptability accumulated through the long-term history.

  7. [Evolutionary process unveiled by the maximum genetic diversity hypothesis].

    Science.gov (United States)

    Huang, Yi-Min; Xia, Meng-Ying; Huang, Shi

    2013-05-01

    As two major popular theories to explain evolutionary facts, the neutral theory and Neo-Darwinism, despite their proven virtues in certain areas, still fail to offer comprehensive explanations to such fundamental evolutionary phenomena as the genetic equidistance result, abundant overlap sites, increase in complexity over time, incomplete understanding of genetic diversity, and inconsistencies with fossil and archaeological records. Maximum genetic diversity hypothesis (MGD), however, constructs a more complete evolutionary genetics theory that incorporates all of the proven virtues of existing theories and adds to them the novel concept of a maximum or optimum limit on genetic distance or diversity. It has yet to meet a contradiction and explained for the first time the half-century old Genetic Equidistance phenomenon as well as most other major evolutionary facts. It provides practical and quantitative ways of studying complexity. Molecular interpretation using MGD-based methods reveal novel insights on the origins of humans and other primates that are consistent with fossil evidence and common sense, and reestablished the important role of China in the evolution of humans. MGD theory has also uncovered an important genetic mechanism in the construction of complex traits and the pathogenesis of complex diseases. We here made a series of sequence comparisons among yeasts, fishes and primates to illustrate the concept of limit on genetic distance. The idea of limit or optimum is in line with the yin-yang paradigm in the traditional Chinese view of the universal creative law in nature.

  8. Genetic diversity of Ascaris in southwestern Uganda.

    Science.gov (United States)

    Betson, Martha; Nejsum, Peter; Llewellyn-Hughes, Julia; Griffin, Claire; Atuhaire, Aaron; Arinaitwe, Moses; Adriko, Moses; Ruggiana, Andrew; Turyakira, Grace; Kabatereine, Narcis B; Stothard, J Russell

    2012-02-01

    Despite the common occurrence of ascariasis in southwestern Uganda, helminth control in the region has been limited. To gain further insights into the genetic diversity of Ascaris in this area, a parasitological survey in mothers (n=41) and children (n=74) living in two villages, Habutobere and Musezero, was carried out. Adult Ascaris worms were collected from infected individuals by chemo-expulsion using pyrantel pamoate treatment. Genetic diversity within these worms was assessed by inspection of DNA sequence variation in a mitochondrial marker and length polymorphism at microsatellite loci. Overall prevalence of ascariasis was 42.5% in mothers and 30.4% in their children and a total of 98 worms was examined from 18 hosts. Sequence analysis of a portion of the mitochondrial cytochrome c oxidase subunit 1 gene revealed 19 different haplotypes, 13 of which had not been previously encountered. Microsatellite analysis using eight loci provided evidence for high gene flow between worm populations from the two villages but comparing these worms with others obtained in a prior study on Unguja, Zanzibar, confirmed little genetic exchange and mixing of worm populations between the two areas. By adding to our understanding of the genetic diversity of Ascaris in Africa, this study provides useful information for monitoring changes in parasite population structure in the face of ongoing and future control. Copyright © 2011 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

  9. Assessment of genetic diversity and variation of Robinia pseudoacacia seeds induced by short-term spaceflight based on two molecular marker systems and morphological traits.

    Science.gov (United States)

    Yuan, C Q; Li, Y F; Sun, P; Sun, Y H; Zhang, G J; Yang, M S; Zhang, Y Y; Li, Y; Wang, L

    2012-12-17

    The black locust (Robinia pseudoacacia) is a forest legume that is highly valued as a honey plant and for its wood. We explored the effect of short-term spaceflight on development of R. pseudoacacia seedlings derived from seeds that endured a 15-day flight; the genetic diversity and variation of plants sampled from space-mutagenized seeds were compared to plants from parallel ground-based control seeds using molecular markers and morphological traits. In the morphology analysis, the space-mutagenized group had apparent variation compared with the control group in morphological traits, including plant height, basal diameter, number of branches, branch stipular thorn length, branch stipular thorn middle width, leaflet vertex angle, and tippy leaf vertex angle. Simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular marker analyses showed a slightly higher levels of genetic diversity in the space-mutagenized group compared to the control group. In the SRAP analysis, the space-mutagenized group had 115 polymorphic bands vs 98 in the controls; 91.27% polymorphic loci vs 77.78% in the controls; 1.9127 ± 0.2834 alleles vs 1.7778 ± 0.4174 in the controls; Nei's genetic diversity (h) was 0.2930 ± 0.1631 vs 0.2688 ± 0.1862 in the controls, and the Shannon's information index (I) was 0.4452 ± 0.2177 vs 0.4031 ± 0.2596 in the controls. The number of alleles was significantly higher in the space-mutagenized group. In the SSR analysis, the space-mutagenized group also had more polymorphic bands (51 vs 46), a greater percentage of polymorphic loci (89.47% vs 80.70%); h was also higher (0.2534 ± 0.1533 vs 0.2240 ± 0.1743), as was I (0.3980 ± 0.2069 vs 0.3501 ± 0.2412). These results demonstrated that the range of genetic variation in the populations of R. pseudoacacia increased after spaceflight. It also suggested that the SSR and SRAP markers are effective markers for studying mutations and genetic diversity in R. pseudoacacia. The data

  10. Dolutegravir reshapes the genetic diversity of HIV-1 reservoirs.

    Science.gov (United States)

    Gantner, Pierre; Lee, Guinevere Q; Rey, David; Mesplede, Thibault; Partisani, Marialuisa; Cheneau, Christine; Beck-Wirth, Geneviève; Faller, Jean-Pierre; Mohseni-Zadeh, Mahsa; Martinot, Martin; Wainberg, Mark A; Fafi-Kremer, Samira

    2018-04-01

    Better understanding of the dynamics of HIV reservoirs under ART is a critical step to achieve a functional HIV cure. Our objective was to assess the genetic diversity of archived HIV-1 DNA over 48 weeks in blood cells of individuals starting treatment with a dolutegravir-based regimen. Eighty blood samples were prospectively and longitudinally collected from 20 individuals (NCT02557997) including: acutely (n = 5) and chronically (n = 5) infected treatment-naive individuals, as well as treatment-experienced individuals who switched to a dolutegravir-based regimen and were either virologically suppressed (n = 5) or had experienced treatment failure (n = 5). The integrase and V3 loop regions of HIV-1 DNA isolated from PBMCs were analysed by pyrosequencing at baseline and weeks 4, 24 and 48. HIV-1 genetic diversity was calculated using Shannon entropy. All individuals achieved or maintained viral suppression throughout the study. A low and stable genetic diversity of archived HIV quasispecies was observed in individuals starting treatment during acute infection. A dramatic reduction of the genetic diversity was observed at week 4 of treatment in the other individuals. In these patients and despite virological suppression, a recovery of the genetic diversity of the reservoirs was observed up to 48 weeks. Viral variants bearing dolutegravir resistance-associated substitutions at integrase position 50, 124, 230 or 263 were detected in five individuals (n = 5/20, 25%) from all groups except those who were ART-failing at baseline. None of these substitutions led to virological failure. These data demonstrate that the genetic diversity of the HIV-1 reservoir is reshaped following the initiation of a dolutegravir-based regimen and strongly suggest that HIV-1 can continue to replicate despite successful treatment.

  11. Effects of complex life cycles on genetic diversity: cyclical parthenogenesis

    Science.gov (United States)

    Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

    2016-01-01

    Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks). PMID:27436524

  12. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    Ivoire. However, no study on the genetic diversity of the species has been performed to date. This study aims at analyzing the diversity and genetic structure of 35 maize accessions using 10 microsatellite markers. These accessions are from ...

  13. Genetic diversity of Echinococcus spp. in Russia.

    Science.gov (United States)

    Konyaev, Sergey V; Yanagida, Tetsuya; Nakao, Minoru; Ingovatova, Galina M; Shoykhet, Yakov N; Bondarev, Alexandr Y; Odnokurtsev, Valeriy A; Loskutova, Kyunnyay S; Lukmanova, Gulnur I; Dokuchaev, Nikolai E; Spiridonov, Sergey; Alshinecky, Mikhail V; Sivkova, Tatyana N; Andreyanov, Oleg N; Abramov, Sergey A; Krivopalov, Anton V; Karpenko, Sergey V; Lopatina, Natalia V; Dupal, Tamara A; Sako, Yasuhito; Ito, Akira

    2013-11-01

    In Russia, both alveolar and cystic echinococcoses are endemic. This study aimed to identify the aetiological agents of the diseases and to investigate the distribution of each Echinococcus species in Russia. A total of 75 Echinococcus specimens were collected from 14 host species from 2010 to 2012. Based on the mitochondrial DNA sequences, they were identified as Echinococcus granulosus sensu stricto (s.s.), E. canadensis and E. multilocularis. E. granulosus s.s. was confirmed in the European Russia and the Altai region. Three genotypes, G6, G8 and G10 of E. canadensis were detected in Yakutia. G6 was also found in the Altai region. Four genotypes of E. multilocularis were confirmed; the Asian genotype in the western Siberia and the European Russia, the Mongolian genotype in an island of Baikal Lake and the Altai Republic, the European genotype from a captive monkey in Moscow Zoo and the North American genotype in Yakutia. The present distributional record will become a basis of public health to control echinococcoses in Russia. The rich genetic diversity demonstrates the importance of Russia in investigating the evolutionary history of the genus Echinococcus.

  14. Hypothesis: Cryptosporidium genetic diversity mirrors national disease notification rate.

    Science.gov (United States)

    Takumi, Katsuhisa; Cacciò, Simone M; van der Giessen, Joke; Xiao, Lihua; Sprong, Hein

    2015-06-06

    Cryptosporidiosis is a gastrointestinal disease affecting many people worldwide. Disease incidence is often unknown and surveillance of human cryptosporidiosis is installed in only a handful of developed countries. A genetic marker that mirrors disease incidence is potentially a powerful tool for monitoring the two primary human infected species of Cryptosporidium. We used the molecular epidemiological database with Cryptosporidium isolates from ZoopNet, which currently contains more than 1400 records with their sampling nations, and the names of the host species from which the isolates were obtained. Based on 296 C. hominis and 195 C. parvum GP60 sequences from human origin, the genetic diversities of Cryptosporidium was estimated for several nations. Notified cases of human cryptosporidiosis were collected from statistics databases for only four nations. Genetic diversities of C. hominis were estimated in 10 nations in 5 continents, and that of C. parvum of human origin were estimated in 15 nations. Correlation with reported incidence of human cryptosporidiosis in four nations (the Netherlands, United States, United Kingdom and Australia) was positive and significant. A linear model for testing the relationship between the genetic diversity and incidence produced a significantly positive estimate for the slope (P-value mirrors notification rates of human cryptosporidiosis was not rejected based on the data presented. Genetic diversity of C. hominis and C. parvum may therefore be an independent and complementary measure for quantifying disease incidence, for which only a moderate number of stool samples from each nation are sufficient data input.

  15. Genetic Diversity in Insect Metal Tolerance

    OpenAIRE

    Thomas J. S. Merritt; Adam J. Bewick

    2017-01-01

    Insects encounter a variety of metals in their environment, many of which are required at some concentration for normal organismal homeostasis, but essentially all of which are toxic at higher concentrations. Insects have evolved a variety of genetic, and likely epigenetic, mechanisms to deal with metal stress. A recurring theme in all these systems is complexity and diversity; even simple, single gene, cases are complex. Of the known gene families, the metallothioneins are perhaps the best u...

  16. Limited Genetic Diversity of Brucella spp.

    OpenAIRE

    Gándara, Benjamín; Merino, Ahidé López; Rogel, Marco Antonio; Martínez-Romero, Esperanza

    2001-01-01

    Multilocus enzyme electrophoresis (MLEE) of 99 Brucella isolates, including the type strains from all recognized species, revealed a very limited genetic diversity and supports the proposal of a monospecific genus. In MLEE-derived dendrograms, Brucella abortus and a marine Brucella sp. grouped into a single electrophoretic type related to Brucella neotomae and Brucella ovis. Brucella suis and Brucella canis formed another cluster linked to Brucella melitensis and related to Rhizobium tropici....

  17. Genetic diversity and population structure of blue-crested lizard ...

    Indian Academy of Sciences (India)

    Weerachai Saijuntha

    2017-06-19

    Jun 19, 2017 ... Indo-Chinese forest lizard; white-lipped lizard; agamid; gene flow; reptile; CO1 gene. although illegal, it is still massively hunted in several .... Genetic diversity of C. mystaceus. Figure 1. Minimum spanning haplotype network of C. mysteceus generated based on partial CO1 sequence corresponds to their.

  18. Analysis of genetic diversity and construction of core collection of ...

    African Journals Online (AJOL)

    Analysis of genetic diversity and construction of core collection of local mulberry varieties from Shanxi Province based on ISSR marker. ... By using stepwise clustering and random methods and the modified heuristic algorithm, 21 core collections were constructed and the ratio of core collection was 28.77%. The result of ...

  19. Estimation of genetic diversity of the Kenyan yam (Dioscorea spp ...

    African Journals Online (AJOL)

    MUTHAMIA

    2013-10-02

    Oct 2, 2013 ... The botany, ethnobotany, use and possible future of yams in West Africa. Econ. Bot. 26:301-318. Beebe S, Sckroch PW, Tohme J, Duque MC, Pedraza F, Nienhuis J. (2000). Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of. RAPD ...

  20. Estimate of genetic diversity in cassutinga ( Croton heliotropiifolius ...

    African Journals Online (AJOL)

    Estimate of genetic diversity in cassutinga (Croton heliotropiifolius) based on molecular markers. Tallita de Oliveira Rocha, Janaina Silva Freitas, Elisa Susilene Lisboa dos Santos, Murilo Marques Scaldaferri, Claudine Gonçalves de Oliveira, Carlos Bernard Moreno Cerqueira-Silva ...

  1. Genetic structure and diversity of the Neem Germplasm Bank from ...

    African Journals Online (AJOL)

    Particular

    2013-05-15

    May 15, 2013 ... The marker data indicated that GBN have three ... formulation of appropriate strategies for management and use of GBN. ..... Dhillon RS, Mohapatra T, Singh S, Boora KS, Singh, K (2007). Assessment of genetic diversity in Azadirachta indica based on DNA fingerprinting. Indian J. Biotech. 6:519-524.

  2. Assessing genetic diversity and phylogeographic structure of duck ...

    African Journals Online (AJOL)

    In this study, the maternal genetic diversity and phylogenetic relationship of Nigerian duck populations were assessed. A total of 591 base pair fragment of the mitochondrial DNA (mtDNA) D-loop region of 87 indigenous ducks from two populations in Nigeria were analyzed. Seven haplotypes and 70 polymorphic sites were ...

  3. Genetic diversity in Jatropha species from different regions of Brazil ...

    African Journals Online (AJOL)

    Genetic diversity in Jatropha species from different regions of Brazil based on morphological characters and inters-simple sequence repeat (ISSR) molecular markers. ... There was no relation between similarity patterns and geographical origin of accesses in the group analysis. Average percentage of polymorphism found ...

  4. Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] varieties ...

    African Journals Online (AJOL)

    Cowpea, Vigna unguiculata (L.) Walp. presents phenotypical variabilities and in order to study the genetic diversity of cultivated Senegalese varieties, two experimental approaches were used. First, a physiological characterization based on nitrogen fixation was used to assess cowpea breeding lines. Inoculation with two ...

  5. Genetic diversity and species delimitation in the opportunistic genus Fonsecaea

    NARCIS (Netherlands)

    Najafzadeh, M.J.; Gueidan, C.; Badali, H.; Gerrits Van Den Ende, A. H.; Xi, L.; de Hoog, G.S.

    2009-01-01

    Genetic diversity and species delimitation were investigated among 39 isolates recovered from clinical and environmental sources in Central and South America, Africa, East Asia and Europe. All had been morphologically identified as Fonsecaea spp. Molecular analyses were based on sequences of the

  6. Genetic diversity among selected genotypes of almond Prunus ...

    African Journals Online (AJOL)

    Average polymorphic information content (PIC) value of 16 selected primers was 0.684 and maximum and minimum PIC value was 0.8687 and 0.2551 for primers S073 and S081, respectively. Cophenetic correlation was found to be 0.89. RAPD data on genetic diversity matched classification of studied genotypes based on ...

  7. Assessment of the genetic diversity of geographically unrelated ...

    African Journals Online (AJOL)

    JOHN

    2005-05-05

    May 5, 2005 ... for the identification of genetic diversity of geographical unrelated strains and analysis of M. aeruginosa strains. AFLPs seem to overcome the major pitfalls present in other PCR based methods, e.g. DAF or RAPD analysis, and appear to be as reproducible, heritable and intraspecific as RFLPs (Law et al., ...

  8. Genetic diversity in Zimbabwean Sanga cattle breeds using ...

    African Journals Online (AJOL)

    Zimbabwe's smallholder land-based livelihoods are dominated by the three local Sanga cattle breeds, namely Mashona, Tuli, and Nkone. A study was carried out to determine genetic diversity and differentiation among conservation populations of these breeds using 16 bovine-specific microsatellite markers. These markers ...

  9. Original Paper Patterns of genetic structure and phenotypic diversity ...

    African Journals Online (AJOL)

    Diversity levels in ten local sorghum guinea varieties (25 panicles per variety) collected from different farms in ... results underline the role of farmer practices in phenotypic and genetic evolution of sorghum. This concept should be well considered ... varietal needs and preferences: applying research station-based breeding ...

  10. Assessment of genetic diversity in different clones of Dalbergia ...

    African Journals Online (AJOL)

    Genetic diversity of forty (40) clones of Dalbergia sissoo Roxb was analyzed using randomly amplified polymorphic DNA (RAPD) markers by selecting 30 decamer primers, which were later reduced to 10 based on the preliminary PCR amplification. A total of 129 distinct DNA fragments (bands) were amplified, of which 104 ...

  11. Genetic diversity analysis and subspecies classification of Thailand ...

    African Journals Online (AJOL)

    Genetic diversity among 126 rice accessions, including 110 Thai landraces and 16 varieties used as subspecies reference, were evaluated by three types of DNA markers, InDel (Insertion/Deletion), inter-simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers. Twelve InDel primer pairs, based on DNA ...

  12. Managing genetic diversity and society needs

    Directory of Open Access Journals (Sweden)

    Arthur da Silva Mariante

    2008-07-01

    Full Text Available Most livestock are not indigenous to Brazil. Several animal species were considered domesticated in the pre-colonial period, since the indigenous people manage them as would be typical of European livestock production. For over 500 years there have been periodic introductions resulting in the wide range of genetic diversity that for centuries supported domestic animal production in the country. Even though these naturalized breeds have acquired adaptive traits after centuries of natural selection, they have been gradually replaced by exotic breeds, to such an extent, that today they are in danger of extinction To avoid further loss of this important genetic material, in 1983 Embrapa Genetic Resources and Biotechnology decided to include conservation of animal genetic resources among its priorities. In this paper we describe the effort to genetically characterize these populations, as a tool to ensure their genetic variability. To effectively save the threatened local breeds of livestock it is important to find a niche market for each one, reinserting them in production systems. They have to be utilized in order to be conserved. And there is no doubt that due to their adaptive traits, the Brazilian local breeds of livestock can play an important role in animal production, to meet society needs.

  13. Genetic diversity of Coccidioides posadasii from Brazil.

    Science.gov (United States)

    Brilhante, Raimunda Sâmia Nogueira; de Lima, Rita Amanda Chaves; Ribeiro, Joyce Fonteles; de Camargo, Zoilo Pires; Castelo-Branco, Débora de Souza Collares Maia; Grangeiro, Thalles Barbosa; Cordeiro, Rossana de Aguiar; Gadelha Rocha, Marcos Fábio; Sidrim, José Júlio Costa

    2013-05-01

    Studies of the genetic variation within populations of Coccidioides posadasii are scarce, especially for those recovered from South America. Understanding the distribution of genotypes among populations is important for epidemiological surveillance. This study evaluated the genetic diversity of 18 Brazilian strains of C. posadasii through the sequencing of the 18-28S region of nuclear rDNA, as well as through RAPD and M13-PCR fingerprinting techniques. The sequences obtained were compared to Coccidioides spp. previously deposited in GenBank. The MEGA5 program was used to perform phylogenetic analyses. Within the C. posadasii clade, a single cluster was observed, containing seven isolates from Ceará, which presented a single nucleotide polymorphism. These isolates were from the same geographical area. The strains of C. posadasii showed a lower rate of genetic diversity in the ITS1 and ITS2 regions. The results of M13 and RAPD-PCR fingerprinting indicated a similar electrophoretic profile. No differences between clinical and environmental isolates were detected. This was the first study assessing the genetic variability of a larger number of C. posadasii isolates from Brazil.

  14. Genetic diversity in Tunisian horse breeds

    Directory of Open Access Journals (Sweden)

    B. Jemmali

    2017-06-01

    Full Text Available This study aimed at screening genetic diversity and differentiation in four horse breeds raised in Tunisia, the Barb, Arab-Barb, Arabian, and English Thoroughbred breeds. A total of 200 blood samples (50 for each breed were collected from the jugular veins of animals, and genomic DNA was extracted. The analysis of the genetic structure was carried out using a panel of 16 microsatellite loci. Results showed that all studied microsatellite markers were highly polymorphic in all breeds. Overall, a total of 147 alleles were detected using the 16 microsatellite loci. The average number of alleles per locus was 7.52 (0.49, 7.35 (0.54, 6.3 (0.44, and 6 (0.38 for the Arab-Barb, Barb, Arabian, and English Thoroughbred breeds, respectively. The observed heterozygosities ranged from 0.63 (0.03 in the English Thoroughbred to 0.72 in the Arab-Barb breeds, whereas the expected heterozygosities were between 0.68 (0.02 in the English Thoroughbred and 0.73 in the Barb breeds. All FST values calculated by pairwise breed combinations were significantly different from zero (p  <  0.05 and an important genetic differentiation among breeds was revealed. Genetic distances, the factorial correspondence, and principal coordinate analyses showed that the important amount of genetic variation was within population. These results may facilitate conservation programs for the studied breeds and enhance preserve their genetic diversity.

  15. Genetic diversity among farmer-preferred cassava landraces in ...

    African Journals Online (AJOL)

    Understanding of genetic diversity among a breeding population is an important requirement for crop improvement as it allows for the selection of diverse parental combinations and formation of heterotic pools for genetic gain. This study was carried out to determine genetic diversity within and among 51 farmer-preferred ...

  16. Genetic gain and gene diversity of seed orchard crops

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Kyu-Suk [Swedish Univ. of Agricultural Sciences, Umeaa (Sweden). Dept. of Forest Genetics and Plant Physiology

    2001-07-01

    Seed orchards are the major tool for deploying the improvement generated by breeding programs and assuring the consistent supply of genetically improved seed. Attainment of genetic gain and monitoring of gene diversity through selection and breeding were studied considering the factors: selection intensity; genetic value; coancestry; fertility variation; and pollen contamination. The optimum goal of a seed orchard is achieved when the orchard population is under an idealized situation, i.e., panmixis, equal gamete contributions from all parental genotypes, non-relatedness and no pollen contamination. In practice, however, due to relatedness among parents, variation in clonal fertility and ramet number, and gene migration from outside, the realized genetic gain and gene diversity deviate from the expectation. In the present study, the genetic value of seed orchard crops (genetic gain, G) could be increased by selective harvest, genetic thinning and/or both. Status number (N{sub S}) was used to monitor the loss of gene diversity in the process of forest tree domestication, and calculated to be reasonably high in most seed orchards. Fertility of parents was estimated based on the assessment of flowering or seed production, which was shown to be under strong genetic control. Variation in fertility among orchard parents was a general feature and reduced the predicted gene diversity of the orchard crop. Fertility variation among parents could be described by the sibling coefficient ({psi}). {psi} was estimated to be 2 (CV = 100% for fertility). In calculating {psi}, it was possible to consider, besides fertility variation, the phenotypic correlation between maternal and parental fertilities, and pollen contamination. Status number was increased by controlling parental fertility, e.g., equal seed harvest, mixing seed in equal proportions and balancing parental contribution. By equalizing female fertility among over-represented parents, it was possible to effect a

  17. Determination of genetic diversity among Turkish durum wheat ...

    African Journals Online (AJOL)

    Wheat landraces represent an important source of genetic variation that can be used for future wheat breeding program. The rich wheat landraces from Turkey have not been sufficiently analyzed genetically. For this reason, genetic diversity and relationship of the landraces must be determined. In this study, genetic diversity ...

  18. Genetic Diversity of Koala Retroviral Envelopes

    Directory of Open Access Journals (Sweden)

    Wenqin Xu

    2015-03-01

    Full Text Available Genetic diversity, attributable to the low fidelity of reverse transcription, recombination and mutation, is an important feature of infectious retroviruses. Under selective pressure, such as that imposed by superinfection interference, gammaretroviruses commonly adapt their envelope proteins to use alternative receptors to overcome this entry block. The first characterized koala retroviruses KoRV subgroup A (KoRV-A were remarkable in their absence of envelope genetic variability. Once it was determined that KoRV-A was present in all koalas in US zoos, regardless of their disease status, we sought to isolate a KoRV variant whose presence correlated with neoplastic malignancies. More than a decade after the identification of KoRV-A, we isolated a second subgroup of KoRV, KoRV-B from koalas with lymphomas. The envelope proteins of KoRV-A and KoRV-B are sufficiently divergent to confer the ability to bind and employ distinct receptors for infection. We have now obtained a number of additional KoRV envelope variants. In the present studies we report these variants, and show that they differ from KoRV-A and KoRV-B envelopes in their host range and superinfection interference properties. Thus, there appears to be considerable variation among KoRVs envelope genes suggesting genetic diversity is a factor following the KoRV-A infection process.

  19. Genetic Diversity of HIV-1 in Tunisia.

    Science.gov (United States)

    El Moussi, Awatef; Thomson, Michael M; Delgado, Elena; Cuevas, María Teresa; Nasr, Majda; Abid, Salma; Ben Hadj Kacem, Mohamed Ali; Benaissa Tiouiri, Hanene; Letaief, Amel; Chakroun, Mohamed; Ben Jemaa, Mounir; Hamdouni, Hayet; Tej Dellagi, Rafla; Kheireddine, Khaled; Boutiba, Ilhem; Pérez-Álvarez, Lucía; Slim, Amine

    2017-01-01

    In this study, the genetic diversity of HIV-1 in Tunisia was analyzed. For this, 193 samples were collected in different regions of Tunisia between 2012 and 2015. A protease and reverse transcriptase fragment were amplified and sequenced. Phylogenetic analyses were performed through maximum likelihood and recombination was analyzed by bootscanning. Six HIV-1 subtypes (B, A1, G, D, C, and F2), 5 circulating recombinant forms (CRF02_AG, CRF25_cpx, CRF43_02G, CRF06_cpx, and CRF19_cpx), and 11 unique recombinant forms were identified. Subtype B (46.4%) and CRF02_AG (39.4%) were the predominant genetic forms. A group of 44 CRF02_AG sequences formed a distinct Tunisian cluster, which also included four viruses from western Europe. Nine viruses were closely related to isolates collected in other African or in European countries. In conclusion, a high HIV-1 genetic diversity is observed in Tunisia and the local spread of CRF02_AG is first documented in this country.

  20. Genetic diversity of koala retroviral envelopes.

    Science.gov (United States)

    Xu, Wenqin; Gorman, Kristen; Santiago, Jan Clement; Kluska, Kristen; Eiden, Maribeth V

    2015-03-17

    Genetic diversity, attributable to the low fidelity of reverse transcription, recombination and mutation, is an important feature of infectious retroviruses. Under selective pressure, such as that imposed by superinfection interference, gammaretroviruses commonly adapt their envelope proteins to use alternative receptors to overcome this entry block. The first characterized koala retroviruses KoRV subgroup A (KoRV-A) were remarkable in their absence of envelope genetic variability. Once it was determined that KoRV-A was present in all koalas in US zoos, regardless of their disease status, we sought to isolate a KoRV variant whose presence correlated with neoplastic malignancies. More than a decade after the identification of KoRV-A, we isolated a second subgroup of KoRV, KoRV-B from koalas with lymphomas. The envelope proteins of KoRV-A and KoRV-B are sufficiently divergent to confer the ability to bind and employ distinct receptors for infection. We have now obtained a number of additional KoRV envelope variants. In the present studies we report these variants, and show that they differ from KoRV-A and KoRV-B envelopes in their host range and superinfection interference properties. Thus, there appears to be considerable variation among KoRVs envelope genes suggesting genetic diversity is a factor following the KoRV-A infection process.

  1. Genetic diversity of Entamoeba: Novel ribosomal lineages from cockroaches.

    Directory of Open Access Journals (Sweden)

    Tetsuro Kawano

    Full Text Available Our current taxonomic perspective on Entamoeba is largely based on small-subunit ribosomal RNA genes (SSU rDNA from Entamoeba species identified in vertebrate hosts with minor exceptions such as E. moshkovskii from sewage water and E. marina from marine sediment. Other Entamoeba species have also been morphologically identified and described from non-vertebrate species such as insects; however, their genetic diversity remains unknown. In order to further disclose the diversity of the genus, we investigated Entamoeba spp. in the intestines of three cockroach species: Periplaneta americana, Blaptica dubia, and Gromphadorhina oblongonota. We obtained 134 Entamoeba SSU rDNA sequences from 186 cockroaches by direct nested PCR using the DNA extracts of intestines from cockroaches, followed by scrutinized BLASTn screening and phylogenetic analyses. All the sequences identified in this study were distinct from those reported from known Entamoeba species, and considered as novel Entamoeba ribosomal lineages. Furthermore, they were positioned at the base of the clade of known Entamoeba species and displayed remarkable degree of genetic diversity comprising nine major groups in the three cockroach species. This is the first report of the diversity of SSU rDNA sequences from Entamoeba in non-vertebrate host species, and should help to understand the genetic diversity of the genus Entamoeba.

  2. Genetic diversity of Entamoeba: Novel ribosomal lineages from cockroaches

    Science.gov (United States)

    Kawano, Tetsuro; Imada, Mihoko; Chamavit, Pennapa; Kobayashi, Seiki; Hashimoto, Tetsuo

    2017-01-01

    Our current taxonomic perspective on Entamoeba is largely based on small-subunit ribosomal RNA genes (SSU rDNA) from Entamoeba species identified in vertebrate hosts with minor exceptions such as E. moshkovskii from sewage water and E. marina from marine sediment. Other Entamoeba species have also been morphologically identified and described from non-vertebrate species such as insects; however, their genetic diversity remains unknown. In order to further disclose the diversity of the genus, we investigated Entamoeba spp. in the intestines of three cockroach species: Periplaneta americana, Blaptica dubia, and Gromphadorhina oblongonota. We obtained 134 Entamoeba SSU rDNA sequences from 186 cockroaches by direct nested PCR using the DNA extracts of intestines from cockroaches, followed by scrutinized BLASTn screening and phylogenetic analyses. All the sequences identified in this study were distinct from those reported from known Entamoeba species, and considered as novel Entamoeba ribosomal lineages. Furthermore, they were positioned at the base of the clade of known Entamoeba species and displayed remarkable degree of genetic diversity comprising nine major groups in the three cockroach species. This is the first report of the diversity of SSU rDNA sequences from Entamoeba in non-vertebrate host species, and should help to understand the genetic diversity of the genus Entamoeba. PMID:28934335

  3. Application of a partitioning procedure based on Rao quadratic entropy index to characterize the temporal evolution of in situ varietal and genetic diversity of bread wheat in France over the period 1981-2006.

    Science.gov (United States)

    Perronne, Rémi; Goldringer, Isabelle

    2017-12-15

    We present and highlight a partitioning procedure based on the Rao quadratic entropy index to assess temporal in situ inter-annual varietal and genetic changes of crop diversity. For decades, Western-European agroecosystems have undergone profound changes, among which a reduction of crop genetic diversity. These changes have been highlighted in numerous studies, but no unified partitioning procedure has been proposed to compute the inter-annual variability in both varietal and genetic diversity. To fill this gap, we tested, adjusted and applied a partitioning procedure based on the Rao quadratic entropy index that made possible to describe the different components of crop diversity as well as to account for the relative acreages of varieties. To emphasize the relevance of this procedure, we relied on a case study focusing on the temporal evolution of bread wheat diversity in France over the period 1981-2006 at both national and district scales. At the national scale, we highlighted a decrease of the weighted genetic replacement indicating that varieties sown in the most recent years were more genetically similar than older ones. At the district scale, we highlighted sudden changes in weighted genetic replacement in some agricultural regions that could be due to fast shifts of successive leading varieties over time. Other regions presented a relatively continuous increase of genetic similarity over time, potentially due to the coexistence of a larger number of co-leading varieties that got closer genetically. Based on the partitioning procedure, we argue that a tendency of in situ genetic homogenization could be compared to some of its potential causes, such as a decrease in the speed of replacement or an increase in between-variety genetic similarity over time.

  4. Genetic diversity in aspen and its relation to arthropod abundance

    Science.gov (United States)

    Zhang, Chunxia; Vornam, Barbara; Volmer, Katharina; Prinz, Kathleen; Kleemann, Frauke; Köhler, Lars; Polle, Andrea; Finkeldey, Reiner

    2015-01-01

    The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen. PMID:25674097

  5. Gene diversity and genetic variation in lung flukes (genus Paragonimus).

    Science.gov (United States)

    Blair, David; Nawa, Yukifumi; Mitreva, Makedonka; Doanh, Pham Ngoc

    2016-01-01

    Paragonimiasis caused by lung flukes (genus Paragonimus) is a neglected disease occurring in Asia, Africa and the Americas. The genus is species-rich, ancient and widespread. Genetic diversity is likely to be considerable, but investigation of this remains confined to a few populations of a few species. In recent years, studies of genetic diversity have moved from isoenzyme analysis to molecular phylogenetic analysis based on selected DNA sequences. The former offered better resolution of questions relating to allelic diversity and gene flow, whereas the latter is more suitable for questions relating to molecular taxonomy and phylogeny. A picture is emerging of a highly diverse taxon of parasites, with the greatest diversity found in eastern and southern Asia where ongoing speciation might be indicated by the presence of several species complexes. Diversity of lung flukes in Africa and the Americas is very poorly sampled. Functional molecules that might be of value for immunodiagnosis, or as targets for medical intervention, are of great interest. Characterisation of these from Paragonimus species has been ongoing for a number of years. However, the imminent release of genomic and transcriptomic data for several species of Paragonimus will dramatically increase the rate of discovery of such molecules, and illuminate their diversity within and between species. © The Author 2015. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1.

    Directory of Open Access Journals (Sweden)

    Binhua Liang

    Full Text Available BACKGROUND: Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. METHODOLOGY/PRINCIPAL FINDINGS: HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. CONCLUSIONS/SIGNIFICANCE: Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies.

  7. A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1

    Science.gov (United States)

    Liang, Binhua; Luo, Ma; Scott-Herridge, Joel; Semeniuk, Christina; Mendoza, Mark; Capina, Rupert; Sheardown, Brent; Ji, Hezhao; Kimani, Joshua; Ball, Blake T.; Van Domselaar, Gary; Graham, Morag; Tyler, Shane; Jones, Steven J. M.; Plummer, Francis A.

    2011-01-01

    Background Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. Methodology/Principal Findings HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB) sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL) and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. Conclusions/Significance Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies. PMID:22039546

  8. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    Science.gov (United States)

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

  9. Review: Genetic diversity and population structure of cotton ...

    African Journals Online (AJOL)

    Cotton (Gossypium spp.) is the world's leading natural fiber crop and is cultivated in diverse temperate and tropical areas. In this sense, molecular markers are important tools for polymorphism identification in genetic diversity analyses. The objective of this study was to evaluate genetic diversity and population structure in ...

  10. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A.

  11. Genetic diversity analysis of stress tolerant rice (Oryza sativa L.)

    African Journals Online (AJOL)

    MD.Farid Islam

    2012-10-23

    Oct 23, 2012 ... can be invaluable in crop breeding. Genetic diversity analysis is used for estimating and establishing of genetic relationship in germplasm collection, identifying diverse parental combinations to create segregating progenies with maximum genetic variability for further selection and introgressing desirable ...

  12. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    2015-12-03

    Dec 3, 2015 ... The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering impor- tant repositories of biological diversity, the genetic ...

  13. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    Unknown

    [Gupta A. K., Chauhan M., Tandon S. N. and Sonia 2005 Genetic diversity and bottleneck studies in the Marwari horse breed. J. Genet. 84, 295–301] ... developed to carry out studies of genetic variation (Brad- ley et al. 1996; Canon et al. ..... 1996 Mitochondrial diversity and the origins of African and. European cattle. Proc.

  14. Genetic diversity in some local chicken breeds using microsatellite markers

    Directory of Open Access Journals (Sweden)

    M. Cassandro

    2010-04-01

    Full Text Available Genetic relationships among Veneto native breeds of chickens were studied on the basis of microsatellites polymorphisms. A total of 100 DNA samples from 2 local chicken breeds (45 Robusta Lionata and 43 Robusta Maculata and a commercial broiler line (12 Golden Comet were analyzed using 19 microsatellite markers. The average number of alleles per locus was 4.05 and the expected heterozigosity resulted lower for the local breeds than the broiler line. The Robusta Lionata breed and the broiler line showed a significant deficit and excess of heterozygotes, respectively, deviating from Hardy-Weinberg equilibrium. Nei’s standard genetic distances corrected for bias due to sampling of individuals (Da, based on allele frequencies, were calculated among breeds. The local breeds resulted very similar confirming the same genetic origin. The results suggested that microsatellite markers are a useful tool for studying the genetic diversity among local chicken breeds.

  15. Genetic and Chemical Diversity in Perovskia abrotanoides Kar. (Lamiaceae) Populations Based on ISSRs Markers and Essential Oils Profile.

    Science.gov (United States)

    Pourhosseini, Seyyed Hossein; Hadian, Javad; Sonboli, Ali; Nejad Ebrahimi, Samad; Mirjalili, Mohammad Hossein

    2018-01-19

    Genetic and the essential oil composition variability among twelve Perovskia abrotanoides populations (PAbPs) growing wild in Iran were assessed by ISSR markers, GC-FID and GC/MS, respectively. Nine selected ISSR primers produced 119 discernible bands, of them 96 (80.7%) being polymorphic. Genetic similarity values among populations ranged between 0.07 and 0.79 which indicated a high level of genetic variation. Polymorphic information content, resolving power and marker index generated by ISSR primers were, 0.31, 6.14, and 3.32, respectively. UPGMA grouped PAbPs into four main clusters. Altogether, 38 chemical compounds were identified in the oils, and a relatively high variation in their contents was found. Camphor (11.9 - 27.5%), 1,8-cineole (11.3 - 21.3%), α-bisabolol (0.0 - 13.1%), α-pinene (5.9 - 10.8%), and δ-3-carene (0.1 - 10.5%) were the major compounds. Oxygenated monoterpenes (32.1 - 35.8%) and monoterpene hydrocarbons (25.7 - 30.4%) were the main groups of compounds in the oils studied. Cluster analysis and principal-component analysis were used to characterize the samples according to oil components. Four main chemotypes were found to be Chemotype I (camphor/1,8-cineol), Chemotype II (1,8-cineole/camphor), Chemotype III (camphor/1,8-cineol/α-bisabolol), and Chemotype IV (camphor/δ-3-carene/α-bisabolol). The information, provided here on P. abrotanoides populations, will be useful to introduce this plant into agricultural systems. © 2018 Wiley-VHCA AG, Zurich, Switzerland.

  16. The Genetic Diversity of the Americas.

    Science.gov (United States)

    Adhikari, Kaustubh; Chacón-Duque, Juan Camilo; Mendoza-Revilla, Javier; Fuentes-Guajardo, Macarena; Ruiz-Linares, Andrés

    2017-08-31

    The history of the Americas involved the encounter of millions of Native Americans, Europeans, and Africans. A variable admixture of these three continental groups has taken place throughout the continent, influenced by demography and a range of social factors. This variable admixture has had a major influence on the genetic makeup of populations across the continent. Here, we summarize the demographic history of the region, highlight some social factors that affected historical admixture, and review major patterns of ancestry across the Western Hemisphere based on genetic data.

  17. Genetic diversity and genetic structure of the Siberian roe deer (Capreolus pygargus) populations from Asia.

    Science.gov (United States)

    Lee, Yun Sun; Markov, Nickolay; Voloshina, Inna; Argunov, Alexander; Bayarlkhagva, Damdingiin; Oh, Jang Geun; Park, Yong-Su; Min, Mi-Sook; Lee, Hang; Kim, Kyung Seok

    2015-08-18

    The roe deer, Capreolus sp., is one of the most widespread meso-mammals of Palearctic distribution, and includes two species, the European roe deer, C. capreolus inhabiting mainly Europe, and the Siberian roe deer, C. pygargus, distributed throughout continental Asia. Although there are a number of genetic studies concerning European roe deer, the Siberian roe deer has been studied less, and none of these studies use microsatellite markers. Natural processes have led to genetic structuring in wild populations. To understand how these factors have affected genetic structure and connectivity of Siberian roe deer, we investigated variability at 12 microsatellite loci for Siberian roe deer from ten localities in Asia. Moderate levels of genetic diversity (H(E) = 0.522 to 0.628) were found in all populations except in Jeju Island, South Korea, where the diversity was lowest (H(E) = 0.386). Western populations showed relatively low genetic diversity and higher degrees of genetic differentiation compared with eastern populations (mean Ar = 3.54 (east), 2.81 (west), mean F(ST) = 0.122). Bayesian-based clustering analysis revealed the existence of three genetically distinct groups (clusters) for Siberian roe deer, which comprise of the Southeastern group (Mainland Korea, Russian Far East, Trans-Baikal region and Northern part of Mongolia), Northwestern group (Western Siberia and Ural in Russia) and Jeju Island population. Genetic analyses including AMOVA (F(RT) = 0.200), Barrier and PCA also supported genetic differentiation among regions separated primarily by major mountain ridges, suggesting that mountains played a role in the genetic differentiation of Siberian roe deer. On the other hand, genetic evidence also suggests an ongoing migration that may facilitate genetic admixture at the border areas between two groups. Our results reveal an apparent pattern of genetic differentiation among populations inhabiting Asia, showing moderate levels of genetic diversity with an

  18. Genetic diversity and population structure: implications for conservation of wild soybean (Glycine soja Sieb. et Zucc) based on nuclear and chloroplast microsatellite variation.

    Science.gov (United States)

    He, Shuilian; Wang, Yunsheng; Volis, Sergei; Li, Dezhu; Yi, Tingshuang

    2012-10-03

    Wild soybean (Glycine soja Sieb. et Zucc) is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from 43 locations sampled across its range in China, Japan and Korea were analyzed using 20 nuclear (nSSRs) and five chloroplast microsatellite markers (cpSSRs) to reveal its genetic diversity and population structure. Relatively high nSSR diversity was found in wild soybean compared with other self-pollinated species, and the region of middle and lower reaches of Yangtze River (MDRY) was revealed to have the highest genetic diversity. However, cpSSRs suggested that Korea is a center of diversity. High genetic differentiation and low gene flow among populations were detected, which is consistent with the predominant self-pollination of wild soybean. Two main clusters were revealed by MCMC structure reconstruction and phylogenetic dendrogram, one formed by a group of populations from northwestern China (NWC) and north China (NC), and the other including northeastern China (NEC), Japan, Korea, MDRY, south China (SC) and southwestern China (SWC). Contrib analyses showed that southwestern China makes the greatest contribution to the total diversity and allelic richness, and is worthy of being given conservation priority.

  19. Great ape genetic diversity and population history

    DEFF Research Database (Denmark)

    Prado-Martinez, Javier; Sudmant, Peter H.; Kidd, Jeffrey M.

    2013-01-01

    Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape...... all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape...... genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations....

  20. Estimating intraspecific genetic diversity from community DNA metabarcoding data

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    2018-04-01

    Full Text Available Background DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs, losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal. Methods This study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package “JAMP” and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii 18 monitoring samples each amplified with four different primer sets and two PCR replicates. Results We detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177–200 OTUs, each containing an average of 2.40–3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stonefly

  1. Genetic diversity affects colony survivorship in commercial honey bee colonies

    Science.gov (United States)

    Tarpy, David R.; vanEngelsdorp, Dennis; Pettis, Jeffrey S.

    2013-08-01

    Honey bee ( Apis mellifera) queens mate with unusually high numbers of males (average of approximately 12 drones), although there is much variation among queens. One main consequence of such extreme polyandry is an increased diversity of worker genotypes within a colony, which has been shown empirically to confer significant adaptive advantages that result in higher colony productivity and survival. Moreover, honey bees are the primary insect pollinators used in modern commercial production agriculture, and their populations have been in decline worldwide. Here, we compare the mating frequencies of queens, and therefore, intracolony genetic diversity, in three commercial beekeeping operations to determine how they correlate with various measures of colony health and productivity, particularly the likelihood of queen supersedure and colony survival in functional, intensively managed beehives. We found the average effective paternity frequency ( m e ) of this population of honey bee queens to be 13.6 ± 6.76, which was not significantly different between colonies that superseded their queen and those that did not. However, colonies that were less genetically diverse (headed by queens with m e ≤ 7.0) were 2.86 times more likely to die by the end of the study when compared to colonies that were more genetically diverse (headed by queens with m e > 7.0). The stark contrast in colony survival based on increased genetic diversity suggests that there are important tangible benefits of increased queen mating number in managed honey bees, although the exact mechanism(s) that govern these benefits have not been fully elucidated.

  2. Investigation of genetic diversity in flixweed ( Descurainia sophia ...

    African Journals Online (AJOL)

    Investigation of genetic diversity in flixweed ( Descurainia sophia ) germplasm from Kerman province using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) molecular markers.

  3. Morphological and molecular genetic diversity of Syrian indigenous ...

    African Journals Online (AJOL)

    Morphological and molecular genetic diversity of Syrian indigenous goat populations. Halima Hassen, Barbara Rischkowsky, Adnan Termanini, Ghassen Jessry, Aynalem Haile, Michael Baum, Samir Lababidi ...

  4. Molecular research on the genetic diversity of Tunisian date palm ...

    African Journals Online (AJOL)

    Molecular research on the genetic diversity of Tunisian date palm ( Phoenix dactylifera L.) using the random amplified microsatellite polymorphism (RAMPO) and amplified fragment length polymorphism (AFLP) methods.

  5. Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

    Directory of Open Access Journals (Sweden)

    Saba Jasim Aljumaili

    2018-01-01

    Full Text Available Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak with 3 released varieties as a control using the 32 simple sequence repeat (SSR markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816 from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

  6. Restoration of coral populations in light of genetic diversity estimates

    Science.gov (United States)

    Shearer, T. L.; Porto, I.; Zubillaga, A. L.

    2009-09-01

    Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using microsatellites. The mean number of alleles per locus across 72 surveyed scleractinian coral populations was 8.27 (±0.75 SE). In addition, population genetic datasets from four species ( Acropora palmata, Montastraea cavernosa, Montastraea faveolata and Pocillopora damicornis) were analyzed to assess the minimum number of donor colonies required to retain specific proportions of the genetic diversity of the population. Rarefaction analysis of the population genetic datasets indicated that using 10 donor colonies randomly sampled from the original population would retain >50% of the allelic diversity, while 35 colonies would retain >90% of the original diversity. In general, scleractinian coral populations are genetically diverse and restoration methods utilizing few clonal genotypes to re-populate a reef will diminish the genetic integrity of the population. Coral restoration strategies using 10-35 randomly selected local donor colonies will retain at least 50-90% of the genetic diversity of the original population.

  7. Genetic Diversity Analysis of Indian Salmon, Eleutheronema tetradactylum from South Asian Countries Based on Mitochondrial COI Gene Sequences

    Directory of Open Access Journals (Sweden)

    Ramakrishnan THIRUMARAISELVI

    2015-12-01

    Full Text Available Eleutheronema tetradactylum is an important commercial fish species exposed to intense exploitation both in Southeast Asian countries and Northern parts of Australia. Research on the population structure of E. tetradactylum in these coastal waters is substantial in order to ensure sustainable use and appropriate resource management. In this study, genetic variation, diversity and population structure of E. tetradactylum among four FAO fishing areas, along South Asian countries, were evaluated using cytochrome c oxidase subunit I (COI gene. Totally 30 sequences of COI gene were collected from four FAO fishing areas. Among these 30 individuals, 18 distinct haplotypes were defined. High levels of haplotype diversity (hd = 0.952 ± 0.096 and nucleotide diversity (π = 0.01536 ± 0.00312 were observed in the population within the Bay of Bengal. No haplotype and nucleotide diversity were observed in South China Sea population. Hierarchical analysis of molecular variance (AMOVA indicated that 0.81% of the genetic variation occurred within the populations, while 7.09% variation occurred among populations. Significant genealogical branches were recognized in North Australian populations (one clade, South China Sea populations (one clade, Arabian Sea and Bay of Bengal populations (one clade on the neighbor-joining tree. These results suggested that E. tetradactylum populations in FAO fishing areas 51, 57 and 61 have developed different genetic structures. Tests of neutral evolution and mismatch distribution suggest that a population growth of E. tetradactylum may take place in these fishing areas.

  8. Genetic diversity of table grape based on morphoagronomic traits Diversidade genética de acessos de uvas de mesa baseada em caracteres morfoagronômicos

    Directory of Open Access Journals (Sweden)

    Patrícia Coelho de Souza Leão

    2011-02-01

    Full Text Available The conservation and characterization of grape (Vitis spp genetic resources in germplasm banks have been the basis of its use in breeding programs that result in development of new cultivars. There are at least 10,000 grape cultivars kept in germplasm collection. The genetic diversity in 136 table grape accessions from the state of Bahia, Brazil, was evaluated. Continuous and discrete morphoagronomic traits were assessed. The clustering analysis by the Tocher otimization method resulted in 30 clusters (considering continuous morphoagronomic traits, and 9 clusters (taking into consideration multicategorical traits. There was no agreement between clusters obtained by both, continuous or discrete phenotypic descriptors, independent of the cluster method analysis used. A satisfactory genetic variability among the table grape accessions was observed.A conservação e caracterização dos recursos genéticos de videira (Vitis spp. em bancos de germoplasma tem sido a base para a sua utilização nos programas de melhoramento, que resultam no desenvolvimento de novas cultivares, estimando-se a existência de pelo menos 10.000 cultivares de uva mantidos em coleções de germoplasma. Avaliou-se a diversidade genética presente em 136 acessos de uvas de mesa de uma coleção de germoplasma do estado da Bahia, com base em caraterísticas morfoagronômicas de variação contínua e discreta. A análise de agrupamento pelo método de Tocher resultou na formação de 30 grupos utilizando-se descritores morfo-agronômicos de variação contínua e 9 grupos, com base em caracteres multicategóricos. Não houve concordância entre os grupos obtidos pela análise de descritores fenotípicos contínuos e discretos, independente do método de agrupamento utilizado. Detectou-se a existência de variabilidade genética satisfatória entre os acessos de uvas de mesa da coleção.

  9. Population genetic diversity and fitness in multiple environments

    Directory of Open Access Journals (Sweden)

    McGreevy Thomas J

    2010-07-01

    Full Text Available Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater and stressful conditions (diluted seawater. The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation

  10. Evaluation of bamboo genetic diversity using morphological and SRAP analyses.

    Science.gov (United States)

    Zhu, S; Liu, T; Tang, Q; Fu, L; Tang, Sh

    2014-03-01

    Bamboo is an important member of the giant grass subfamily Bambusoideae of Poaceae. In this study, 13 bamboo accessions belonging to 5 different genera were subjected to morphological evaluation and sequence-related amplified polymorphism (SRAP) analysis. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis was used to construct a dendrogram and to estimate the genetic distances among accessions. On the basis of morphological characteristics, the 13 accessions were distinctly classified into 2 major clusters; 3 varieties, PPYX, PGNK, and PLYY were grouped as cluster A, and 10 accessions were categorized under cluster B. Similarity coefficients ranging from 0.23 to 0.96 indicated abundant genetic variation among bamboo varieties. Approximately 38 SRAP primer combinations generated 186 bands, with 150 bands (80.65%) showing polymorphisms among the 13 accessions. Based on SRAP analysis, 13 bamboo accessions were grouped into 3 major clusters. Five species comprised Cluster I (PASL, PLYY, PTSC, SCNK, and BMAK), which belongs to genus Phyllostachys. Cluster II consisted of 5 varieties, PASL, PLYY, PTSC, SCNK, and BMAK; Cluster III included 3 varieties, PGNK, PLSY, and BMRS. Comparison of the results generated by morphological and SRAP analyses showed that the classification based on SRAP markers was more concordant to the taxonomic results of Gamble than that performed using morphological characters, thus suggesting that SRAP analysis is more efficient in evaluating genetic diversity in bamboos compared to morphological analysis. The SRAP technique serves as an alternative method in assessing genetic diversity within bamboo collections.

  11. Genetic diversity and kelp forest vulnerability to climatic stress.

    Science.gov (United States)

    Wernberg, Thomas; Coleman, Melinda A; Bennett, Scott; Thomsen, Mads S; Tuya, Fernando; Kelaher, Brendan P

    2018-01-30

    Genetic diversity confers adaptive capacity to populations under changing conditions but its role in mediating impacts of climate change remains unresolved for most ecosystems. This lack of knowledge is particularly acute for foundation species, where impacts may cascade throughout entire ecosystems. We combined population genetics with eco-physiological and ecological field experiments to explore relationships among latitudinal patterns in genetic diversity, physiology and resilience of a kelp ecosystem to climate stress. A subsequent 'natural experiment' illustrated the possible influence of latitudinal patterns of genetic diversity on ecosystem vulnerability to an extreme climatic perturbation (marine heatwave). There were strong relationships between physiological versatility, ecological resilience and genetic diversity of kelp forests across latitudes, and genetic diversity consistently outperformed other explanatory variables in contributing to the response of kelp forests to the marine heatwave. Population performance and vulnerability to a severe climatic event were thus strongly related to latitudinal patterns in genetic diversity, with the heatwave extirpating forests with low genetic diversity. Where foundation species control ecological structure and function, impacts of climatic stress can cascade through the ecosystem and, consequently, genetic diversity could contribute to ecosystem vulnerability to climate change.

  12. Population structure and genetic diversity of Sinibrama macrops from Ou River and Ling River based on mtDNA D-loop region analysis, China.

    Science.gov (United States)

    Zhao, Liangjie; Chenoweth, Erica L; Liu, Qigen

    2018-03-01

    In order to understand the influence of human activities such as habitat fragmentation on freshwater fish population evolution, we investigated and compared the genetic diversity and phylogeography of Sinibrama macrops populations in the Oujiang River and Ling River. Mitochondrial control region sequences (D-loop region) of 131 specimens from six populations were obtained and analyzed. The diversity of main stream in the Ou River was lower than that in Ling River. Changtan population showed the lowest diversity (H = 0.646 ± 0.077; π = 0.00060 ± 0.00820). Pairwise F ST , gene flow (Nm), and genetic distance (Da) indicated that Longquan and Changtan significantly differentiate from other populations. Nested clade phylogeographical analysis (NCPA) showed some clades and total cladogram experienced isolation by distance. In conclusion, the populations from severely fragmented Ou River have the lower diversity and more intense differentiation than that from the mainstream of Ling River, Changtan population present the lowest diversity and were isolated by the dam construction.

  13. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications.

    Science.gov (United States)

    Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

    2017-01-01

    Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

  14. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications.

    Directory of Open Access Journals (Sweden)

    Christophe Dufresnes

    Full Text Available Cannabis (hemp and marijuana is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs in 1 324 samples selected specifically for fibre (24 hemp varieties and drug (15 marijuana varieties production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

  15. The genetic diversity of wild rescuegrass is associated with ...

    Indian Academy of Sciences (India)

    c Indian Academy of Sciences. ONLINE RESOURCES. The genetic diversity of wild rescuegrass is associated with precipitation levels. ROMINA ... For correspondence. E-mail: nayub@cnia.inta.gov.ar. the analysis of its genetic diversity seem to be essential to conserve this species and to evaluate the agronomic poten-.

  16. Genetic diversity in Kenyan populations of Acacia senegal (L.) willd ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-18

    Jul 18, 2008 ... diversity (Houston and Houston, 1993). So, the conclusion that spatial organization of local populations and the concomitant patterns of gene flow are important determinants of the level of genetic diversity within each population and of a species becoming genetically diffe- rentiated over its range (Yeh, ...

  17. Genetic diversity, taxonomy and legumins implications of seed ...

    African Journals Online (AJOL)

    Conrad Prof

    2013-04-24

    Apr 24, 2013 ... polyacrylamide gel electrophoresis (SDS-PAGE) to estimate protein content diversity and the possible genetic relatedness. 28.3% similarity and 71.7% proteomic polymorphism was scored for the species. The high variability expressed by the lot reflects the genetic diversity amongst Fabaceae population.

  18. Assessment of genetic diversity among sixty bread wheat ( Triticum ...

    African Journals Online (AJOL)

    Assessment of genetic diversity among wheat cultivars is important to ensure that a continuous pool of cultivars with varying desirable traits is maintained. In view of this, a molecular study was conducted to assess the genetic diversity of sixty wheat cultivars using sixty microsatellite markers. Amplified alleles from each ...

  19. Genetic diversity of Pakistani maize genotypes using chromosome ...

    African Journals Online (AJOL)

    For improvement of maize crop presence of genetic diversity in the germplasm is very important. This study was conducted to determine genetic diversity among 17 Pakistani maize genotypes using 10 simple sequence repeat (SSR) primer sets. All the amplification products were in the range of <250-750 bp. To estimate the ...

  20. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

  1. Analysis of genetic diversity and estimation of inbreeding coefficient ...

    African Journals Online (AJOL)

    Analysis of genetic diversity and estimation of inbreeding coefficient within Caspian horse population using microsatellite markers. ... structure and to the assessment of genetic diversity that may be helpful to horse breeders in designing and managing breeding or conservation strategies for the Caspian horse breed.

  2. Genetic diversity and association of ISSR markers with the ...

    African Journals Online (AJOL)

    Tung tree is a useful woody oil plant in the world. In this study, both the genetic diversity and biochemical traits were analyzed in order to improve the breeding methods on tung tree. The mean genetic similarity coefficient (Gs), the mean Nei's gene diversity (h) and the mean Shannon's information index (I) of tung tree were ...

  3. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 ...

  4. Genetic diversity of Myanmar rice and their implementation on ...

    African Journals Online (AJOL)

    Genetic diversity of Myanmar rice and their implementation on management methods. ... The importance of the conservation on on-farm landraces of Oryza sativa and its wild relatives was proposed in order to ensure the genetic resources for further breeding and conserve biological diversity. Key words: Oryza sativa, rice, ...

  5. DNA landmarks for genetic diversity assessment in tea genotypes ...

    African Journals Online (AJOL)

    Tea (Camellia sinensis) is one of the most important non-alcoholic beverages of the world. Natural genetic diversity in tea has been reduced due to continue selection in favor of desirable traits. The present study was conducted to estimate genetic diversity in tea genotypes cultivated in Pakistan using 20 randomly amplified ...

  6. Genetic diversity among natural populations of Ottelia acuminata ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... Genetic diversity among geographically separated populations of Nepenthes mirabilis. Biologia Brat. 61: 295-298. Farès K, Guasmi F, Touil L, Triki T, Ferchichi A (2009). Genetic diversity of pistochio tree using inter-simple sequence repeat markers. ISSR supported by morphological and chemical markers.

  7. Genetic diversity of Escherichia coli isolated from commercial swine ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... The infectious diseases caused by E. coli are very serious. Analysis of E. coli strains genetic diversity is important for epidemiology. The objective of this study was to use REP-PCR and ERIC-PCR for the analysis of genetic diversity among E. coli strains isolated from commercial swine farms in Sichuan ...

  8. Assessment of genetic diversity in Indian rice germplasm (Oryza ...

    Indian Academy of Sciences (India)

    DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-à-vis QTL ...

  9. Genetic diversity in Ethiopian field pea ( Pisum sativum L ...

    African Journals Online (AJOL)

    Field pea is an ancient legume crop grown mainly for food in Ethiopia. Even though, there are over one thousand five hundred field pea collections, only a few studies has been conducted on the magnitude and pattern of genetic diversity at molecular level particularly with SSR markers. In this study, genetic diversity of 142 ...

  10. DNA landmarks for genetic diversity assessment in tea genotypes ...

    African Journals Online (AJOL)

    Bilal

    2011-11-07

    Nov 7, 2011 ... Tea (Camellia sinensis) is one of the most important non-alcoholic beverages of the world. Natural ... present study was conducted to estimate genetic diversity in tea genotypes cultivated in Pakistan using. 20 randomly ..... genetic diversity in Oolong tea germplasms by AFLP fingerprinting. J. Tea Sci.

  11. Study on genetic diversity in Pakistani wheat varieties using simple ...

    African Journals Online (AJOL)

    Common wheat ( Triticum aestivum L.) is a grass species, cultivated world wide. Globally, it is the most important human food grain and ranks second in total production as a cereal crop behind maize. Genetic diversity evaluation of germplasm is the basis of improvement in wheat. In the present study genetic diversity of 10 ...

  12. Genetic diversity analysis of rice cultivars from various origins using ...

    African Journals Online (AJOL)

    Genetic diversity is of paramount importance for the success of any plant breeding program. An experiment was conducted to assess the extent of genetic diversity and similarity of 24 rice cultivars from various origins using 29 simple sequence repeat (SSR) markers. A total of 144 alleles were detected at the 29 SSR primer ...

  13. Phenotypic and molecular evaluation of genetic diversity of rapeseed

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... The genetic diversity and relationships among rapeseed genotypes were evaluated using quantitative analysis ...... Utility of. AFLP markers for the assessment of genetic diversity within Brassica nigra germplasm. Plant Breed. 123: 13-16. Nyende AB (2008). Biotechnology in plant nutrient management for.

  14. Genetic diversity enhances restoration success by augmenting ecosystem services.

    Directory of Open Access Journals (Sweden)

    Laura K Reynolds

    Full Text Available Disturbance and habitat destruction due to human activities is a pervasive problem in near-shore marine ecosystems, and restoration is often used to mitigate losses. A common metric used to evaluate the success of restoration is the return of ecosystem services. Previous research has shown that biodiversity, including genetic diversity, is positively associated with the provision of ecosystem services. We conducted a restoration experiment using sources, techniques, and sites similar to actual large-scale seagrass restoration projects and demonstrated that a small increase in genetic diversity enhanced ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention. In our experiment, plots with elevated genetic diversity had plants that survived longer, increased in density more quickly, and provided more ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention. We used the number of alleles per locus as a measure of genetic diversity, which, unlike clonal diversity used in earlier research, can be applied to any organism. Additionally, unlike previous studies where positive impacts of diversity occurred only after a large disturbance, this study assessed the importance of diversity in response to potential environmental stresses (high temperature, low light along a water-depth gradient. We found a positive impact of diversity along the entire depth gradient. Taken together, these results suggest that ecosystem restoration will significantly benefit from obtaining sources (transplants or seeds with high genetic diversity and from restoration techniques that can maintain that genetic diversity.

  15. Genetic diversity enhances restoration success by augmenting ecosystem services.

    Science.gov (United States)

    Reynolds, Laura K; McGlathery, Karen J; Waycott, Michelle

    2012-01-01

    Disturbance and habitat destruction due to human activities is a pervasive problem in near-shore marine ecosystems, and restoration is often used to mitigate losses. A common metric used to evaluate the success of restoration is the return of ecosystem services. Previous research has shown that biodiversity, including genetic diversity, is positively associated with the provision of ecosystem services. We conducted a restoration experiment using sources, techniques, and sites similar to actual large-scale seagrass restoration projects and demonstrated that a small increase in genetic diversity enhanced ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). In our experiment, plots with elevated genetic diversity had plants that survived longer, increased in density more quickly, and provided more ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). We used the number of alleles per locus as a measure of genetic diversity, which, unlike clonal diversity used in earlier research, can be applied to any organism. Additionally, unlike previous studies where positive impacts of diversity occurred only after a large disturbance, this study assessed the importance of diversity in response to potential environmental stresses (high temperature, low light) along a water-depth gradient. We found a positive impact of diversity along the entire depth gradient. Taken together, these results suggest that ecosystem restoration will significantly benefit from obtaining sources (transplants or seeds) with high genetic diversity and from restoration techniques that can maintain that genetic diversity.

  16. Genetic diversity and phylogenetic analysis of two Tunisian bivalves (Mactridae) Mactra corallina (Linnaeus, 1758) and Eastonia rugosa (Helbling, 1799) based on COI gene sequences.

    Science.gov (United States)

    Chetoui, Imene; Denis, Françoise; Boussaid, Mohamed; Telahigue, Khoula; El Cafsi, M'Hamed

    2016-01-01

    A partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) was used as a genetic marker for a genetic diversity and phylogenetic analysis (DNA barcoding) of two Mactridae species, Mactra corallina and Eastonia rugosa, collected from the Tunisian coast. These Mactridae species could be distinguished by DNA barcoding techniques and they will be considered as monophyletic clades with the Neighbor-Joining (NJ) tree. The genetic structure detected that E. rugosa presents three haplotypes with a high frequency of HER1 (0.89). However, M. corralina shared 14 haplotypes. The haplotypic diversity (H) was equal to 0.205 and 0.954, respectively, for E. rugosa and M. corallina. While the nucleotide diversity (π) was higher for M. corallina (π=0.0818), the mismatch distribution showed a unimodal curve for E. rugosa (a recent sudden demographic expansion) and a multimodal distribution for M. corallina (size stability). Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  17. Fatty Acid Diversity is Not Associated with Neutral Genetic Diversity in Native Populations of the Biodiesel Plant Jatropha curcas L.

    Science.gov (United States)

    Martínez-Díaz, Yesenia; González-Rodríguez, Antonio; Rico-Ponce, Héctor Rómulo; Rocha-Ramírez, Víctor; Ovando-Medina, Isidro; Espinosa-García, Francisco J

    2017-01-01

    Jatropha curcas L. (Euphorbiaceae) is a shrub native to Mexico and Central America, which produces seeds with a high oil content that can be converted to biodiesel. The genetic diversity of this plant has been widely studied, but it is not known whether the diversity of the seed oil chemical composition correlates with neutral genetic diversity. The total seed oil content, the diversity of profiles of fatty acids and phorbol esters were quantified, also, the genetic diversity obtained from simple sequence repeats was analyzed in native populations of J. curcas in Mexico. Using the fatty acids profiles, a discriminant analysis recognized three groups of individuals according to geographical origin. Bayesian assignment analysis revealed two genetic groups, while the genetic structure of the populations could not be explained by isolation-by-distance. Genetic and fatty acid profile data were not correlated based on Mantel test. Also, phorbol ester content and genetic diversity were not associated. Multiple linear regression analysis showed that total oil content was associated with altitude and seasonality of temperature. The content of unsaturated fatty acids was associated with altitude. Therefore, the cultivation planning of J. curcas should take into account chemical variation related to environmental factors. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  18. Genetic Diversity of Indigofera tinctoria L. in Java and Madura Islands as Natural Batik Dye based on Intersimple Sequence Repeat Markers

    Directory of Open Access Journals (Sweden)

    Muhammad Rifqi Hariri

    2017-09-01

    Full Text Available Indigo leaves (Indigofera tinctoria L. are utilized as a source of batik dye in Java and Madura islands, Indonesia. Batik makers from the islands collect indigo leaves from wild plants. Continuous collection of wild plants from their natural habitat may decrease their diversity. The present research was conducted to analyze the genetic diversity and population structure of I. tinctoria L. from Java and Madura. 55 indigo accessions were collected from 10 locations in Java and Madura. The indigo DNA was extracted and amplified using 15 ISSR primers. A total of 123 bands showed 50-90% polymorphic loci. PCA and UPGMA were used to analyze the data. All indigo accessions were clustered into 4 groups at a 60% similarity coefficient: a group consisting of Madura accessions, a group consisting of East Java accessions, a group consisting of Central Java accessions, and a group consisting of West Java accessions. Accessions collected from the same or adjacent populations tended to show similar ISSR characteristics. The genetic diversity of indigo in Java and Madura islands is relatively high (%P = 68.3, but the diversity residing within each population is lower (37% than that between populations (63%.

  19. Beauveria bassiana: Quercetinase production and genetic diversity

    Science.gov (United States)

    Eula Maria de M. B., Costa; Fabiana Cristina, Pimenta; Christian, Luz; Valéria de, Oliveira; Marília, Oliveira; Elda, Bueno; Silvana, Petrofeza

    2011-01-01

    Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detected by random amplified polymorphic DNA (RAPD) analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP) did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase. PMID:24031599

  20. Genetic diversity and trait genomic prediction in a pea diversity panel.

    Science.gov (United States)

    Burstin, Judith; Salloignon, Pauline; Chabert-Martinello, Marianne; Magnin-Robert, Jean-Bernard; Siol, Mathieu; Jacquin, Françoise; Chauveau, Aurélie; Pont, Caroline; Aubert, Grégoire; Delaitre, Catherine; Truntzer, Caroline; Duc, Gérard

    2015-02-21

    Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being

  1. The genetic diversity of strawberry (Fragaria ananassa Duch. hybrids based on ISSR markers - doi: 10.4025/actasciagron.v35i4.16737

    Directory of Open Access Journals (Sweden)

    Claudinéia Ferreira Nunes

    2013-05-01

    Full Text Available The strawberry is an important agricultural crop in Brazil. However, most of the commercial genotypes currently in cultivation in Brazil were developed in other countries with environmental adaptations often inadequate for the regional conditions. In this work, inter-simple sequence repeat markers were used to determine the genetic variability and the loci segregation profiles of 84 strawberry hybrids obtained from a genetic breeding program at the ‘Empresa de Pesquisa Agropecuária de Minas Gerais.’ The hybrids were produced from crosses involving the following progenitors: ‘Toyonoka’ x ‘Sweet Charlie’, ‘Camino Real’ x ‘Sweet Charlie’, ‘Oso Grande’ x ‘Sweet Charlie’, ‘Oso Grande’ x ‘Toyonoka’, ‘Dover’ x ‘Oso Grande’, and ‘Camino Real’ x ‘Toyonoka’. Fourteen genotypes were randomly sampled for each hybrid combination and evaluated. The results showed that the genetic profiles of the hybrids from each test cross were very diverse, most likely due to the high heterozygosity of the genome of each progenitor involved, which might indicate the presence of adequate genetic diversity among the hybrids to allow for the selection of new cultivars with agronomic traits that are more suitable to environmental conditions in Brazil.

  2. Genetic diversity of Sclerocarya birrea subspecies birrea ...

    African Journals Online (AJOL)

    Yomi

    2012-01-03

    Jan 3, 2012 ... population. Shannon's index was also estimated for the whole sample considered as a single population. To analyse genetic structure, genetic distances were constructed using the Nei's original measures of genetic identity and genetic distance (Nei, 1972). The degree of differentiation among popu-.

  3. Genetic diversity and kelp forest vulnerability to climatic stress

    OpenAIRE

    Wernberg, Thomas; Coleman, Melinda A.; Bennett, Scott; Thomsen, Mads S.; Tuya, Fernando; Kelaher, Brendan P.

    2018-01-01

    Genetic diversity confers adaptive capacity to populations under changing conditions but its role in mediating impacts of climate change remains unresolved for most ecosystems. This lack of knowledge is particularly acute for foundation species, where impacts may cascade throughout entire ecosystems. We combined population genetics with eco-physiological and ecological field experiments to explore relationships among latitudinal patterns in genetic diversity, physiology and resilience of a ke...

  4. Genetic diversity of faba bean ( Vicia faba L.) populations revealed ...

    African Journals Online (AJOL)

    Shannon indexes ranges from 0.166 to 0.248 with an average of 0.207. The genetic diversity within population of 0.743 was clearly higher than that of among population genetic diversity (Dst = 0.138), indicating an out-crossing predominance in the studied populations. The Dst value showed that 15.6% of the total genetic ...

  5. Assessment of the genetic diversity of Kenyan coconut germplasm ...

    African Journals Online (AJOL)

    Genetic diversity and relationship among 48 coconut individuals (Cocos nucifera L.) collections from the Coastal lowland of Kenya were analyzed using 15 simple sequence repeat (SSR) primer pairs. Diversity parameters were calculated using Popgene Software version 1.31. The gene diversity values ranged from 0.0408 ...

  6. The loss of genetic diversity in the Chinese paddlefish (Psephurus ...

    Indian Academy of Sciences (India)

    Unknown

    agement strategies for species conservation. Genetic diversity surveys in endangered populations typically determine the variation currently maintained in ... (Fang et al. 2002a, 2003), and genetic differentiation of populations (Wan et al. 2003b) of endangered animals. Besides a reliable genetic marker, detecting the loss of.

  7. Assessment of genetic diversity in sorghum accessions using ...

    African Journals Online (AJOL)

    Genetic polymorphism present among sorghum accessions was low, as evidenced by the high level of similarity in the AFLP marker profiles of different sorghum accessions. Pair-wise genetic similarity coefficients ranged from 0.87 to 0.99, with an average of 0.92. This indicates low levels of genetic diversity among tested ...

  8. Assessment of the genetic diversity in five generations of a ...

    African Journals Online (AJOL)

    SERVER

    time, and genetic similarity could reach closer to 100% at 18-19 generation of this line. Key words: Litopenaeus vannamei, genetic diversity, genetic drift, ... of exotic pathogens (Batalha et al., 2002). Apart from the remarkable development of shrimp culture in ..... distance among the stocks (Table 4). y = 0.2948Ln(x) + 0.1385.

  9. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    High genetic diversity was observed among the landraces for both marker systems. STRUCTURE analysis revealed 4 clusters of genetically differentiated groups of landraces. Cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance between landraces increasing ...

  10. Genetic diversity in Cucurbita pepo landraces from northern ...

    African Journals Online (AJOL)

    The dendrogram mainly grouped the populations according to their mature fruit colour, and then according to their geographical origin. All genetic parameters indicated that there was plentiful genetic diversity in C. pepo landraces of northern KwaZulu-Natal, South Africa. Key words: Cucurbita pepo landraces, genetic ...

  11. Genetic diversity of four protected indigenous chicken breeds in ...

    African Journals Online (AJOL)

    The genetic diversity of four protected indigenous chicken breeds was evaluated with 25 microsatellite markers. Polymorphism information content (PIC), heterozygosity with the estimator of genetic differentiation FST and Nei's genetic distance were evaluated. The results showed that these four protected local chicken ...

  12. Contrasting genetic diversity among Oryza longistaminata (A. Chev ...

    African Journals Online (AJOL)

    Molecular markers have been used extensively in studying genetic diversity, genetic relationships and germplasm management. However, the understanding of between and within population genetic variation and how it is partitioned on the basis of geographic origin is crucial as this helps to improve sampling efficiency.

  13. Genetic diversity analysis of the medicinal herb Plantago ovata ...

    African Journals Online (AJOL)

    Hierarchical cluster analysis using SPSS method showed genetic variation amongst genotypes dividing them into three major clusters comprising 10, seven and one genotypes, respectively. The result of present study indicates that RAPD analysis has determined the genetic relationships and estimated the genetic diversity ...

  14. Genetic diversity among natural populations of Ottelia acuminata ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... ISSR is a dominant molecular marker revealed in mass, and has ... used reliably as molecular markers in genetic studies for .... Genetic diversity among geographically separated populations of Nepenthes mirabilis. Biologia Brat. 61: 295-298. Farès K, Guasmi F, Touil L, Triki T, Ferchichi A (2009). Genetic.

  15. Genetic diversity among some blackberry cultivars and their ...

    African Journals Online (AJOL)

    In this study, genetic diversity among these blackberry cultivars and their genetic relationship with Boysenberry and raspberry were analyzed using AFLP markers. Our results indicated that Blackberry cultivars from North America had narrow genetic background which can pose a problem for future breeding programs.

  16. Multiple paternity does not depend on male genetic diversity.

    Science.gov (United States)

    Thonhauser, Kerstin E; Raveh, Shirley; Penn, Dustin J

    2014-07-01

    Polyandry is common in many species and it has been suggested that females engage in multiple mating to increase the genetic diversity of their offspring (genetic diversity hypothesis). Multiple paternity occurs in 30% of litters in wild populations of house mice, Mus musculus musculus , and multiple-sired litters are genetically more diverse than single-sired ones. Here, we aimed to test whether female house mice produce multiple-sired litters when they have the opportunity to produce genetically diverse litters. We assessed the rates of multiple paternity when females could choose to mate with two males that were genetically dissimilar to each other (i.e. nonsiblings and MHC dissimilar) compared with when females could choose to mate with two males that were genetically similar to each other (i.e. siblings and shared MHC alleles). Multiple mating may depend upon a female's own condition, and, therefore, we also tested whether inbred (from full-sibling matings) females were more likely to produce multiple-sired progeny than outbred controls. Overall we found that 29% of litters had multiple sires, but we found no evidence that females were more likely to produce multiple-sired litters when they had the opportunity to mate with genetically dissimilar males compared with controls, regardless of whether females were inbred or outbred. Thus, our findings do not support the idea that female mice increase multiple paternity when they have the opportunity to increase the genetic diversity of their offspring, as expected from the genetic diversity hypothesis.

  17. Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea

    Directory of Open Access Journals (Sweden)

    Dong Hwan Lee

    2014-06-01

    Full Text Available The plant pathogenic bacterial genus Pectobacteirum consists of heterogeneous strains. The P. carotovorum species is a complex strain showing divergent characteristics, and a new subspecies named P. carotovorum subsp. brasiliensis has been identified recently. In this paper, we re-identified the P. carotovorum subsp. brasiliensis isolates from those classified under the subspecies carotovorum and newly isolated P. carotovorum subsp. brasiliensis strains. All isolates were able to produce plant cell-wall degrading enzymes such as pectate lyase, polygalacturonase, cellulase and protease. We used genetic and biochemical methods to examine the diversity of P. carotovorum subsp. brasiliensis isolates, and found genetic diversity within the brasiliensis subsp. isolates in Korea. The restriction fragment length polymorphism analysis based on the recA gene revealed a unique pattern for the brasiliensis subspecies. The Korean brasiliensis subsp. isolates were divided into four clades based on pulsed-field gel electrophoresis. However, correlations between clades and isolated hosts or year could not be found, suggesting that diverse brasiliensis subsp. isolates existed.

  18. Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea.

    Science.gov (United States)

    Lee, Dong Hwan; Kim, Jin-Beom; Lim, Jeong-A; Han, Sang-Wook; Heu, Sunggi

    2014-06-01

    The plant pathogenic bacterial genus Pectobacteirum consists of heterogeneous strains. The P. carotovorum species is a complex strain showing divergent characteristics, and a new subspecies named P. carotovorum subsp. brasiliensis has been identified recently. In this paper, we re-identified the P. carotovorum subsp. brasiliensis isolates from those classified under the subspecies carotovorum and newly isolated P. carotovorum subsp. brasiliensis strains. All isolates were able to produce plant cell-wall degrading enzymes such as pectate lyase, polygalacturonase, cellulase and protease. We used genetic and biochemical methods to examine the diversity of P. carotovorum subsp. brasiliensis isolates, and found genetic diversity within the brasiliensis subsp. isolates in Korea. The restriction fragment length polymorphism analysis based on the recA gene revealed a unique pattern for the brasiliensis subspecies. The Korean brasiliensis subsp. isolates were divided into four clades based on pulsed-field gel electrophoresis. However, correlations between clades and isolated hosts or year could not be found, suggesting that diverse brasiliensis subsp. isolates existed.

  19. Assessment of genetic diversity in rice [Oryza sativa L.] germplasm based on agro-morphology traits and zinc-iron content for crop improvement.

    Science.gov (United States)

    Roy, Subhas Chandra; Sharma, B D

    2014-04-01

    Genetic resources of landraces (84 cultivars) were collected from various agro-ecological regions of West Bengal and adjoining areas and characterized based on qualitative and quantitative agro-morphological descriptors along with zinc (Zn) and iron (Fe) content. The DUS protocol was employed to study 16 agro-morphological passport data such as: vegetative data (anthocyanin pigmentation, plant habit), reproductive data (flag leaf attitude, stigma colour, panicle attitude), including eight grain quality traits: grain length, grain width, 1000 grains weight, kernel length, kernel breadth etc. Highest seed weight was found in cultivar Khechri (32.04 g/1000 seeds), collected from Sundarban and least seed weight was 9.6 g/1000seeds in Katharibhog. Maturity duration was found very short (2 cm) in one cultivar Jungli (2.3 cm). Seeds per panicle were 180 in Chinisakkar (medium range), 177 in Dudheswar, and 151 in Ladua. Flag leaf was found in erect condition in late observation in Dudheswar, Enda and Ghiosh. Seventeen cultivars were grouped in the aromatic rice category out of total 84 local landraces. Twenty-one cultivars were with awn, whose length ranges from 1.6 mm (Anandi) to 22.5 mm (Tulaipanji). Kernel colour varies from red, yellowish, brownish, creamy white to white. Kernel length varies from 4 mm to 8 mm and breadth 1.90 mm to 3 mm. Kernel length/breadth ration varied from 1.6 to 3.9. Highest ratio of L/B was found in Pusa Basmati 1(3.9) and lowest in Dudhey (1.6). Elongation ration was highest in Kalokure (2.07) and lowest in Phoolpakri (0.62). Nutritional values of mineral contents of iron (Fe) and zinc (Zn) were estimated in all cultivars by Atomic Absorption Spectrophotometic method. Iron concentration varies from 0.25 μg/g to 34.8 μg/g and zinc from 0.85 μg/g to 195.3 μg/g in the landraces. Highest iron containing rice was Swetonunia with 34.8 μg/g and highest amount of Zn was found in Nepali Kalam which was 195.3 μg/g. Anaerobic

  20. Intra- and interspecific genetic diversity of New Zealand hairworms (Nematomorpha).

    Science.gov (United States)

    Tobias, Zachary J C; Yadav, Arun K; Schmidt-Rhaesa, Andreas; Poulin, Robert

    2017-07-01

    Hairworms (Nematomorpha) are a little-known group of parasites, and despite having been represented in the taxonomic literature for over a century, the implementation of molecular genetics in studies of hairworm ecology and evolution lags behind that of other parasitic taxa. In this study, we characterize the genetic diversity of the New Zealand nematomorph fauna and test for genetic structure within the most widespread species found. We provide new mitochondrial and nuclear ribosomal sequence data for three previously described species from New Zealand: Gordius paranensis, Parachordodes diblastus and Euchordodes nigromaculatus. We also present genetic data on a previously reported but undescribed Gordius sp., as well as data from specimens of a new Gordionus sp., a genus new for New Zealand. Phylogenetic analyses of CO1 and nuclear rDNA regions correspond with morphological classification based on scanning electron microscopy, and demonstrate paraphyly of the genus Gordionus and the potential for cryptic species within G. paranensis. Population-level analyses of E. nigromaculatus showed no genetic differentiation among sampling locations across the study area, in contrast to previously observed patterns in known and likely definitive hosts. Taken together, this raises the possibility that factors such as definitive host specificity, intermediate host movement, and passive dispersal of eggs and larvae may influence host-parasite population co-structure in hairworms.

  1. Hidden genetic diversity in the green alga Spirogyra (Zygnematophyceae, Streptophyta

    Directory of Open Access Journals (Sweden)

    Chen Charlotte

    2012-06-01

    Full Text Available Abstract Background The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate. Results We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclear ribosomal DNA (SSU rDNA strands of different origin. The resulting SSU rDNA sequences were used for phylogenetic analyses using complex evolutionary models (posterior probability, maximum likelihood, neighbor joining, and maximum parsimony methods. The sequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53 individual clones, but our results still support monophyly of the genus. Our data set did not contain a single slow-evolving taxon that would have been placed on a shorter branch compared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a secondary loss of the 1506 group I intron, which formed a long-branched group within the genus. The phylogenetic relationship to the genus Spirotaenia was not resolved satisfactorily. The genetic distance within the genus Spirogyra exceeded the distances measured within any other genus of the remaining Zygnemataceae included in this study. Conclusion Overall, we define eight distinct clades of Spirogyra, one of them including the genus Sirogonium. A large number of non-homoplasious synapomorphies (NHS; 114 NHS in total was found for Spirogyra (41 NHS and for each clade (totaling 73 NHS. This emphasizes the high genetic diversity of this genus and the distance to the remaining Zygnematophyceae.

  2. Genetic diversity of canine olfactory receptors

    Directory of Open Access Journals (Sweden)

    Hitte Christophe

    2009-01-01

    Full Text Available Abstract Background Evolution has resulted in large repertoires of olfactory receptor (OR genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations. Results We sequenced 109 OR genes considered representative of the whole OR canine repertoire, which consists of more than 800 genes, in a cohort of 48 dogs of six different breeds. SNP frequency showed the overall level of polymorphism to be high. However, the distribution of SNP was highly heterogeneous among OR genes. More than 50% of OR genes were found to harbour a large number of SNP, whereas the rest were devoid of SNP or only slightly polymorphic. Heterogeneity was also observed across breeds, with 25% of the SNP breed-specific. Linkage disequilibrium within OR genes and OR clusters suggested a gene conversion process, consistent with a mean level of polymorphism higher than that observed for introns and intergenic sequences. A large proportion (47% of SNP induced amino-acid changes and the Ka/Ks ratio calculated for all alleles with a complete ORF indicated a low selective constraint with respect to the high level of redundancy of the olfactory combinatory code and an ongoing pseudogenisation process, which affects dog breeds differently. Conclusion Our demonstration of a high overall level of polymorphism, likely to modify the ligand-binding capacity of receptors distributed differently within the six breeds tested, is the first step towards understanding why Labrador Retrievers and German Shepherd Dogs have a much greater potential for use as sniffer dogs than Pekingese dogs or Greyhounds. Furthermore, the heterogeneity in OR polymorphism observed raises questions as to why, in a context in which most OR genes are highly polymorphic, a subset of

  3. Does genetic diversity hinder parasite evolution in social insect colonies?

    DEFF Research Database (Denmark)

    Hughes, William Owen Hamar; Boomsma, Jacobus Jan

    2006-01-01

    Polyandry is often difficult to explain because benefits of the behaviour have proved elusive. In social insects, polyandry increases the genetic diversity of workers within a colony and this has been suggested to improve the resistance of the colony to disease. Here we examine the possible impact...... of host genetic diversity on parasite evolution by carrying out serial passages of a virulent fungal pathogen through leaf-cutting ant workers of known genotypes. Parasite virulence increased over the nine-generation span of the experiment while spore production decreased. The effect of host relatedness...... upon virulence appeared limited. However, parasites cycled through more genetically diverse hosts were more likely to go extinct during the experiment and parasites cycled through more genetically similar hosts had greater spore production. These results indicate that host genetic diversity may indeed...

  4. Genetic diversity of Histoplasma and Sporothrix complexes based on sequences of their ITS1-5.8S-ITS2 regions from the BOLD System.

    Science.gov (United States)

    Estrada-Bárcenas, Daniel Alfonso; Vite-Garín, Tania; Navarro-Barranco, Hortensia; de la Torre-Arciniega, Raúl; Pérez-Mejía, Amelia; Rodríguez-Arellanes, Gabriela; Ramirez, Jose Antonio; Humberto Sahaza, Jorge; Taylor, Maria Lucia; Toriello, Conchita

    2014-01-01

    High sensitivity and specificity of molecular biology techniques have proven usefulness for the detection, identification and typing of different pathogens. The ITS (Internal Transcribed Spacer) regions of the ribosomal DNA are highly conserved non-coding regions, and have been widely used in different studies including the determination of the genetic diversity of human fungal pathogens. This article wants to contribute to the understanding of the intra- and interspecific genetic diversity of isolates of the Histoplasma capsulatum and Sporothrix schenckii species complexes by an analysis of the available sequences of the ITS regions from different sequence databases. ITS1-5.8S-ITS2 sequences of each fungus, either deposited in GenBank, or from our research groups (registered in the Fungi Barcode of Life Database), were analyzed using the maximum likelihood (ML) method. ML analysis of the ITS sequences discriminated isolates from distant geographic origins and particular wild hosts, depending on the fungal species analyzed. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  5. Genetic diversity and structure found in samples of Eritrean bread wheat

    DEFF Research Database (Denmark)

    Desta, Zeratsion Abera; Orabi, Jihad; Jahoor, Ahmed

    2014-01-01

    Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple...... sequence repeat markers. A total of 539 alleles were detected. The allele number per locus ranged from 2 to 21, with a mean allele number of 9.2. The average genetic diversity index was 0.66, with values ranging from 0.01 to 0.89. Comparing the three genomes of wheat, the B genome had the highest genetic...... diversity (0.66) and the D genome the lowest diversity (0.61). A STRUCTURE analysis based on the Bayesian model-based cluster analysis followed by a graphical representation of the distances by non-parametric multidimensional scaling revealed a distinct partition of the Eritrean wheat accessions into two...

  6. GENETIC DIVERSITY, PARENTAGE VERIFICATION AND GENETIC BOTTLENECKS EVALUATION IN IRANIAN TURKMEN HORSE BREED.

    Science.gov (United States)

    Rahimi-Mianji, G; Nejati-Javaremi, A; Farhadi, A

    2015-09-01

    The present study was undertaken to genetically evaluate Turkmen horses for genetic diversity and to evaluate whether they have experienced any recent genetic bottlenecks. A total of 565 individuals from Turkmen horses were characterized for within breed diversity using 12 microsatellite markers. The estimated mean allelic diversity was (9.42 ± 1.78) per locus, with a total of 131 alleles in genotyped samples. A high level of genetic variability within this breed was observed in terms of high values of effective number of alleles (4.70 ± 1.36), observed heterozygosity (0.757 ± 0.19), expected Nei's heterozygosity (0.765 ± 0.13), and polymorphism information content (0.776 ± 0.17). The estimated cumulative probability of exclusion of wrongly named parents (PE) was high, with an average value of 99.96% that indicates the effectiveness of applied markers in resolving of parentage typing in Turkmen horse population. The paternity testing results did not show any misidentification and all selected animals were qualified based on genotypic information using a likelihood-based method. Low values of Wright's fixation index, F(IS) (0.012) indicated low levels of inbreeding. A significant heterozygote excess on the basis of different models, as revealed from Sign and Wilcoxon sign rank test suggested that Turkmen horse population is not in mutation-drift equilibrium. But, the Mode-shift indicator test showed a normal 'L' shaped distribution for allelic class and proportion of alleles, thus indicating the absence of bottleneck events in the recent past history of this breed. Further research work should be carrying out to clarify the cause of discrepancy observed forbottleneck results in this breed. In conclusion, despite unplanned breeding in Turkmen horse population, this breed still has sufficient genetic variability and could provide a valuable source of genetic material that may use for meeting the demands of future breeding programs.

  7. Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger

    Science.gov (United States)

    Menzies, Brandon R.; Renfree, Marilyn B.; Heider, Thomas; Mayer, Frieder; Hildebrandt, Thomas B.; Pask, Andrew J.

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago. PMID:22530022

  8. Genetic diversity of hepatitis C virus in Ethiopia.

    Science.gov (United States)

    Hundie, Gadissa Bedada; Raj, V Stalin; GebreMichael, Daniel; Pas, Suzan D; Haagmans, Bart L

    2017-01-01

    Hepatitis C virus (HCV) is genetically highly divergent and classified in seven major genotypes and approximately hundred subtypes. These genotypes/subtypes have different geographic distribution and response to antiviral therapy. In Ethiopia, however, little is known about their molecular epidemiology and genetic diversity. The aim of this study was to investigate the distribution and genetic diversity of HCV genotypes/subtypes in Ethiopia, using 49 HCV RNA positive samples. HCV genotypes and subtypes were determined based on the sequences of the core and the nonstructural protein 5B (NS5B) genomic regions. Phylogenetic analysis revealed that the predominant was genotype 4 (77.6%) followed by 2 (12.2%), 1 (8.2%), and 5 (2.0%). Seven subtypes were identified (1b, 1c, 2c, 4d, 4l, 4r and 4v), with 4d (34.7%), 4r (34.7%) and 2c (12.2%) as the most frequent subtypes. Consistent with the presence of these subtypes was the identification of a potential recombinant virus. One strain was typed as genotype 2c in the NS5B region sequence and genotype 4d in the core region. In conclusion, genotype 4 HCV viruses, subtypes 4d and 4r, are most prevalent in Ethiopia. This genotype is considered to be difficult to treat, thus, our finding has an important impact on the development of treatment strategies and patient management in Ethiopia.

  9. The investigation of genetic diversity and evolution of Daweishan Mini chicken based on the complete mitochondrial (mt)DNA D-loop region sequence.

    Science.gov (United States)

    Jia, Xiao-Xu; Tang, Xiu-Jun; Lu, Jun-Xian; Fan, Yan-Feng; Chen, Da-Wei; Tang, Meng-Jun; Gu, Rong; Gao, Yu-Shi

    2016-07-01

    This study evaluated the genetic diversity and origin of Daweishan Mini chickens using mtDNA sequence polymorphism. Blood samples from 30 Daweishan Mini chickens were collected. The complete D-loop was PCR amplified, sequenced and compared with the DNA data of five Red Junglefowl (Gallus gallus) subspecies. Eighteen variable sites that defined six haplotypes were observed. The six haplotypes were clustered into four clades (A, B, D and E), of which clade A and B were dominant. Clades Aand B were clustered with G.g. spadiceus, indicating these two clades may have originated from this subspecies. These results show there is diversity in the middle of the mtDNA D-loop, and indicate there are multiple maternal origins for Daweishan Mini chickens. It appears that G.g. spadiceus contributed more to the evolution of the Daweishan Mini chickens breed than the other four subspecies tested here.

  10. Low genetic diversity and high genetic differentiation among ...

    African Journals Online (AJOL)

    Possible reasons for the high population genetic differentiation and the low levels of genetic variation within populations are inbreeding and genetic drift. Of a total of 26 known populations, 14 are now extinct, five during the course of this study. Action to prevent complete extinction of the species is therefore urgent.

  11. Understanding diversity in coral-algal symbiosis: a cluster-based approach to interpreting fine-scale genetic variation in the genus Symbiodinium

    Science.gov (United States)

    Correa, A. M. S.; Baker, A. C.

    2009-03-01

    Reef corals associate with an extraordinary diversity of dinoflagellate endosymbionts (genus Symbiodinium), and this diversity has become critical to understanding how corals respond to environmental changes. A popular molecular marker for Symbiodinium diversity, the Internal Transcribed Spacer-2 (ITS-2) region of ribosomal DNA, has revealed hundreds of distinct variants that are generally interpreted as representing different species, even though many have not been systematically tested for functional or ecological differentiation. Many of these variants are only minimally divergent from one another (1 bp or less), and others occupy basal nodes of traditional species phylogenies (“living ancestors”), indicating that some Symbiodinium ITS-2 diversity may represent intraspecific sequence variation. This hypothesis was tested for Symbiodinium clades A- D (the dominant symbionts of reef corals) through the construction of statistical parsimony networks of ITS-2 sequence diversity, and identification of clusters of closely related sequences within these networks. Initial assessments indicated that ecological differentiation exists between, but not within, these clusters. This approach, although imperfect in its ability to identify species boundaries in all cases, nevertheless dramatically reduces “species” diversity in Symbiodinium (from ~175 to 35). This testable alternative hypothesis indicates that, in Symbiodinium, “species” consist of clusters of closely related ITS-2 sequences diverging from ancestral variants that are typically ecologically dominant. A cluster-based view of Symbiodinium ITS-2 diversity improves our ability to: (1) construct well-supported symbiont phylogenies; (2) establish functional niches for symbiont species; and (3) understand flexibility and specificity within coral-algal symbioses. This cluster-based approach can ultimately be integrated with emerging population-level datasets (microsatellites and microsatellite flanking

  12. Genetic diversity of Escherichia coli isolated from commercial swine ...

    African Journals Online (AJOL)

    PCR) for the analysis of genetic diversity among Escherichia coli strains isolated from commercial swine farms in Sichuan province of China. Thirty four strains of E. coli were selected by selective medium and conventional biochemical test from ...

  13. Isolation, genetic diversity and identification of a virulent pathogen of ...

    African Journals Online (AJOL)

    Isolation, genetic diversity and identification of a virulent pathogen of eriophyid mite, Aceria guerreronis (Acari: Eriophyidae) by DNA marker in Karnataka, India. Basavaraj Kalmath, B Mallik, S Onkarappa, R Girish, N Srinivasa ...

  14. Genetic diversity analysis of various red spider mite- resistant ...

    African Journals Online (AJOL)

    User

    2011-05-02

    resistant cotton (Gossypium hirsutum) cultivars that are applied in cultivar identification and breeder's right protection of cottons. The genomic DNA was used as template and random primers were used to analyze the genetic diversity.

  15. Genetic diversity assessment of farmers' and improved potato ...

    African Journals Online (AJOL)

    Genetic diversity assessment of farmers' and improved potato (Solanum tuberosum) cultivars from Eritrea using simple sequence repeat (SSR) markers. Biniam Mesfin Ghebreslassie, S. Mwangi Githiri, Tadesse Mehari, Remmy W. Kasili, Marc Ghislain, Eric Magembe ...

  16. Assessment of genetic diversity among sugarcane cultivars using ...

    African Journals Online (AJOL)

    Assessment of genetic diversity among sugarcane cultivars using novel microsatellite markers. Manish Dev Sharma, Upma Dobhal, Prashant Singh, Shailender Kumar, AK Gaur, SP Singh, AS Jeena, Eapon P Koshy, S Kumar ...

  17. Genetic diversity analysis of various red spider miteresistant upland ...

    African Journals Online (AJOL)

    resistant cotton (Gossypium hirsutum) cultivars that are applied in cultivar identification and breeder's right protection of cottons. The genomic DNA was used as template and random primers were used to analyze the genetic diversity of 21 accessions ...

  18. (AFLP) analysis of genetic diversity and relationship of Chinese ...

    African Journals Online (AJOL)

    Administrator

    2011-05-30

    May 30, 2011 ... and 25 cultivars that originated from China with fluorescent amplified fragment length polymorphism molecular markers were ... Key words: Rosa rugosa, genetic diversity and relationship, amplified fragment length polymorphism. INTRODUCTION ... northern Japan (Ohwi, 1965), the Korean Peninsula.

  19. Genetic diversity and molecular characterization of physic nut ...

    African Journals Online (AJOL)

    ajl

    2013-02-27

    specific genetic ... diversity studies, molecular markers have been applied to identify and to select genotypes with ..... Biologia floral e polinização artificial de pinhão-manso no norte de. Minas Gerais. Pesq. Agropec. Bras.

  20. Distribution and genetic diversity of the terrestrial slugs Arion lusitanicus Mabille, 1868 and Arion rufus (Linnaeus, 1758) in Poland based on mitochondrial DNA.

    Science.gov (United States)

    Soroka, Marianna; Kozłowski, Jan; Wiktor, Andrzej; Kałuski, Tomasz

    2009-01-01

    The slugs Arion lusitanicus and Arion rufus inhabit ecologically degraded areas and are serious vegetation pests. In recent years, new localities of these species have been found in various parts of Poland. Here we study the morphology of 90 specimens from 9 populations of slugs. The morphology of the genital system allowed for the identification of 60 A. lusitanicus specimens from 6 populations and 30 A. rufus individuals from another 3 localities. In order to describe their genetic diversity at the level of the individual, population, and species, we compared sequences of the mitochondrial cytochrome oxidase subunit I (cox1) gene. The morphological analysis revealed that each of the studied populations comprised a single species, which was also confirmed by the molecular assay. We obtained 674-bp sequences of the cox1 gene for each species that showed a total of eight haplotypes. The genetic diversity of A. lusitanicus individuals ranged from 0.5% to 2.1%, whereas that of A. rufus was twice as low: 0.4-1.0%. The difference between the two species within the cox1 gene was at the level of 12%. Three A. lusitanicus and two A. rufus populations were found to be monomorphic. Large inter-population variability was found within each of the studied species, which suggests that the Polish populations of A. lusitanicus may have originated from repeated, separate introductions arriving from various parts of Europe.

  1. Genetic diversity and phylogeography of highly zoonotic Echinococcus granulosus genotype G1 in the Americas (Argentina, Brazil, Chile and Mexico) based on 8279bp of mtDNA.

    Science.gov (United States)

    Laurimäe, Teivi; Kinkar, Liina; Andresiuk, Vanessa; Haag, Karen Luisa; Ponce-Gordo, Francisco; Acosta-Jamett, Gerardo; Garate, Teresa; Gonzàlez, Luis Miguel; Saarma, Urmas

    2016-11-01

    Echinococcus granulosus is a taeniid cestode and the etiological agent of an infectious zoonotic disease known as cystic echinococcosis (CE) or hydatid disease. CE is a serious public health concern in many parts of the world, including the Americas, where it is highly endemic in many regions. Echinococcus granulosus displays high intraspecific genetic variability and is divided into multiple genotypes (G1-G8, G10) with differences in their biology and etiology. Of these, genotype G1 is responsible for the majority of human and livestock infections and has the broadest host spectrum. However, despite the high significance to the public and livestock health, the data on genetic variability and regional genetic differences of genotype G1 in America are scarce. The aim of this study was to evaluate the genetic variability and phylogeography of G1 in several countries in America by sequencing a large portion of the mitochondrial genome. We analysed 8279bp of mtDNA for 52 E. granulosus G1 samples from sheep, cattle and pigs collected in Argentina, Brazil, Chile and Mexico, covering majority of countries in the Americas where G1 has been reported. The phylogenetic network revealed 29 haplotypes and a high haplotype diversity (Hd=0.903). The absence of phylogeographic segregation between different regions in America suggests the importance of animal transportation in shaping the genetic structure of E. granulosus G1. In addition, our study revealed many highly divergent haplotypes, indicating a long and complex evolutionary history of E. granulosus G1 in the Americas. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Genetic diversity and population structure in Meconopsis ...

    African Journals Online (AJOL)

    This species is distributed in Qinghai, Xizang, Sichuan, Shanxi ,Gansu and Hubei provinces of the People's Republic of China. Genetic variation of ... Nei's coefficient of differentiation (GST) was found to be high (0.2320), also confirming the relatively high level of genetic differentiation within populations. By UPGMA cluster ...

  3. Genetic diversity and relationships among indigenous Mozambican ...

    African Journals Online (AJOL)

    Population genetic variability was relatively high when compared to other African breeds. Only 4.5% of the total genetic variation could be ... The results support the hypothesis of the Bovino de Tete cattle being a result of crossbreeding between Sanga and Zebu breeds. This study presents the first extensive information on ...

  4. ONLINE RESOURCES Assessment of Genetic Diversity and ...

    Indian Academy of Sciences (India)

    Sony

    including null alleles, mutation, nature of the plant, selection process, small population size and heterozygote deficiency. The most important factor is sampling effect called genetic drift which causes a random change in genotypic frequencies. Evaluation of genetic variation and cluster analysis. The results obtained from ...

  5. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Directory of Open Access Journals (Sweden)

    Daniel Garrido-Sanz

    Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

  6. Genetic diversity of seagrass seeds influences seedling morphology and biomass.

    Science.gov (United States)

    Randall Hughes, A; Hanley, Torrance C; Schenck, Forest R; Hays, Cynthia G

    2016-12-01

    Genetic diversity can influence ecological processes throughout ontogeny, yet whether diversity at early life history stages is important in long-lived taxa with overlapping generations is unclear. Seagrass systems provide some of the best evidence for the ecological effects of genetic diversity among adult shoots, but we do not know if the genetic diversity of seeds and seedlings also influences seagrass ecology. We tested the effects of seagrass (Zostera marina) seed diversity and relatedness on germination success, seedling morphology, and seedling production by comparing experimental assemblages of seeds collected from single reproductive shoots ("monocultures") to assemblages of seeds collected from multiple reproductive shoots ("polycultures"). There was no difference in seedling emergence, yet seedlings from polycultures had larger shoots above and below ground than seedlings from monocultures at the end of the 1-yr experiment. Genetic relatedness of the seedlings predicted some aspects of shoot morphology, with more leaves and longer roots and shoots at intermediate levels of relatedness, regardless of seed diversity. Our results suggest that studies of only adult stages may underestimate the importance of genetic diversity if the benefits at early life history stages continue to accrue throughout the life cycle. © 2016 by the Ecological Society of America.

  7. Genetic diversity of a newly established population of golden eagles on the Channel Islands, California

    Science.gov (United States)

    Sonsthagen, Sarah A.; Coonan, Timothy J.; Latta, Brian C.; Sage, George K.; Talbot, Sandra L.

    2012-01-01

    Gene flow can have profound effects on the genetic diversity of a founding population depending on the number and relationship among colonizers and the duration of the colonization event. Here we used data from nuclear microsatellite and mitochondrial DNA control region loci to assess genetic diversity in golden eagles of the recently colonized Channel Islands, California. Genetic diversity in the Channel Island population was low, similar to signatures observed for other recent colonizing island populations. Differences in levels of genetic diversity and structure observed between mainland California and the islands suggests that few individuals were involved in the initial founding event, and may have comprised a family group. The spatial genetic structure observed between Channel Island and mainland California golden eagle populations across marker types, and genetic signature of population decline observed for the Channel Island population, suggest a single or relatively quick colonization event. Polarity in gene flow estimates based on mtDNA confirm an initial colonization of the Channel Islands by mainland golden eagles, but estimates from microsatellite data suggest that golden eagles on the islands were dispersing more recently to the mainland, possibly after reaching the carrying capacity of the island system. These results illustrate the strength of founding events on the genetic diversity of a population, and confirm that changes to genetic diversity can occur within just a few generations.

  8. The study of genetic diversity in some Iranian accessions of ...

    African Journals Online (AJOL)

    Hyoscyamus sp. is well known as a natural source of two main tropan alkaloids including hyoscyamine and scopolamine. The environmental conditions make a very wide diversity of this herb in Iran. This study was conducted to evaluate the genetic diversity within a set of 45 Iranian accessions of Hyoscyamus sp. using ...

  9. The characterization of goat genetic diversity : Towards a genomic approach

    NARCIS (Netherlands)

    Ajmone-Marsan, P.; Colli, L.; Han, J. L.; Achilli, A.; Lancioni, H.; Joost, S.; Crepaldi, P.; Pilla, F.; Stella, A.; Taberlet, P.; Boettcher, P.; Negrini, R.; Lenstra, J. A.

    2014-01-01

    The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers

  10. Assessment of the genetic diversity of Kenyan coconut germplasm ...

    African Journals Online (AJOL)

    HP-PROBOOK

    2016-10-05

    Oct 5, 2016 ... Genetic diversity and relationship among 48 coconut individuals (Cocos nucifera L.) collections from the Coastal lowland of ... Marker. CAC23 had the highest PIC and revealed highest gene diversity values in this study. Analysis of the ..... and Oceania (IPGRI-APO), Serdang, Selangor, Malaysia. pp. 1-350.

  11. Genetic diversity analysis of mustard (Brassica spp.) germplasm ...

    African Journals Online (AJOL)

    sunny t

    successfully cultivated between Aman and Boro rice rotation without affecting this popular cropping pattern. So, it is urgent to analyze the genetic diversity and its response for the selection of short duration mustard genotypes for increasing our cropping intensity. Diversity at marker loci is currently the most feasible strategy ...

  12. Genetic diversity of Tamarindus indica populations: Any clues on the ...

    African Journals Online (AJOL)

    Tamarindus indica is a domesticated species of high economic value for the Sahel region. Despite this importance, very few data is available on its diversity as well as its structure leading to controversial discussions on its origin. Thus it is questionable whether the knowledge of its genetic diversity and organisation may ...

  13. Genetic diversity in pigeonpea [Cajanus cajan (L.) Millsp ...

    African Journals Online (AJOL)

    USER

    2010-05-31

    May 31, 2010 ... Genetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversity,. India and a presumed secondary centre of diversity in East Africa were evaluated using six microsatellite markers. Forty-seven (47) alleles were detected in the populations studied, with a mean of.

  14. Assessment of genetic diversity among wheat somaclonal variants ...

    African Journals Online (AJOL)

    use

    2011-10-26

    Oct 26, 2011 ... yield potential, wide adaptation, and durable resistance to important diseases such as the rusts. ... diversity levels among adapted, wheat germplasm can provide predictive estimates of genetic ..... diversity among Tibetan wheat, common wheat and European spelt wheat revealed by RAPD markers, ...

  15. Classification of genetic diversity and choice of parents for ...

    African Journals Online (AJOL)

    Thirty-one accessions of cowpea of diverse eco-geographic origins were evaluated for genetic diversity using principal component analysis (PCA), single linkage cluster analysis (SLCA) and canonical techniques. The accessions were classified into six groups by PCA and SLCA while canonical technique identified five ...

  16. Genetic diversity of endangered populations of Butia capitata ...

    African Journals Online (AJOL)

    The flora and fauna of the Cerrado biome in central Brazil both show great diversity and high levels of endemism. Butia capitata is a palm native to this biome that has significant economic, social, and environmental value. We sought to identify and quantify the genetic diversity of four fragmented populations of B. capitata ...

  17. Analysis of genetic diversity in bambara groundnut [ Vigna ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity among 100 selected bambara groundnut [Vigna subterranea (L.) Verdc] landraces from a diverse geographic area of Tanzania. Eleven informative AFLP primer combinations generated a total of 49 scorable polymorphic amplification ...

  18. Genetic diversity in pigeonpea [ Cajanus cajan (L.) Millsp ...

    African Journals Online (AJOL)

    Genetic relationships among 88 pigeonpea accessions from a presumed centre of origin and diversity, India and a presumed secondary centre of diversity in East Africa were evaluated using six microsatellite markers. Forty-seven (47) alleles were detected in the populations studied, with a mean of eight alleles per locus.

  19. Molecular assessment of genetic diversity in mung bean germplasm

    Indian Academy of Sciences (India)

    2008-04-02

    Apr 2, 2008 ... wider range of diversity but also groups the accessions ac- cording to their field performance for ... minous out group for all studies to test whether our reaction conditions were optimized to resolve it as a ...... Mignouna H. D., Ng N. Q., Ikea J. and Thotapilly G. 1998 Genetic diversity in cowpea as revealed by ...

  20. Analysis of genetic diversity in accessions of Irvingia gabonensis ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity and relationships among 15 accessions of Irvingia gabonensis collected from Cameroun, Gabon, and Nigeria. Twelve AFLP+3 primers produced 384 polymorphic fragments. Average genetic distance (AGD) between the 15 accessions ...

  1. Genetic diversity of Sorghum bicolor (L.) Moench landraces from ...

    African Journals Online (AJOL)

    ABEL

    2015-04-22

    Apr 22, 2015 ... preservation of their genetic potential. The objective of this study was to assess the genetic diversity of sorghum (Sorghum bicolor (L.) Moench) cultivated in the Northwest of Benin and to reveal certain fundamental evolutionary mechanisms. A total of 61 accessions of sorghum landraces belonging to the.

  2. Assessment and characterization of genetic diversity in Withania ...

    African Journals Online (AJOL)

    ... transfer of useful genes, thus maximizing the use of such available germplasms as genetic resource materials for breeders. The present input, first of its kind in Ashwagandha, will thus assist the marker assisted crop improvement programme. Key words: Withania somnifera, genetic diversity, RAPD, AFLP, polymorphism, ...

  3. Assessment of genetic diversity in Sudanese maize (Zea mays L ...

    African Journals Online (AJOL)

    Jane

    2011-08-08

    Aug 8, 2011 ... 3Commission for Biotechnology and Genetic Engineering, National Centre for Research, P.O. Box 2404, Khartoum,. Sudan. Accepted 17 June, 2011. The randomly amplified polymorphic DNA (RAPD) molecular markers were used to assess genetic diversity in 27 Sudanese maize genotypes. Ten primers ...

  4. Study on genetic diversity in Pakistani wheat varieties using simple ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... Full Length Research Paper. Study on genetic diversity in Pakistani wheat varieties using simple sequence repeat (SSR) markers. Bahadar Zeb, Imtiaz Ahmad Khan, Shahid Ali*, Sardar Bacha, Saqib Mumtaz and Zahoor. Ahmed Swati. Institute of Biotechnology and Genetic Engineering NWFP, Agricultural ...

  5. Genetic Diversity of Indigenous Chickens in Cameroon | Fotsa ...

    African Journals Online (AJOL)

    Genetic Diversity of Indigenous Chickens in Cameroon. ... Bulletin of Animal Health and Production in Africa ... Over time, the adaptation to harsh environmental conditions by the indigenous chickens resulted in a huge genetic potential that goes beyond the mere short-term objectives of sources of income, food protein, and ...

  6. Genetic diversity and population structure of sweet cassava using ...

    African Journals Online (AJOL)

    The objective of this study was to evaluate the population structure and genetic diversity among 66 sweet cassava (Manihot esculenta Crantz) traditional accessions collected in Maringa, Parana, Brazil, using microsatellite molecular markers. Population structure was analyzed by means of genetic distances and ...

  7. Genetic diversity and population structure of 10 Chinese indigenous ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 89; Issue 1. Genetic diversity and population structure of 10 Chinese indigenous egg-type duck breeds assessed by microsatellite polymorphism. Li Hui-Fang Song Wei-Tao Shu Jing-Ting Chen Kuan-Wei Zhu Wen-Qi Han Wei Xu Wen-Juan. Research Article Volume 89 Issue 1 ...

  8. Supplementary data: Genetic diversity among old Portuguese bread ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity among old Portuguese bread wheat cultivars and botanical varieties evaluated by ITS rDNA PCR-RFLP markers. A. Carvalho, H. Guedes-Pinto and J. Lima-Brito. J. Genet. 88, 363–367. Table 1. Passport data of the old Portuguese bread wheat cultivars (2n = 6x = 42;. AABBDD).

  9. The loss of genetic diversity in the Chinese paddlefish (Psephurus ...

    Indian Academy of Sciences (India)

    Unknown

    The loss of genetic diversity in the Chinese paddlefish. (Psephurus gladius Martens) as revealed by DNA fingerprinting. XUE-CHANG WU*. College of Life Sciences and the Key Laboratory of Conservation Genetics and Reproductive Biology for Endangered. Wild Animals of the Ministry of Education, Zhejiang University, ...

  10. Low genetic diversity of Phytophthora infestans population in potato ...

    African Journals Online (AJOL)

    AJL

    This study reveals the genetic diversity of P. infestans population in north China. A total of. 134 strains of P. ... Key words: Phytophthora infestans, population genetics, simple-sequence repeat (SSR), potato late blight. INTRODUCTION .... growth (about 5 to 7 days), the white mycelia of P. infestans were transferred to fresh ...

  11. Genetic diversity of bitter taste receptor gene family in Sichuan ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 95; Issue 3. Genetic diversity of bitter taste receptor gene family in Sichuan domestic and Tibetan chicken populations. YUAN SU DIYAN LI UMA GAUR YAN WANG NAN WU BINLONG CHEN HONGXIAN XU HUADONG YIN YAODONG HU QING ZHU. RESEARCH ARTICLE ...

  12. Analysis of Genetic diversity and reltionships in local Tunisian barley ...

    African Journals Online (AJOL)

    Yomi

    Genetic diversity and environmental associations of wild barley, Hordeum spontaneum, in Turkey. Genetica, 68: 203-213. Nagaoka T, Ogihara Y (1997). Applicability of inter-simple sequence repeat polymorphism in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor. Appl. Genet. 94: 597-602.

  13. Genetic diversity of Indonesia milkfish ( Chanos chanos ) using ...

    African Journals Online (AJOL)

    Genetic diversity of milkfish (Chanos chanos) from Indonesia was investigated using amplified fragment length polymorphism (AFLP) markers. A total of 255 loci were detected by combination of seven primers from 130 individuals collected at seven locations. AFLP analysis provided useful information in determining genetic ...

  14. Genetic diversity of Bambara groundnut ( Vigna subterranea (L ...

    African Journals Online (AJOL)

    The existence of genetic diversity in germplasm collections is crucial for cultivar development. Genetic relationships among 105 Bambara groundnuts (Vigna subterranea (L) Verdc.) accessions from Kenya were evaluated using 12 microsatellite markers. The Bambara landraces were collected from farmers in the western ...

  15. Genetic diversity and population structure of the marbled rockfish ...

    Indian Academy of Sciences (India)

    water pollution. The only genetic work on the rockfishes was undertaken by Dong et al. (2008) in Zhejiang, People's. Republic of China. This study used eight enzyme markers and reported a low level of polymorphism of only 27.78%. The objective of the present study was to assess the genetic diversity within populations ...

  16. Assessment of genetic diversity in Indian rice germplasm (Oryza ...

    Indian Academy of Sciences (India)

    Assessment of genetic diversity in Indian rice germplasm. (Oryza sativa L.): use of random versus trait linked microsatellite markers. Sheel Yadav, Ashutosh Singh, ..... Supplementary data, J. Genet. 92, 545–557. Table 3. Details of markers for yield related functional genes in rice. SSR marker. Chromosome. Forward primer.

  17. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

  18. Genetic diversity of indigenous chicken ecotypes in Jordan

    African Journals Online (AJOL)

    Jane

    2010-10-11

    Oct 11, 2010 ... conservation of genetic resources of indigenous chicken breeds in Jordan. For more general view, Siegel et al. (1992) studied the genetic diversity among wild jungle fowl and commercial chickens, using RAPD fingerprinting technique, and provided information to assess the gene- tic variation and propose ...

  19. Genetic diversity analysis of pearl millet (Pennisetum glauccum [L ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... assess the degree of polymorphisms within and among genotypes and to investigate if this approach was suitable for genetic studies of pearl ... markers for the assessment of genetic diversity and choosing parents for developing ..... RAPD mapping in a doubled haploid population of rice (Oryza sativa L.).

  20. Estimation of genetic diversity between three Saudi sheep breeds ...

    African Journals Online (AJOL)

    Estimation of genetic diversity between three Saudi sheep breeds using DNA markers. AAG Adam, NB Hamza, MAW Salim, KS Khalil. Abstract. The genetic variation of Najdi, Harri and Awassi breeds of Saudi sheep prevailing in Raniah province of Makka district were assessed and compared to Sudanese Desert sheep ...

  1. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    2015-12-03

    Dec 3, 2015 ... of an elite germplasm collection of Jatropha curcas L., a biofuel plant. Plant Sci. 176, 505–513. Varshney R. K., Chabane K., Hendre P. S., Aggarwal R. K. and. Graner A. 2007 Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and con- servation of genetic ...

  2. Molecular evaluation of genetic diversity and association studies in ...

    Indian Academy of Sciences (India)

    Molecular evaluation of genetic diversity and association studies in rice. (Oryza sativa L.) C. Vanniarajan, K. K. Vinod and Andy Pereira. J. Genet. 91, 9–19. Table 1. Chromosome-wise distribution of SSR alleles and their number (k), polymorphic information content (PIC) and allele discrimination index (Dm). Chromosome.

  3. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Among the mixed models analysed, mixed linear model (MLM) identified 21 quantitative trait loci for lint percentage and seed quality traits, such as seed protein and oil. Establishing genetic diversity, population structure and marker trait associations for the seed quality traits could be valuable in understanding the genetic ...

  4. Genetic diversity in Egyptian and Saudi goat breeds using ...

    African Journals Online (AJOL)

    SARAH

    2013-12-30

    Dec 30, 2013 ... Genomic DNA was extracted from whole blood of each sample and microsatellites techniques were used for analysis of DNA. The results showed that, the total ... other with only little genetic exchange between the geographically isolated populations. Key words: Microsatellites, Goats, Genetic diversity, ...

  5. Genetic relationships and diversity of Jatropha curcas accessions in ...

    African Journals Online (AJOL)

    This study has been undertaken to assess the extent of genetic diversity in a representative set of 16 accessions of Jatropha curcas. Inter-simple sequence repeat (ISSR) analysis was used to establish the genetic relationship among the accessions. From the eight ISSR primers used, the number of amplicons per primers ...

  6. Genetic diversity analysis and conservation of the Chinese herb ...

    African Journals Online (AJOL)

    Salvia miltiorrhiza is an economically important floral herb. However, little work has been conducted to further our understanding of the genetics of this herb. In this study, a representative set of germplasm of. S. miltiorrhiza populations was used to analyze genetic diversity using amplified fragment length polymorphism ...

  7. Analysis of genetic diversity in pigeon pea germplasm using ...

    Indian Academy of Sciences (India)

    Pigeon pea (Cajanus cajan), an important legume crop is predominantly cultivated in tropical and subtropical regions of Asia and Africa. It is normally considered to have a low degree of genetic diversity, an impediment in undertaking crop improvement programmes.We have analysed genetic polymorphism of domesticated ...

  8. Inter simple sequence repeat analysis of genetic diversity of five ...

    African Journals Online (AJOL)

    This paper studied the genetic diversity of five cultivated pepper species using inter simple sequence repeat (ISSR) analysis. The amplicons of 13 out of 15 designed primers were stable polymorphic and therefore were used as genetic biomarkers. 135 total clear bands were obtained, of which 102 were polymorphic bands ...

  9. Assessing genetic diversity of perennial ryegrass ( Lolium perenne L ...

    African Journals Online (AJOL)

    In this study, inter-simple sequence repeat (ISSR) markers were used to compare genetic diversity between commercial cultivars and natural germplasm which were obtained from Europe, Africa, Asia, and North America. There was a relatively high genetic variation in the whole collection judged by the polymorphism rate ...

  10. Assessment of genetic diversity among Capsicum annuum L ...

    African Journals Online (AJOL)

    Vast genetic diversity is available in chilli which may facilitate the breeder to develop new varieties, provided the genetic distance between the accessions is properly understood. In this study, 45 accessions of chilli collected from Chilli Research Station, Devihosur, Haveri district of Karnataka State were subjected for RAPD ...

  11. Genetic diversity of a native chicken breed in Iran

    Indian Academy of Sciences (India)

    2National Animal Breeding Center, P.O. Box 3111212290 Isfahan, Iran. [Nasr Esfahani E., Eskandarinasab M. P., Esmaeil Khanian S., Nikmard M. and Molaee V. 2012 Genetic diversity of a native chicken breed in Iran. J. Genet. 91, e28–e31. Online only: http://www.ias.ac.in/jgenet/OnlineResources/91/e28.pdf]. Introduction.

  12. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    uqhdesma

    2016-10-12

    Oct 12, 2016 ... with genetic distance between landraces increasing with an increase in geographic distance. The ... the extent and structure of crop genetic diversity is ...... Ribosomal DNA spacer length polymorphism in barley. Mendelian inheritance, chromosomal location and population dynamics. Proc. Natl. Acad. Sci.

  13. Genetic diversity in green gram [Vigna radiata (L.)] landraces ...

    African Journals Online (AJOL)

    GRACE

    2006-07-03

    Jul 3, 2006 ... substantially increased our knowledge of the genetics of plant populations. These results have important implications for the conservation strategy. Information on the levels and distribution of genetic diversity of any plant species may contribute to the knowledge of their evolutionary history and potential, ...

  14. Genetic diversity in cocoa germplasm of southern Cameroon ...

    African Journals Online (AJOL)

    The range of polymorphism of about 194 cocoa accessions collected in farms in Southern Cameroon during field surveys and 71 Trinitario and Upper Amazon clones available in genebanks on-station was assessed using 13 SSR markers. The gene diversity, genetic differentiation and genetic similarities were analysed for ...

  15. Morphological and molecular genetic diversity of Syrian indigenous ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-05-04

    May 4, 2016 ... Domestic goats in Syria may provide an interesting source of genetic variability due to its proximity to the centers of domestication. This study aimed to assess the morphological variation, genetic diversity and population substructure of the Syrian goat populations. Commonly, three goat genotypes are.

  16. Genetic diversity of Myanmar rice and their implementation on ...

    African Journals Online (AJOL)

    AMAJU

    2011-02-21

    Feb 21, 2011 ... Myanmar has diverse agronomic landscape and potentially preserves high level of genetic resources for important crop species. ... bank population maintained by seed-propagation in a genebank for several generations and an “on- ..... of artificial and natural factors affecting the genetic. Yamanaka et al.

  17. Genetic diversity of Przewalski's gazelle using noninvasive DNA and ...

    African Journals Online (AJOL)

    According to the genetic similarity and geographical closeness, we suggested that six populations should be managed as three separate conservation units and habitat corridors should be built to link the Yuanzhe, Hudong-Ketu, Haergai and Sand Island populations. Key words: Habitat fragment, genetic diversity, ...

  18. Genetic diversity of Bambara groundnut (Vigna subterranea (L ...

    African Journals Online (AJOL)

    FORRESTER

    2015-01-28

    Jan 28, 2015 ... The existence of genetic diversity in germplasm collections is crucial for cultivar development. Genetic relationships among 105 Bambara groundnuts (Vigna subterranea (L) Verdc.) accessions from Kenya were evaluated using 12 microsatellite markers. The Bambara landraces were collected from farmers ...

  19. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

    Science.gov (United States)

    Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

    2016-11-14

    Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (H E  = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (H E  = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher

  20. Genomic patterns inAcropora cervicornisshow extensive population structure and variable genetic diversity.

    Science.gov (United States)

    Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

    2017-08-01

    Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

  1. Genetic diversity in farm animals - A review

    NARCIS (Netherlands)

    Groeneveld, L. F.; Lenstra, J. A.; Eding, H.; Toro, M. A.; Scherf, B.; Pilling, D.; Negrini, R.; Finlay, E. K.; Jianlin, H.; Groeneveld, E.; Weigend, S.

    2010-01-01

    Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition,

  2. Promiscuity, sexual selection, and genetic diversity: a reply to Spurgin.

    Science.gov (United States)

    Lifjeld, Jan T; Gohli, Jostein; Johnsen, Arild

    2013-10-01

    We recently reported a positive association between female promiscuity and genetic diversity across passerine birds, and launched the hypothesis that female promiscuity acts as a balancing selection, pressure maintaining genetic diversity in populations (Gohli et al.2013). Spurgin (2013) questions both our analyses and interpretations. While we agree that the hypothesis needs more comprehensive empirical testing, we find his specific points of criticism unjustified. In a more general perspective, we call for a more explicit recognition of female mating preferences as mechanisms of selection in population genetics theory. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  3. The structural diversity of artificial genetic polymers.

    Science.gov (United States)

    Anosova, Irina; Kowal, Ewa A; Dunn, Matthew R; Chaput, John C; Van Horn, Wade D; Egli, Martin

    2016-02-18

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Genetic diversity of six populations of red hybrid tilapia, using microsatellites genetic markers

    Directory of Open Access Journals (Sweden)

    Boris Briñez R.

    2011-05-01

    Full Text Available Objective. To determine and evaluate the genetic diversity of six populations of red hybrid tilapia, with the purpose to assess the potential benefit of a future breeding program conducted at the Research Center for Aquaculture (Ceniacua, Colombia. Material and methods. A total of 300 individuals, representing a wide genetic variability, were genotyped using a fluorescent microsatellite marker set of 5 gene-based SSRs in 6 different farms belonging to 4 States of Colombia. Results. The result showed that the mean number of alleles per locus per population was 8.367. The population 5 had the highest mean number of alleles with 9.6 alleles, followed by population 4 with 9.4 alleles, population 2 with 9.2, population 3 with 8.0, population 1 with 7.2 and population 6 with 6.8 alleles. The analysis of the distribution of genetic variation was (17.32% among population, while among individuals within populations was (28.55% and within individuals was high (54.12%. The standard diversity indices showed that population 4 was the more variable (mean He=0.837 followed by population 1 (mean He=0.728, population 3 (mean He=0.721, population 5 (mean He=0.705, population 2 (mean He=0.690, population 6 (mean He=0.586. Highly significant deviations from Hardy–Weinberg, exhibited all of the populations, mostly due to deficits of heterozygotes. Genotype frequencies at loci UNH 106 of population 5 and loci UNH 172 of population 6 were Hardy-Weinberg equilibrium (HWE. Conclusions. The results of this study, contribute to the genetic breeding program of Tilapia, conduced by the Research Center for Aquaculture. The Fst distance showed that the samples are differentiated genetically and it is possible to use at the beginning of the genetic program. However, it is recommended to introduce others individuals to the crossbreeding program.

  5. Radiation induced mutants in elite genetic background for the augmentation of genetic diversity

    International Nuclear Information System (INIS)

    Kumar, V.; Bhagwat, S.G.

    2011-01-01

    Rice (Oryza sativa L.), an important food crop for India, shows large genetic diversity. However, despite the large genetic resource, high genetic similarity is reported in cultivated varieties indicating genetic erosion. Radiation induced mutations provide genetic variability in elite background. In the present study, twenty gamma ray induced mutants of rice variety WL112 (carrying sd-1 semi-dwarfing gene) were analysed for genetic diversity using microsatellite markers. The high range of genetic diversity among mutants indicated that the mutants possess potential for enhancing variability in rice. Cluster analysis showed presence of five clusters having small sub-clusters. Earliness, semi-dwarf stature or resistance to blast disease observed among the mutants showed that these will be useful in breeding programmes. (author)

  6. Assessment of genetic diversity of sweet potato in Puerto Rico.

    Science.gov (United States)

    Rodriguez-Bonilla, Lorraine; Cuevas, Hugo E; Montero-Rojas, Milly; Bird-Pico, Fernando; Luciano-Rosario, Dianiris; Siritunga, Dimuth

    2014-01-01

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied.

  7. Genetics of equine insect bite hypersensitivity and genetic diversity in horses

    NARCIS (Netherlands)

    Shrestha, Merina

    2017-01-01

    Genetic variation contributing to the phenotypic variation was utilized in this thesis to understand the genetic background of a complex trait IBH, and to understand genetic diversity and relationships between various horse populations.

    IBH is the most common skin allergic disorder in

  8. COMPARITIVE GENETIC DIVERSITY ANALYSIS OF OAT (Avena ...

    African Journals Online (AJOL)

    knsccf

    ... diversity, inter-simple sequence repeats (ISSR), morphology, oat, relationship. INTRODUCTION. Oat (Avena sativa L.) is one of the most important forage and feed crops of the world. Oat is used as green fodder, straw, hay or silage. Oat grain makes a good balanced concentrate in the rations for poultry, cattle, sheep and.

  9. Genetic diversity analysis of Tinospora cordifolia germplasm ...

    Indian Academy of Sciences (India)

    2012-04-03

    Apr 3, 2012 ... Wiley Eastern Limited, New Delhi, India. Shinde V. M. and Dhalwal K. 2010 DNA fingerprinting of. Tinospora cordifolia using RAPD analysis. J. Global Pharma. Tech. 2, 38–42. Singh S., Singh D. R., Faseela F., Kumar N., Damodaran V. and. Srivastava R. C. 2011. Diversity of 21 taro (Colocasia esculenta.

  10. Increased genetic diversity of HIV-1 circulating in Hong Kong.

    Directory of Open Access Journals (Sweden)

    Jonathan Hon-Kwan Chen

    Full Text Available HIV-1 group M strains are characterized into 9 pure subtypes and 48 circulating recombinant forms (CRFs. Recent studies have identified the presence of new HIV-1 recombinants in Hong Kong and their complexity continues to increase. This study aims to characterize the HIV-1 genetic diversity in Hong Kong. Phylogenetic analyses were performed by using HIV-1 pol sequences including protease and partial reverse transcriptase isolated from 1045 local patients in Hong Kong from 2003 to 2008. For the pol sequences with unassigned genotype, the evidence of recombination was determined by using sliding-window based bootscan plots and their env C2V3 region were also sequenced. Epidemiological background of these patients was further collected. The pol phylogenetic analyses highlighted the extent of HIV-1 genetic diversity in Hong Kong. Subtype B (450/1045; 43.1% and CRF01_AE (469/1045; 44.9% variants were clearly predominant. Other genotypes (126/1045; 12.1% including 3 defined subtypes, 10 CRFs, 1 unassigned subtype and 33 recombinants with 11 different mosaic patterns were observed. Recombinants of subtype B and CRF01_AE were mainly found among local Chinese MSM throughout 2004 to 2008, while the CRF02_AG and subtype G recombinants were circulating among non-Chinese Asian population in Hong Kong through heterosexual transmission starting from 2008. Our study demonstrated the complex recombination of HIV-1 in Hong Kong and the need in developing surveillance system for tracking the distribution of new HIV-1 genetic variants.

  11. Genetic diversity of Carica papaya as revealed by AFLP markers.

    Science.gov (United States)

    Kim, M S; Moore, P H; Zee, F; Fitch, M M M; Steiger, D L; Manshardt, R M; Paull, R E; Drew, R A; Sekioka, T; Ming, R

    2002-06-01

    Genetic relationships among Carica papaya cultivars, breeding lines, unimproved germplasm, and related species were established using amplified fragment length polymorphism (AFLP) markers. Seventy-one papaya accessions and related species were analyzed with nine EcoRI-MseI primer combinations. A total of 186 informative AFLP markers was generated and analyzed. Cluster analysis suggested limited genetic variation in papaya, with an average genetic similarity among 63 papaya accessions of 0.880. Genetic diversity among cultivars derived from the same or similar gene pools was smaller, such as Hawaiian Solo hermaphrodite cultivars and Australian dioecious cultivars with genetic similarity at 0.921 and 0.912, respectively. The results indicated that self-pollinated hermaphrodite cultivars were as variable as open-pollinated dioecious cultivars. Genetic diversity between C. papaya and six other Carica species was also evaluated. Carica papaya shared the least genetic similarity with these species, with an average genetic similarity of 0.432; the average genetic similarity among the six other species was 0.729. The results from AFLP markers provided detailed estimates of the genetic variation within and among papaya cultivars, and supported the notion that C. papaya diverged from the rest of Carica species early in the evolution of this genus.

  12. New data on sterlet (Acipenser ruthenus L. genetic diversity in the middle and Lower Danube sections, based on mitochondrial DNA analyses

    Directory of Open Access Journals (Sweden)

    Cvijanović Gorčin

    2015-01-01

    Full Text Available Poor regulated fishery, pollution, fragmentation and loss of habitat are most important factors influencing decline of sterlet population worldwide. In Middle and Lower Danube region, this species still have significant economic importance since wilde populations are commercially exploited, while Upper Danube populations are dependent on stocking efforts in order to maintain their presence in open waters. Aim of present study is to analyze genetic diversity of sterlet populations from the Middle and Lower Danube and Lower Tisza rivers, as a prerequisite for their effective conservation and management. Analysis of a highly variable D-loop fragment of mitochondrial DNA detected five new haplotypes, while the eight previously identified haplotypes had extended their previous range. Genetic variability could be attributed almost entirely to individuals, with observed lack of population structure. Negative values of neutrality test indicate recent expansion on some sampling locations. Adittionaly, gene flow analysis between Lower and Middle Danube region showed intensive exchange of speciemens. At the same time analysis showed some influence of Tisza dam on gene flow between samples from Tisza and Middle Danube section.Our study indicated the need for a careful planning of sterlet stocking programmes and inclusion of demographic data or catch time-series. [Projekat Ministarstva nauke Republike Srbije, br. 173045

  13. Genetic diversity and population structure in Meconopsis ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-05-24

    May 24, 2010 ... Meconopsis quintuplinervia is regarded as a valuable medicinal plant in Tibetan medicinal system. This species is distributed in Qinghai, Xizang, Sichuan, Shanxi ,Gansu and Hubei provinces of the People's. Republic of China. Genetic variation of 16 M. quintuplinervia populations sampled from Qinghai ...

  14. Genetic fingerprinting and phylogenetic diversity of Staphylococcus ...

    African Journals Online (AJOL)

    Genetic fingerprinting of 18 different isolates of Staphylococcus aureus from Nigeria using random amplified polymorphic DNA (RAPD) was carried out. Ten out of 100 Operon primers showed polymorphism among the isolates tested generating 88 bands, 51 of which were polymorphic with sizes ranging between 200 and ...

  15. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Quinta de Prados, 5001-801 Vila Real, Portuga; BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, Lisboa, Portugal; Departamento de Genética, Facultad de Biologia, ...

  16. Genetic diversity and population structure among sorghum ...

    African Journals Online (AJOL)

    The Western Ethiopian region harbors a unique set of sorghum germplasm adapted to conditions not conventional to sorghums grown in other parts of the world. Accessions from the region possess unique resistance to multiple leaf and grain diseases. This study is aimed at exploring the extent of genetic variation and ...

  17. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    1Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Quinta de Prados,. 5001-801 Vila Real, Portugal. 2Departamento de Genética, Facultad de Biologia, Universidad Complutense, C/ José Antonio Novais, 12,. 28040 Madrid, Spain. 3BioISI- Biosystems & Integrative Sciences Institute, ...

  18. Genetic diversity of Chlamydia pecorum strains in wild koala locations across Australia and the implications for a recombinant C. pecorum major outer membrane protein based vaccine.

    Science.gov (United States)

    Kollipara, Avinash; Polkinghorne, Adam; Wan, Charles; Kanyoka, Pride; Hanger, Jon; Loader, Joanne; Callaghan, John; Bell, Alicia; Ellis, William; Fitzgibbon, Sean; Melzer, Alistar; Beagley, Kenneth; Timms, Peter

    2013-12-27

    The long term survival of the koala (Phascolarctos cinereus) is at risk due to a range of threatening processes. A major contributing factor is disease caused by infection with Chlamydia pecorum, which has been detected in most mainland koala populations and is associated with ocular and genital tract infections. A critical aspect for the development of vaccines against koala chlamydial infections is a thorough understanding of the prevalence and strain diversity of C. pecorum infections across wild populations. In this study, we describe the largest survey (403 koalas from eight wild populations and three wildlife hospitals) examining the diversity of C. pecorum infections. 181 of the 403 koalas tested (45%) positive for C. pecorum by species-specific quantitative PCR with infection rates ranging from 20% to 61% in the eight wild populations sampled. The ompA gene, which encodes the chlamydial major outer membrane protein (MOMP), has been the major target of several chlamydial vaccines. Based on our analysis of the diversity of MOMP amino types in the infected koalas, we conclude that, (a) there exists significant diversity of C. pecorum strains in koalas, with 10 distinct, full length C. pecorum MOMP amino types identified in the 11 koala locations sampled, (b) despite this diversity, there are predicted T and B cell epitopes in both conserved as well as variable domains of MOMP which suggest cross-amino type immune responses, and (c) a recombinant MOMP-based vaccine consisting of MOMP "F" could potentially induce heterotypic protection against a range of C. pecorum strains. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  19. [Genetic diversity of microsatellite loci in captive Amur tigers].

    Science.gov (United States)

    Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

    2004-09-01

    The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten

  20. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    Science.gov (United States)

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  1. SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars

    Directory of Open Access Journals (Sweden)

    Xiaoyan Song

    2016-05-01

    Full Text Available In potato breeding, it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance. A promising alternative is diploid breeding. Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits. In this study, we used SSR markers to evaluate the genetic diversity of diploid potato cultivars. To screen polymorphic SSR markers, 55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships. Among them, 12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars. The primers produced 6 to 18 bands with an average of 8.2 bands per primer. In total, 98 bands were amplified from 192 cultivars, and 97 of them were polymorphic. Cluster analysis using UPGMA showed the genetic relationships of all accessions tested: 186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers, and the 192 diploid cultivars were divided into 11 groups, and 83.3% constituted the first group. Clustering results showed relatively low genetic diversity among 192 diploid cultivars, with closer relationship at the molecular level. The results can provide molecular basis for diploid potato breeding.

  2. Genetic Diversity of Turf-Type Tall Fescue Using Diversity Arrays Technology

    Czech Academy of Sciences Publication Activity Database

    Baird, J. H.; Kopecký, David; Lukaszewski, A.J.; Green, R. J.; Bartoš, Jan; Doležel, Jaroslav

    2012-01-01

    Roč. 52, č. 1 (2012), s. 408-412 ISSN 0011-183X Institutional research plan: CEZ:AV0Z50380511 Keywords : Festuca arundinacea * Diversity Arrays Technology (DArT) * Low genetic polymorphism Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.513, year: 2012

  3. Genetic diversity assessed by microsatellite markers in sweet corn cultivars

    Directory of Open Access Journals (Sweden)

    Ana Daniela Lopes

    2015-12-01

    Full Text Available Information on genetic diversity is essential to the characterization and utilization of germplasm. The genetic diversity of twenty-two sweet corn cultivars (seventeen open-pollinated varieties, OPV, and five hybrids, H was investigated by applying simple sequence repeat markers. A total of 257 primers were tested, of which 160 were found to be usable in terms of high reproducibility for all the samples tested; 45 were polymorphic loci, of which 30 were used to assess the genetic diversity of sweet corn cultivars. We detected a total of 86 alleles using 30 microsatellite primers. The mean polymorphism was 82 %. The highest heterozygosity values (Ho = 0.20 were found in the PR030-Doce Flor da Serra and BR427 III OPVs, whereas the lowest values (0.14 were recorded in the MG161-Branco Doce and Doce Cubano OPVs. The polymorphism information content ranged from 0.19 (Umc2319 to 0.71 (Umc2205. The analysis of molecular variance revealed that most of the genetic variability was concentrated within the cultivars of sweet corn (75 %, with less variability between them (25 %. The consensus tree derived from the neighbor-joining (NJ algorithm using 1,000 bootstrapping replicates revealed seven genetically different groups. Nei’s diversity values varied between 0.103 (Doce do Hawai × CNPH-1 cultivars and 0.645 (Amarelo Doce × Lili cultivars, indicating a narrow genetic basis. The Lili hybrid was the most distant cultivar, as revealed by Principal Coordinates Analysis and the NJ tree. This study on genetic diversity will be useful for planning future studies on sweet corn genetic resources and can complement the breeding programs for this crop.

  4. Genetic diversity and trait genomic prediction in a pea diversity panel

    OpenAIRE

    Burstin, Judith; Salloignon, Pauline; Chabert Martinello, Marianne; Magnin Robert, Jean-Bernard; Siol, Mathieu; Jacquin, Françoise; Chauveau, Aurelie; Pont, Caroline; Aubert, Gregoire; Delaitre, Catherine; Truntzer, Caroline; Duc, Gérard

    2015-01-01

    Background Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR)...

  5. Feasible Initial Population with Genetic Diversity for a Population-Based Algorithm Applied to the Vehicle Routing Problem with Time Windows

    Directory of Open Access Journals (Sweden)

    Marco Antonio Cruz-Chávez

    2016-01-01

    Full Text Available A stochastic algorithm for obtaining feasible initial populations to the Vehicle Routing Problem with Time Windows is presented. The theoretical formulation for the Vehicle Routing Problem with Time Windows is explained. The proposed method is primarily divided into a clustering algorithm and a two-phase algorithm. The first step is the application of a modified k-means clustering algorithm which is proposed in this paper. The two-phase algorithm evaluates a partial solution to transform it into a feasible individual. The two-phase algorithm consists of a hybridization of four kinds of insertions which interact randomly to obtain feasible individuals. It has been proven that different kinds of insertions impact the diversity among individuals in initial populations, which is crucial for population-based algorithm behavior. A modification to the Hamming distance method is applied to the populations generated for the Vehicle Routing Problem with Time Windows to evaluate their diversity. Experimental tests were performed based on the Solomon benchmarking. Experimental results show that the proposed method facilitates generation of highly diverse populations, which vary according to the type and distribution of the instances.

  6. Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras.

    Science.gov (United States)

    Lopez, Ana Cecilia; Ortiz, Andres; Coello, Jorge; Sosa-Ochoa, Wilfredo; Torres, Rosa E Mejia; Banegas, Engels I; Jovel, Irina; Fontecha, Gustavo A

    2012-11-26

    Understanding the population structure of Plasmodium species through genetic diversity studies can assist in the design of more effective malaria control strategies, particularly in vaccine development. Central America is an area where malaria is a public health problem, but little is known about the genetic diversity of the parasite's circulating species. This study aimed to investigate the allelic frequency and molecular diversity of five surface antigens in field isolates from Honduras. Five molecular markers were analysed to determine the genotypes of Plasmodium vivax and Plasmodium falciparum from endemic areas in Honduras. Genetic diversity of ama-1, msp-1 and csp was investigated for P. vivax, and msp-1 and msp-2 for P. falciparum. Allelic frequencies were calculated and sequence analysis performed. A high genetic diversity was observed within Plasmodium isolates from Honduras. A different number of genotypes were elucidated: 41 (n = 77) for pvama-1; 23 (n = 84) for pvcsp; and 23 (n = 35) for pfmsp-1. Pvcsp sequences showed VK210 as the only subtype present in Honduran isolates. Pvmsp-1 (F2) was the most polymorphic marker for P. vivax isolates while pvama-1 was least variable. All three allelic families described for pfmsp-1 (n = 30) block 2 (K1, MAD20, and RO33), and both allelic families described for the central domain of pfmsp-2 (n = 11) (3D7 and FC27) were detected. However, K1 and 3D7 allelic families were predominant. All markers were randomly distributed across the country and no geographic correlation was found. To date, this is the most complete report on molecular characterization of P. vivax and P. falciparum field isolates in Honduras with regards to genetic diversity. These results indicate that P. vivax and P. falciparum parasite populations are highly diverse in Honduras despite the low level of transmission.

  7. Relationship of genetic diversity and niche centrality: a survey and analysis.

    Science.gov (United States)

    Lira-Noriega, Andrés; Manthey, Joseph D

    2014-04-01

    The distribution of genetic diversity within and among populations in relation to species' geographic ranges is important to understanding processes of evolution, speciation, and biogeography. One hypothesis predicts that natural populations at geographic range margins will have lower genetic diversity relative to those located centrally in species' distributions owing to a link between geographic and environmental marginality; alternatively, genetic variation may be unrelated with geographic marginality via decoupling of geographic and environmental marginality. We investigate the predictivity of geographic patterns of genetic variation based on geographic and environmental marginality using published genetic diversity data for 40 species (insects, plants, birds, mammals, worms). Only about half of species showed positive relationships between geographic and environmental marginality. Three analyses (sign test, multiple linear regression, and meta-analysis of correlation effect sizes) showed a negative relationship between genetic diversity and distance to environmental niche centroid, but no consistent relationship of genetic diversity with distance to geographic range center. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  8. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

    Directory of Open Access Journals (Sweden)

    Windig Jack J

    2008-07-01

    Full Text Available Abstract Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. Non-genetic aspects included threats (e.g. low population size, low preferences by farmers and current merits (economic, ecological and cultural merits. Threat analysis identified eight of the 14 breeds as threatened. Analysis of current merits showed that sub-alpine and arid-lowland breeds contribute most to farmer livelihoods in comparison to other breeds. The highest contribution to the genetic diversity conserved was from the Simien breed. Simien showed high between-breed (low between-breed kinship = 0.04 as well as high within-breed diversity (low within-breed kinship = 0.09 and high HE = 0.73 and allelic richness = 6.83. We combined the results on threat status, current breed merits and contributions to genetic diversity to produce a ranking of the 14 breeds for conservation purposes. Our results balance the trade-offs between conserving breeds as insurance against future uncertainties and current sustainable utilization. The ranking of breeds provides a basis for conservation strategies for Ethiopian sheep and contributes to a regional or global conservation plan.

  9. Landscape, population structure and genetic diversity of Stomoxys calcitrans

    Directory of Open Access Journals (Sweden)

    Dsouli Aymes N.

    2009-03-01

    Full Text Available To investigate whether different landscapes could affect genetic diversity and structure of the cosmopolitan diptera Stomoxys calcitrans, populations from Gabon and southern France were studied using dominant amplified fragment length polymorphism (AFLP markers. Gabon is characterized by a forested closed landscape, and southern France by an open Mediterranean landscape. The genetic diversity between Gabon and France populations did not differ significantly (P > 0.05. Contrary to our expectation, this study shows a moderate level of genetic differentiation between these two distant countries (Fst = 0.0979 and a low genetic structure among Gabonese and French populations (Fst = 0.0291 and 0.0275 respectively. This result could indicate the capacities of S. calcitrans populations to sustain a high level of gene flow, despite geographic distance and isolation.

  10. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    Directory of Open Access Journals (Sweden)

    Bisgaard Magne

    2011-02-01

    Full Text Available Abstract Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies.

  11. Ortholog identification in genera of high genetic diversity and evolution

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Frisvad, Jens Christian

    In the era of high-throughput sequencing, comparative genomics is vastly used in the discovery of genetic diversity between species, but also in defining the core and pan genome of single species to whole genera. Current comparative approaches are implementing ortholog identification to establish...... genome annotations, gene or protein evolutions or defining functional features in individual species and groups.......In the era of high-throughput sequencing, comparative genomics is vastly used in the discovery of genetic diversity between species, but also in defining the core and pan genome of single species to whole genera. Current comparative approaches are implementing ortholog identification to establish...

  12. Entropy and Information Approaches to Genetic Diversity and its Expression: Genomic Geography

    Directory of Open Access Journals (Sweden)

    William B. Sherwin

    2010-07-01

    Full Text Available This article highlights advantages of entropy-based genetic diversity measures, at levels from gene expression to landscapes. Shannon’s entropy-based diversity is the standard for ecological communities. The exponentials of Shannon’s and the related “mutual information” excel in their ability to express diversity intuitively, and provide a generalised method of considering microscopic behaviour to make macroscopic predictions, under given conditions. The hierarchical nature of entropy and information allows integrated modeling of diversity along one DNA sequence, and between different sequences within and among populations, species, etc. The aim is to identify the formal connections between genetic diversity and the flow of information to and from the environment.

  13. Genetic diversity of noroviruses in Brazil

    Directory of Open Access Journals (Sweden)

    Julia Monassa Fioretti

    2011-12-01

    Full Text Available Norovirus (NoV infections are a major cause of acute gastroenteritis outbreaks around the world. In Brazil, the surveillance system for acute diarrhoea does not include the diagnosis of NoV, precluding the ability to assess its impact on public health. The present study assessed the circulation of NoV genotypes in different Brazilian states by partial nucleotide sequencing analysis of the genomic region coding for the major capsid viral protein. NoV genogroup II genotype 4 (GII.4 was the prevalent (78% followed by GII.6, GII.7, GII.12, GII.16 and GII.17, demonstrating the great diversity of NoV genotypes circulating in Brazil. Thus, this paper highlights the importance of a virological surveillance system to detect and characterize emerging strains of NoV and their spreading potential.

  14. Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene.

    Science.gov (United States)

    Martin, Simon H; Möst, Markus; Palmer, William J; Salazar, Camilo; McMillan, W Owen; Jiggins, Francis M; Jiggins, Chris D

    2016-05-01

    A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. Copyright © 2016 by the Genetics Society of America.

  15. Genetic diversity of Echinococcus granulosus in center of Iran.

    Science.gov (United States)

    Pestechian, Nader; Hosseini Safa, Ahmad; Tajedini, Mohammadhasan; Rostami-Nejad, Mohammad; Mousavi, Mohammad; Yousofi, Hosseinali; Haghjooy Javanmard, Shaghayegh

    2014-08-01

    Hydatid cyst caused by Echinococcus granulosus is one of the most important parasitic diseases around the world and many countries in Asia, including Iran, are involved with this infection. This disease can cause high mortality in humans as well as economic losses in livestock. To date, several molecular methods have been used to determine the genetic diversity of E. granulosus. So far, identification of E. granulosus using real-time PCR fluorescence-based quantitative assays has not been studied worldwide, also in Iran. Therefore, the aim of this study was to investigate the genetic diversity of E. granulosus from center of Iran using real-time PCR method. A total of 71 hydatid cysts were collected from infected sheep, goat, and cattle slaughtered in Isfahan, Iran during 2013. DNA was extracted from protoscolices and/or germinal layers from each individual cyst and used as template to amplify the mitochondrial cytochrome c oxidase subunit 1 gene (cox1) (420 bp). Five cattle isolates out of 71 isolates were sterile and excluded from further investigation. Overall, of 66 isolates, partial sequences of the cox1 gene of E. granulosus indicated the presence of genotypes G1 in 49 isolates (74.2%), G3 in 15 isolates (22.7%), and G6 in 2 isolates (3.0%) in infected intermediate hosts. Sixteen sequences of G1 genotype had microgenetic variants, and they were compared to the original sequence of cox1. However, isolates identified as G3 and G6 genotypes were completely consistent with original sequences. G1 genotype in livestock was the dominant genotype in Isfahan region, Iran.

  16. Genetic diversity of symbiotic cyanobacteria in Cycas revoluta (Cycadaceae).

    Science.gov (United States)

    Yamada, Shuntaro; Ohkubo, Satoshi; Miyashita, Hideaki; Setoguchi, Hiroaki

    2012-09-01

    The diversity of cyanobacterial species within the coralloid roots of an individual and populations of Cycas revoluta was investigated based on 16S rRNA gene sequences. Sixty-six coralloid roots were collected from nine natural populations of cycads on Kyushu and the Ryukyu Islands, covering the entire distribution range of the species. Approximately 400 bp of the 5'-end of 16S rRNA genes was amplified, and each was identified by denaturing gradient gel electrophoresis. Most coralloid roots harbored only one cyanobiont, Nostoc, whereas some contained two or three, representing cyanobiont diversity within a single coralloid root isolated from a natural habitat. Genotypes of Nostoc within a natural population were occasionally highly diverged and lacked DNA sequence similarity, implying genetic divergence of Nostoc. On the other hand, Nostoc genotypes showed no phylogeographic structure across the distribution range, while host cycads exhibited distinct north-south differentiation. Cycads may exist in symbiosis with either single or multiple Nostoc strains in natural soil habitats. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  17. Genetic diversity of pestivirus isolates in cattle from Western Austria.

    Science.gov (United States)

    Hornberg, Andrea; Fernández, Sandra Revilla; Vogl, Claus; Vilcek, Stefan; Matt, Monika; Fink, Maria; Köfer, Josef; Schöpf, Karl

    2009-03-30

    The genetic diversity of bovine viral diarrhoea virus (BVDV) isolates in infected cattle from Tyrol and Vorarlberg (Austria) was investigated. Blood samples were collected within the compulsory Austrian BVDV control programme during 2005 and 2006. The 5'-untranslated region (5'-UTR) and partially the N-terminal autoprotease (N(pro)) were amplified by one-step reverse transcriptase-polymerase chain reaction (RT-PCR) and the PCR products were subsequently sequenced. Phylogenetic analysis based on 5'-UTR and N(pro) sequences demonstrated that almost all isolates (307/310) were of the BVDV-1 genotype. They were clustered into eight different subtypes, here listed by their frequency of occurrence: BVDV-1h (143), BVDV-1f (79), BVDV-1b (41), BVDV-1d (28), BVDV-1e (6), BVDV-1a (4), BVDV-1g (3) and BVDV1-k (3). Two pestivirus isolates were typed as BVDV-2 and one isolate as BDV closely related to Gifhorn strain (BDV-3). Correlation among isolates could only be observed at the farm level, i.e., within a herd. However, no correlation between the genetic and geographical distances could be observed above the farm level. Because of the wide distribution of certain BVDV-1 subtypes and the low prevalence of herd-specific strains, a determination of tracing routes of infection was not possible. Furthermore, recombination events were not detected.

  18. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...... in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number...... of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated...

  19. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.).

    Science.gov (United States)

    Li, Pirui; Zhang, Fei; Chen, Sumei; Jiang, Jiafu; Wang, Haibin; Su, Jiangshuo; Fang, Weimin; Guan, Zhiyong; Chen, Fadi

    2016-06-01

    Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits.

  20. Assessment of genetic diversity of Lycoris longituba (Amaryllidaceae ...

    Indian Academy of Sciences (India)

    To take right measures to protect wild resources of L. longituba, it is important to study the range of genetic variation, genetic structure, diversification trend and other factors affecting genetic structure of the populations of this important and sparsely distributed species. Presently, many biochemical and DNA-based markers.

  1. Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

    Science.gov (United States)

    van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  2. Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

    Science.gov (United States)

    Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  3. Mapping genetic diversity of cherimoya (Annona cherimola Mill.: application of spatial analysis for conservation and use of plant genetic resources.

    Directory of Open Access Journals (Sweden)

    Maarten van Zonneveld

    Full Text Available There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill., a Neotropical fruit tree species. We present spatial analyses to (1 improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs; and (2 formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could

  4. Endemic and widespread coral reef fishes have similar mitochondrial genetic diversity.

    Science.gov (United States)

    Delrieu-Trottin, Erwan; Maynard, Jeffrey; Planes, Serge

    2014-12-22

    Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  5. Defining the landscape of adaptive genetic diversity.

    Science.gov (United States)

    Eckert, Andrew J; Dyer, Rodney J

    2012-06-01

    Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.). © 2012 Blackwell Publishing Ltd.

  6. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    Science.gov (United States)

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  7. genetic diversity among sorghum landraces of southwestern

    African Journals Online (AJOL)

    ACSS

    2016-05-14

    May 14, 2016 ... colour and threshability were major traits responsible for the observed clustering (P<0.001). Principal .... first to the flag leaf. Leaf length data were taken from the base to tip of the leaf, leaf width on the widest part of the same leaf, exertion length from ligule of flag .... selection based on perception for yield,.

  8. Genetic diversity and relationship analysis among accessions of ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) DNA markers were used to assess the genetic diversity and relationships between 55 accessions of genus Aegilops, including the species Aegilops triuncialis L. (UUCC), Aegilops geniculata Roth (MMUU), Aegilops cylindrica Host (CCDD) and Aegilops umbellulata Zhuk ...

  9. Genetic diversity in Balkhi, Hashtnagri and Michni sheep ...

    African Journals Online (AJOL)

    Morphological and genetic diversity among the three neighboring sheep breeds native to Central valley of Khyber Pukhtunkhwa (KP, Pakistan) was investigated. A total number of 138 non relative individuals of Balkhi (46), Hashtnagri (44) and Michni (48) was sampled for morphological as well as molecular characters ...

  10. Assessment of genetic diversity in Triticum spp. and Aegilops spp ...

    African Journals Online (AJOL)

    Genetic diversity among some wild relatives of wheat was estimated using amplified fragment length polymorphism (AFLP) and morphological markers. Thirty one Triticum and Aegilops genotypes including twenty-four Triticum and Aegilops accessions belonging to five diploid (Triticum baeoticum, Triticum monococcum, ...

  11. Low genetic diversity of Phytophthora infestans population in potato ...

    African Journals Online (AJOL)

    Late blight, caused by Phytophthora infestans is the most important disease of potato (Solanum tuberosum). This study reveals the genetic diversity of P. infestans population in north China. A total of 134 strains of P. infestans were isolated from different agricultural fields in Hebei, Liaoning, Jinlin and Heilongjiang Provinces ...

  12. Evaluation of genetic diversity in rice using simple sequence repeats ...

    African Journals Online (AJOL)

    The genetic diversity of 64 rice genotypes using 20 SSR primers on chromosome number 7-12 was investigated. DNA was extracted by modified cetyl trimethyl ammonium bromide (CTAB) method. The banding pattern was recorded in the form of 0-1 data sheet which was analyzed using unweighted pair group method with ...

  13. Genetic diversity and conservation of Mexican forest trees

    Science.gov (United States)

    C. Wehenkel; S. Mariscal-Lucero; J.P. Jaramillo-Correa; C.A. López-Sánchez; J.J. Vargas Hernández; C. Sáenz-Romero

    2017-01-01

    Over the last 200 years, humans have impacted the genetic diversity of forest trees. Because of widespread deforestation and over-exploitation, about 9,000 tree species are listed worldwide as threatened with extinction, including more than half of the ~600 known conifer taxa. A comprehensive review of the floristic-taxonomic literature compiled a list of 4,331...

  14. Genetic diversity in coastal and inland desert populations of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-14

    Nov 14, 2011 ... This study compared the genetic diversity within and among six naturally growing coastal and inland populations of Peganum harmala by using random amplified polymorphic DNA (RAPD) technique. Seven primers generated a total of 63 RAPD bands (loci) of which 60 (95.24%) were polymorphic across.

  15. Assessment of genetic diversity of sweet potato in Puerto Rico

    Science.gov (United States)

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand ...

  16. Assessment of genetic diversity in French bean ( Phaseolus vulgaris ...

    African Journals Online (AJOL)

    RAPD molecular markers were used to evaluate the genetic diversity in the fourteen varieties of French bean (Phaseolus vulgaris) of three eco-geographical regions of Bangladesh. Out of the 20 primers only, 6 yielded polymorphic banding patterns. In total, 40 different DNA bands were reproducibly obtained, out of which ...

  17. Assessment of genetic diversity in French bean (Phaseolus vulgaris ...

    African Journals Online (AJOL)

    ONOS

    2010-08-09

    Aug 9, 2010 ... RAPD molecular markers were used to evaluate the genetic diversity in the fourteen varieties of French bean (Phaseolus vulgaris) of three eco-geographical regions of Bangladesh. Out of the 20 primers only,. 6 yielded polymorphic banding patterns. In total, 40 different DNA bands were reproducibly ...

  18. Analysis of genetic diversity of muga silkworm (Antheraea ...

    African Journals Online (AJOL)

    USER

    2010-03-22

    Mar 22, 2010 ... Eleven populations of muga silkworm, Antheraea assamensis Helfer, the golden silk yarn producer of northeast India, was subjected to RAPD marker analysis in order to assess its genetic diversity. The genomic DNA extracted from muga silkworms were analysed using 50 random primers among which 36.

  19. Genetic Diversity of Local and Introduced Sweet Potato [Ipomoea ...

    African Journals Online (AJOL)

    This study was therefore conducted to estimate the genetic diversity of 114 Sweet potato [Ipomoea batatas (L.) Lam] accessions obtained from Nigeria, Asia, Latin America and Local collections along with two improved varieties. Accessions were planted in 2012/13 cropping season at Haramaya University, eastern Ethiopia ...

  20. Genetic diversity of Fusarium wilt races of pigeonpea in major ...

    African Journals Online (AJOL)

    Fusarium wilt is a serious fungal disease in pigeonpea (Cajanus cajan) which causes severe yield loses (up to 90%). Genetic diversity in pigeonpea wilt pathogen [Fusarium udum (fud)] was characterised using 14 isolates collected from major pulse growing regions of India. Twenty four RAPD primers generated a total of ...

  1. Genetic diversity assessment of wild and cultivated varieties of ...

    African Journals Online (AJOL)

    The present study deals with evaluation of genetic diversity and pedigree analysis through RAPD analysis. A total number of 40 Jatropha curcas accessions collected from different geographical regions and 43 random decamer primers were screened to assess polymorphism. 10 primers were amplified and 94 polymorphic ...

  2. Human immunodeficiency virus type-1 (HIV-1) genetic diversity and ...

    African Journals Online (AJOL)

    The presence of human immunodeficiency virus (HIV) type-1 diversity has an impact on vaccine efficacy and drug resistance. It is important to know the circulating genetic variants and associated drug-resistance mutations in the context of scale up of antiretroviral therapy (ART) in Nigeria. The objective of this study was to ...

  3. Genetic diversity in two populations of Limicolaria aurora (Jay, 1839 ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-06-22

    Jun 22, 2016 ... savannah) and Benin City (tropical rain forest) in Nigeria and possibly delimit the populations into sub species. A total of one hundred and ten specimens of L. aurora made up ..... Environmental stress such as drought could possibly have influenced genetic diversity in New Bussa with lower annual rainfall ...

  4. Evaluation of genetic diversity of Portuguese Pinus sylvestris L ...

    Indian Academy of Sciences (India)

    strategies and use of forest germplasm, as well as defini- tion of genetic relationships (Laurentin 2009). .... differentiation among populations in this pine species, given that RAPD produced a higher number of bands ... According to Tikhonova (2009) the strategy to conserve diversity of Scots pine from natural stands and ...

  5. Genetic diversity and chemical polymorphism of Tunisian Lavandula ...

    African Journals Online (AJOL)

    Population differentiation performed on combined data yielded similar to that shown using each marker separately. Conservation strategies should take into account the levels of genetic diversity and chemical variation in relation to population and bioclimate. Keywords: Lavandula multifida, Tunisia, natural populations, ...

  6. Genetic diversity of Annona senegalensis Pers. populations as ...

    African Journals Online (AJOL)

    Annona senegalensis Pers. is one of the wild fruit tree for domestication in southern Africa. An assessment of the genetic diversity in A. senegalensis would assist in planning for future germplasm collection, conservation and fruit domestication programmes. During 2004 to 2006 nine populations were collected from different ...

  7. Genetic Diversity and Relationships in the Turkey species of the ...

    African Journals Online (AJOL)

    ILHAN

    2011-11-16

    Nov 16, 2011 ... Amplified fragment length polymorphism (AFLP) DNA markers were used to assess the genetic diversity and relationships between 55 accessions of genus Aegilops, including the species Aegilops triuncialis L. (UUCC), Aegilops geniculata Roth (MMUU), Aegilops cylindrica Host (CCDD) and Aegilops.

  8. Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    Hierarchical Approaches to the Analysis of Genetic Diversity in Plants: A Systematic Overview. ME Osawaru, MC Ogwu, RO Aiwansoba. Abstract. Hierarchical analysis highlights the nature of relationship between and among type samples as outlined by standard descriptors. It produces an output called dendrogram, which ...

  9. Assessment of genetic diversity analysis in contrasting sugarcane ...

    African Journals Online (AJOL)

    Sugarcane is an important crop in the country economically, politically and sociologically. It is the second largest agro-industry next to textiles. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 28 sugarcane genotypes were ...

  10. Molecular Mechanisms Influencing Genetic Diversity of Campylobacter jejuni

    NARCIS (Netherlands)

    Gaasbeek, E.J.

    2009-01-01

    Campylobacter jejuni is an important food-borne pathogen, causing human bacterial gastroenteritis. Throughout the years several methods have been developed for typing C. jejuni. These methods uncovered the existence of enormous genetic diversity within the species. Stable lineages of C. jejuni are

  11. Genetic diversity of intensive cultured and wild tiger shrimp Penaeus ...

    African Journals Online (AJOL)

    The objective of this study was to assess the genetic diversity of intensive cultured and wild tiger shrimp Penaeus monodon (Fabricius) in Malaysia using six microsatellite markers (CSCUPmo1, CSCUPmo2, CSCUPmo3, CSCUPmo4, CSCUPmo6 and CSCUPmo7). The mean numbers of allele, observed heterozygosis, ...

  12. Genetic diversity of Przewalski's gazelle using noninvasive DNA and ...

    African Journals Online (AJOL)

    Cynthia

    2015-04-01

    Apr 1, 2015 ... The Przewalski's gazelle (Procapra przewalskii) is endemic to China and the total current population of the species is only about several hundred. In order to understand the genetic structure and diversity of the Przewalski's gazelle in China for the purpose of guiding conservation initiatives, we examined ...

  13. Evaluation of genetic diversity in the golden apple snail, Pomacea ...

    African Journals Online (AJOL)

    The genetic diversity of Pomacea canaliculata, collected from Los Banos (LB) in Philippines and Yuyao (YY), Taizhou (TZ), Fuzhou (FZ), Guangzhou (GZ), Nanning (NN), Kunming (KM) in China, was studied by using the inter simple sequence repeat (ISSR) technique. A total of 498 loci from 140 individuals were amplified ...

  14. Genetic diversity studies and identification of SSR markers ...

    Indian Academy of Sciences (India)

    2013-08-13

    Aug 13, 2013 ... Abstract. Genetic diversity and identification of simple sequence repeat markers correlated with Fusarium wilt resistance was performed in a set of 36 elite cultivated pigeonpea genotypes differing in levels of resistance to Fusarium wilt. Twenty-four polymorphic sequence repeat markers were screened ...

  15. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

    2011-01-01

    Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprisin...

  16. Analysis of the genetic diversity of four rabbit genotypes using ...

    African Journals Online (AJOL)

    Dr.Ola

    2013-05-15

    May 15, 2013 ... diseases or market conditions. A considerable number of genetic diversity studies for several livestock species have been carried out during recent years by research. *Corresponding author. E-mail: ola.galal@agr.kfs.edu.eg or olagalal2002@yahoo.com , Tel/Fax: +2-0479102930. Abbreviations: APRI ...

  17. Assessment of genetic diversity among maize accessions using inter ...

    African Journals Online (AJOL)

    Assessment of genetic diversity among maize accessions using inter simple sequence repeats (ISSR) markers. AT do Amaral Júnior, EC de Oliveira, LSA Gonçalves, CA Scapim, LS Candido, TR da Conceição Silva, C Vittorazzi, KS da Cunha ...

  18. Genetic diversity of Cryptosporidium spp. in captive reptiles

    Czech Academy of Sciences Publication Activity Database

    Xiao, L.; Ryan, U. M.; Graczyk, T. K.; Limor, J.; Li, L.; Kombert, M.; Junge, R.; Sulaiman, I. M.; Zhou, L.; Arrowood, M. J.; Koudela, Břetislav; Modrý, David; Lal, A. A.

    2004-01-01

    Roč. 70, č. 2 (2004), s. 891-899 ISSN 0099-2240 R&D Projects: GA ČR GA524/00/P015 Institutional research plan: CEZ:AV0Z6022909 Keywords : Cryptosporidium * reptiles * genetic diversity Subject RIV: EG - Zoology Impact factor: 3.810, year: 2004

  19. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    Unknown

    . 295. Genetic diversity and bottleneck studies in the Marwari horse breed. A. K. GUPTA 1 *, M. CHAUHAN 1 , S. N. TANDON 1 and SONIA 2. 1National Research Centre on Equines, Sirsa Road, Hisar 125 001, India. 2Guru Jambeshwar ...

  20. Molecular evaluation of genetic diversity and association studies in ...

    Indian Academy of Sciences (India)

    In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination ...

  1. Appraisal of biochemical and genetic diversity of mango cultivars ...

    African Journals Online (AJOL)

    Mango (Mangifera indica L.) is one of the oldest fruit crops and is broadly cultivated worldwide. To determine the level of genetic diversity, a total of 13 mango genotypes have been collected from different farms of Fayoum oasis in Egypt and were analyzed using molecular (DNA) and biochemical (SDS-PAGE) markers ...

  2. Population genetic diversity of marble goby (Oxyeleotris marmoratus ...

    Indian Academy of Sciences (India)

    Cheng Zhao

    2017-12-08

    Dec 8, 2017 ... east Asia, especially in Malaysia, Singapore, Thailand and. Vietnam (Inger ... cial culture of marble goby has suffered from germplasm ..... Southeast Asia. Through long-term artificial breeding, the genetic diversity of the cultured marble goby popula- tions were relatively low compared to Vietnam population.

  3. Genetic diversity and population structure of 10 Chinese indigenous ...

    Indian Academy of Sciences (India)

    times become extinct. This loss of genetic diversity within and among breeds is a negative trend, not only from the perspective of culture, but also with regard to utility. Traits, genotypes and alleles with possible economic interest are at risk of being lost. Further, breeds are exposed to a great loss of alleles and haplotypes as ...

  4. Genetic diversity, phylogeographic structure and effect of selection ...

    Indian Academy of Sciences (India)

    Abdulhakeem B. Ajibike

    2017-12-11

    Dec 11, 2017 ... Abstract. In this study, the maternal genetic diversity, phylogenetic relationship and effect of natural selection on indigenous chickens from Nigeria were assessed. A total of 397-bp fragment of the mitochondrial DNA (mtDNA) D-loop region of 171 indigenous chickens from four populations of Nigeria and ...

  5. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    user

    2011-02-28

    Feb 28, 2011 ... Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. Ting Ji, Ling Yin and Guohong Chen*. College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China. Accepted 18 January, 2011. Using 21 microsatellite markers ...

  6. Evaluation of genetic diversity in rice using SSR markers

    African Journals Online (AJOL)

    hemant

    2012-10-18

    Oct 18, 2012 ... The polymorphism information content (PIC) value for the SSR loci ranged from 0.36 to. 0.98. Higher PIC values were associated ... Since each marker system has specific advantages and disadvantages, the choice of the marker ... The objective of current studies was to estimate the genetic diversity among ...

  7. Genetic diversity in Ethiopian mustard ( Bbrassica carinata a. braun ...

    African Journals Online (AJOL)

    In this study, genetic diversity in 60 Ethiopian mustard genotypes, collected from 16 regions of Ethiopia, were assessed using the techniques of cluster and ... for the majority of traits of interest: seed yield/plot, seed yield/plant, biomass/plot, biomass/plant, plant height, number of pods/plant, 1000 seeds' weight and oil content ...

  8. Genetic diversity of taraxacum germplasm revealed by sequence ...

    African Journals Online (AJOL)

    Sequence-related amplified polymorphism (SRAP) and morphological markers were employed to determine the genetic diversity and relations among 11 population of taraxacum in northeast of China. Data on 34 morphological traits were collected and analyzed. A total of 795 polymorphic SRAP's bands were scored with ...

  9. Genetic structure and diversity of East African taro [ Colocasia ...

    African Journals Online (AJOL)

    Taro [Colocasia esculenta (L) Schott] is mainly produced in Africa by small holder farmers and plays an important role in the livelihood of millions of poor people in less developed countries. The genetic diversity of East African taro has not been determined. This study utilizes six microsatellite primers to analyze five ...

  10. Some insights into the phenotypic and genetic diversity of ...

    African Journals Online (AJOL)

    Deon

    objectives: to describe pig production systems, get a phenotypic description of the pigs and to characterize ... aimed at combining data on production systems, physical attributes and genetic diversity in order to build a .... condition scores of pigs and chemical composition of pig feed resources in a semi-arid smallholder.

  11. A study of patrilineal genetic diversity in Iranian indigenous horse ...

    African Journals Online (AJOL)

    Autosomal markers and mtDNA have been used in horse phylogenetic studies. These studies display evolutionary events that happened in both sexes or only in females. It is necessary to investigate genetic diversity in Y-specific markers for clarifying contribution of males in horse domestication. The Y chromosome ...

  12. Analysis of genetic diversity in mango ( Mangifera indica L.) using ...

    African Journals Online (AJOL)

    Glutamate oxaloacetate transaminase, malate dehydrogenase and peroxidase analysis possessed 8, 10 and 7 zymotypes, respectively, and genotypes were grouped into different electrophoretic zymotypes which indicated higher level of genetic diversity of mango. For glutamate oxaloacetate transminase, G6 was the most ...

  13. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    Generally, Tigray and Amhara regions showed moderate to high diversity in ISSR analysis. ... other crops. The main purpose of its cultivation in. Ethiopia is to use it as a medicinal plant. It is used for human abdominal ache and diarrhea. Moreover, L. ... of 10 primers were obtained from the Genetic Research Laboratory.

  14. Genetic diversity and germplasm resource research on tung tree ...

    African Journals Online (AJOL)

    Tung tree is an important woody oil-rich plant in the world. In order to determine the genetic diversity, germplasm resource and breeding method on tung tree, inter-simple sequence repeats (ISSR) was used to investigate the cultivars in China. Among the total 110 bands amplified with 12 primers, 90 were polymorphic.

  15. Population genetic diversity of marble goby (Oxyeleotris marmoratus ...

    Indian Academy of Sciences (India)

    Cheng Zhao

    2017-12-08

    Dec 8, 2017 ... E-mail: yinshaowu@163.com. Cheng Zhao and Xiaoping Zhu contributed equally to this work. Keywords. marble goby; genetic diversity; mtDNA control region; microsatellite; population structure. mtDNA is highly polymorphic and it has 5–10 times rate of nucleotide substitution than nuclear DNA (Aquadro.

  16. Genetic diversity among some blackberry cultivars and their ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... Key words: Blackberry, Boysenberry, raspberry, genetic diversity, AFLP markers. INTRODUCTION. Blackberries are fruiting-bearing species of genus Rubus subgenus Rubus of Rosaceae family (Clark et al., 2007). Germplasm Resources Information Network describes 13 subgenera for the genus Rubus ...

  17. Examination of genetic diversity in common bean (Phaseolus ...

    African Journals Online (AJOL)

    HP

    2015-02-11

    Feb 11, 2015 ... To study the pattern of genetic diversity in 45 genotypes of common bean, 19 RAPD primers were used. Of 253 bands produced, 236 bands (94.22%) were polymorphic in which maximum number (20 polymorphic bands) were observed in the profiles of the primer OPB-07. Highest PIC value (0.79) was.

  18. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    The present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat by genome DNA fingerprinting as revealed by random amplified polymorphic DNA (RAPD) analysis. Ten decamer RAPD primers (OPG-1, OPG-2, OPG-3, OPG-4, OPG-5, OPA-3, OPA-4, OPA-5, OPA-8, and OPA-15) ...

  19. The use of microsatellite markers for genetic diversity assessment of ...

    African Journals Online (AJOL)

    In this study, gene diversity and genetic relationships among 30 genotypes of genus Hordeum from Kerman province (Iran) were assessed using 10 simple sequence repeat (SSR) primers. Seven of these markers were highly polymorphic. A total of 96 alleles were detected. The number of alleles per microsatellite marker ...

  20. Assessment of genetic diversity of rice ( Oryza sativa ) cultivars using ...

    African Journals Online (AJOL)

    A set of 36 polymorphic simple sequence repeat (SSR) primers well distributed on all the 12 rice chromo-somes have been used to assess the genetic diversity among the rice varieties. A total of 98 alleles were detected with an average of 2.78 alleles per locus across 39 genotypes. The number of alleles varied from two to ...

  1. Assessment of genetic diversity for some Iraqi date palms ( Phoenix ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphisms (AFLP) were used to evaluate the genetic diversity between 18 date palm (Phoenix dactylifera L.) varieties (11 females and 7 males) collected from the center of Iraq. Six primer pairs were applied to detect polymorphism between varieties. A total of 83 polymorphic AFLP fragments ...

  2. Genetic diversity and relationship analysis of the Brassica napus ...

    African Journals Online (AJOL)

    Oilseed rape (Brassica napus L.) is an important oilseed crop worldwide. The objective of this research was to study the genetic diversity and relationships of B. napus accessions using simple sequence repeat (SSR). A set of 217 genotypes was characterized using 37 SSR markers of mapping on the B. napus genome.

  3. Genetic diversity and population structure of Caragana microphylla ...

    African Journals Online (AJOL)

    Caragana microphylla Lam. is a long-lived shrub species in the semi-arid, arid and desert regions. To determine the genetic diversity and population structure of C. microphylla Lam., 17 wild populations from the central and eastern part of Inner Mongolia were analyzed by inter-simple sequence repeat. 18 primers produced ...

  4. Genetic diversity analysis of stress tolerant rice ( Oryza sativa L ...

    African Journals Online (AJOL)

    Genetic diversity analysis of stress tolerant rice (Oryza sativa L.) A S M Faridul Islam, M Raihan Ali, Glenn B Gregorio, M Rafiqul Islam. Abstract. Fourteen rice genotypes, composed of six salt tolerant, three submergence tolerant, two drought tolerant genotypes along with three high yielding genotypes, released from ...

  5. Genetic diversity of two Tunisian sheep breeds using random ...

    African Journals Online (AJOL)

    Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity and population structure in six sheep populations belonging to two native Tunisian breeds (the Barbarine and the Western thin tail). A total of 96 samples were typed using eight RAPD primers. 62 bands were scored, of which 44 ...

  6. Evaluation of genetic diversity in barley ( Hordeum vulgare L.) from ...

    African Journals Online (AJOL)

    This study aimed to determine the genetic diversity and relationships among barley varieties (Hordeum vulgare L.) growing at Wollo Highland areas by using hordein and agro-morphological traits. Twenty (20) varieties were laid down in randomized complete block design (RCBD) design with three replications; they were ...

  7. Genetic diversity and in vitro antibiotic susceptibility profile of ...

    African Journals Online (AJOL)

    We assessed the genetic diversity of forty Salmonella isolates obtained from selected domestic water and waste water sources in the Eastern Cape Province of South Africa using DNA fingerprinting and antibiotic susceptibility profile as test indices. Restriction digests and SDS/PAGE as well as the DNA dendograms of the ...

  8. Assessment of genetic diversity in Triticum spp. and Aegilops spp ...

    African Journals Online (AJOL)

    SERVER

    2008-03-04

    Mar 4, 2008 ... polymorphism (AFLP) and morphological markers. Thirty one Triticum and Aegilops genotypes ..... modern breeding would go hand in hand with a large decrease in diversity, which could threaten ... Aegilops tauschii genepool and the evolution of hexaploid wheat. Theor. Appl. Genet. 97: 657–670. Friebe B ...

  9. Study of genetic diversity in finger millet (Eleusine coracana L ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... Radioactive detection. Yes/No. No. Yes/No. No. Yes/No. Yes/No. Development costs. Medium. Low. Medium. Medium/High. High. Medium. Start-up costs. Medium/High. Low. Medium. High. High. Medium. Applications. Genetic diversity, polyploidy, hybridization, phylogeny, mating system. Fingerprinting,.

  10. Study of genetic diversity in Sudanese sesame (Sesamum indicum L ...

    African Journals Online (AJOL)

    The random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Sesame indicum (L.). RAPD technique was carried out in a set of 10 sesame germplasm collected from different regions of Sudan. A total of 64 polymorphisms (6.4 polymorphic markers per primer) out of 75 reproducible ...

  11. Preliminary molecular analysis of the genetic diversity of some ...

    African Journals Online (AJOL)

    In the arid and semi arid areas, salt bush (Atriplex) represents an important forage resource. The characterization of the genetic diversity of these species is useful for their classification, their conservation and their improvement. In this context, we used the random amplified polymorphic DNA-polymerase chain reaction ...

  12. Genetic diversity of bottle gourd ( Lagenaria siceraria (Molina) Standl.)

    African Journals Online (AJOL)

    Bottle gourd (Lagenaria siceraria (Molina) Standl.) is an important crop in rural communities in South Africa but it remains under-researched. The objective of this study was to assess the genetic diversity present amongst bottle gourd landraces grown by smallholder farmers in South Africa using morphological traits and 11 ...

  13. Genetic diversity in coastal and inland desert populations of ...

    African Journals Online (AJOL)

    This study compared the genetic diversity within and among six naturally growing coastal and inland populations of Peganum harmala by using random amplified polymorphic DNA (RAPD) technique. Seven primers generated a total of 63 RAPD bands (loci) of which 60 (95.24%) were polymorphic across all individuals.

  14. Assessment of genetic diversity in sorghum accessions using ...

    African Journals Online (AJOL)

    uwerhiavwe

    3Agricultural Research Council - Grain Crops Institute, Private Bag X1251, Potchefstroom 2520, South Africa. Accepted 21 February, 2013. Amplified ... the main areas of sorghum domestication (Deu et al.,. 1994). Assessment of sorghum ... characterise genetic diversity within and among crop species and these will help in ...

  15. Genetic diversity of important rice cultivars of Kashmir valley using ...

    African Journals Online (AJOL)

    27,RM-72, RM-107 and RM-154 were used to estimate the genetic diversity of eight indica rice cultivars significant for rice breeding programme in the temperate Kashmir Province of India. The SSR primers used, specific to five different ...

  16. Genetic diversity and population structure among isolates of the ...

    African Journals Online (AJOL)

    Bipolaris oryzae, the rice brown spot fungus is one of the pathological threats to rice crop worldwide. The genetic diversity among the Indian isolates of brown spot pathogen was studied using inter-simple sequence repeats (ISSR). Considerable intraspecific variability among the isolates of B. oryzae was revealed.

  17. Application of SRAP in the genetic diversity of Tricholoma matsutake ...

    African Journals Online (AJOL)

    GREGORY

    2010-09-20

    Sep 20, 2010 ... Key words: Genetic diversity, Tricholoma matsutake, fungi, sequence related amplified polymorphism (SRAP). INTRODUCTION. The ectomycorrhizal fungus Tricholoma matsutake is one of the most delicious and valuable edible mushrooms in ... and one each from Korea, Japan, France, and Morocco,.

  18. Genetic diversity of maize genotypes on the basis of morpho ...

    African Journals Online (AJOL)

    In this investigation, an attempt was made to assess the genetic diversity among 91 maize (Zea mays L.) genotypes using morpho-physiological and molecular markers. Variability was observed for six morpho-physiological traits namely, SPAD chlorophyll meter reading, canopy temperature, plant height, yield per plant, ...

  19. Genetic diversity of indigenous chicken ecotypes in Jordan | Al ...

    African Journals Online (AJOL)

    DNA polymorphism of 4 indigenous chicken ecotypes was assessed in Jordan using random amplified polymorphic DNA (RAPD) markers. 10 RAPD markers showed high genetic diversity values in the 4 ecotypes located in the northern, eastern, western and southern provinces of Jordan. The effective number of alleles per ...

  20. Analysis of genetic diversity and construction of core collection of ...

    African Journals Online (AJOL)

    Jane

    2011-06-03

    Jun 3, 2011 ... Genetic diversity of 73 local mulberry varieties from Shanxi Province were screened using ISSR markers, with l5 primers combinations selected for their reproducibility and polymorphism. 129 bands were amplified, of which 115 bands showed polymorphism and the ratio of polymorphism bands was.

  1. Assessment of the genetic diversity conservation in three tall coconut

    African Journals Online (AJOL)

    Assessment of the genetic diversity conservation in three tall coconut (Cocos nucifera L.) accessions regenerated by controlled pollination, using microsatellite markers. Saraka Didier Martial Yao, Konan Jean Louis Konan, N'Da Désiré Pokou, Kouamé Jean Noel Konan, Auguste Emmanuel Issali, Raoul Sylvère Sie, Bi Irié ...

  2. Genetic diversity and historical demography of kuruma shrimp ...

    African Journals Online (AJOL)

    Two varieties (I and II) of kuruma shrimp (Penaeus japonicus) were found in the north of South China Sea (SCS) and Taiwan Strait (TS). To estimate the demographic history and genetic diversity of this species complex off China, 141 individuals were collected from the East China Sea (ECS), TS and SCS and 27 variety 2 ...

  3. Analysis of genetic diversity in pigeon pea germplasm using ...

    Indian Academy of Sciences (India)

    MANEESHA

    2017-08-16

    Aug 16, 2017 ... Asia and Africa. It is normally considered to have a low degree of genetic diversity, an impediment in undertaking crop improvement programmes. ... of environmental conditions. ..... Th, Thailand; It, Italy; B, Barbados; Ta, Taiwan; J, Jamaica; V, Venezuela; UK, United Kingdom; My, Myanmar; U, Uganda; G,.

  4. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

  5. DNA methylation and genetic diversity analysis of genus Cycas in ...

    African Journals Online (AJOL)

    mallory

    2012-01-12

    Jan 12, 2012 ... Key words: Cycas, DNA methylation, genetic diversity, methylation sensitive amplification polymorphism .... Cliffs and steep slopes on Khao Chamao mountain (eastern. Thailand). C. clivicola subsp. clivicola (Cli). 7-9, 10-12. M, F. Limestone cliffs, sea shore, evergreen forest, dry ... cytosine at both strands.

  6. Assessment of genetic diversity in Sudanese maize ( Zea mays L ...

    African Journals Online (AJOL)

    The randomly amplified polymorphic DNA (RAPD) molecular markers were used to assess genetic diversity in 27 Sudanese maize genotypes. Ten primers were used, resulting in the amplification of 59 fragments, of which 53 (89.33) were polymorphic. The maximum number of fragment bands (10) were produced by the ...

  7. Genetic diversity of Mycobacterium tuberculosis in Mbarara, South ...

    African Journals Online (AJOL)

    Background: We determined the genetic diversity of mycobacteria isolated from tuberculosis patients in Mbarara Uganda, using region of difference (RD) analysis and spacer oligonucleotide typing (spoligotyping). Methods: Sputum samples were cultured on Lowenstein Jensen media. The isolates were characterized using ...

  8. Genetic diversity of Pogonatherum paniceum (Lam.) Hack in ...

    African Journals Online (AJOL)

    Inter-simple sequence repeats markers were used to estimate the genetic diversity of Pogonatherum paniceum (Lam.) Hack. from Sichuan Province, Yunnan Province, Chongqing City and Guangxi Zhuang Autonomous Region in China. 100 primers were carried out on 22 wild populations, 14 could produce highly ...

  9. Genetic diversity of Pogonatherum paniceum (Lam.) Hack. in ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) markers were used to estimate the genetic diversity of Pogonatherum paniceum (Lam.) Hack. from Sichuan Province, Yunnan Province, Chongqing City and. Guangxi Zhuang autonomous Region in China. 10 primer combinations were carried out on 180 different individuals ...

  10. Assessment of genetic diversity among accessions of two traditional ...

    African Journals Online (AJOL)

    Assessment of genetic diversity among accessions of two traditional leafy vegetables (Acmella uliginosa (L.) and Justicia tenella (Nees) T.) consumed in Benin using amplified fragment length polymorphism (AFLP) markers. K Adéoti, A Rival, A Dansi, BS Ahohuendo, S Santoni, T Beule, A Nato, Y Henry, A Ahanchédé, ...

  11. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-20

    Jul 20, 2009 ... Full Length Research Paper. Molecular analysis of genetic diversity in elite II synthetic hexaploid wheat screened against Barley yellow dwarf virus. Huma Saffdar1 ... The history of cultiva- ted wheat and human .... and viewed under the UV light chamber using the computer pro- gram UVIPhotoMW.

  12. Molecular assessment of genetic diversity in cluster bean ...

    Indian Academy of Sciences (India)

    pestle in a 1.5 mL conical micro-centrifuge tubes with liquid nitrogen. Dneasy. ® plant mini kit protocols ... products was drawn using unweighted pair group method us- ing arithmetic averages algorithm (UPGMA) .... Mignouna H. D., Ng N. Q., Ikea J. and Thotapilly G. 1998 Genetic diversity in cowpea as revealed by random ...

  13. Genetic diversity of Ascaris in southwestern Uganda

    DEFF Research Database (Denmark)

    Betson, Martha; Nejsum, Peter; Llewellyn-Hughes, Julia

    2012-01-01

    Despite the common occurrence of ascariasis in southwestern Uganda, helminth control in the region has been limited. To gain further insights into the genetic diversity of Ascaris in this area, a parasitological survey in mothers (n=41) and children (n=74) living in two villages, Habutobere and M...

  14. Genetic diversity in green gram [Vigna radiata (L.)] landraces ...

    African Journals Online (AJOL)

    Green gram [Vigna radiata (L.)] landraces were collected from various localities of Southern Tamil Nadu, India, to determine the extent of genetic diversity at DNA level by random amplified polymorphic DNA (RAPD) analysis using 20 decamer primers. All the primers produced polymorphic amplification products with some ...

  15. Genetic diversity and population structure of begomoviruses infecting sweet potato

    Science.gov (United States)

    Begomoviruses infecting sweet potatoes (Ipomoea batatas) exhibit high genetic diversity, and approximately eight species including Sweet potato leaf curl virus (SPLCV) have been described from different regions around the world. In this study, the complete genomic sequences of 17 geographically dist...

  16. Genetic diversity of Santalum album using random amplified ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-06

    Jul 6, 2009 ... Sandalwood is found distributed all over the country with over 90% of the area in Karnataka and Tamil Nadu. It is of great economic importance because of its fragrant heartwood and oil. In the present study Random Amplified Polymorphic DNA (RAPD) technique was used to accesses the genetic diversity ...

  17. Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers*

    Directory of Open Access Journals (Sweden)

    Ocelák M.

    2015-12-01

    Full Text Available The diversity and genetic relationships in 173 sacha inchi samples were analyzed using ISSR markers. Thirty ISSR primers were used, only 8 showed variability in tested samples. ISSR fragments ranged from 200 to 2500 bp. The mean number of bands per primer was 12 and the average number of polymorphic bands per primer was 11. The lowest percentages of polymorphic bands (27%, gene diversity (0.103, and Shannon’s information index (0.15 were exhibited by the Santa Lucia population, which was also geographically most distant. This fact may be attributed to a very small size of this group. In contrast, the Dos de Mayo population exhibited the highest percentage of polymorphic bands (78%, and the Santa Cruz population the highest Nei’s gene diversity index (0.238 and Shannon’s information index (0.357. The obtained level of genetic variability was 36% among tested populations and 64% within populations. Although the diversity indices were low, a cluster analysis revealed 8 clusters containing mainly samples belonging to individual populations. Principal coordinate analysis clearly distinguished Chumbaquihui, Pucallpa, Dos de Mayo, and Aguas de Oro populations, the others were intermixed. The obtained results indicated the level of genetic diversity present in this location of Peru, although it is influenced by anthropological aspects and independent on the geographical distances.

  18. Determination of genetic diversity among some almond accessions

    Directory of Open Access Journals (Sweden)

    Pinar Hasan

    2015-01-01

    Full Text Available More recently the use of different molecular markers in fruit species to determine particularly genetic diversity, genetic relationships and cultivar identification has been gained more importance. In the study, 13 randomly amplified polimorfic DNA (RAPD and 4 inter-simple sequence repeat (ISSR markers were used to evaluate genetic relationships among 95 almong accessions (26 foreign cultivars and 69 national cultivars and selections. The all plant material found in Almond Germplasm Repository in Gaziantep, Turkey. Both RAPD and ISSR markers distinguished the almond cultivars and selections in various levels. 17 RAPD and ISSR markers yielded a total of 73 scorable bands, which 51 are polymorphic. The two marker system exhibited variation with regard to average band sizes and polymorphism ratio. The average polymorphism was higher in ISSR (88% compared to RAPD (74%. RAPD and ISSR marker systems were found to be useful for determining genetic diversity among almong genotypes and cultivars. Combining of two dendrograms obtained through these markers show different clustering of 96 almond specimens without geographical isolation. These results supported that almonds in Turkey indicated considerable genetic diversity.

  19. [Study on Genetic Diversity of Twelve Natural Zanthoxylum dissitum Populations].

    Science.gov (United States)

    Li, Meng; Wang, Ping; Sun, Ji-kang; Zhou, Tao; Fe, Ming-liang

    2014-12-01

    The genetic diversity of twelve natural Zanthoxylum dissitum populations, which is a species of Chinese herbal medicines to four provinces of southwest China, has been investigated. By inter-simple sequence repeat markers (ISSR), the eight primers, which could amplify stable, clear and highly polymorphic bands, were screened from 100 candidate primers. 150 total ISSR discernible bands and 147 polymorphic were amplified by the eight checked primers. On one hand, the percentage of polymorphic bands was 98.0%, on the other hand, the population level the percent of polymorphic bands ranged from 26.0% to 62.0%. The Shannon's information index within species (Hsp) was 0.4175, while the values within population (Hpop) were ranged from 0.1328 to 0.3267. Analysis of molecular variance (ANOVA) revealed that the population genetic variation accounted for 47.98% but the intraspecific variation for 52.02%. The high level of genetic diversity exists not only in population but also in species. A high degree of genetic differentiation populations is approved to exist in Zanthoxylum dissitum. These results lay a theoretical foundation for genetic diversity analysis of Zanthoxylum dissitum.

  20. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    Science.gov (United States)

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.