WorldWideScience

Sample records for stable genetic diversity

  1. Stable genetic diversity despite parasite and pathogen spread in honey bee colonies

    Science.gov (United States)

    Jara, Laura; Muñoz, Irene; Cepero, Almudena; Martín-Hernández, Raquel; Serrano, José; Higes, Mariano; De la Rúa, Pilar

    2015-10-01

    In the last decades, the rapid spread of diseases, such as varroosis and nosemosis, associated with massive honey bee colonies mortality around the world has significantly decreased the number and size of honey bee populations and possibly their genetic diversity. Here, we compare the genetic diversity of Iberian honey bee colonies in two samplings performed in 2006 and 2010 in relation to the presence of the pathogenic agents Nosema apis, Nosema ceranae, and Varroa destructor in order to determine whether parasite and pathogen spread in honey bee colonies reflects changes in genetic diversity. We found that the genetic diversity remained similar, while the incidence of N. ceranae increased and the incidence of N. apis and V. destructor decreased slightly. These results indicate that the genetic diversity was not affected by the presence of these pathogenic agents in the analyzed period. However, the two groups of colonies with and without Nosema/Varroa detected showed significant genetic differentiation (G test). A detailed analysis of the allelic segregation of microsatellite loci in Nosema/Varroa-negative colonies and parasitized ones revealed two outlier loci related to genes involved in immune response.

  2. Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes.

    Directory of Open Access Journals (Sweden)

    S Elizabeth Alter

    Full Text Available Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.

  3. [Genetic diversity of microorganisms].

    Science.gov (United States)

    Li, Juan; Zhang, Ke-Qin

    2012-11-01

    Microorganisms are important components of the biosphere in maintaining the ecological balance. With the development of molecular biology techniques, researches on the microbial genetic diversity have been developed from morphological and/or protein levels to molecular level. The development of high-throughout sequencing and metagenomics technology not only provide more abundant information and powerful evidence for understanding microbial diversities, but also have great significance for rational utilization and protection of biological resources. The advances in research on genetic diversity of microorganisms, such as separation and identification, population genetic structure, speciation, phylogeny, and evolution of microorganisms, were discussed in this paper.

  4. Low genetic diversity and genetic differentiation among ...

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... (2003) examined genetic diversity of tropical abalone H. asinina originating from Thai waters by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of 18S and 16S rDNAs, and the lack of genetic heterogeneity were confirmed. Recently, significant genetic differentiation ...

  5. Genetic diversity increases population productivity in a sessile marine invertebrate.

    Science.gov (United States)

    Aguirre, J David; Marshall, Dustin J

    2012-05-01

    Reductions in genetic diversity can have widespread ecological consequences: populations with higher genetic diversity are more stable, productive and resistant to disturbance or disease than populations with lower genetic diversity. These ecological effects of genetic diversity differ from the more familiar evolutionary consequences of depleting genetic diversity, because ecological effects manifest within a single generation. If common, genetic diversity effects have the potential to change the way we view and manage populations, but our understanding of these effects is far from complete, and the role of genetic diversity in sexually reproducing animals remains unclear. Here, we examined the effects of genetic diversity in a sexually reproducing marine invertebrate in the field. We manipulated the genetic diversity of experimental populations and then measured individual survival, growth, and fecundity, as well as the size of offspring produced by individuals in high and low genetic diversity populations. Overall, we found greater genetic diversity increased performance across all metrics, and that complementarity effects drove the increased productivity of our high-diversity populations. Our results show that differences in genetic diversity among populations can have pervasive effects on population productivity within remarkably short periods of time.

  6. Human Capital and Genetic Diversity

    OpenAIRE

    Sequeira, Tiago; Santos, Marcelo,; Ferreira-Lopes, Alexandra

    2013-01-01

    The determinants of human capital have been studied sparsely in the literature. Although there is a huge literature on the determinants of schooling linked with the quality of schooling, there are not many contributions that explore the deep determinants of investment in, quantity and quality of human capital. This paper investigates the relationship between human capital and the ancestral genetic diversity of populations. It highlights a strong hump-shaped relationship between genetic divers...

  7. Genetic diversity in Trichomonas vaginalis.

    Science.gov (United States)

    Meade, John C; Carlton, Jane M

    2013-09-01

    Recent advances in genetic characterisation of Trichomonas vaginalis isolates show that the extensive clinical variability in trichomoniasis and its disease sequelae are matched by significant genetic diversity in the organism itself, suggesting a connection between the genetic identity of isolates and their clinical manifestations. Indeed, a high degree of genetic heterogeneity in T vaginalis isolates has been observed using multiple genotyping techniques. A unique two-type population structure that is both local and global in distribution has been identified, and there is evidence of recombination within each group, although sexual recombination between the groups appears to be constrained. There is conflicting evidence in these studies for correlations between T vaginalis genetic identity and clinical presentation, metronidazole susceptibility, and the presence of T vaginalis virus, underscoring the need for adoption of a common standard for genotyping the parasite. Moving forward, microsatellite genotyping and multilocus sequence typing are the most robust techniques for future investigations of T vaginalis genotype-phenotype associations.

  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. 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...

  10. 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

  11. Assessing Plant Genetic Diversity by Molecular Tools

    OpenAIRE

    Linda Mondini; Arshiya Noorani; Pagnotta, Mario A.

    2009-01-01

    This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity. In recent years, there has been a significant increase in the application of molecular genetic methods for assessing the conservation and use of plant genetic resources. Molecular techniques have been applied in the analysis of specific genes, as well as to increase understanding of gene action, generate genetic maps and assist in the development of gene transfer technologi...

  12. An Anthropocene map of genetic diversity.

    Science.gov (United States)

    Miraldo, Andreia; Li, Sen; Borregaard, Michael K; Flórez-Rodríguez, Alexander; Gopalakrishnan, Shyam; Rizvanovic, Mirnesa; Wang, Zhiheng; Rahbek, Carsten; Marske, Katharine A; Nogués-Bravo, David

    2016-09-30

    The Anthropocene is witnessing a loss of biodiversity, with well-documented declines in the diversity of ecosystems and species. For intraspecific genetic diversity, however, we lack even basic knowledge on its global distribution. We georeferenced 92,801 mitochondrial sequences for >4500 species of terrestrial mammals and amphibians, and found that genetic diversity is 27% higher in the tropics than in nontropical regions. Overall, habitats that are more affected by humans hold less genetic diversity than wilder regions, although results for mammals are sensitive to choice of genetic locus. Our study associates geographic coordinates with publicly available genetic sequences at a massive scale, yielding an opportunity to investigate both the drivers of this component of biodiversity and the genetic consequences of the anthropogenic modification of nature. Copyright © 2016, American Association for the Advancement of Science.

  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 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.

  15. 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.

  16. 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

  17. High genetic diversity of Jatropha curcas assessed by ISSR.

    Science.gov (United States)

    Díaz, B G; Argollo, D M; Franco, M C; Nucci, S M; Siqueira, W J; de Laat, D M; Colombo, C A

    2017-05-31

    Jatropha curcas L. is a highly promising oilseed for sustainable production of biofuels and bio-kerosene due to its high oil content and excellent quality. However, it is a perennial and incipiently domesticated species with none stable cultivar created until now despite genetic breeding programs in progress in several countries. Knowledge of the genetic structure and diversity of the species is a necessary step for breeding programs. The molecular marker can be used as a tool for speed up the process. This study was carried out to assess genetic diversity of a germplasm bank represented by J. curcas accessions from different provenance beside interspecific hybrid and backcrosses generated by IAC breeding programs using inter-simple sequence repeat markers. The molecular study revealed 271 bands of which 98.9% were polymorphic with an average of 22.7 polymorphic bands per primer. Genetic diversity of the germplasm evaluated was slightly higher than other germplasm around the world and ranged from 0.55 to 0.86 with an average of 0.59 (Jaccard index). Cluster analysis (UPGMA) revealed no clear grouping as to the geographical origin of accessions, consistent with genetic structure analysis using the Structure software. For diversity analysis between groups, accessions were divided into eight groups by origin. Nei's genetic distance between groups was 0.14. The results showed the importance of Mexican accessions, congeneric wild species, and interspecific hybrids for conservation and development of new genotypes in breeding programs.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2010-05-24

    May 24, 2010 ... genetic structure of M. quintuplinervia has probably been shaped by its breeding modes, biogeographic history and human impact ... Key words: Meconopsis quintuplinervia Regel, genetic diversity, random amplified polymorphic DNA markers, ..... inbreeding depression and facilitate quality control of drug.

  19. 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 ...

  20. 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.

  1. Nephronophthisis: A Genetically Diverse Ciliopathy

    Directory of Open Access Journals (Sweden)

    Roslyn J. Simms

    2011-01-01

    Full Text Available Nephronophthisis (NPHP is an autosomal recessive cystic kidney disease and a leading genetic cause of established renal failure (ERF in children and young adults. Early presenting symptoms in children with NPHP include polyuria, nocturia, or secondary enuresis, pointing to a urinary concentrating defect. Renal ultrasound typically shows normal kidney size with increased echogenicity and corticomedullary cysts. Importantly, NPHP is associated with extra renal manifestations in 10–15% of patients. The most frequent extrarenal association is retinal degeneration, leading to blindness. Increasingly, molecular genetic testing is being utilised to diagnose NPHP and avoid the need for a renal biopsy. In this paper, we discuss the latest understanding in the molecular and cellular pathogenesis of NPHP. We suggest an appropriate clinical management plan and screening programme for individuals with NPHP and their families.

  2. MULTIVARIATE DIVERSITY, HERITABILITY AND GENETIC ...

    African Journals Online (AJOL)

    La caractérisation de la variabilité génétique existante est une Characterisation of exiting genetic variability is a préalable dans des activités d'amélioration cultural. La présente étude était conçue pour évaluer la variabilité génétique parmi les génotypes svlectionnés de tef Eragrostis, Zucc.Trotter (Tef) dans cinq zones ...

  3. 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.

  4. [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.

  5. Diversity of potato genetic resources.

    Science.gov (United States)

    Machida-Hirano, Ryoko

    2015-03-01

    A considerable number of highly diverse species exist in genus Solanum. Because they can adapt to a broad range of habitats, potato wild relatives are promising sources of desirable agricultural traits. Potato taxonomy is quite complex because of introgression, interspecific hybridization, auto- and allopolyploidy, sexual compatibility among many species, a mixture of sexual and asexual reproduction, possible recent species divergence, phenotypic plasticity, and the consequent high morphological similarity among species. Recent researchers using molecular tools have contributed to the identification of genes controlling several types of resistance as well as to the revision of taxonomical relationships among potato species. Historically, primitive forms of cultivated potato and its wild relatives have been used in breeding programs and there is still an enormous and unimaginable potential for discovering desirable characteristics, particularly in wild species Different methods have been developed to incorporate useful alleles from these wild species into the improved cultivars. Potato germplasm comprising of useful alleles for different breeding objectives is preserved in various gene banks worldwide. These materials, with their invaluable information, are accessible for research and breeding purposes. Precise identification of species base on the new taxonomy is essential for effective use of the germplasm collection.

  6. Genetic diversity of salt tolerance in Miscanthus

    NARCIS (Netherlands)

    Chen, Charlie; Schoot, van der Hanneke; Dehghan, Shiva; Alvim Kamei, Claire L.; Schwarz, Kai Uwe; Meyer, Heike; Visser, Richard G.F.; Linden, van der Gerard

    2017-01-01

    Miscanthus is a woody rhizomatous C4 grass that can be used as a CO2 neutral biofuel resource. It has potential to grow in marginal areas such as saline soils, avoiding competition for arable lands with food crops. This study explored genetic diversity for salt tolerance in Miscanthus and discovered

  7. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    Abstract. The objective of this study was to quantify the molecular diversity and to determine the genetic relationships among Secale spp. and among cultivars of Secale cereale using RAPDs, ISSRs and sequence analysis of six exons of ScMATE1 gene. Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD ...

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

    African Journals Online (AJOL)

    ACSS

    Classic F-statistics revealed the highest intra-specific polymorphism recorded for E. africana (32.45%), followed by E. coracana (16.83%); implying .... Genetic diversity and eco-geographical distribution of Eleusine species. 47 regions of Ethiopia as a ... were collected from the central highlands, west, northwest, northern and ...

  9. Cryptic genetic diversity in Dientamoeba fragilis.

    Science.gov (United States)

    Johnson, J A; Clark, C G

    2000-12-01

    Uncertainty surrounding the role of Dientamoeba fragilis in human disease could be due in part to the existence of pathogenic and nonpathogenic variants. Evidence for two genetically distinct forms was obtained using PCR-restriction fragment length polymorphism analysis of ribosomal genes. Future studies in humans will need to take D. fragilis diversity into account.

  10. Cryptic Genetic Diversity in Dientamoeba fragilis

    OpenAIRE

    Johnson, Jeanette A.; Clark, C. Graham

    2000-01-01

    Uncertainty surrounding the role of Dientamoeba fragilis in human disease could be due in part to the existence of pathogenic and nonpathogenic variants. Evidence for two genetically distinct forms was obtained using PCR-restriction fragment length polymorphism analysis of ribosomal genes. Future studies in humans will need to take D. fragilis diversity into account.

  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. Using microsatellite markers to assess genetic diversity ...

    African Journals Online (AJOL)

    bobby

    2013-05-15

    May 15, 2013 ... YAO et al. 2809. Table 1. Populations of tall coconut palm including three parental (G0) and three regenerated (G1) populations investigated in the present study of the genetic diversity by microsatellite markers. Population code, origin and sample size are also shown. Population. Generation. Codea. Origin.

  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...

  14. 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 cerealeusing RAPDs, ISSRs and sequence analysis of six exons ofScMATE1gene.Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR ...

  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. Genetic diversity of eleven European pig breeds.

    Science.gov (United States)

    Laval, G; Iannuccelli, N; Legault, C; Milan, D; Groenen, M A; Giuffra, E; Andersson, L; Nissen, P H; Jørgensen, C B; Beeckmann, P; 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 heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly reduced heterozygosity. Breed differentiation was significant as shown by the high among-breed fixation index (overall F(ST)= 0.27), and confirmed by the clustering based on the genetic distances between individuals, which grouped essentially all individuals in 11 clusters corresponding to the 11 breeds. The genetic distances between breeds were first used to construct phylogenetic trees. The trees indicated that a genetic drift model might explain the divergence of the two German breeds, but no reliable phylogeny could be inferred among the remaining breeds. The same distances were also used to measure the global diversity of the set of breeds considered, and to evaluate the marginal loss of diversity attached to each breed. In that respect, the French Basque breed appeared to be the most "unique" in the set considered. This study, which remains to be extended to a larger set of European breeds, indicates that using genetic distances between breeds of farm animals in a classical taxonomic approach may not give clear resolution, but points to their usefulness in a prospective evaluation of diversity.

  17. Genetic diversity of eleven European pig breeds

    Directory of Open Access Journals (Sweden)

    Foulley Jean-Louis

    2000-03-01

    Full Text Available Abstract 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 heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly reduced heterozygosity. Breed differentiation was significant as shown by the high among-breed fixation index (overall FST = 0.27, and confirmed by the clustering based on the genetic distances between individuals, which grouped essentially all individuals in 11 clusters corresponding to the 11 breeds. The genetic distances between breeds were first used to construct phylogenetic trees. The trees indicated that a genetic drift model might explain the divergence of the two German breeds, but no reliable phylogeny could be inferred among the remaining breeds. The same distances were also used to measure the global diversity of the set of breeds considered, and to evaluate the marginal loss of diversity attached to each breed. In that respect, the French Basque breed appeared to be the most "unique" in the set considered. This study, which remains to be extended to a larger set of European breeds, indicates that using genetic distances between breeds of farm animals in a classical taxonomic approach may not give clear resolution, but points to their usefulness in a prospective evaluation of diversity.

  18. Assessing Plant Genetic Diversity by Molecular Tools

    Directory of Open Access Journals (Sweden)

    Linda Mondini

    2009-08-01

    Full Text Available This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity. In recent years, there has been a significant increase in the application of molecular genetic methods for assessing the conservation and use of plant genetic resources. Molecular techniques have been applied in the analysis of specific genes, as well as to increase understanding of gene action, generate genetic maps and assist in the development of gene transfer technologies. Molecular techniques have also had critical roles in studies of phylogeny and species evolution, and have been applied to increase our understanding of the distribution and extent of genetic variation within and between species. These techniques are well established and their advantages as well as limitations have been realized and described in this work. Recently, a new class of advanced techniques has emerged, primarily derived from a combination of earlier, more basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques, in order to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. Some of the advanced marker techniques utilize newer classes of DNA elements, such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. The most important and recent advances made in molecular marker techniques are discussed in this review, along with their applications, advantages and limitations applied to plant sciences.

  19. Genetic diversity of Syrian Arabian horses.

    Science.gov (United States)

    Almarzook, S; Reissmann, M; Arends, D; Brockmann, G A

    2017-08-01

    Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added. Observed heterozygosis (Ho ) ranged between 0.30 and 0.32, expected heterozygosity (He ) between 0.30 and 0.31 and inbreeding coefficients (Fis ) between -0.02 and -0.05, indicating high genetic diversity within Syrian strains. Likewise, the genetic differentiation between the three Syrian strains was very low (Fst  horses. Among Arabian horses, we found three clusters containing either horses from the USA or horses from Syria or horses from Syria and the USA together. Individuals from the same Syrian Arabian horse strain were spread across different sub-clusters. When analyzing Syrian Arabian horses alone, the best population differentiation was found with three distinct clusters. In contrast to expectations from the studbook, these clusters did not coincide with strain affiliation. Although this finding supports the hypothesis of three founders, the genetic information is not consistent with the currently used strain designation system. The information can be used to reconsider the current breeding practice. Beyond that, Syrian Arabian horses are an important reservoir for genetic diversity. © 2017 Stichting International Foundation for Animal Genetics.

  20. 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....

  1. 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 ...

  2. Inbreeding levels in swine: Ramifications for Genetic Diversity

    Science.gov (United States)

    Globally, genetic diversity of livestock populations is contracting. Knowing the true extent of the contraction is needed to develop effective conservation strategies. While contractions of genetic diversity have been documented at the breed level, little within breed documentation has occurred. ...

  3. Global genetic diversity of Aedes aegypti.

    Science.gov (United States)

    Gloria-Soria, Andrea; Ayala, Diego; Bheecarry, Ambicadutt; Calderon-Arguedas, Olger; Chadee, Dave D; Chiappero, Marina; Coetzee, Maureen; Elahee, Khouaildi Bin; Fernandez-Salas, Ildefonso; Kamal, Hany A; Kamgang, Basile; Khater, Emad I M; Kramer, Laura D; Kramer, Vicki; Lopez-Solis, Alma; Lutomiah, Joel; Martins, Ademir; Micieli, Maria Victoria; Paupy, Christophe; Ponlawat, Alongkot; Rahola, Nil; Rasheed, Syed Basit; Richardson, Joshua B; Saleh, Amag A; Sanchez-Casas, Rosa Maria; Seixas, Gonçalo; Sousa, Carla A; Tabachnick, Walter J; Troyo, Adriana; Powell, Jeffrey R

    2016-11-01

    Mosquitoes, especially Aedes aegypti, are becoming important models for studying invasion biology. We characterized genetic variation at 12 microsatellite loci in 79 populations of Ae. aegypti from 30 countries in six continents, and used them to infer historical and modern patterns of invasion. Our results support the two subspecies Ae. aegypti formosus and Ae. aegypti aegypti as genetically distinct units. Ae. aegypti aegypti populations outside Africa are derived from ancestral African populations and are monophyletic. The two subspecies co-occur in both East Africa (Kenya) and West Africa (Senegal). In rural/forest settings (Rabai District of Kenya), the two subspecies remain genetically distinct, whereas in urban settings, they introgress freely. Populations outside Africa are highly genetically structured likely due to a combination of recent founder effects, discrete discontinuous habitats and low migration rates. Ancestral populations in sub-Saharan Africa are less genetically structured, as are the populations in Asia. Introduction of Ae. aegypti to the New World coinciding with trans-Atlantic shipping in the 16th to 18th centuries was followed by its introduction to Asia in the late 19th century from the New World or from now extinct populations in the Mediterranean Basin. Aedes mascarensis is a genetically distinct sister species to Ae. aegypti s.l. This study provides a reference database of genetic diversity that can be used to determine the likely origin of new introductions that occur regularly for this invasive species. The genetic uniqueness of many populations and regions has important implications for attempts to control Ae. aegypti, especially for the methods using genetic modification of populations. © 2016 John Wiley & Sons Ltd.

  4. 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 ...

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

    Indian Academy of Sciences (India)

    Abstract. Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. 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 ...

  6. 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 ...

  7. Analysis of genetic diversity in some durum wheat ( Triticum durum ...

    African Journals Online (AJOL)

    An experiment was conducted to examine the magnitude of genetic diversity and characters contributing to genetic diversity among 23 durum wheat genotypes grown at Adet, northwest Ethiopia, in 2010 main cropping season. Genetic divergence was carried out according to Mahalanobis D2 statistics. Genetic distance ...

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

    African Journals Online (AJOL)

    SARAH

    2013-12-30

    Dec 30, 2013 ... Objective: The genetic polymorphism within and among three indigenous goat breeds found in Egypt (Barki and ... with only little genetic exchange between the geographically isolated populations. Key words: Microsatellites, Goats, Genetic diversity, Genotype. INTRODUCTION ..... conservation strategies.

  9. GENETIC DIVERSITY IN CZECH HAFLINGER HORSES

    Directory of Open Access Journals (Sweden)

    Luboš Vostrý

    2015-09-01

    Full Text Available The Haflinger as a small moutain horse breed originated from the South Tyrol district as a cross of Alpen Mountain breeds with Araber. This breed was expanding to Czech Republic during the last 25 years. The aim of this study was to analyse genetic diversity within the population using microsatellite markers. A total of 95 alleles have been detected. The highest frequency 88.18% showed allele 101 (HTG 6. The heterosigosity varied from 0.25 (HTG 6 to 0.84 (VHL 20, genetic diversity reached 0.6–0.8. The heterozygosity of the whole population studied is FIS= -0.013. The average effective number of allele per locus was 2.93 with standard deviation 1.54, with minimal and maximal level 1.30 and 7.83, respectively. Average polymorphism information content per locus was 0.608 with standard derivation 0.146, with minimal and maximal level 0.208 and 0.824, respectively. The results showed that breeding program of Czech Haflinger is optimal, including optimized mating strategies. The diversity of the population Czech Haflinger, based on a small number of microsatellites, seems to be sufficient.

  10. 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.

  11. 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.

  12. Conservation implications of species–genetic diversity correlations

    Directory of Open Access Journals (Sweden)

    Aapo Kahilainen

    2014-12-01

    Full Text Available Despite its importance for the long-term viability of populations and functioning of ecosystems, the genetic diversity of populations is seldom given explicit consideration in conservation prioritization. Research on the species–genetic diversity correlation (SGDC suggests that species diversity within a community and intrapopulation genetic diversity are positively correlated, due to the parallel influences of environmental characteristics (area, connectivity, and environmental heterogeneity on both levels of diversity. A positive locality scale SGDC (i.e. α-SGDC thus provides potential for simultaneous conservation of both species diversity within a locality and intrapopulation genetic diversity. However, caution is needed, since in some situations environmental characteristics can influence species diversity and genetic diversity differently, resulting in a negative α-SGDC. In such cases there can be a conflict between conservation of species diversity within localities and genetic diversity within populations. SGDCs provide useful information also for conservation planning, which considers compositional differences between localities, since the mechanisms behind α-SGDCs can also drive correlations between differentiation of community and genetic compositions (i.e. β-SGDCs. We suggest that emphasizing locality area and connectivity between similar localities in conservation planning best conserves both species and intrapopulation genetic diversity, and that focusing on highly complementary species richness may compromise conservation of genetic diversity.

  13. Genetic diversity in Stylosanthes capitata ACCESS

    Directory of Open Access Journals (Sweden)

    Janaina Azevedo Martuscello

    2015-12-01

    Full Text Available The objective of this study was to evaluate the genetic diversity and the relative importance of morphological traits for the study of genetic diversity among Stylosanthes capitata genotypes. Ten open-pollinated families (297-2, 49-5, 1064-4, 49-4, 1095-5, 141-6, 1064-6, 297-6, 625-3, and 111-3, previously selected by the Embrapa Gado de Corte improvement program, and the Campo Grande cultivar as control were evaluated. A completely randomized design consisting of four repetitions was used. The following morphological traits were studied: type of growth, length, width and length-to-width ratio of the central and lateral leaflets, plant height, stem length, and number of secondary ramifications. Mahalanobis generalized distance was calculated using the phenotypic means for each trait and the matrix of residual variances and covariances. Once the dissimilarity matrix was obtained, the families and Campo Grande cultivar were grouped using Ward’s method. Canonical variables were also analyzed using the phenotypic mean of the traits studied and the matrix of residual variances and covariances. Cluster analysis by Ward’s method permitted to divide the 11 genotypes into five groups. Canonical analysis was efficient since it permitted to summarize the total variation observed in the nine morphological traits into only three canonical variables, which accounted for 81.65% of the total variation in the data. The importance of the traits for clustering was also analyzed. Central leaflet width, length-to-width ratio of the central and lateral leaflets, lateral leaflet width and secondary ramifications were the most important traits for the evaluation of genetic diversity among Stylosanthes capitata genotypes.

  14. Pyrosequencing and genetic diversity of microeukaryotes

    DEFF Research Database (Denmark)

    Harder, Christoffer Bugge

    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...... to identify the thousands of DNA sequences, and Article II contributes to this by a morphological and phylogenetic characterization and naming of two new genera of flagellates found in Danish soil. The fact that it is possible to find two unknown and genetically divergent lineages in a few grams of soil from...... to evaluate the explanatory power of individual genes and their mutual consistency. The fact that ITS, the most widely used marker in fungi, did not show the best taxonomic resolution serves to put the heavy reliance upon a single marker (18S) in protozoology into perspective....

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

    African Journals Online (AJOL)

    Contrasting genetic diversity among Oryza longistaminata (A. Chev et Roehr) populations from different geographic origins using AFLP. ... The mean Nei's genetic diversity for all the 176 loci in the 48 populations was 0.302 and diversity for populations within countries ranged from 0.1161 to 0.2126. Partitioning of between ...

  16. Genetic diversity of Chrysichthys nigrodigitatus in the Lagos lagoon ...

    African Journals Online (AJOL)

    s

    2012-11-13

    Nov 13, 2012 ... Mitochondrial DNA control region sequences were used to investigate the genetic diversity of populations of Chrysichthys ..... to our result. Therefore, combination of both mtDNA and nuclear DNA markers must be ... genetic structure pattern similar to freshwater species and genetic diversity similar to ...

  17. Analysis of genetic diversity in Eucalyptus grandis (Hill ex Maiden ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-04

    Jul 4, 2008 ... Population genetic theory predicts that the decrease in the genetic diversity limits species ability to keep pace with the changing selection pressure (Young and. Merrian, 1992). The release of genetically diverse material is a prere- quisite for preventing inbreeding depression in future generations. Hence ...

  18. Effects of landscape fragmentation on genetic diversity of Stipa ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... determine if and how these disturbances have impacted on genetic structure of S. krylovii populations, ... Key words: Stipa krylovii roshev, genetic diversity, landscape fragmentation, patch, habitat isolation, ISSR marker, rangeland ..... duce inbreeding depression in order to maintain the diversity of genetic ...

  19. Genetic diversity in selected stud and commercial herds of the ...

    African Journals Online (AJOL)

    Assignment methods (based on STRUCTURE software) revealed a real structure consisting of four genetic populations (K = 4). Estimates of genetic diversity did not support the hypothesis of significant loss of genetic diversity in any individual Afrikaner herd. Heterozygosity estimates ranged from 0.456 - 0.737 within ...

  20. AFLP analysis on genetic diversity and population structure of small ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... Bohai Bay, Yellow Sea and East China Sea were analyzed using amplified fragment length polymorphism. (AFLP). Ninety-one ... Key words: Small yellow croaker, Larimichthys polyactis, genetic population structure, genetic diversity, AFLP. ... gene mapping, linkage and genetic diversity of species.

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

    African Journals Online (AJOL)

    The understanding of genetic diversity within local crop varieties constitutes an important step in the 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 ...

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

    African Journals Online (AJOL)

    Genetic diversity based on the characterization of genetic makeup, using molecular markers is of utmost importance for breeders in crop improvement programme. A total of 26 microsatellite primers were used to determine the genetic diversity among 40 sugarcane genotypes including their parents. The polymerase chain ...

  3. Genetic Diversity of Local and Introduced Sweet Potato [Ipomoea ...

    African Journals Online (AJOL)

    Efficient use of plant genetic diversity is a prerequisite for the development of crop varieties in meeting the challenges of food security and poverty alleviation. Understanding the variation and diversity of the genetic resources of crop species is therefore the first step to efficient utilization and genetic resource conservation.

  4. 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.

  5. Genetic diversity in Oroxylum indicum (L.) Vent. (Bignoniaceae), a ...

    African Journals Online (AJOL)

    Genetic diversity in Oroxylum indicum (L.) Vent. (Bignoniaceae), a vulnerable medicinal plant by random amplified polymorphic DNA marker. ... results show that the genetic diversity of this species is low, possibly depicting a difficulty in adapting to environmental variations. This distributive pattern of genetic variation of O.

  6. Rarity and genetic diversity in Indo–Pacific Acropora corals

    Science.gov (United States)

    Richards, Zoe T; Oppen, Madeleine J H

    2012-01-01

    Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo–Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome. PMID:22957189

  7. Rarity and genetic diversity in Indo-Pacific Acropora corals.

    Science.gov (United States)

    Richards, Zoe T; Oppen, Madeleine J H

    2012-08-01

    Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo-Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome.

  8. 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.

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

    Science.gov (United States)

    Blum, Michael J; Bagley, Mark J; Walters, David M; Jackson, Suzanne A; Daniel, F Bernard; Chaloud, Deborah J; Cade, Brian 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.

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

    African Journals Online (AJOL)

    R Madhusudhana

    We studied genetic diversity in 31 sorghum parents using 413 sorghum simple sequence repeats (SSR) markers ..... BT × 623 and its derivative,. ICSB38 grouped ..... Pedigree- vs. DNA marker-based genetic similarity estimates in Cotton. Crop.

  11. 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.

  12. Genetic Diversity of Croatian Common Bean Landraces

    Directory of Open Access Journals (Sweden)

    Klaudija Carović-Stanko

    2017-04-01

    Full Text Available In Croatia, the majority of the common bean production is based on local landraces, grown by small-scale farmers in low input production systems. Landraces are adapted to the specific growing conditions and agro-environments and show a great morphological diversity. These local landraces are in danger of genetic erosion caused by complex socio-economic changes in rural communities. The low profitability of farms and their small size, the advanced age of farmers and the replacement of traditional landraces with modern bean cultivars and/or other more profitable crops have been identified as the major factors affecting genetic erosion. Three hundred accessions belonging to most widely used landraces were evaluated by phaseolin genotyping and microsatellite marker analysis. A total of 183 different multi-locus genotypes in the panel of 300 accessions were revealed using 26 microsatellite markers. Out of 183 accessions, 27.32% were of Mesoamerican origin, 68.31% of Andean, while 4.37% of accessions represented putative hybrids between gene pools. Accessions of Andean origin were further classified into phaseolin type II (“H” or “C” and III (“T”, the latter being more frequent. A model-based cluster analysis based on microsatellite markers revealed the presence of three clusters in congruence with the results of phaseolin type analysis.

  13. Genetic Diversity of Croatian Common Bean Landraces.

    Science.gov (United States)

    Carović-Stanko, Klaudija; Liber, Zlatko; Vidak, Monika; Barešić, Ana; Grdiša, Martina; Lazarević, Boris; Šatović, Zlatko

    2017-01-01

    In Croatia, the majority of the common bean production is based on local landraces, grown by small-scale farmers in low input production systems. Landraces are adapted to the specific growing conditions and agro-environments and show a great morphological diversity. These local landraces are in danger of genetic erosion caused by complex socio-economic changes in rural communities. The low profitability of farms and their small size, the advanced age of farmers and the replacement of traditional landraces with modern bean cultivars and/or other more profitable crops have been identified as the major factors affecting genetic erosion. Three hundred accessions belonging to most widely used landraces were evaluated by phaseolin genotyping and microsatellite marker analysis. A total of 183 different multi-locus genotypes in the panel of 300 accessions were revealed using 26 microsatellite markers. Out of 183 accessions, 27.32% were of Mesoamerican origin, 68.31% of Andean, while 4.37% of accessions represented putative hybrids between gene pools. Accessions of Andean origin were further classified into phaseolin type II ("H" or "C") and III ("T"), the latter being more frequent. A model-based cluster analysis based on microsatellite markers revealed the presence of three clusters in congruence with the results of phaseolin type analysis.

  14. Application of SRAP in the genetic diversity of Tricholoma matsutake ...

    African Journals Online (AJOL)

    ... genetic variation was detected within individual populations. Dongning maintained a higher genetic diversity while Hunchun was lower. The analyses found a significant positive correlation between genetic distance and geographical distance and no correlation between genetic distance and altitudinal differences among ...

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

    African Journals Online (AJOL)

    Cynthia

    2015-04-01

    Apr 1, 2015 ... Microsatellites are currently one of the markers of choice for the molecular characterization of animal genetic diversity and conservation genetics. In this study, we examined the genetic structure of six populations in the Qinghai Lake region and Tianjun using noninvasive genetic methods. This study is to ...

  16. Investigating Genetic Diversity of Foeniculum Vulgare Mill using Molecular Markers

    OpenAIRE

    Omid Jadidi; Mansour Kalantar

    2016-01-01

    Medicinal plants are considered valuable genetic resources in Iran. One of these medicinal as well as spice plants is Foeniculum Vulgare Mill from Umbellifetae family used in different industries such as food, medicine, and cosmetics. It seems that due to different climate conditions in Iran this plant represents a high and valuable genetic diversity; therefore, management of genetic resources protection and obtaining information about genetic diversity will help awareness of evolution pro...

  17. 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

  18. Genetic diversity of human RNase 8

    Directory of Open Access Journals (Sweden)

    Chan Calvin C

    2012-01-01

    Full Text Available Abstract Background Ribonuclease 8 is a member of the RNase A family of secretory ribonucleases; orthologs of this gene have been found only in primate genomes. RNase 8 is a divergent paralog of RNase 7, which is lysine-enriched, highly conserved, has prominent antimicrobial activity, and is expressed in both normal and diseased skin; in contrast, the physiologic function of RNase 8 remains uncertain. Here, we examine the genetic diversity of human RNase 8, a subject of significant interest given the existence of functional pseudogenes (coding sequences that are otherwise intact but with mutations in elements crucial for ribonucleolytic activity in non-human primate genomes. Results RNase 8 expression was detected in adult human lung, spleen and testis tissue by quantitative reverse-transcription PCR. Only two single-nucleotide polymorphisms and four unique alleles were identified within the RNase 8 coding sequence; nucleotide sequence diversity (π = 0.00122 ± 0.00009 per site was unremarkable for a human nuclear gene. We isolated transcripts encoding RNase 8 via rapid amplification of cDNA ends (RACE and RT-PCR which included a distal potential translational start site followed by sequence encoding an additional 30 amino acids that are conserved in the genomes of several higher primates. The distal translational start site is functional and promotes RNase 8 synthesis in transfected COS-7 cells. Conclusions These results suggest that RNase 8 may diverge considerably from typical RNase A family ribonucleases and may likewise exhibit unique function. This finding prompts a reconsideration of what we have previously termed functional pseudogenes, as RNase 8 may be responding to constraints that promote significant functional divergence from the canonical structure and enzymatic activity characteristic of the RNase A family.

  19. 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), ... A relatively high level of genetic differentiation among populations was detected based on Nei's gene diversity analysis (Gst = 0.2001) and analysis of ...

  20. Genetic diversity in green gram accessions as revealed by STMS ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-28

    Nov 28, 2011 ... gram using wild relatives. Key words: Genetic diversity, green gram, Vigna radiata, STMS. INTRODUCTION. Among Vigna group, in economic terms, green gram is the most ... Molecular markers employed for the analysis of genetic diversity in green ..... and is critical to their conservation and management.

  1. 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 ...

  2. Application of SRAP in the genetic diversity of Tricholoma matsutake ...

    African Journals Online (AJOL)

    GREGORY

    2010-09-20

    Sep 20, 2010 ... mushrooms. The study firstly applied SRAP technique into genetic diversity of T. matsutake. A total of. 129 strains from 13 geographical locations in northeastern China, were amplified by using ... of the most delicious and valuable edible mushrooms in ..... to examine the genetic diversity in basidiomycetes.

  3. 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 ...

  4. 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 ...

  5. 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 ...

  6. 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 ...

  7. Genetic diversity in some Turkish pepper (Capsicum annuum L ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... genotypes had comparatively higher genetic diversity. Key words: Capsicum annuum, AFLP, Genetic diversity. INTRODUCTION. Pepper (Capsicum annuum L; 2n = 2x = 24) are important vegetable species both worldwide and in. Turkey with the 24.80 and 1.75 million t of production on. 1.725 millions and ...

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

    Indian Academy of Sciences (India)

    2013-12-11

    Dec 11, 2013 ... Abstract. Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. ... carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of ..... allelic data was analysed using the computer package Dar- win (ver.

  9. 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.

  10. Genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    The Ethiopian genetic center is considered to be one of the secondary centers of diversity for the common bean. This study was conducted to characterize the distribution of genetic diversity between and within ecological/geographical regions of Ethiopia. A germplasm sample of 116 landrace accessions was developed, ...

  11. 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 ...

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

    African Journals Online (AJOL)

    The present study was undertaken to genetically evaluate Caspian horses for genetic diversity and to asses whether they have experienced recent population bottlenecks. A total of 100 individuals were characterized for within breed diversity using 16 microsatellite markers. The estimated mean number of alleles was 8.69 ...

  13. 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 ...

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

    African Journals Online (AJOL)

    Mwale

    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 ...

  15. Genetic diversity of the monomeric prolamins and hordein in hulless ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-05-04

    May 4, 2009 ... Alvarez GB, Broccoli A, Martin LM (2006a). Genetic diversity and structure in a natural Hordeum chilense populations based on gliadins analysis.PL. Syst. Evol. 261: 11-18. Alvarez GB, Broccoli A, Martin LM (2006b). Variability and genetic diversity for gliadins in natural populations of Hordeum chilense.

  16. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    The presence of sufficient genetic diversity in the germplam is an important prerequisite for the improve-ment and efficient use of available material. Traditionally, the data on agronomic, morphological and physiological plants traits are used to estimate the genetic diversity. But now molecular markers are available for ...

  17. 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.

  18. 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.

  19. 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.

  20. Beauveria bassiana: quercetinase production and genetic diversity

    Directory of Open Access Journals (Sweden)

    Eula Maria de M. B Costa

    2011-03-01

    Full Text Available 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.

  1. 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

  2. Genetic Diversity of Salt Tolerance in Miscanthus

    Science.gov (United States)

    Chen, Chang-Lin; van der Schoot, Hanneke; Dehghan, Shiva; Alvim Kamei, Claire L.; Schwarz, Kai-Uwe; Meyer, Heike; Visser, Richard G. F.; van der Linden, C. Gerard

    2017-01-01

    Miscanthus is a woody rhizomatous C4 grass that can be used as a CO2 neutral biofuel resource. It has potential to grow in marginal areas such as saline soils, avoiding competition for arable lands with food crops. This study explored genetic diversity for salt tolerance in Miscanthus and discovered mechanisms and traits that can be used to improve the yield under salt stress. Seventy genotypes of Miscanthus (including 57 M. sinensis, 5 M. sacchariflorus, and 8 hybrids) were evaluated for salt tolerance under saline (150 mM NaCl) and normal growing conditions using a hydroponic system. Analyses of shoot growth traits and ion concentrations revealed the existence of large variation for salt tolerance in the genotypes. We identified genotypes with potential for high biomass production both under control and saline conditions that may be utilized for growth under marginal, saline conditions. Several relatively salt tolerant genotypes had clearly lower Na+ concentrations and showed relatively high K+/Na+ ratios in the shoots under salt stress, indicating that a Na+ exclusion mechanism was utilized to prevent Na+ accumulation in the leaves. Other genotypes showed limited reduction in leaf expansion and growth rate under saline conditions, which may be indicative of osmotic stress tolerance. The genotypes demonstrating potentially different salt tolerance mechanisms can serve as starting material for breeding programs aimed at improving salinity tolerance of Miscanthus. PMID:28261243

  3. Endemic insular and coastal Tunisian date palm genetic diversity.

    Science.gov (United States)

    Zehdi-Azouzi, Salwa; Cherif, Emira; Guenni, Karim; Abdelkrim, Ahmed Ben; Bermil, Aymen; Rhouma, Soumaya; Salah, Mohamed Ben; Santoni, Sylvain; Pintaud, Jean Christophe; Aberlenc-Bertossi, Frédérique; Hannachi, Amel Salhi

    2016-04-01

    The breeding of crop species relies on the valorisation of ancestral or wild varieties to enrich the cultivated germplasm. The Tunisian date palm genetic patrimony is being threatened by diversity loss and global climate change. We have conducted a genetic study to evaluate the potential of spontaneous coastal resources to improve the currently exploited Tunisian date palm genetic pool. Eighteen microsatellite loci of Phoenix dactylifera L. were used to compare the genetic diversity of coastal accessions from Kerkennah, Djerba, Gabès and continental date palm accessions from Tozeur. A collection of 105 date palms from the four regions was analysed. This study has provided us with an extensive understanding of the local genetic diversity and its distribution. The coastal date palm genotypes exhibit a high and specific genetic diversity. These genotypes are certainly an untapped reservoir of agronomically important genes to improve cultivated germplasm in continental date palm.

  4. 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-.

  5. Molecular Markers for Genetic Diversity Studies in African Leafy Vegetables

    OpenAIRE

    Omondi, Emmanuel O.; Debener, Thomas; Linde, Marcus; Abukutsa-Onyango, Mary; Dinssa, Fekadu F.; Winkelmann, Traud

    2016-01-01

    African leafy vegetables are becoming important crops in tackling nutrition and food security in many parts of sub-Saharan Africa, since they provide important micronutrients and vitamins, and help resource-poor farm families bridge lean periods of food shortage. Genetic diversity studies are essential for crop improvement programmes as well as germplasm conservation efforts, and research on genetic diversity of these vegetables using molecular markers has been increasing over time. Diversity...

  6. Phenotypic diversity in the Ethiopian noug germplasm | Genet ...

    African Journals Online (AJOL)

    Based on the characters studied and small collections evaluated, the centres of diversity for noug appears to be in Gojjam, Welega and Shewa, and further exploration efforts should be undertaken in these regions. Key Words: Diversity index, genetic diversity, germplasm, Guizotia abyssinica Cass., oilseed (African Crop ...

  7. Patterns of genetic structure and phenotypic diversity in sorghum ...

    African Journals Online (AJOL)

    The importance of phenotypic intra-varietal diversity in early, intermediate and late maturing varieties varied in relation to the observed trait. The genetic analysis specified that the highest diversity rates were in the late maturing varieties (3.3 for allelic richness and 0.47 for gene diversity). Factorial Discriminant Analysis on ...

  8. Differences in genetic diversity in Holstein cattle with high and low genetic merit

    NARCIS (Netherlands)

    Engelsma, K.A.; Veerkamp, R.F.; Calus, M.P.L.; Windig, J.J.

    2010-01-01

    Evaluations of genetic diversity in Holstein cattle based on pedigree data, indicate a decrease in genetic diversity in Holstein cattle, because of a lower effective population size and a higher relatedness compared to other cattle breeds. However, pedigree based diversity reflects only the overall

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

    Indian Academy of Sciences (India)

    2015-12-03

    Dec 3, 2015 ... tant repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of ..... Peakall R. and Smouse P. E. 2012 GenAlEx 6.5: genetic analysis in. Excel. Population genetic software for teaching and research—an update. Bioinformatics 28, 2537–2539.

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

    African Journals Online (AJOL)

    SERVER

    obtained for F5, F6, F7, F8 and F9 generations revealed a progressive increasing of genetic similarity throughout the five stocks, ... Key words: Litopenaeus vannamei, genetic diversity, genetic drift, inbreeding, RAPD. INTRODUCTION ..... here which could be accounted to inbreeding depression. The increase of the effective ...

  11. An understanding of the underlying genetic diversity within and ...

    African Journals Online (AJOL)

    AMuchugi

    2016-08-03

    Aug 3, 2016 ... understanding of the genetic diversity and the extent of distribution of genetic variation available within a species. (Muchugi et al., 2012). A wide genetic base provides the ability to withstand potential inbreeding depression through future generations of farmer propagation. (Frankham, 2010). However, little ...

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

    Indian Academy of Sciences (India)

    The genetic structure and diversity of 10 Chinese indigenous egg-type duck breeds were investigated using 29 microsatellite markers. ... genetic variability originated from differences among breeds, with all loci contributing significantly. An unrooted ..... be made for this breed to avoid inbreeding depression and genetic drift.

  13. Genetic diversity analysis of Labeo gonius (Hamilton, 1822) in three ...

    African Journals Online (AJOL)

    a

    2013-05-08

    May 8, 2013 ... gonius from three different sized reservoirs viz., Dhaura, Baigul and Nanak Sagar reservoir of. Uttarakhand by applying allozyme ... Key words: Allozyme, Labeo gonius, genetic diversity, population genetics. INTRODUCTION ... Generally, individuals with greater genetic variability have higher growth rates ...

  14. 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 ...

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

    African Journals Online (AJOL)

    In this condition, the gene pool of local chicken is experiencing a dangerous erosion of its original genetic diversity. The presence of relevant tropical genetic mutations can be associated with any poultry genetic improvement. Urgent conservation measures that will pave the way for subsequent progress are imperative.

  16. Genetic diversity of indigenous chicken ecotypes in Jordan

    African Journals Online (AJOL)

    Jane

    2010-10-11

    Oct 11, 2010 ... vation of genetic resources of indigenous chicken ecotypes in Jordan. Key words: Polymorphism, conservation, allele numbers, genetic distance, RAPD markers. INTRODUCTION. DNA diversity is continuously suffering erosion in several fields of animal genetic resources. This is especially true.

  17. Analysis of genetic diversity in Arrhenatherum elatius Germplasm ...

    African Journals Online (AJOL)

    Jane

    2011-07-25

    Jul 25, 2011 ... Key words: Arrhenatherum elatius, genetic diversity, inter-simple sequence repeat (ISSR) markers. INTRODUCTION. Arrhenatherum elatius (L.) ... markers, to provide evidence for genetic improvement, and to evaluate the applicability of this ..... cations in aquaculture. Genet. Aquacult. 238: 31-37. Mahmoud ...

  18. 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

  19. Stable isotope signatures reflect dietary diversity in European forest moths.

    Science.gov (United States)

    Adams, Marc-Oliver; Seifert, Carlo Lutz; Lehner, Lisamarie; Truxa, Christine; Wanek, Wolfgang; Fiedler, Konrad

    2016-01-01

    Information on larval diet of many holometabolous insects remains incomplete. Carbon (C) and nitrogen (N) stable isotope analysis in adult wing tissue can provide an efficient tool to infer such trophic relationships. The present study examines whether moth feeding guild affiliations taken from literature are reflected in isotopic signatures. Non-metric multidimensional scaling and permutational analysis of variance indicate that centroids of dietary groups differ significantly. In particular, species whose larvae feed on mosses or aquatic plants deviated from those that consumed vascular land plants. Moth δ(15)N signatures spanned a broader range, and were less dependent on species identity than δ(13)C values. Comparison between moth samples and ostensible food sources revealed heterogeneity in the lichenivorous guild, indicating only Lithosia quadra as an obligate lichen feeder. Among root-feeding Agrotis segetum, some specimens appear to have developed on crop plants in forest-adjacent farm land. Reed-feeding stem-borers may partially rely on intermediary trophic levels such as fungal or bacterial growth. Diagnostic partitioning of moth dietary guilds based on isotopic signatures alone could not be achieved, but hypotheses on trophic relationships based on often vague literature records could be assessed with high resolution. Hence, the approach is well suited for basic categorization of moths where diet is unknown or notoriously difficult to observe (i.e. Microlepidoptera, lichen-feeders).

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

    African Journals Online (AJOL)

    The results exhibit a strong genetic differentiation which is obviously due to genetic drift in the isolated populations. The genetic structure of M. quintuplinervia has probably been shaped by its breeding modes, biogeographic history and human impact (both grazing and collection for medicinal purposes). This research might ...

  1. Stable cycling in discrete-time genetic models.

    Science.gov (United States)

    Hastings, A

    1981-11-01

    Examples of stable cycling are discussed for two-locus, two-allele, deterministic, discrete-time models with constant fitnesses. The cases that cycle were found by using numerical techniques to search for stable Hopf bifurcations. One consequence of the results is that apparent cases of directional selection may be due to stable cycling.

  2. Genetic diversity increases insect herbivory on oak saplings.

    Directory of Open Access Journals (Sweden)

    Bastien Castagneyrol

    Full Text Available A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Quercus robur half-sib families. We quantified genetic diversity at the plot level by genotyping all oak saplings and assessed overall damage caused by ectophagous and endophagous herbivores along a gradient of increasing genetic diversity. Damage due to ectophagous herbivores increased with the genetic diversity in oak sapling populations as a result of higher levels of damage in mixtures than in monocultures for all families (complementarity effect rather than because of the presence of more susceptible oak genotypes in mixtures (selection effect. Assemblages of different oak genotypes would benefit polyphagous herbivores via improved host patch location, spill over among neighbouring saplings and diet mixing. By contrast, genetic diversity was a poor predictor of the abundance of endophagous herbivores, which increased with individual sapling apparency. Plant genetic diversity may not provide sufficient functional contrast to prevent tree sapling colonization by specialist herbivores while enhancing the foraging of generalist herbivores. Long term studies are nevertheless required to test whether the effect of genetic diversity on herbivory change with the ontogeny of trees and local adaptation of specialist herbivores.

  3. Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance.

    Science.gov (United States)

    Schou, Mads F; Loeschcke, Volker; Bechsgaard, Jesper; Schlötterer, Christian; Kristensen, Torsten N

    2017-12-01

    The effective population size (Ne ) is a central factor in determining maintenance of genetic variation. The neutral theory predicts that loss of variation depends on Ne , with less genetic drift in larger populations. We monitored genetic drift in 42 Drosophila melanogaster populations of different adult census population sizes (10, 50 or 500) using pooled RAD sequencing. In small populations, variation was lost at a substantially lower rate than expected. This observation was consistent across two ecological relevant thermal regimes, one stable and one with a stressful increase in temperature across generations. Estimated ratios between Ne and adult census size were consistently higher in small than in larger populations. The finding provides evidence for a slower than expected loss of genetic diversity and consequently a higher than expected long-term evolutionary potential in small fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent with this hypothesis, the X-chromosome, which is largely free of recessive deleterious alleles due to hemizygosity in males, fits neutral expectations even in small populations. Our experiments provide experimental answers to a range of unexpected patterns in natural populations, ranging from variable diversity on X-chromosomes and autosomes to surprisingly high levels of nucleotide diversity in small populations. © 2017 John Wiley & Sons Ltd.

  4. Genetic Diversity and Diversity of Environment: Mathematical Aspects

    Science.gov (United States)

    1967-01-01

    case, and the stable distribution in the other, have been found ex- plicitly for certain special cases, and in symbolic form in more general cases. (See...phisnms," Evolution, Vol. 14 (1960), pp. 458-472. [27] G. MALECOT, Les Mathematiques de l’Heredite (edited by Libraries de l’Academiiie de Medicine

  5. Genetic Diversity of Plasmodium falciparum in Haiti: Insights from Microsatellite Markers.

    Directory of Open Access Journals (Sweden)

    Tamar E Carter

    Full Text Available Hispaniola, comprising Haiti and the Dominican Republic, has been identified as a candidate for malaria elimination. However, incomplete surveillance data in Haiti hamper efforts to assess the impact of ongoing malaria control interventions. Characteristics of the genetic diversity of Plasmodium falciparum populations can be used to assess parasite transmission, which is information vital to evaluating malaria elimination efforts. Here we characterize the genetic diversity of P. falciparum samples collected from patients at seven sites in Haiti using 12 microsatellite markers previously employed in population genetic analyses of global P. falciparum populations. We measured multiplicity of infections, level of genetic diversity, degree of population geographic substructure, and linkage disequilibrium (defined as non-random association of alleles from different loci. For low transmission populations like Haiti, we expect to see few multiple infections, low levels of genetic diversity, high degree of population structure, and high linkage disequilibrium. In Haiti, we found low levels of multiple infections (12.9%, moderate to high levels of genetic diversity (mean number of alleles per locus = 4.9, heterozygosity = 0.61, low levels of population structure (highest pairwise Fst = 0.09 and no clustering in principal components analysis, and moderate linkage disequilibrium (ISA = 0.05, P<0.0001. In addition, population bottleneck analysis revealed no evidence for a reduction in the P. falciparum population size in Haiti. We conclude that the high level of genetic diversity and lack of evidence for a population bottleneck may suggest that Haiti's P. falciparum population has been stable and discuss the implications of our results for understanding the impact of malaria control interventions. We also discuss the relevance of parasite population history and other host and vector factors when assessing transmission intensity from genetic diversity data.

  6. Tartary Buckwheat Genetic Diversity in the Himalayas Associated with Farmer Landrace Diversity and Low Dietary Dependence

    OpenAIRE

    Weijuan Huang; Devra I. Jarvis; Selena Ahmed; Chunlin Long

    2017-01-01

    While crop genetic diversity supports ecological processes and food security, there have been few cross-cultural studies evaluating the influence of cultural and dietary factors on the conservation of genetic resources. This study examines genetic diversity patterns of tartary buckwheat in 18 smallholder farming communities across five regions of China (Yunnan Province, Tibet Autonomous Region and Sichuan Province) and Bhutan managed by Yi, Tibetan, and Bhutanese farmers using ethnobotanical ...

  7. Limited intra-genetic diversity in Dientamoeba fragilis housekeeping genes.

    Science.gov (United States)

    Stensvold, Christen Rune; Clark, C Graham; Röser, Dennis

    2013-08-01

    Dientamoeba fragilis is a common intestinal parasite of unsettled clinical significance. Differences in clinical outcome of parasitic infections may reflect parasite genetic diversity, and so tools to study intra-genetic diversity that could potentially reflect differences in clinical phenotypes are warranted. Here, we show that genetic analysis of three D. fragilis housekeeping genes enables clear distinction between the two known genotypes, but that integration of housekeeping genes in multi-locus sequencing tools for D. fragilis may have limited epidemiological and clinical value due to no further added genetic resolution. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. 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.

  9. Development and molecular-genetic characterization of a stable Brassica allohexaploid.

    Science.gov (United States)

    Gupta, Mehak; Atri, Chhaya; Agarwal, Neha; Banga, Surinder Singh

    2016-11-01

    We report first-time synthesis of a stable Brassica allohexaploid. It may evolve into a new species and also advance our understanding of pairing regulation and genome evolution in complex allopolyploids. Crop Brassicas include both monogenomic and digenomic species. A trigenomic Brassica (AABBCC) is not known to exist in nature. Past attempts to synthesize a stable allohexaploid were not successful due to aberrant meiosis and very high proportion of aneuploid plants in the selfed progenies. We report the development of a stable allohexaploid Brassica (2n = 54; AABBCC). Genomic in situ hybridization confirmed the complete assemblage of three genomes. Only allohexaploids involving B. rapa cv. R01 (2n = 20; AA) as pollinator with a set of B. carinata (2n = 34; BBCC) were stable. These exhibited a high proportion (0.78-0.94) of pollen mother cells with normal meiosis and an excellent hexaploid ratio (0.80-0.94) in the selfed progenies. Stability of two allohexaploid combinations was demonstrated from H1 to H4 generations at two very diverse locations in India. Graphical genotyping of allohexaploids allowed detection of chromosome fragment exchanges among three genomes. These were much smaller for meiotically stable allohexaploids as compared to unstable ones. The putative hexaploids were morphologically closer to the female donor, B. carinata, for leaf morphology, inflorescence structure and flower shape. The newly formed allohexaploid may also provide unique opportunities to investigate the immediate genetic and genomic consequences of a Brassica allohexaploid with three resident genomes.

  10. Modelling the loss of genetic diversity in vole populations in a spatially and temporally varying environment

    DEFF Research Database (Denmark)

    Topping, Christopher John; Østergaard, Siri; Pertoldi, Cino

    2003-01-01

    incorporating explicit genetics provide a promising new approach to the evaluation of the effect of animal behaviour, and random and man-induced events on the genetic composition of populations. They also provide a new platform from which to investigate the implication of real world deviations from assumptions...... conditions, but exclude factors such as animal behaviour, environmental structure, and breeding biology, all of which influence genetic diversity. Most populations are unique in some of these characteristics, and therefore may be unsuitable for the classical approach. Here, an alternative approach using......Altering environmental conditions affects the genetic composition of populations via demographic and selective responses by creating of variety of population substructuring types. Classical genetic approaches can predict the genetic composition of populations under long-term or structurally stable...

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

    African Journals Online (AJOL)

    ACSS

    V.P., Rajaram, V., Hash, C.T. and Thakur, R.P.. 2010. SSR allelic diversity in relation to morphological traits and resistance to grain mould in sorghum. Crop and Pasture Science. 61:230-240. Salimath, S., Olivera, A., Godwin, I. and. Bennetzen, J. 1995. Assesment of genome origins and diversity in the genus Eleusine.

  12. 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.

  13. Genetic diversity in Satureja species determined by sequence ...

    Indian Academy of Sciences (India)

    ANITA NAMAYANDEH

    www.ias.ac.in/jgenet/OnlineResources/96/e5.pdf]. Introduction. The genetic diversity of 50 Satureja species was evaluated in three distinct geographical regions of Iran using sequence- related amplified polymorphism (SRAP) markers. Eleven.

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

    African Journals Online (AJOL)

    Yomi

    evaluated using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR). A high level of ... Key words: Barley, RAPD markers, SSR markers, genetic diversity. INTRODUCTION ..... regression approach. Cancer. Res.

  15. Population genetic diversity of marble goby (Oxyeleotris marmoratus ...

    Indian Academy of Sciences (India)

    Navya

    2017-03-31

    Innovation Center for Marine Bio-Industry Technology of Jiangsu Province,. Lianyungang, Jiangsu 222005, China. #These authors contributed equally to this work. Short title: Population genetic diversity analysis of marble goby.

  16. Genetic diversity of natural Tunisian Lavandula multifida L ...

    African Journals Online (AJOL)

    Proprietaire

    2013-02-13

    Feb 13, 2013 ... Key words: Lavandula multifida, genetic diversity, population structure, isozymes, random amplified polymorphic DNA (RAPDs). ... based on morphological, cytogenetic and reproductive traits (Upson et al., 2000; ...... leucanthemifolius var. casablancae): evidence from chloroplast DNA and random amplified ...

  17. Evaluation of genetic diversity in Pyrus germplasm native to Azad ...

    African Journals Online (AJOL)

    hope&shola

    2010-12-06

    Dec 6, 2010 ... ... and limits of the molecular technique in assessing the genetic diversity and relation- ..... ecological dissimilarity. These results also indicate .... interspecific hybrids and extent of self-fertility in Pyrus. Bull. Torrey. Bot. Club, 98: ...

  18. 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 ...

  19. 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 ...

  20. Genetic diversity of grape germplasm as revealed by microsatellite ...

    African Journals Online (AJOL)

    group method with arithmetic averages (UPGMA) clustering analysis. These results will be useful for the exploitation of grape germplasm in basic and applied research. Key words: Vitis vinifera L., simple sequence repeat (SSR), genetic diversity, ...

  1. Genetic diversity and historical demography of Chinese shrimp ...

    African Journals Online (AJOL)

    Genetic diversity and historical demography of Chinese shrimp Feneropenaeus chinensis in Yellow Sea and Bohai Sea based on mitochondrial DNA analysis. YL Li, XY Kong, ZN Yu, J Kong, S Ma, LM Chen ...

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

    Indian Academy of Sciences (India)

    2012-04-03

    Apr 3, 2012 ... T. cordifolia is dio- cious in nature and is primarily propagated through vegeta- tive means. This condition precludes genetic recombination and reshuffling of genes that is manifested in the form of genetic variation. The species is used in almost every house- hold in the Himalayan region of India for the cure ...

  3. Genetic diversity and structure in two protected Posidonia oceanica meadows.

    Science.gov (United States)

    Micheli, Carla; D'Esposito, Daniela; Belmonte, Alessandro; Peirano, Andrea; Valiante, Luigi Maria; Procaccini, Gabriele

    2015-08-01

    Posidonia oceanica meadows growing along the west Mediterranean coastline are under continuous anthropogenic pressure. The way meadow health correlates with genetic and genotypic diversity in P. oceanica, is still under debate. Here we report a microsatellite analysis of two P. oceanica meadows living in protected areas of the Ligurian (Monterosso al Mare, MPA of "Cinque Terre") and central Tyrrhenian Sea (Santa Marinella, regional Site of Community Importance). Both meadows were recently classified as "disturbed", according to shoot density and other phenological parameters. Between the two meadows, Santa Marinella showed higher genetic diversity, while clear genetic substructure was present in both sites, reflecting high spatial heterogeneity. The present study suggests that genetic diversity does not match unequivocally with shoot density and leaf morphology and that small scale intra-meadow heterogeneity is an important factor to consider for establishing the relation between genetic/genotypic variability and health of natural seagrass meadows. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Culture, population structure, and low genetic diversity in Pleistocene hominins.

    Science.gov (United States)

    Premo, L S; Hublin, Jean-Jacques

    2009-01-06

    Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage has been low for more than 500,000 years, but the mechanism responsible for suppressing genetic diversity in Pleistocene hominin populations without similarly affecting that of their hominoid contemporaries remains unknown. Here we use agent-based simulation to study the effect of culturally mediated migration on neutral genetic diversity in structured populations. We show that, in populations structured by culturally mediated migration, selection can suppress neutral genetic diversity over thousands of generations, even in the absence of bottlenecks or expansions in census population size. In other words, selection could have suppressed the effective population size of Pleistocene hominins for as long as the degree of cultural similarity between regionally differentiated groups played an important role in mediating intraspecific gene flow.

  5. Inference of genetic diversity in popcorn S3 progenies.

    Science.gov (United States)

    Pena, G F; do Amaral, A T; Ribeiro, R M; Ramos, H C C; Boechat, M S B; Santos, J S; Mafra, G S; Kamphorst, S H; de Lima, V J; Vivas, M; de Souza Filho, G A

    2016-05-09

    Molecular markers are a useful tool for identification of complementary heterotic groups in breeding programs aimed at the production of superior hybrids, particularly for crops such as popcorn in which heterotic groups are not well-defined. The objective of the present study was to analyze the genetic diversity of 47 genotypes of tropical popcorn to identify possible heterotic groups for the development of superior hybrids. Four genotypes of high genetic value were studied: hybrid IAC 125, strain P2, and varieties UENF 14 and BRS Angela. In addition, 43 endogamous S3 progenies obtained from variety UENF 14 were used. Twenty-five polymorphic SSR-EST markers were analyzed. A genetic distance matrix was obtained and the following molecular diversity parameters were estimated: number of alleles, number of effective alleles, polymorphism information content (PIC), observed and expected heterozygosities, Shannon diversity index, and coefficient of inbreeding. We found a moderate PIC and high diversity index, indicating that the studied population presents both good discriminatory ability and high informativeness for the utilized markers. The dendrogram built based on the dissimilarity matrix indicated six distinct groups. Our findings demonstrate the genetic diversity among the evaluated genotypes and provide evidence for heterotic groups in popcorn. Furthermore, the functional genetic diversity indicates that there are informative genetic markers for popcorn.

  6. 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.

  7. 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.

  8. 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.|info:eu-repo/dai/nl/067852335

    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

  9. 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.

  10. 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 ...

  11. 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 ...

  12. 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.

  13. 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 ...

  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. 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. Assessment of genetic diversity among accessions of two traditional ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) markers were used to evaluate the genetic diversity and explore the genetic relationship among accessions of Acmella uliginosa and Justicia tenella, two leaf vegetables collected from different areas in the northwest and northeast parts of Benin (West Africa). The total ...

  17. Genetic diversity is a predictor of mortality in humans

    NARCIS (Netherlands)

    N.A. Bihlmeyer (Nathan A.); J. Brody (Jennifer); G.D. Smith; K.L. Lunetta (Kathryn); M.A. Nalls (Michael); J.A. Smith (Jennifer A); T. Tanaka (Toshiko); G. Davies (Gail); L. Yu (Lei); S.S. Mirza (Saira); A. Teumer (Alexander); J. Coresh (Josef); J.S. Pankow (James); N. Franceschini (Nora); A. Scaria (Anish); J. Oshima (Junko); B.M. Psaty (Bruce); V. Gudnason (Vilmundur); G. Eiriksdottir (Gudny); T.B. Harris (Tamara); H. Li (Hanyue); D. Karasik (David); D.P. Kiel (Douglas P.); M. Garcia (Melissa); Y. Liu (YongMei); J.D. Faul (Jessica D.); S.L. Kardia (Sharon L.r); W. Zhao (Wei); L. Ferrucci (Luigi); M.M. Allerhand (Michael); D.C. Liewald (David C.); P. Redmond (Paul); J.M. Starr (John); P.L. de Jager (Philip); D.A. Evans (Denis); N. Direk (Nese); M.A. Ikram (Arfan); A.G. Uitterlinden (André); G. Homuth (Georg); R. Lorbeer (Roberto); H.J. Grabe (Hans Jörgen); L.J. Launer (Lenore); J. Murabito (Joanne); A. Singleton (Andrew); D.R. Weir (David); S. Bandinelli (Stefania); I.J. Deary (Ian J.); D.A. Bennett (David A.); H.W. Tiemeier (Henning); T. Kocher (Thomas); T. Lumley (Thomas); D.E. Arking (Dan)

    2014-01-01

    textabstractBACKGROUND: It has been well-established, both by population genetics theory and direct observation in many organisms, that increased genetic diversity provides a survival advantage. However, given the limitations of both sample size and genome-wide metrics, this hypothesis has not been

  18. 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 ...

  19. Assessment of genetic diversity among maize accessions using inter ...

    African Journals Online (AJOL)

    NRCC

    2011-11-07

    Nov 7, 2011 ... The narrow genetic base of popcorn has been of concern to the breeders of this cultivar, hence the present research ... the common maize assembled in the group I confirmed that the compared analysis of genetic diversity was more ..... inbreeding depression is also strong, thus favoring abrupt changes in ...

  20. Evaluation of genetic diversity in Sulla coronaria from different ...

    African Journals Online (AJOL)

    Five oligonucleotides generating 116 markers complementary to simple sequence repeats were used in order to characterize wild and cultivated ecotypes of Sulla coronaria and assess genetic diversity suitable in breeding programs. While analysing populations, a large genetic variability was revealed and supported by ...

  1. 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 .... 10 µl volume mix consisting of 5 U Dreamtaq polymerase enzyme. (Thermo scientific corp ..... constraints in bambara groundnut production, marketing and consumption in the brong ahafo ...

  2. Genetic diversity and differentiation in roses: A gardenrose perspective

    NARCIS (Netherlands)

    Vukosavljev, M.; Zhang, J.; Esselink, G.; Westende, van 't W.P.C.; Cox, P.; Visser, R.G.F.; Arens, P.; Smulders, M.J.M.

    2013-01-01

    tFor the first time genetic diversity among modern garden rose cultivars has been evaluated using a setof 24 microsatellite markers covering most chromosomes. A total of 518 different alleles were obtainedin the set of 138 rose cultivars and this led to the conclusion that in terms of genetic

  3. 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- ...

  4. 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).

  5. Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    Hierarchical analysis highlights the nature of relationship between and among type samples as outlined by standard descriptors. It produces an output called dendrogram, which depicts the hierarchical structure of genetic interaction in clusters/groups. Genetic diversity is the variation of heritable characteristics in a ...

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

    African Journals Online (AJOL)

    STORAGESEVER

    2010-01-18

    Jan 18, 2010 ... Analysis of genetic diversity and estimation of inbreeding coefficient within Caspian horse population using microsatellite markers. Hosein Shahsavarani and Ghodrat Rahimi-Mianji*. Laboratory for Molecular Genetics and Animal Biotechnology, Department of Animal Science, Faculty of Animal Science.

  7. 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, ...

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

    African Journals Online (AJOL)

    Population structure was analyzed by means of genetic distances and probabilistic models; allelic frequencies were used in order to assess the genetic diversity indexes (Ht, Ho, PIC, % polymorphism and number of alleles) for each locus studied. All evaluated loci were polymorphic and the average was highly heterozygote ...

  9. 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 ...

  10. Genetic diversity of Cameroon native goat populations revealed by ...

    African Journals Online (AJOL)

    A total of seventeen caprine microsatellite markers were used on 169 goats to investigate genetic diversity of eight Cameroon native goats and to assess genetic differentiation with the east African small goat. All microsatellites showed a high polymorphic content (PIC) of more than 0.5 in almost all ecotypes.

  11. 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.

  12. Genetic diversity of taraxacum germplasm revealed by sequence ...

    African Journals Online (AJOL)

    Genetic diversity of taraxacum germplasm revealed by sequence-related amplified polymorphism (SRAP) analysis. ... African Journal of Biotechnology ... The genetic relationships analyzed with un-weighed pairgroup method with arithmetic mean (UPMGA) showed that 11 population of taraxacum were grouped into three ...

  13. Genetic diversity among varieties and wild species accessions of ...

    African Journals Online (AJOL)

    Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on SSR markers. ... African Journal of Biotechnology ... To assess the genetic relations inPisum genus and to examine putative duplicate accessions, 20 pea varieties (Pisum sativum L.) with 57 accessions from wild Pisum ...

  14. Genetic diversity in Oroxylum indicum (L.) Vent. (Bignoniaceae), a ...

    African Journals Online (AJOL)

    SERVER

    2008-02-05

    Feb 5, 2008 ... Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in. Oroxylum indicum (L.) Vent (Bignoniaceae) a vulnerable medicinal plant collected from eight locations in Andhra Pradesh, India. High level of genetic similarity was observed in the collected accessions.

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

    African Journals Online (AJOL)

    Genetic diversity in Egyptian and Saudi goat breeds using microsatellite markers. KF Mahrous, SYM Alakilli, LM Salem, SHA El-Aziem, AA El-Hanafy. Abstract. Objective: The genetic polymorphism within and among three indigenous goat breeds found in Egypt (Barki and Zaraibi) and in Saudi Arabia (Ardi) was detected by ...

  16. Genetic diversity of intensive cultured and wild tiger shrimp Penaeus ...

    African Journals Online (AJOL)

    Inbreeding as negative factor perhaps promote a significant increase of the genetic similarity of the captive populations, consequently leading to greater disease susceptibility and impairment of both the growth and final size of the shrimps. Therefore evaluating genetic diversity and inbreeding required for improvement of ...

  17. Analysis of genetic diversity among cultivated enset (Ensete ...

    African Journals Online (AJOL)

    user

    2011-11-09

    Nov 9, 2011 ... Genetic diversity of wild Cofea arabica populations in. Ethiopia as a contribution to conservation and use planning. Ecology and Development series. Doctoral Thesis. University of Bonn,. Germany, No. 44. Yeh FC, Yang RC, Boyle T (1999). Population genetic analysis of codominant markers and qualitative ...

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

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 2. Genetic diversity and population structure of blue-crested lizard, Calotes ... These two lineages are separated by mountain ranges, which play an important role as natural barriers blocking gene flow. Our finding reveal at least two cryptic lineages represented in C.

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

    Indian Academy of Sciences (India)

    Okhotsk Sea in eastern Siberia, and from beyond the sub- arctic forests of northern Scandinavia to arid, mountain- ous southern areas of Spain (Labra et al. 2006; Pyhäjärvi et al. ... in light of global climatic changes. Keywords. genetic diversity; ISSR; RAPD; Pinus sylvestris L. Journal of Genetics Vol. 92, Online Resources.

  20. 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 ...

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-02-04

    Feb 4, 2009 ... Genetic diversity of Pakistani maize genotypes using chromosome specific simple sequence repeat (SSR) primer sets. Zamarud Shah1*, Iqbal Munir1 Shahid Ali2, Arshad Iqbal1, Saqib Mumtaz1, Rab Nwaz3 and. Zahoor Ahmed Swati1. 1Institute of Biotechnology and Genetic Engineering, Faculty of Crop ...

  2. Genetic diversity Study of Dioscoreas Using Morphological Traits ...

    African Journals Online (AJOL)

    Prof. Ogunji

    or molecular markers. Isozymes, being biochemical expressions of the genetic make-up of the plant, can be used to greatly improve the accuracy of cultivar identification. Bressan et al. (2014) used isozymes analysis in delineating yam cultivars into different species. The results revealed clear genetic diversity of the yam.

  3. Genetic diversity of Annona senegalensis Pers. populations as ...

    African Journals Online (AJOL)

    Administrator

    2007-05-16

    May 16, 2007 ... assessment of the genetic diversity in A. senegalensis would assist in planning for future germplasm collection, conservation and fruit .... templates in 20 µl total volume. The amplifications were conducted ... The SSRs were screened on Genetic Analyzer model 3730 XL automated DNA sequencer, G5 dye ...

  4. Assessment of genetic diversity within sour cherry clones

    DEFF Research Database (Denmark)

    Clausen, S. K.; Andersen, S. B.; Henriksen, K.

    2013-01-01

    of improved breeding material. However, no differences in allele profile were found between or within the clones, calling into question the extent of the available genetic diversity and indicating that the observed variance in yield may have to be explained by other genetic mechanisms, including epigenetic...

  5. 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.

  6. 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 ...

  7. 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 ...

  8. 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 ...

  9. 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 ...

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

    African Journals Online (AJOL)

    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 distinguished in Syria, ...

  11. 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 ...

  12. Genetic diversity in Indian FCV and burley tobacco cultivars

    Indian Academy of Sciences (India)

    term tobacco improvement and reduction of vulnerability of the crop. Prior to the availability of DNA-based markers, most genetic diversity studies in various crops were carried out using morphological markers. Molecular markers have become useful tools to provide a relatively unbiased method of quantifying genetic ...

  13. 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 ...

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

    African Journals Online (AJOL)

    hope&shola

    2006-02-03

    Feb 3, 2006 ... 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. 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 ...

  16. Genetic diversity studies and identification of SSR markers ...

    Indian Academy of Sciences (India)

    Genetic diversity studies and identification of SSR markers associated with Fusarium wilt (Fusarium udum) resistance in cultivated pigeonpea (Cajanus cajan) ... Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanas 221 005, India; Department of Mycology and ...

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

    African Journals Online (AJOL)

    SARAH

    2013-12-30

    Dec 30, 2013 ... Serrano M, Calvo JH, Martínez M, Marcos-Carcavilla A,. Cuevas J, González C, Jurado JJ, de Tejada PD. (2009). Microsatellite based genetic diversity and population structure of the endangered. Spanish Guadarrama goat breed. BMC Genet. 10: 61. Slatkin, M. (1985): Gene flow in natural populations.

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

    African Journals Online (AJOL)

    In summary, the farmers' cultivars are distinct from the Kenyan and Rwandese materials and represent more genetic diversity than the varieties imported into Eritrea. This finding is of interest to national breeding program to use the farmer's materials as source of genetic variation for traits of interest. Keywords: Potato, simple ...

  19. Genetic diversity in farm animals - A review

    NARCIS (Netherlands)

    Groeneveld, L. F.; Lenstra, J. A.|info:eu-repo/dai/nl/067852335; Eding, H.; Toro, M. A.; Scherf, B.; Pilling, D.; Negrini, R.; Finlay, E. K.; Jianlin, H.; Groeneveld, E.|info:eu-repo/dai/nl/315030267; 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,

  20. Genetic Diversity in Urban and Rural Indigenous Mexico

    OpenAIRE

    López, John Emilio William

    2016-01-01

    The goal of this study was to examine the genetic diversity of indigenous (and semi-indigenous) populations in Mexico and determine if any genetic variation correlated to culture and language. Mexico’s indigenous populations have not been extensively studied using contemporary genetic typing systems; the ones conducted used too few loci, or very small sample sizes. Mexico has 291 living native languages derived from twelve separate and distinct linguistic families divided into 68 major ...

  1. 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.

  2. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

    Directory of Open Access Journals (Sweden)

    Sara Melito

    Full Text Available BACKGROUND: Helichrysum italicum (Asteraceae is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. METHODS: H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. KEY RESULTS: The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. CONCLUSIONS: The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil.

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    Afrooz Alimohamadi

    2012-12-01

    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 term of 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.  

  5. 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.

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

    African Journals Online (AJOL)

    2011-12-12

    Dec 12, 2011 ... with Mycobacterium tuberculosisBeijing genotype strains is associated with polymorphisms in SLC11A1/NRAMP1 in Indonesian patients with tuberculosis. J. Infect. Dis. 2009; 200: 1671-1674. Hershberg, R., Lipatov, M., Small, P. M.,. 16. et al. High functional diversity inMycobacterium tuberculosisdriven.

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

    African Journals Online (AJOL)

    2011-12-12

    Dec 12, 2011 ... (11, 13), or in the Canary Islands in Spain (14). Finally, recent studies have reported associations between. M. tuberculosis lineages and specific ..... 27. et al. Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in. Cameroon. J. Clin. Microbiol. 2003 ...

  8. 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 ...

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

    African Journals Online (AJOL)

    Pairwise FST values however indicated that all populations were significantly differentiated (p < 0.01). STRUCTURE clustering analysis showed that Volta population split from the Guinea Savanna population. Grasscutter populations in Ghana are genetically differentiated according to agro-ecological zones and the Volta ...

  10. 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 ...

  11. 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...

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

    African Journals Online (AJOL)

    knsccf

    The genotypic classification agreed closely with the grouping observed in .... reaction was performed in the form of master mix to minimize error. Amplification .... Relationships among 20 genotypes of oat visualized by principal component analysis (PCoA) of rainfed plot observations based genetic similarities. The numbers ...

  13. 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.

  14. Polishing the craft of genetic diversity creation in directed evolution.

    Science.gov (United States)

    Tee, Kang Lan; Wong, Tuck Seng

    2013-12-01

    Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field. © 2013. Published by Elsevier Inc. All rights reserved.

  15. 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.

  16. 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.

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

    Science.gov (United States)

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    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.

  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

    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......% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations.......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...

  19. 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

  20. Genetic Diversity among Ancient Nordic Populations

    Science.gov (United States)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R.; Kivisild, Toomas; Dissing, Jørgen

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (∼2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture. PMID:20689597

  1. Genetic diversity among ancient Nordic populations.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13% than among extant Danes and Scandinavians (approximately 2.5% as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  2. The study of relatedness and genetic diversity in cranes

    Science.gov (United States)

    Gee, G.F.; Dessauer, H.C.; Longmire, J.; Briles, W.E.; Simon, R.C.; Wood, Don A.

    1992-01-01

    The U.S. Fish and Wildlife Service (Service) is responsible for recovery of endangered species in the wild and, when necessary, maintenance in captivity. These programs provide an immediate measure of insurance against extinction. A prerequisite inherent in all of these programs is the preservation of enough genetic diversity to maintain a viable population and to maintain the capacity of the population to respond to change. Measures of genetic diversity examine polymorphic genes that are not influenced by selection pressures. Examples of these techniques and those used to determine relatedness are discussed. Studies of genetic diversity, electrophoresis of blood proteins, relatedness, blood typing, and restriction fragment length polymorphisms which are being used by the Patuxent Wildlife Research Center are discussed in detail.

  3. Genetic diversity and population differentiation of Sclerotinia sclerotiorum collected from canola in China and in USA

    Science.gov (United States)

    Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity wa...

  4. Tartary Buckwheat Genetic Diversity in the Himalayas Associated with Farmer Landrace Diversity and Low Dietary Dependence

    Directory of Open Access Journals (Sweden)

    Weijuan Huang

    2017-10-01

    Full Text Available While crop genetic diversity supports ecological processes and food security, there have been few cross-cultural studies evaluating the influence of cultural and dietary factors on the conservation of genetic resources. This study examines genetic diversity patterns of tartary buckwheat in 18 smallholder farming communities across five regions of China (Yunnan Province, Tibet Autonomous Region and Sichuan Province and Bhutan managed by Yi, Tibetan, and Bhutanese farmers using ethnobotanical surveys and DNA barcoding. Findings emphasize that high dietary dependence linked to a single crop may result in simplification of genetic diversity as well as agricultural systems and landscapes more broadly. We advocate for the diversification of crops in agricultural systems as well as diets through the integration of scientific research and farmers’ ecological knowledge and practices towards meeting global food security while supporting environmental well-being through biodiversity conservation.

  5. Landscape, population structure and genetic diversity of Stomoxys calcitrans.

    Science.gov (United States)

    Dsouli Aymes, N; Mavoungou, J F; De Stordeur, E; Duvallet, G

    2009-03-01

    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.

  6. Genetic diversity analysis of fruit characteristics of hawthorn germplasm.

    Science.gov (United States)

    Su, K; Guo, Y S; Wang, G; Zhao, Y H; Dong, W X

    2015-12-07

    One hundred and six accessions of hawthorn intraspecific resources, from the National Germplasm Repository at Shenyang, were subjected to genetic diversity and principal component analysis based on evaluation data of 15 fruit traits. Results showed that the genetic diversity of hawthorn fruit traits varied. Among the 15 traits, the fruit shape variable coefficient had the most obvious evaluation, followed by fruit surface state, dot color, taste, weight of single fruit, sepal posture, peduncle form, and metula traits. These are the primary traits by which hawthorn could be classified in the future. The principal component demonstrated that these traits are the most influential factors of hawthorn fruit characteristics.

  7. Bartonella Prevalence and Genetic Diversity in Small Mammals from Ethiopia

    DEFF Research Database (Denmark)

    Meheretu, Yonas; Leirs, Herwig E.l.; Welegerima, Kiros

    2013-01-01

    More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp of the Barto......More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp...

  8. Danish apple cultivars: genetic diversity, parentage and breeding potential

    DEFF Research Database (Denmark)

    Larsen, Bjarne; Pedersen, Carsten; Ørgaard, Marian

    2017-01-01

    Abstract We made a genetic analysis of about 500 apple cultivars, which either originate from Denmark or have been of greater importance in Denmark. To study the diversity and parentage among the cultivars, 15 SSR markers were used. A new PCR-based protocol for identification of S-alleles was dev......Abstract We made a genetic analysis of about 500 apple cultivars, which either originate from Denmark or have been of greater importance in Denmark. To study the diversity and parentage among the cultivars, 15 SSR markers were used. A new PCR-based protocol for identification of S...

  9. Assessment of genetic diversity in Brazilian barley using SSR markers

    Directory of Open Access Journals (Sweden)

    Jéssica Rosset Ferreira

    2016-03-01

    Full Text Available Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC, with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs.

  10. Castor bean organelle genome sequencing and worldwide genetic diversity analysis.

    Directory of Open Access Journals (Sweden)

    Maximo Rivarola

    Full Text Available Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.

  11. The spatio-temporal dynamics of neutral genetic diversity

    OpenAIRE

    Bonnefon, Olivier; Coville, Jérôme; Garnier, Jimmy; Hamel, François; Roques, Lionel

    2014-01-01

    International audience; The notions of pulled and pushed solutions of reaction-dispersal equations introduced by Garnier et al. (2012) and Roques et al. (2012) are based on a decomposition of the solutions into several components. In the framework of population dynamics, this decomposition is related to the spatio-temporal evolution of the genetic structure of a population. The pulled solutions describe a rapid erosion of neutral genetic diversity, while the pushed solutions are associated wi...

  12. 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.

  13. 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.

  14. Reduced genetic diversity and alteration of gene flow in a fiddler crab due to mangrove degradation.

    Directory of Open Access Journals (Sweden)

    Alex Nehemia

    Full Text Available The fiddler crab Austruca occidentalis is a dominant species in mangrove forests along the East African coast. It enhances soil aeration and, through its engineering activities, makes otherwise-inaccessible food available for other marine organisms. Despite its importance, the habitat of A. occidentalis is threatened by human activities. Clearing the mangroves for salt farming and selective logging of mangroves trees continue to jeopardise mangrove ecosystems in the Western Indian Ocean. This study aims to use partial mitochondrial COI gene sequences and nuclear microsatellites to determine whether salt farming activities in mangroves have a negative impact on the genetic diversity and gene flow of A. occidentalis collected along the Tanzania coast. The level of genetic diversity for both mitochondrial DNA and nuclear microsatellites are relatively lower in samples from salt ponds compared to natural mangrove sites. Analysis of molecular variance (AMOVA among all populations showed low but significant differentiation (COI: Fst = 0.022, P < 0.05; microsatellites: Fst = 0.022, P < 0.001. A hierarchical AMOVA indicates lower but significant genetic differentiation among populations from salt ponds and natural mangroves sites (COI: Fct = 0.033, P < 0.05; microsatellites: Fct = 0.018, P = < 0.01. These results indicate that salt farming has a significant negative impact on the genetic diversity of A. occidentalis. Since higher genetic diversity contributes to a stable population, restoring the cleared habitats might be the most effective measures for the conservation of genetic diversity and hence adaptive potential to environmental change in this species.

  15. 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.

  16. 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.

  17. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

    2011-01-01

    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...

  18. Genetic diversity, phylogeographic structure and effect of selection ...

    Indian Academy of Sciences (India)

    Abdulhakeem B. Ajibike

    2017-12-11

    Dec 11, 2017 ... culture to address poverty in Africa: opportunities and challenges. (eds. J. E. O. Rege, A. M. Nyamu and D. Sendalo), pp. 293–298. ILRI Publications, Nairobi. Mtileni B. J., Muchadeyi F. C., Maiwashe A., Groeneveld. E., Groeneveld L. F., Dzama K. and Weigend S. 2011. Genetic diversity and conservation of ...

  19. 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...... hinder the ability of parasites to adapt while cycling within social insect colonies....

  20. Microsatellite genotyping reveals high genetic diversity but low ...

    African Journals Online (AJOL)

    JMwacharos

    2016-03-16

    Mar 16, 2016 ... Genetic diversity and structure of goats within an early ... due to their recognized features and characteristics. The ... Genomic DNA was extracted from whole blood using. DNeasy® Blood and Tissue Kit (Qiagen GmbH, Germany). DNA concentration and purity were assessed using the BioPhotometer.

  1. 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.

  2. Genetic diversity of intensive cultured and wild tiger shrimp Penaeus ...

    African Journals Online (AJOL)

    Mahdi

    2011-02-25

    Feb 25, 2011 ... Brood stock showed lower genetic diversity value than wild population. However, with an observed heterozygosity (Hobs) below expectations it would be necessary to introduce cross breeding among hatcheries to reduce the risk of inbreeding depression. Microsatellite markers analysis was able to ...

  3. 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 ...

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

    African Journals Online (AJOL)

    Based on the previous migratory scenarios, the Cameroon native goats may have various maternal origins, Indian, Middle East and south Mediterranean regions. The results are useful for conservation and subsequent investigations may be undertaken to broaden genetic diversity particularly for production purpose.

  5. Genetic diversity of ochratoxigenic Aspergillus section Nigri , using ...

    African Journals Online (AJOL)

    This study evaluates the genetic diversity of ochratoxigenic Aspergillus section Nigri using RAPD and VCG techniques. Results obtained revealed OPX 07 as the most informative of the tested RAPD markers generating 12 polymorphic bands while the least bands were generated by OPR 19. Of the 40 Aspergillus section ...

  6. 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 ... In addition, due to the greater number of markers per assay, the AFLP technique seems to be more informative than the RAMPO method.

  7. Analysis of genetic Diversity and relationships of Tanzania local ...

    African Journals Online (AJOL)

    Genetic diversity among seven Tanzanian goat populations (Ujiji, Sukuma, Ugogo, Maasai, Mbeya, Newala and Coastal goats) was investigated by determining polymorphisms at 19 microsatellite DNA loci, West African Dwarf Tswana, Landim and Toggenburg were included to serve as reference breeds. Among the ...

  8. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    Full Length Research Paper ... The study was conducted to assess the genetic diversity of L. sativum population from Ethiopia using inter simple sequence repeat (ISSR) marker. Molecular data generated from ISSR ... the ISSR data was used to construct unweighted pair group method with arithmetic mean (UPGMA) and.

  9. 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 ...

  10. 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 ...

  11. 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 ...

  12. 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 ...

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

    Indian Academy of Sciences (India)

    The genetic structure and diversity of 10 Chinese indigenous egg-type duck breeds were investigated using 29 microsatellite markers. The total number of animals examined were 569, on average 57 animals per breed were selected. The microsatellite marker set analysed provided 177 alleles (mean 6.1 alleles per locus, ...

  14. 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...

  15. Comparative evaluation of genetic diversity using RAPD, SSR and ...

    Indian Academy of Sciences (India)

    [Panwar P., Nath M., Yadav V. K. and Kumar A. 2010 Comparative evaluation of genetic diversity using RAPD, SSR and cytochome P450 gene based markers ... sity analysis, the present study aimed to evaluate the relative usefulness of RAPD .... primer ranged from 3 to 15, and size of the products ranged from 300 bp to ...

  16. 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 ...

  17. A study of patrilineal genetic diversity in Iranian indigenous horse ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-28

    Nov 28, 2011 ... 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, excluding the pseudoautosomal region, is inherited as a single nonrecombinant unit.

  18. 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 ...

  19. 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 ...

  20. Genetic Diversity in Ethiopian Field Pea (Pisum sativum L ...

    African Journals Online (AJOL)

    Ethiopian field pea germplasm were investigated using SSR markers. ... that markers used in this study would be useful for genetic diversity analysis of pea. .... Statistical Analysis. Euclidean distance was used for the cluster analysis, i.e. the square distance between two vectors. Principal component analysis (PC) was done ...

  1. 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 ...

  2. Evaluation of genetic diversity in rice using simple sequence repeats ...

    African Journals Online (AJOL)

    The dendrogram revealed 8 major distinct clusters. Higher range of similarity values for related genotypes using simple sequence repeats (SSR) provides greater confidence for the assessment of genetic diversity and relationships. The polymorphism information content (PIC) value for the SSR loci ranged from 0.36 to 0.98.

  3. Examination of genetic diversity in common bean ( Phaseolus ...

    African Journals Online (AJOL)

    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 observed for the ...

  4. (SSR) marker- assisted genetic diversity among upland Bt- and non ...

    African Journals Online (AJOL)

    Student

    2011-11-02

    Nov 2, 2011 ... new elite cotton cultivars. Key words: Bt-cotton, dissimilarity matrix, DNA polymorphism, genetic diversity, SSR marker. INTRODUCTION. Cotton is the world's most imperative natural textile fiber and a valuable oil seed crop. Cotton is the main cash crop of Pakistan and provides cotton fiber to the national.

  5. Genetic diversity of Plasmodium falciparum field isolates from south ...

    African Journals Online (AJOL)

    Conclusion: The allelic distributions however were similar to those previously reported in other endemic malaria countries. Future studies will be designed to include other malaria endemic regions of Nigeria such as the oil exploration regions. Keywords: Genetic diversity; Plasmodium; Merozoite surface protein, monoclonal ...

  6. Genetic diversity of Santalum album using random amplified ...

    African Journals Online (AJOL)

    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 among 30 accessions of S. album collected from different parts of South India. A total of 248 polymorphic amplicons were ...

  7. Genetic diversity and in vitro antibiotic susceptibility profile of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-04-06

    Apr 6, 2009 ... sulfomethoxazole. Key words: Genetic diversity, Salmonella, water, antibiotic susceptibility. INTRODUCTION ... The emergence of antibiotic resistant bacterial patho- gens has become a major public health .... sludge tank; strains 26, 32, 36, 37, 38, 39 and 40 isolated from Amalinda waste water plant's ...

  8. 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 ...

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

    African Journals Online (AJOL)

    Flixweed plant bearing the scientific title of 'Descurainia sophia' is recognized across the planet as well as in Iran, as an herbal medicine. The present study investigates the genetic diversity of germplasm of flixweed in Kerman Province using and inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA ...

  10. 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 ...

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

    African Journals Online (AJOL)

    Biniam M

    2016-08-31

    Aug 31, 2016 ... Sixty three potato clones (51 farmers' and 12 varieties) from Eritrea, 18 and 12 varieties from Kenya and. Rwanda, respectively were characterized using 12 highly polymorphic simple sequence repeat (SSR) markers. The study was designed to assess the genetic diversity and varietal distinctness among ...

  12. Genetic diversity analysis in the Hypericum perforatum populations ...

    African Journals Online (AJOL)

    Genetic diversity analysis in the Hypericum perforatum populations in the Kashmir valley by using inter-simple sequence repeats (ISSR) markers. Shazia Farooq, MA Siddiqui, PC Ray, MQ Sheikh, Sheikh Shahnawaz, M Ashraf Bhat, MR Mir, MZ Abdin, Imtiyaz Ahmad, Jamsheed Javid, Prasant Yadav, M Masroor, Mariyam ...

  13. 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 ...

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... Key words: Triticum aestivum L., SSR markers, genetic diversity. INTRODUCTION. In Pakistan wheat is grown on 8358 thousand hectares with a total production of 21.6 million/tons giving an aver- age yield of 2.39 tons ha-1. Wheat occupies 70% of Rabi and 37% of total cropped area of Pakistan. In NWFP,.

  15. An understanding of the underlying genetic diversity within and ...

    African Journals Online (AJOL)

    AMuchugi

    2016-08-03

    Aug 3, 2016 ... Four primer combinations produced a total of 223 polymorphic bands. Both the natural and on-farm populations had high genetic diversity ranging from H = 0.2892 to H = 0.1278. Principal ... The integrity and quality of the DNA was ... amplified fragments with fluorescent-labeled EcoRI primers having.

  16. Assessment of Genetic diversity in mutant cowpea lines using ...

    African Journals Online (AJOL)

    FKOLADE

    2016-11-09

    Nov 9, 2016 ... for crop improvement, hence the need to broaden the genetic base of any crop. This study was done in order to further enhance this in cowpea. While assessing diversity and phylogenetic relationship with other mutants and their parents, each unique mutant was also characterized. Randomly amplified ...

  17. 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 ...

  18. AFLP analysis on genetic diversity and population structure of small ...

    African Journals Online (AJOL)

    The population genetic structure and diversity of small yellow croaker Larimichthys polyactis in the Bohai Bay, Yellow Sea and East China Sea were analyzed using amplified fragment length polymorphism (AFLP). Ninety-one individuals were collected from six locations representing three stocks of small yellow croaker.

  19. 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 ...

  20. Genetic diversity of Santalum album using random amplified ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-06

    Jul 6, 2009 ... Santalum album is a parasitic, evergreen tree growing primarily in south Central India, in the dry ... species belonging to the family santalaceae ... superior trees. Therefore, assessment of genetic diversity is vital in developing effective conservation strategies (Loveless, 1992) and sustainable manage-.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... America in this study. Key words: Blackberry, Boysenberry, raspberry, genetic diversity, AFLP markers. INTRODUCTION ... Germplasm Resources Information Network describes 13 subgenera for the genus Rubus ... polymorphisms) markers are highly reproducible multi-locus marker system developed by ...

  2. Genetic diversity and differentiation of Pseudophoenix (Arecaceae) in Hispaniola

    Science.gov (United States)

    Technical Abstract Pseudophoenix ekmanii Burret, P. lediniana Read, and P. vinifera (Mart.) Becc. (Arecaceae) are endemic to Hispaniola. The more wide-ranging P. sargentii H.Wendl. ex Sarg. occurs on this island as well. The population genetic diversity and structure of Pseudophoenix was investigate...

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

    African Journals Online (AJOL)

    Common bread wheat has very low genetic diversity. Plant breeders find it difficult to get appropriate germplasm which can be used for bread wheat improvement. Wild plant species is one of the potential sources for conferring resistant genes which can be exploited for bread wheat improvement. The challenge is to utilize ...

  4. Genetic diversity, classification and comparative study on the larval ...

    African Journals Online (AJOL)

    Genetic diversity, classification and comparative study on the larval phenotypic data in 54 oval cocoon strains of Iran silkworm Bombyx mori (Lepidoptera: ... However, the strains of the same origin did not grouped together, demonstrating that they might have from different biological and development performance.

  5. 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.

  6. Genetic diversity analysis of some exotic, Indian and mutant ...

    African Journals Online (AJOL)

    USER

    2010-06-28

    Jun 28, 2010 ... Key words: Brassica carinata, Brassica juncea, Brassica napus, RAPD markers, polymorphism, genetic diversity. INTRODUCTION. Brassica is cosmopolitan in distribution occupying a pro- minent place in world's agrarian economy as vegetables, oilseed, feed and fodder, green manure and condiment.

  7. Assessing genetic diversity in Valencia peanut germplasm using SSR markers

    Science.gov (United States)

    Valencia peanuts (Arachis hypogaea L.ssp. fastigiata var. fastigiata) are well known for their in-shell market value. Assessment of genetic diversity of the available Valencia germplasm is key to the success of developing improved cultivars with desirable agronomic and quality traits. In the pres...

  8. 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 ...

  9. Genetic diversity of Kenyan Prosopis populations based on random ...

    African Journals Online (AJOL)

    MUTURI

    In combination, these traits may enhance the invasiveness of plant hybrids. The introduction of Prosopis ... Description of sample populations, plant sampling and reference species. Six naturally established Prosopis ...... boosted genetic diversity in the invasive range of black cherry. (Prunus serotina; Rosaceae). Ann. Bot.

  10. Multi-objective Uniform-diversity Genetic Algorithm (MUGA)

    OpenAIRE

    Jamali, Ali; Nariman-zadeh, Nader; Atashkari, Kazem

    2008-01-01

    A new multi-objective uniform-diversity genetic algorithm (MUGA) has been proposed and successfully used for some test functions and for thermodynamic cycle optimization of ideal turbojet engines. It has been shown that the performance of this algorithm is superior to that

  11. Genetic diversity and reproductive success in mandrills (Mandrillus sphinx).

    Science.gov (United States)

    Charpentier, M; Setchell, J M; Prugnolle, F; Knapp, L A; Wickings, E J; Peignot, P; Hossaert-McKey, M

    2005-11-15

    Recent studies of wild animal populations have shown that estimators of neutral genetic diversity, such as mean heterozygosity, are often correlated with various fitness traits, such as survival, disease susceptibility, or reproductive success. We used two estimators of genetic diversity to explore the relationship between heterozygosity and reproductive success in male and female mandrills (Mandrillus sphinx) living in a semifree ranging setting in Gabon. Because social rank is known to influence reproductive success in both sexes, we also examined the correlation between genetic diversity and social rank in females, and acquisition of alpha status in males, as well as length of alpha male tenure. We found that heterozygous individuals showed greater reproductive success, with both females and males producing more offspring. However, heterozygosity influenced reproductive success only in dominant males, not in subordinates. Neither the acquisition of alpha status in males, nor social rank in females, was significantly correlated with heterozygosity, although more heterozygous alpha males showed longer tenure than homozygous ones. We also tested whether the benefits of greater genetic diversity were due mainly to a genome-wide effect of inbreeding depression or to heterosis at one or a few loci. Multilocus effects best explained the correlation between heterozygosity and reproductive success and tenure, indicating the occurrence of inbreeding depression in this mandrill colony.

  12. 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....

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

    African Journals Online (AJOL)

    AJL

    compositions and changes in population genetic structure of P. infestans, especially the .... Allele frequencies for SSR markers in 134 P. infestans strains from the four provinces collected in 2008 and 2009. SSR locus Allele Hebei Liaoning Jilin Heilongjiang 2008 2009 Overall Gene diversity. G11. 156. 0.02. 0.00. 0.13. 0.03.

  14. Evaluation of genetic diversity in rice using SSR markers

    African Journals Online (AJOL)

    hemant

    2012-10-18

    Oct 18, 2012 ... como doadora de alelos para aumento da producao e da tolerancia a seca do arroz (Oryza sativa) via analise de ABQTLs. Thesis,. Universidade Federal de Goias. Ravi M, Geethanjali S, Sameeyafarheen F, Maheswaran M (2003). Molecular marker based genetic diversity analysis in rice (Oryza sativa L.) ...

  15. Genetic diversity of Pogonatherum paniceum (Lam.) Hack. in ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-04-06

    Apr 6, 2009 ... 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.

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

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... strains of E. coli were selected by selective medium and conventional biochemical test from fresh stool samples of swines in ... extragenic palindrome PCR (REP-PCR), 34 E. coli isolates were clustered to 19 ERIC-PCR genotypes ..... genetic diversity of Clostridium perfringens from chicken by REP-. PCR.

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

    African Journals Online (AJOL)

    Conrad Prof

    2013-04-24

    Apr 24, 2013 ... protein mix, and the resultant relationship based on seed storage proteins instigates a review of erstwhile taxonomic, agricultural ... Key words: Fabaceae, seed protein, polymorphism, genetic diversity, taxonomy, single protein. ..... Fassini PG, Noda RB, Ferreira ES, Silva MA, Neves VA, Demonte A. (2011).

  18. Genetic diversity and bottleneck analysis of Yunnan mithun ( Bos ...

    African Journals Online (AJOL)

    Mithun or gayal (Bos frontalis) is endemic to the Gaoligongshan Mountains and Drung River Basin in Yunnan, China; a rare and endangered Bos species. To evaluate the genetic diversity and bottleneck effect of Yunnan mithun population, we screened 16 bovine microsatellite loci of Yunnan mithun (N = 34) to provide ...

  19. 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...

  20. 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 ...

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

    African Journals Online (AJOL)

    ajl

    2013-02-27

    Feb 27, 2013 ... 4Agricultural Research Company of Minas Gerais (EPAMIG), Uberaba, Minas Gerais, Brazil. 5Departament of Agricultural Sciences, State University of Montes Claros, Janaúba, Minas Gerais, Brazil. Accepted 5 October, 2012. The genetic diversity among 46 accessions of physic nut was estimated with Nei ...

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

    African Journals Online (AJOL)

    Charles Moses Lyimo

    2013-12-21

    Dec 21, 2013 ... Animal Science. Abstract. The study aimed to evaluate the genetic diversity of Tanzanian chicken populations through phylogenetic relationship, and to trace the history of Tanzanian indigenous chickens. Five ecotypes of. Tanzanian local chickens (Ching'wekwe, Kuchi, Morogoro-medium, Pemba and ...

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

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-05-04

    May 4, 2016 ... for molecular characterization of domestic animals. Therefore, the present study was aimed to analyse the. Syrian goat genetic diversity and differentiation using recommended morphological traits (FAO, 2012) and microsatellite markers (FAO, 2004) to inform the design of rational goat breeds improvement ...

  4. Assessment of genetic diversity of Lycoris longituba (Amaryllidaceae ...

    Indian Academy of Sciences (India)

    On the other hand, the colour type in XY pop- ulation was mainly white. These results were in accordance with the analysis based on RAPDs in that the dissimilarity of morphological types among the three populations was con- firmed by the genetic diversity data. The reason may be that natural hybridization of many fertile ...

  5. 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 ...

  6. 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 ...

  7. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    was conducted to assess the genetic diversity of L. sativum population from Ethiopia using inter simple sequence repeat (ISSR) marker. Molecular ... human abdominal ache and diarrhea. Moreover, L. sativum is also used to treat ..... Composition and Physical Properties of Cress (Lepidium sativum L.) and Field Pennycress ...

  8. Genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    fire7-

    2016-12-28

    Dec 28, 2016 ... The Ethiopian genetic center is considered to be one of the secondary centers of diversity for the ... accessions was developed, which represented different common bean production ecologies and seed .... The size of the bubbles does not correspond to number of genotypes sampled in each location.

  9. Genetic diversity of the blast fungus, Magnaporthe grisea (Hebert ...

    African Journals Online (AJOL)

    Genetic diversity of the blast fungus, Magnaporthe grisea (Hebert) Barr, in Burkina Faso. Y Séré, A Onasanya, A Afolabi, HD Mignouna, K Akator. Abstract. Trapping nurseries trialed at two screening sites in Burkina Faso appeared to be an effective tool to characterize the virulence spectrum of blast populations using limited ...

  10. Genetic diversity in barley landraces (Hordeum vulgare L. subsp ...

    Indian Academy of Sciences (India)

    Genetic diversity in barley landraces (Hordeum vulgare L. subsp. vulgare) originated from Crescent Fertile region as detected by seed storage proteins. RIM MZID FARHAT CHIBANI RAYDA BEN AYED MOHSEN HANANA JOELLE BREIDI RABIH KABALAN SAMIH EL-HAJJ HASSAN MACHLAB AHMED REBAI LAMIS ...

  11. Genetic diversity in barley landraces (Hordeum vulgare L. subsp ...

    Indian Academy of Sciences (India)

    Genetic diversity in barley landraces (Hordeum vulgare L. subsp. vulgare) originated from Crescent Fertile region as detected by seed storage proteins. RIM MZID1∗, FARHAT CHIBANI2, RAYDA BEN AYED3, MOHSEN HANANA1, JOELLE BREIDI4,. RABIH KABALAN4, SAMIH EL-HAJJ5, HASSAN MACHLAB6, AHMED ...

  12. Assessment of genetic diversity in Isabgol (Plantago ovata Forsk ...

    African Journals Online (AJOL)

    sandeep kaswan

    Assessment of genetic diversity in Isabgol (Plantago ovata Forsk.) using random amplified polymorphic DNA. (RAPD) and inter-simple sequence repeat (ISSR) markers for developing crop improvement strategies. Vineet Kaswan*, Arunabh Joshi and S. R. Maloo. Department of Molecular Biology and Biotechnology, ...

  13. 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 ...

  14. Genetic diversity, phylogeographic structure and effect of selection ...

    Indian Academy of Sciences (India)

    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 four commercial egg line ...

  15. 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 ...

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

    African Journals Online (AJOL)

    The Croton heliotropiifolius (Euphorbiaceae family) is a shrubby plant that has attracted attention both by the need for conservation as for their pharmacological potential. The present study aimed to characterize the diversity and structure genetic of a population of C. heliotropiifolius present in a forest fragment in the city of ...

  17. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-20

    Jul 20, 2009 ... synthetic hexaploid wheat screened against Barley ... present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat ..... (Saffdar, 2007). Similar results were also obser- ved by De Freitas et al. (2000) in relation to the stem rust disease. The dendrogram showed ...

  18. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... Res. 5: 643-652. Capili JB (1990). Isozyme and mitochondrial DNA restriction endonuclease analysis of three strains of O. nilitocus. Dissertation,. University of Wales. D'Amato ME, Corach D (1996). Genetic diversity of populations of the freshwater shrimp Macrobrachium bordello (Caridae: Palaemonidae).

  19. 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 ...

  20. 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 ...

  1. 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 ...

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

    African Journals Online (AJOL)

    In this study, genetic diversity of 142 contrasting Ethiopian field pea germplasm were investigated using SSR markers. Euclidean Distance Matrix clustered the collections into seven distinct groups. There were 20 collections in Cluster I, 11 in Cluster II, 5 in Cluster III, 41 in Cluster IV, 17 in Cluster V, 18 in Cluster VI and 30 in ...

  3. 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 ...

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

    African Journals Online (AJOL)

    Bilal

    2011-11-07

    Nov 7, 2011 ... As the available land for tea cultivation is limited, improved breeding strategies with reduced pro- duction costs are getting increasing importance. Natural genetic diversity in tea has been reduced at an alarming rate mainly because of selection and breeding for desirable traits (Kaundun and Park, 2002).

  5. 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 ...

  6. 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 ...

  7. 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 ...

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

    African Journals Online (AJOL)

    Genetic relatedness and diversity in 32 almond genotypes were analysed using random amplified polymorphic DNA (RAPD) markers. All the genotypes maintained at Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, India comprised ten exotic introductions and 22 indigenous selections. Using 16 selected ...

  9. 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 ...

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

    African Journals Online (AJOL)

    Review: Genetic diversity and population structure of cotton ( Gossypium hirsutum L. race latifolium H. ) using microsatellite markers. ... African Journal of Biotechnology ... Four groups were identified applying different methods (the probabilistic method, Principal Coordinates Analysis and Neighbor Joining tree). American ...

  11. 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.

  12. 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

  13. 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.

  14. Thai pigs and cattle production, genetic diversity of livestock and strategies for preserving animal genetic resources

    Directory of Open Access Journals (Sweden)

    Kesinee Gatphayak

    2013-03-01

    Full Text Available This paper reviews the current situation of livestock production in Thailand, genetic diversity and evaluation, as well as management strategies for animal genetic resources focusing on pigs and cattle. Sustainable conservation of indigenous livestock as a genetic resource and vital components within the agricultural biodiversity domain is a great challenge as well as an asset for the future development of livestock production in Thailand.

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

    OpenAIRE

    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 horses, caused by bites of midges, predominantly Culicoides species. It affects various horse breeds worldwide. With no effective treatment, IBH degrades horse health and causes economic loss. In this th...

  16. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Directory of Open Access Journals (Sweden)

    Sascha van der Meer

    Full Text Available Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68, which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  17. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Science.gov (United States)

    van der Meer, Sascha; Jacquemyn, Hans

    2015-01-01

    Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  18. Population connectivity buffers genetic diversity loss in a seabird.

    Science.gov (United States)

    Ramírez, Oscar; Gómez-Díaz, Elena; Olalde, Iñigo; Illera, Juan Carlos; Rando, Juan Carlos; González-Solís, Jacob; Lalueza-Fox, Carles

    2013-05-20

    Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems' threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory's shearwater (Calonectris borealis). We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia. Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.

  19. Genetic diversity in a germplasm bank of Oenocarpus mapora (Arecaceae).

    Science.gov (United States)

    Moura, E F; de Oliveira, M S P

    2012-11-26

    Oenocarpus mapora is an Amazonian palm species commonly used by native populations for food and in folk medicine. We measured genetic variability, using RAPD markers, of material kept in a germplasm bank composed of accessions sampled from the Brazilian Amazon. These included 74 individuals from 23 accessions sampled from 9 localities in three States of the Brazilian Amazon. Jaccard genetic similarities were calculated based on 137 polymorphic bands, amplified by 15 primers. Dendrograms constructed based on the genetic similarities among individuals and sample localities demonstrated genetic separation of Acre State from the States of Amazonas and Pará. Two models in three hierarchical levels were considered for AMOVA: one considering the grouping of sampling sites in each state, and the other considering sampling sites in each subgroup formed by the dendrograms. The first model showed no significant genetic variation among states. On the other hand, genetic variation among subgroups was significant. In this model, the within-sample-site genetic diversity was 47.15%, which is considered to be low, since O. mapora is allogamous. By means of Bayesian analysis, the sample sites were clustered into five groups, and their distribution was similar to what we found in the dendrograms based on genetic similarity.

  20. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Science.gov (United States)

    Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, θ = 0.07) were

  1. Genetic Diversity and Population Structure of Theileria annulata in Oman.

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    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

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

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    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.

  3. The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler.

    Science.gov (United States)

    Wright, David J; Spurgin, Lewis G; Collar, Nigel J; Komdeur, Jan; Burke, Terry; Richardson, David S

    2014-05-01

    Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool. © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  4. 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.

  5. Microalgal diversity fosters stable biomass productivity in open ponds treating wastewater.

    Science.gov (United States)

    Cho, Dae-Hyun; Choi, Jung-Woon; Kang, Zion; Kim, Byung-Hyuk; Oh, Hee-Mock; Kim, Hee-Sik; Ramanan, Rishiram

    2017-05-16

    It is established that biodiversity determines productivity of natural ecosystems globally. We have proved that abiotic factors influenced biomass productivity in engineered ecosystems i.e. high rate algal ponds (HRAPs), previously. This study demonstrates that biotic factors, particularly microalgal diversity, play an essential role in maintaining stable biomass productivity in HRAP treating municipal wastewater by mutualistic adaptation to environmental factors. The current study examined data from the second year of a two-year study on HRAP treating municipal wastewater. Microalgal diversity, wastewater characteristics, treatment efficiency and several environmental and meteorological factors were documented. Multivariate statistical analyses reveal that microalgae in uncontrolled HRAPs adapt to adverse environmental conditions by fostering diversity. Subsequently, five dominant microalgal strains by biovolume were isolated, enriched, and optimum conditions for high biomass productivity were ascertained. These laboratory experiments revealed that different microalgal strains dominate in different conditions and a consortium of these diverse taxa help in sustaining the algae community from environmental and predatory pressures. Diversity, niche or seasonal partitioning and mutualistic growth are pertinent in microalgal cultivation or wastewater treatment. Therefore, enrichment of selective species would deprive the collective adaptive ability of the consortium and encourage system vulnerability especially in wastewater treatment.

  6. Date Palm Genetic Diversity Analysis Using Microsatellite Polymorphism.

    Science.gov (United States)

    Khierallah, Hussam S M; Bader, Saleh M; Hamwieh, Alladin; Baum, Michael

    2017-01-01

    Date palm (Phoenix dactylifera L.) is considered one of the great socioeconomic resources in the Middle East and the Arab regions. The tree has been and still is at the center of the comprehensive agricultural development. The number of known date palm cultivars, distributed worldwide, is approximately 3000. The success of genetic diversity conservation or any breeding program depends on an understanding of the amount and distribution of the genetic variation already in existence in the genetic pool. Development of suitable DNA molecular markers for this tree may allow researchers to estimate genetic diversity, which will ultimately lead to the genetic conservation of date palm. Simple sequence repeats (SSRs) are DNA strands, consisting of tandemly repeated mono-, di-, tri-, tetra-, or penta-nucleotide units that are arranged throughout the genomes of most eukaryotic species. Microsatellite markers, developed from genomic libraries, belong to either the transcribed region or the non-transcribed region of the genome, and there is rarely available information on their functions. Microsatellite sequences are especially suited to distinguish closely related genotypes due to a high degree of variability making them ideally suitable in population studies and the identification of closely related cultivars. This chapter focuses on the methods employed to characterize date palm genotypes using SSR markers.

  7. Turtle carapace anomalies: the roles of genetic diversity and environment.

    Directory of Open Access Journals (Sweden)

    Guillermo Velo-Antón

    Full Text Available BACKGROUND: Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3% to 69% in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium. CONCLUSIONS/SIGNIFICANCE: Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants and heritability of anomalies would be useful to better understand the complex origin of anomalies in natural populations.

  8. Microbial diversity and the genetic nature of microbial species.

    Science.gov (United States)

    Achtman, Mark; Wagner, Michael

    2008-06-01

    The earth contains a huge number of largely uncharacterized Bacteria and Archaea. Microbiologists are struggling to summarize their genetic diversity and classify them, which has resulted in heated debates on methods for defining species, mechanisms that lead to speciation and whether microbial species even exist. This Review proposes that decisions on the existence of species and methods to define them should be guided by a method-free species concept that is based on cohesive evolutionary forces. It summarizes current approaches to defining species and the problems of these approaches, and presents selected examples of the population genetic patterns at and below the species level.

  9. Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers

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    Ermis Yanes Paz

    2012-01-01

    Full Text Available The Cuban pineapple germplasm collection represents the genetic diversity of pineapple cultivated in that country and includes other important genotypes obtained from the germplasm collections in Brazil and Martinique. The collection has previously been characterized with morphological descriptors but a molecular characterization has been lacking. With this aim, 56 six genotypes of A. comosus and one of Bromelia pinguin were analyzed with a total of 191 AFLP markers. A dendrogram that represents the genetic relationships between these samples based on the AFLP results showed a low level of diversity in the Cuban pineapple collection. All Ananas comosus accessions, being the majority obtained from farmers in different regions in Cuba, are grouped at distances lower than 0.20. Molecular characterization was in line with morphological characterization. These results are useful for breeding and conservation purposes.

  10. Isolation of genetically diverse Marburg viruses from Egyptian fruit bats.

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    Jonathan S Towner

    2009-07-01

    Full Text Available In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus based on detection of Marburg virus RNA in 31/611 (5.1% bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were collected nine months apart, demonstrating long-term virus circulation. The bat colony was estimated to be over 100,000 animals using mark and re-capture methods, predicting the presence of over 5,000 virus-infected bats. The genetically diverse virus genome sequences from bats and miners closely matched. These data indicate common Egyptian fruit bats can represent a major natural reservoir and source of Marburg virus with potential for spillover into humans.

  11. A genomic scale map of genetic diversity in Trypanosoma cruzi

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    Ackermann Alejandro A

    2012-12-01

    Full Text Available Abstract Background Trypanosoma cruzi, the causal agent of Chagas Disease, affects more than 16 million people in Latin America. The clinical outcome of the disease results from a complex interplay between environmental factors and the genetic background of both the human host and the parasite. However, knowledge of the genetic diversity of the parasite, is currently limited to a number of highly studied loci. The availability of a number of genomes from different evolutionary lineages of T. cruzi provides an unprecedented opportunity to look at the genetic diversity of the parasite at a genomic scale. Results Using a bioinformatic strategy, we have clustered T. cruzi sequence data available in the public domain and obtained multiple sequence alignments in which one or two alleles from the reference CL-Brener were included. These data covers 4 major evolutionary lineages (DTUs: TcI, TcII, TcIII, and the hybrid TcVI. Using these set of alignments we have identified 288,957 high quality single nucleotide polymorphisms and 1,480 indels. In a reduced re-sequencing study we were able to validate ~ 97% of high-quality SNPs identified in 47 loci. Analysis of how these changes affect encoded protein products showed a 0.77 ratio of synonymous to non-synonymous changes in the T. cruzi genome. We observed 113 changes that introduce or remove a stop codon, some causing significant functional changes, and a number of tri-allelic and tetra-allelic SNPs that could be exploited in strain typing assays. Based on an analysis of the observed nucleotide diversity we show that the T. cruzi genome contains a core set of genes that are under apparent purifying selection. Interestingly, orthologs of known druggable targets show statistically significant lower nucleotide diversity values. Conclusions This study provides the first look at the genetic diversity of T. cruzi at a genomic scale. The analysis covers an estimated ~ 60% of the genetic diversity present in the

  12. Human immunodeficiency virus type-1 (HIV-1) genetic diversity and ...

    African Journals Online (AJOL)

    PROGMANAGER

    2013-04-24

    Apr 24, 2013 ... Human immunodeficiency virus type-1 (HIV-1) genetic diversity and prevalence of antiretroviral drug resistance mutations in treatment-naïve adults in Jos,. North Central Nigeria. Anejo-Okopi J. A.1*, Agbaji O. O.1,2, Agaba P. A.1,3, Ugoagwu P. O.1, Were K.4, Onywera H.4,. Owiti P.4, Isa S. E1,2, Otecko N.4 ...

  13. Nephelium lappaceum L. genetic diversity by morphological and molecular characterization

    OpenAIRE

    De Andrade, Renata Aparecida [UNESP; Wickert, Ester [UNESP; Martins, Antonio Baldo Geraldo [UNESP; De Andrade, Mariana Macedo Costa [UNESP; De Macedo Lemos, Eliana Gertrudes [UNESP

    2011-01-01

    The rambutan (Nephelium lappaceum) is an exotic fruit with great market potential in Brazil. However, there are few available informations about plants with potential for cultivation, because great morphologic variation is observed among plants and for consequence, little uniformity in the orchards and in the fruits. This research had for objective to evaluate the genetic diversity of a collection of rambutan plants obtained by seeds through morfo-chemical analyses of plants and fruits and by...

  14. Female promiscuity and genetic diversity in passerine birds

    OpenAIRE

    Gohli, Jostein

    2014-01-01

    This dissertation is about female promiscuity in passerine birds. By using comparative analytical approaches, I have tried to determine why there is such variation in the frequency of this behaviour. I have found that promiscuous species/populations have higher genetic diversity both at neutral loci and at loci directly involved in the recognition of pathogens. These observations may point to benefits from heterozygosity-fitness correlation or increased immunocompetence in offspring. The corr...

  15. Genetic diversity and recombination analysis of sweepoviruses from Brazil

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    Albuquerque Leonardo C

    2012-10-01

    Full Text Available Abstract Background Monopartite begomoviruses (genus Begomovirus, family Geminiviridae that infect sweet potato (Ipomoea batatas around the world are known as sweepoviruses. Because sweet potato plants are vegetatively propagated, the accumulation of viruses can become a major constraint for root production. Mixed infections of sweepovirus species and strains can lead to recombination, which may contribute to the generation of new recombinant sweepoviruses. Results This study reports the full genome sequence of 34 sweepoviruses sampled from a sweet potato germplasm bank and commercial fields in Brazil. These sequences were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic diversity and patterns of genetic exchange in sweepoviruses isolated from Brazil, as well as to review the classification and nomenclature of sweepoviruses in accordance with the current guidelines proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV. Co-infections and extensive recombination events were identified in Brazilian sweepoviruses. Analysis of the recombination breakpoints detected within the sweepovirus dataset revealed that most recombination events occurred in the intergenic region (IR and in the middle of the C1 open reading frame (ORF. Conclusions The genetic diversity of sweepoviruses was considerably greater than previously described in Brazil. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of sweepovirus species and strains and provided valuable new information for understanding the diversity and evolution of sweepoviruses.

  16. Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

    Science.gov (United States)

    Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

    2017-01-01

    Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

  17. Extraordinary Genetic Diversity in a Wood Decay Mushroom.

    Science.gov (United States)

    Baranova, Maria A; Logacheva, Maria D; Penin, Aleksey A; Seplyarskiy, Vladimir B; Safonova, Yana Y; Naumenko, Sergey A; Klepikova, Anna V; Gerasimov, Evgeny S; Bazykin, Georgii A; James, Timothy Y; Kondrashov, Alexey S

    2015-10-01

    Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10(-8) (95% CI: 1.1 × 10(-8) to 4.1 × 10(-8)) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. 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.

  19. 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.

  20. Population genetics of Trypanosoma brucei rhodesiense: clonality and diversity within and between foci.

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    Craig W Duffy

    2013-11-01

    Full Text Available African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda and Southern (Malawi Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics.

  1. Genetic diversity of Poa pratensis L. depending on geographical origin and compared with genetic markers

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    Magdalena Szenejko

    2016-09-01

    Full Text Available Background Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. Methods The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA. Results The low value of Dice’s coefficient (0.369 along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. Discussion The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability.

  2. 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

  3. Genetic diversity of the Eurasian Otter (Lutra lutra) population in Israel.

    Science.gov (United States)

    Cohen, Tali Magory; Narkiss, Tamar; Dolev, Amit; Ben-Ari, Yossi; Kronfeld-Schor, Noga; Guter, Amichai; Saltz, David; Bar-Gal, Gila Kahila

    2013-03-01

    The Israeli population of Eurasian otter (Lutra lutra) marks the Palearctic southern boundary of the species' distribution in the Levant. During the 20th century, the otter population in Israel experienced a dramatic decline due to anthropogenic habitat alterations. Currently, the otter population in Israel is estimated at about 100 individuals and defined as "Critically Endangered". The aim of this research was to characterize the Israeli otter population in order to determine its genetic diversity and fragmentation state for conservation purposes. Monitoring spraint sites during 2000-2011 along active and historic otter distribution regions indicate both stable and unstable otter subpopulations, mainly along the Jordan River. Four otter subpopulations, representing 57 individuals, were characterized by 12 microsatellites, previously used to characterize the European otter populations. The genetic results indicated three subpopulations correlating with three geographical regions: the Hula Valley, Sea of Galilee, and the Harod Valley. A moderate genetic diversity (F (st) = 0.087-0.123) was found among the subpopulations, suggesting sporadic interactions between individuals from distinct geographical locations along the Jordan Rift Valley. The Israeli otter population was found to be very small, demographically remote and genetically distinct, harboring unique alleles absent from the studied European populations. Therefore, immediate conservation actions are recommended to prevent the deterioration of the isolated, unique, and critically endangered otter population in Israel.

  4. Characterisation of the genetic diversity of Brucella by multilocus sequencing

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    MacMillan Alastair P

    2007-04-01

    Full Text Available Abstract Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs. Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in

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

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    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.

  6. Genetic variants regulating expression levels and isoform diversity during embryogenesis.

    Science.gov (United States)

    Cannavò, Enrico; Koelling, Nils; Harnett, Dermot; Garfield, David; Casale, Francesco P; Ciglar, Lucia; Gustafson, Hilary E; Viales, Rebecca R; Marco-Ferreres, Raquel; Degner, Jacob F; Zhao, Bingqing; Stegle, Oliver; Birney, Ewan; Furlong, Eileen E M

    2017-01-19

    Embryonic development is driven by tightly regulated patterns of gene expression, despite extensive genetic variation among individuals. Studies of expression quantitative trait loci (eQTL) indicate that genetic variation frequently alters gene expression in cell-culture models and differentiated tissues. However, the extent and types of genetic variation impacting embryonic gene expression, and their interactions with developmental programs, remain largely unknown. Here we assessed the effect of genetic variation on transcriptional (expression levels) and post-transcriptional (3' RNA processing) regulation across multiple stages of metazoan development, using 80 inbred Drosophila wild isolates, identifying thousands of developmental-stage-specific and shared QTL. Given the small blocks of linkage disequilibrium in Drosophila, we obtain near base-pair resolution, resolving causal mutations in developmental enhancers, validated transcription-factor-binding sites and RNA motifs. This fine-grain mapping uncovered extensive allelic interactions within enhancers that have opposite effects, thereby buffering their impact on enhancer activity. QTL affecting 3' RNA processing identify new functional motifs leading to transcript isoform diversity and changes in the lengths of 3' untranslated regions. These results highlight how developmental stage influences the effects of genetic variation and uncover multiple mechanisms that regulate and buffer expression variation during embryogenesis.

  7. Genetic and phenotypic diversity of Rhizobium isolates from Southern Ecuador

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    Roldán Torres-Gutiérrez

    Full Text Available ABSTRACT Rhizobium-legume symbioses play relevant roles in agriculture but have not been well studied in Ecuador. The aim of this study was to characterize the genetic and phenotypic diversity of Rhizobium isolates associated with Phaseolus vulgaris from southern Ecuador. Morpho-cultural characterization, biochemical tests and physiological analyses were conducted to authenticate and determine the diversity of bacteria Rhizobium-like isolates. The genetic diversity of the isolates was determined by molecular techniques, which consisted of bacteria DNA extraction and amplification and sequencing of the 16S rRNA gene. The nodulation parameters and nitrogen fixation for P. vulgaris under greenhouse conditions were also assessed to determine the phenotypic diversity among isolates. Furthermore, bacteria indole-acetic-acid production was evaluated by the colorimetric method. Morpho-cultural and biochemical characteristic assessments demonstrated that Rhizobium-like bacteria was associated with the P. vulgaris nodules. The diversity among the isolates, as determined by physiological analyses, revealed the potential of several isolates to grow at different pH values, salinity conditions and temperatures. Partial sequencing of the 16S rRNA gene identified the Rhizobium genus in every sampling site. From a total of 20 aligned sequences, nine species of Rhizobium were identified. Nodule formation and biomass, as well as nitrogen fixation, showed an increase in plant phenotypic parameters, which could be influenced by IAA production, especially for the strains R. mesoamericanum NAM1 and R. leguminosarum bv. viciae COL6. These results demonstrated the efficiency of native symbiotic diazotrophic strains inoculants for legume production. This work can serve as the basis for additional studies of native Rhizobium strains and to help spread the use of biofertilizers in Ecuadorian fields.

  8. A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species.

    Science.gov (United States)

    Souza, Helena Augusta Viana E; Collevatti, Rosane Garcia; Lima-Ribeiro, Matheus S; Lemos-Filho, José Pires de; Lovato, Maria Bernadete

    2017-01-01

    The relative role of Pleistocene climate changes in driving the geographic distribution and genetic diversity of South American species is not well known, especially from open biomes such as the Cerrado, the most diverse tropical savanna, encompassing high levels of endemism. Here the effects of Quaternary climatic changes on demographic history, distribution dynamics and genetic diversity of Dimorphandra mollis, an endemic tree species widely distributed in the Cerrado, were investigated. A total of 38 populations covering most of the distribution of D. mollis were analysed using internal transcribed spacer (ITS) sequences and nuclear microsatellite variation [simple sequence repeats (SSRs)]. The framework incorporated statistical phylogeography, coalescent analyses and ecological niche modelling (ENM). Different signatures of Quaternary climatic changes were found for ITS sequences and SSRs corresponding to different time slices. Coalescent analyses revealed large and constant effective population sizes, with high historical connectivity among the populations for ITS sequences and low effective population sizes and gene flow with recent population retraction for SSRs. ENMs indicated a slight geographical range retraction during the Last Glacial Maximum. A large historical refugium across central Brazil was predicted. Spatially explicit analyses showed a spatial cline pattern in genetic diversity related to the paleodistribution of D. mollis and to the centre of its historical refugium. The complex genetic patterns found in D. mollis are the result of a slight geographical range retraction during the Last Glacial Maximum followed by population expansion to the east and south from a large refugium in the central part of the Cerrado. This historical refugium is coincident with an area predicted to be climatically stable under future climate scenarios. The identified refugium should be given high priority in conservation polices to safeguard the evolutionary

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

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    Juan Miguel Cordero-Solórzano

    2015-06-01

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

  10. Peach genetic resources: diversity, population structure and linkage disequilibrium

    Science.gov (United States)

    2013-01-01

    Background Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars. Results In total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: ‘Yu Lu’ and ‘Hakuho’. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the ‘Yu Lu’ subpopulation there

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

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    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.

  12. Limited genetic diversity preceded extinction of the Tasmanian tiger.

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    Brandon R Menzies

    Full Text Available 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.

  13. 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.

  14. 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

  15. Invasion success in Cogongrass (Imperata cylindrica): A population genetic approach exploring genetic diversity and historical introductions

    Science.gov (United States)

    Rima D. Lucardi; Lisa E. Wallace; Gary N. Ervin

    2014-01-01

    Propagule pressure significantly contributes to and limits the potential success of a biological invasion, especially during transport, introduction, and establishment. Events such as multiple introductions of foreign parent material and gene flow among them can increase genetic diversity in founding populations, often leading to greater invasion success. We applied...

  16. Molecular markers: a potential resource for ginger genetic diversity studies.

    Science.gov (United States)

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  17. Phylogeography, genetic structure, and diversity in the dhole (Cuon alpinus).

    Science.gov (United States)

    Iyengar, A; Babu, V N; Hedges, S; Venkataraman, A B; Maclean, N; Morin, P A

    2005-07-01

    The Asiatic wild dog or dhole was once very widely distributed across Asia but now has a very fragmented range. In this first genetic study of this little-known species, we obtained information on genetic diversity, phylogeography, and social structure using both mitochondrial control region sequencing and microsatellite genotyping of noninvasive faecal samples from wild populations, as well as from museum and captive samples. A pattern largely consistent with isolation by distance across the Asian mainland was observed, with no clear subspecies distinctions. However, two major phylogeographical groupings were found across the mainland, one extending from South, Central, and North India (south of the Ganges) into Myanmar, and the other extending from India north of the Ganges into northeastern India, Myanmar, Thailand and the Malaysian Peninsula. We propose a scenario involving glaciation events that could explain this pattern. The origin of the dhole populations in Sumatra and Java is enigmatic and requires further study. Very low levels of genetic diversity were observed among wild dholes from Baluran National Park in Java, Indonesia, but in contrast, high levels were observed in Mudumalai Wildlife Sanctuary in South India.

  18. On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary centre of diversity

    OpenAIRE

    Roullier, C; Kambouo, R; Paofa, J; McKey, D; Lebot, V

    2013-01-01

    New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm p...

  19. Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia

    Science.gov (United States)

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages. PMID:24376692

  20. Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia.

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    Marta Maccari

    Full Text Available There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia. Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.

  1. Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia.

    Science.gov (United States)

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.

  2. Diversity Controlling Genetic Algorithm for Order Acceptance and Scheduling Problem

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    Cheng Chen

    2014-01-01

    Full Text Available Selection and scheduling are an important topic in production systems. To tackle the order acceptance and scheduling problem on a single machine with release dates, tardiness penalty, and sequence-dependent setup times, in this paper a diversity controlling genetic algorithm (DCGA is proposed, in which a diversified population is maintained during the whole search process through survival selection considering both the fitness and the diversity of individuals. To measure the similarity between individuals, a modified Hamming distance without considering the unaccepted orders in the chromosome is adopted. The proposed DCGA was validated on 1500 benchmark instances with up to 100 orders. Compared with the state-of-the-art algorithms, the experimental results show that DCGA improves the solution quality obtained significantly, in terms of the deviation from upper bound.

  3. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

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    Carolyn A. Young

    2015-04-01

    Full Text Available The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization. The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine.

  4. Evolutionary rates and genetic diversities of mixed potyviruses in Narcissus.

    Science.gov (United States)

    Ohshima, Kazusato; Nomiyama, Rei; Mitoma, Shinichiro; Honda, Yuki; Yasaka, Ryosuke; Tomimura, Kenta

    2016-11-01

    There is no attempt to evaluate evolutionary rates, timescales and diversities of viruses collected from mixedly infected hosts in nature. Plants of the genus Narcissus are a monocotyledon and are susceptible to several viruses. In this study, narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected in Japan, and these were investigated for potyvirus infections using potyvirus-specific primers. Individual narcissus plants were found frequently to be mixedly infected with different potyviruses, different isolates and quasispecies of same virus. The viruses were potyviruses and a macluravirus in the family Potyviridae, namely Narcissus late season yellows virus (NLSYV), Narcissus yellow stripe virus (NYSV), Narcissus degeneration virus (NDV), Cyrtanthus elatus virus A (CyEVA) and Narcissus latent virus (NLV). Genetic diversities of coat protein coding region of different virus species were different; NYSV and CyEVA were most diverse whereas NDV was least. Evolutionary rates of all five narcissus viruses were 1.33-7.15×10-3nt/site/year and were similar. The most recent common ancestors (TMRCAs) varied between virus species; NYSV and CyEVA were the oldest whereas NDV was the youngest. Thus, the oldness of TMRCAs of the viruses correlated well with the greatness of nucleotide diversities. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Centennial olive trees as a reservoir of genetic diversity.

    Science.gov (United States)

    Díez, Concepción M; Trujillo, Isabel; Barrio, Eladio; Belaj, Angjelina; Barranco, Diego; Rallo, Luis

    2011-10-01

    Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin. The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars. Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives. This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity.

  6. Centennial olive trees as a reservoir of genetic diversity

    Science.gov (United States)

    Díez, Concepción M.; Trujillo, Isabel; Barrio, Eladio; Belaj, Angjelina; Barranco, Diego; Rallo, Luis

    2011-01-01

    Background and Aims Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin. Methods The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars. Key Results Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives. Conclusions This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity. PMID:21852276

  7. Genetic diversity of Dactylorhiza incarnata (Orchidaceae in northern Poland

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    Aleksandra M. Naczk

    2016-05-01

    Full Text Available The genetic structure of Dactylorhiza incarnata var. incarnata populations is shaped not only by historical events such as recolonization after ice sheet retreat or limited seed and pollen dispersal, but also the bottleneck effect. During the last decade, D. incarnata var. incarnata has also experienced a strong decline in population numbers and sizes, due to habitat loss and fragmentation. In the present research genetic diversity was examined in eight populations located in northern Poland, using six nuclear microsatellites loci. At the species level our results showed a moderate mean level of genetic diversity (A = 4.67; Ae = 2.73; Rs = 4.48; Ho = 0.438; FIS = 0.224, which varied among the studied populations (A: 2.17–3.67; Ae: 1.55–2.69; Rs: 1.31–1.61; Ho: 0.292–0.631; FIS: −0.283–0.340. A considerable overabundance of homozygotes was detected in four populations (FIS within the range of 0.067–0.340, and in the remaining populations an excess of heterozygotes was observed. The average apparent out-crossing rate was also calculated (ta = 0.980, and primarily indicated a tendency to out-cross within the species. Moderate genetic differentiation was found among the studied populations (FST = 0.149; RST = 0.174; p < 0.05. The differentiation of the populations corresponded to relatively low gene flow value (Nm = 0.426 among populations, which amounted to only one migrant every second generation.

  8. Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations.

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    Martin, Alicia R; Gignoux, Christopher R; Walters, Raymond K; Wojcik, Genevieve L; Neale, Benjamin M; Gravel, Simon; Daly, Mark J; Bustamante, Carlos D; Kenny, Eimear E

    2017-04-06

    The vast majority of genome-wide association studies (GWASs) are performed in Europeans, and their transferability to other populations is dependent on many factors (e.g., linkage disequilibrium, allele frequencies, genetic architecture). As medical genomics studies become increasingly large and diverse, gaining insights into population history and consequently the transferability of disease risk measurement is critical. Here, we disentangle recent population history in the widely used 1000 Genomes Project reference panel, with an emphasis on populations underrepresented in medical studies. To examine the transferability of single-ancestry GWASs, we used published summary statistics to calculate polygenic risk scores for eight well-studied phenotypes. We identify directional inconsistencies in all scores; for example, height is predicted to decrease with genetic distance from Europeans, despite robust anthropological evidence that West Africans are as tall as Europeans on average. To gain deeper quantitative insights into GWAS transferability, we developed a complex trait coalescent-based simulation framework considering effects of polygenicity, causal allele frequency divergence, and heritability. As expected, correlations between true and inferred risk are typically highest in the population from which summary statistics were derived. We demonstrate that scores inferred from European GWASs are biased by genetic drift in other populations even when choosing the same causal variants and that biases in any direction are possible and unpredictable. This work cautions that summarizing findings from large-scale GWASs may have limited portability to other populations using standard approaches and highlights the need for generalized risk prediction methods and the inclusion of more diverse individuals in medical genomics. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  9. Investigation and Analysis of Genetic Diversity of Diospyros Germplasms Using SCoT Molecular Markers in Guangxi.

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    Libao Deng

    Full Text Available Knowledge about genetic diversity and relationships among germplasms could be an invaluable aid in diospyros improvement strategies.This study was designed to analyze the genetic diversity and relationship of local and natural varieties in Guangxi Zhuang Autonomous Region of China using start codon targeted polymorphism (SCoT markers. The accessions of 95 diospyros germplasms belonging to four species Diospyros kaki Thunb, D. oleifera Cheng, D. kaki var. silverstris Mak, and D. lotus Linn were collected from different eco-climatic zones in Guangxi and were analyzed using SCoT markers.Results indicated that the accessions of 95 diospyros germplasms could be distinguished using SCoT markers, and were divided into three groups at similarity coefficient of 0.608; these germplasms that belong to the same species were clustered together; of these, the degree of genetic diversity of the natural D. kaki var. silverstris Mak population was richest among the four species; the geographical distance showed that the 12 natural populations of D. kaki var. silverstris Mak were divided into two groups at similarity coefficient of 0.19. Meanwhile, in order to further verify the stable and useful of SCoT markers in diospyros germplasms, SSR markers were also used in current research to analyze the genetic diversity and relationship in the same diospyros germplasms. Once again, majority of germplasms that belong to the same species were clustered together. Thus SCoT markers were stable and especially useful for analysis of the genetic diversity and relationship in diospyros germplasms.The molecular characterization and diversity assessment of diospyros were very important for conservation of diospyros germplasm resources, meanwhile for diospyros improvement.

  10. Investigation and Analysis of Genetic Diversity of Diospyros Germplasms Using SCoT Molecular Markers in Guangxi.

    Science.gov (United States)

    Deng, Libao; Liang, Qingzhi; He, Xinhua; Luo, Cong; Chen, Hu; Qin, Zhenshi

    2015-01-01

    Knowledge about genetic diversity and relationships among germplasms could be an invaluable aid in diospyros improvement strategies. This study was designed to analyze the genetic diversity and relationship of local and natural varieties in Guangxi Zhuang Autonomous Region of China using start codon targeted polymorphism (SCoT) markers. The accessions of 95 diospyros germplasms belonging to four species Diospyros kaki Thunb, D. oleifera Cheng, D. kaki var. silverstris Mak, and D. lotus Linn were collected from different eco-climatic zones in Guangxi and were analyzed using SCoT markers. Results indicated that the accessions of 95 diospyros germplasms could be distinguished using SCoT markers, and were divided into three groups at similarity coefficient of 0.608; these germplasms that belong to the same species were clustered together; of these, the degree of genetic diversity of the natural D. kaki var. silverstris Mak population was richest among the four species; the geographical distance showed that the 12 natural populations of D. kaki var. silverstris Mak were divided into two groups at similarity coefficient of 0.19. Meanwhile, in order to further verify the stable and useful of SCoT markers in diospyros germplasms, SSR markers were also used in current research to analyze the genetic diversity and relationship in the same diospyros germplasms. Once again, majority of germplasms that belong to the same species were clustered together. Thus SCoT markers were stable and especially useful for analysis of the genetic diversity and relationship in diospyros germplasms. The molecular characterization and diversity assessment of diospyros were very important for conservation of diospyros germplasm resources, meanwhile for diospyros improvement.

  11. Genetic diversity, structure and differentiation in cultivate walnut (Juglans regia L.)

    Science.gov (United States)

    M. Aradhya; K. Woeste; D. Velasco

    2012-01-01

    An analysis of genetic structure and differentiation in cultivated walnut (Juglans regia) using 15 microsatellite loci revealed a considerable amount of genetic variation with a mild genetic structure indicating five genetic groups corresponding to the centers of diversity within the home range of walnut in Eurasia. Despite the narrow genetic...

  12. Genetic Competence Drives Genome Diversity in Bacillus subtilis

    Science.gov (United States)

    Chevreux, Bastien; Serra, Cláudia R; Schyns, Ghislain; Henriques, Adriano O

    2018-01-01

    Abstract Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them. PMID:29272410

  13. Temporal genetic patterns of diversity and structure evidence chaotic genetic patchiness in a spiny lobster.

    Science.gov (United States)

    Villacorta-Rath, Cecilia; Souza, Carla A; Murphy, Nicholas P; Green, Bridget S; Gardner, Caleb; Strugnell, Jan M

    2018-01-01

    Population structure of many marine organisms is spatially patchy and varies within and between years, a phenomenon defined as chaotic genetic patchiness. This results from the combination of planktonic larval dispersal and environmental stochasticity. Additionally, in species with bi-partite life, postsettlement selection can magnify these genetic differences. The high fecundity (up to 500,000 eggs annually) and protracted larval duration (12-24 months) and dispersal of the southern rock lobster, Jasus edwardsii, make it a good test species for chaotic genetic patchiness and selection during early benthic life. Here, we used double digest restriction site-associated DNA sequencing (ddRADseq) to investigate chaotic genetic patchiness and postsettlement selection in this species. We assessed differences in genetic structure and diversity of recently settled pueruli across four settlement years and between two sites in southeast Australia separated by approximately 1,000 km. Postsettlement selection was investigated by identifying loci under putative positive selection between recently settled pueruli and postpueruli and quantifying differences in the magnitude and strength of the selection at each year and site. Genetic differences within and among sites through time in neutral SNP markers indicated chaotic genetic patchiness. Recently settled puerulus at the southernmost site exhibited lower genetic diversity during years of low puerulus catches, further supporting this hypothesis. Finally, analyses of outlier SNPs detected fluctuations in the magnitude and strength of the markers putatively under positive selection over space and time. One locus under putative positive selection was consistent at both locations during the same years, suggesting the existence of weak postsettlement selection. © 2017 John Wiley & Sons Ltd.

  14. Neonicotinoid pesticides can reduce honeybee colony genetic diversity

    Science.gov (United States)

    Troxler, Aline; Retschnig, Gina; Gauthier, Laurent; Straub, Lars; Moritz, Robin F. A.; Neumann, Peter; Williams, Geoffrey R.

    2017-01-01

    Neonicotinoid insecticides can cause a variety of adverse sub-lethal effects in bees. In social species such as the honeybee, Apis mellifera, queens are essential for reproduction and colony functioning. Therefore, any negative effect of these agricultural chemicals on the mating success of queens may have serious consequences for the fitness of the entire colony. Queens were exposed to the common neonicotinoid pesticides thiamethoxam and clothianidin during their developmental stage. After mating, their spermathecae were dissected to count the number of stored spermatozoa. Furthermore, their worker offspring were genotyped with DNA microsatellites to determine the number of matings and the genotypic composition of the colony. Colonies providing the male mating partners were also inferred. Both neonicotinoid and control queens mated with drones originating from the same drone source colonies, and stored similar number of spermatozoa. However, queens reared in colonies exposed to both neonicotinoids experienced fewer matings. This resulted in a reduction of the genetic diversity in their colonies (i.e. higher intracolonial relatedness). As decreased genetic diversity among worker bees is known to negatively affect colony vitality, neonicotinoids may have a cryptic effect on colony health by reducing the mating frequency of queens. PMID:29059234

  15. Genetic diversity in the SIR model of pathogen evolution.

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    Isabel Gordo

    Full Text Available We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR. We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts, where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0(1+s is higher than the fitness of the resident strain (R(0. We show that this invasion probability is given by the relative increment in R(0 of the new pathogen (s. By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  16. Enhancing (crop) plant photosynthesis by introducing novel genetic diversity.

    Science.gov (United States)

    Dann, Marcel; Leister, Dario

    2017-09-26

    Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis. Here, we argue for a novel approach that outsources crop photosynthesis to a cyanobacterium that is amenable to adaptive evolution. This system offers numerous advantages, including a short generation time, virtually unlimited population sizes and high mutation rates, together with a versatile toolbox for genetic manipulation. On such a synthetic bacterial platform, 10 000 years of (crop) plant evolution can be recapitulated within weeks. Limitations of this system arise from its unicellular nature, which cannot reproduce all aspects of crop photosynthesis. But successful establishment of such a bacterial host for crop photosynthesis promises not only to enhance the performance of eukaryotic photosynthesis but will also reveal novel facets of the molecular basis of photosynthetic flexibility.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'. © 2017 The Author(s).

  17. Genetic diversity among five T4-like bacteriophages

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    Bertrand Claire

    2006-05-01

    Full Text Available Abstract Background Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Results Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Conclusion Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4

  18. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

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    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

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

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    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

  20. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum.

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    Jane E Stewart

    Full Text Available Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum, highbush blueberry (V. corymbosum, and southern highbush blueberry (V. corymbosum hybrids from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing

  1. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum

    Science.gov (United States)

    Stewart, Jane E.; Brooks, Kyle; Brannen, Phillip M.; Cline, William O.; Brewer, Marin T.

    2015-01-01

    Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population

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

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    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.

  3. Late Quaternary loss of genetic diversity in muskox (Ovibos

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    Mol Dick

    2005-10-01

    Full Text Available Abstract Background The modern wildherd of the tundra muskox (Ovibos moschatus is native only to the New World (northern North America and Greenland, and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial sequence data (hypervariable region and cytochrome b from muskox fossil material recovered from localities in northeastern Asia and the Arctic Archipelago of northern North America, dating from late Pleistocene to late Holocene, and compared our results to existing databases for modern muskoxen. Results Two classes of haplotypes were detected in the fossil material. "Surviving haplotypes" (SHs, closely similar or identical to haplotypes found in modern muskoxen and ranging in age from ~22,000 to ~160 yrbp, were found in all New World samples as well as some samples from northeastern Asia. "Extinct haplotypes" (EHs, dating between ~44,000 and ~18,000 yrbp, were found only in material from the Taimyr Peninsula and New Siberian Islands in northeastern Asia. EHs were not found in the Holocene muskoxen specimens available for this study, nor have they been found in other studies of extant muskox populations. Conclusion We provisionally interpret this evidence as showing that genetic variability was reduced in muskoxen after the Last Glacial Maximum but before the mid-Holocene, or roughly within the interval 18,000-4,000 yrbp. Narrowing this gap further will require the recovery of more fossils and additional genetic information from this interval.

  4. Parallel responses of species and genetic diversity to El Nino Southern Oscillation-induced environmental destruction

    NARCIS (Netherlands)

    Cleary, D.F.R.; Fauvelot, C.Y.; Genner, J.; Menken, S.B.J.; Mooers, A.O.

    2006-01-01

    Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to

  5. Genetic diversity of Ostreopsis ovata (Dinophyceae) from Malaysia.

    Science.gov (United States)

    Pin, L C; Teen, L P; Ahmad, A; Usup, G

    2001-05-01

    The genus Ostreopsis is an important component of benthic and epiphytic dinoflagellate assemblages in coral reefs and seaweed beds of Malaysia. Members of the species may produce toxins that contribute to ciguatera fish poisoning. In this study, two species have been isolated and cultured, Ostreopsis ovata and Ostreopsis lenticularis. Analyses of the 5.8S subunit and internal transcribed spacer regions ITS1 and ITS2 of the ribosomal RNA gene sequences of these two species showed that they are separate species, consistent with morphological designations. The nucleotide sequences of the 5.8S subunit and ITS1 and ITS2 regions of the rRNA gene were also used to evaluate the interpopulation and intrapopulation genetic diversity of O. ovata found in Malaysian waters. Results showed a low level of sequence divergence within populations. At the interpopulation level, the rRNA gene sequence distinguished two groups of genetically distinct strains, representative of a Malacca Straits group (isolates from Port Dickson) and a South China Sea group (isolates from Pulau Redang and Kota Kinabalu). Part of the sequences in the ITS regions may be useful in the design of oligonucleotide probes specific for each group. Results from this study show that the ITS regions can be used as genetic markers for taxonomic, biogeographic, and fine-scale population studies of this species.

  6. The Nuclear DNA Content and Genetic Diversity of Lampetra morii.

    Directory of Open Access Journals (Sweden)

    Xinyu Yan

    Full Text Available We investigated the nuclear DNA content and genetic diversity of a river lamprey, the Korean lamprey Lampetra morii, which is distributed in the northeast of China. L. morii spends its whole life cycle in fresh water, and its adult size is relatively small (~160 mm long compared with that of other lampreys. The haploid nuclear DNA content of L. morii is 1.618 pg (approximately 1.582 Gb in germline cells, and there is ~15% germline DNA loss in somatic cells. These values are significantly smaller than those of Petromyzon marinus, a lamprey with a published draft genome. The chromosomes of L. morii are small and acrocentric, with a diploid modal number of 2n = 132, lower than some other lampreys. Sequence and AFLP analyses suggest that the allelic polymorphism rate (~0.14% based on examined nuclear and mitochondrial DNA sequences of L. morii is much lower than that (~2% of P. marinus. Phylogenetic analysis based on a mitochondrial DNA fragment confirms that L. morii belongs to the genus Lampetra, which, together with the genus Lethenteron, forms a sister group to P. marinus. These genetic background data are valuable for subsequent genetic and genomic research on L. morii.

  7. Genetic diversity revealed by AFLP markers in Albanian goat breeds

    Directory of Open Access Journals (Sweden)

    Hoda Anila

    2012-01-01

    Full Text Available The amplified fragment length polymorphism (AFLP technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei’s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright’s FST index, Nei’s unbiased genetic distance and Reynolds’ genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds’ genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard’s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

  8. Genetic diversity of water use efficiency in Jerusalem artichoke (Helianthus tuberosus L.) germplasm

    Science.gov (United States)

    Genetic diversity in crop germplasm is an important resource for crop improvement, but information on genetic diversity is rare for Jerusalem artichoke, especially for traits related to water use efficiency. The objectives of this study were to investigate genetic variations for water use and water...

  9. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra

    2014-01-01

    , trends and potentials of the world's tree genetic resources to support sustainable growth. The state of the genetic diversity will be based on trends in population distributions and diversity patterns for selected species. The productivity of the genetic resource of trees in current use will reflect...... distributions (patterns of genetic variation of key adaptive traits in the ecological space) of selected species is a realistic way of assessing the trend of intra-specific variation, and thus provides a state indicator of tree genetic diversity also able to reflect possible pressures threatening genetic...

  10. Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain.

    Science.gov (United States)

    Naito, Tadasuke; Mori, Kotaro; Ushirogawa, Hiroshi; Takizawa, Naoki; Nobusawa, Eri; Odagiri, Takato; Tashiro, Masato; Ohniwa, Ryosuke L; Nagata, Kyosuke; Saito, Mineki

    2017-03-15

    Vaccination is considered the most effective preventive means for influenza control. The development of a master virus with high growth and genetic stability, which may be used for the preparation of vaccine viruses by gene reassortment, is crucial for the enhancement of vaccine performance and efficiency of production. Here, we describe the generation of a high-fidelity and high-growth influenza vaccine master virus strain with a single V43I amino acid change in the PB1 polymerase of the high-growth A/Puerto Rico/8/1934 (PR8) master virus. The PB1-V43I mutation was introduced to increase replication fidelity in order to design an H1N1 vaccine strain with a low error rate. The PR8-PB1-V43I virus exhibited good replication compared with that of the parent PR8 virus. In order to compare the efficiency of egg adaptation and the occurrence of gene mutations leading to antigenic alterations, we constructed 6:2 genetic reassortant viruses between the A(H1N1)pdm09 and the PR8-PB1-V43I viruses; hemagglutinin (HA) and neuraminidase (NA) were from the A(H1N1)pdm09 virus, and the other genes were from the PR8 virus. Mutations responsible for egg adaptation mutations occurred in the HA of the PB1-V43I reassortant virus during serial egg passages; however, in contrast, antigenic mutations were introduced into the HA gene of the 6:2 reassortant virus possessing the wild-type PB1. This study shows that the mutant PR8 virus possessing the PB1 polymerase with the V43I substitution may be utilized as a master virus for the generation of high-growth vaccine viruses with high polymerase fidelity, low error rates of gene replication, and reduced antigenic diversity during virus propagation in eggs for vaccine production. IMPORTANCE Vaccination represents the most effective prophylactic option against influenza. The threat of emergence of influenza pandemics necessitates the ability to generate vaccine viruses rapidly. However, as the influenza virus exhibits a high mutation rate

  11. [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

  12. The role of historical and contemporary processes on phylogeographic structure and genetic diversity in the Northern Cardinal, Cardinalis cardinalis

    Directory of Open Access Journals (Sweden)

    Navarro-Sigüenza Adolfo G

    2011-05-01

    Full Text Available Abstract Background Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis. Results Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species' range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America. Conclusion We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in C. cardinalis. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered

  13. 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.

  14. Pedigree analysis for conservation of genetic diversity and purging.

    Science.gov (United States)

    Wellmann, R; Pfeiffer, I

    2009-06-01

    We present an approach to describe and evaluate changes in genetic diversity and to calculate bounds for improvement. This pedigree-based analysis was applied to the Kromfohrländer dog (FCI Gr9 Sec10). Pedigrees trace back to the foundation of the breed and were available for 5527 individuals. Based on this dataset the population structure and historical bottlenecks were studied. Distributions of allele frequencies were estimated by Monte Carlo simulation. To monitor changes in mating systems throughout the breeding history, the homozygosity of alleles was compared with their expectations in Hardy-Weinberg equilibrium. Different breeding lines were identified by hierarchical cluster analysis and were characterized by ancestor contributions. Our calculations showed that the founder event in 1945 was followed by two bottlenecks. One was caused by strong selection in a very small population, and the other was triggered by rigorous disease management. The necessary amount of purging that arised due to the bottlenecks was also discussed.

  15. Genetic diversity of Dekkera bruxellensis yeasts isolated from Australian wineries.

    Science.gov (United States)

    Curtin, Chris D; Bellon, Jennifer R; Henschke, Paul A; Godden, Peter W; de Barros Lopes, Miguel A

    2007-05-01

    Yeasts of the genus Dekkera and its anamorph Brettanomyces represent a significant spoilage issue for the global wine industry. Despite this, there is limited knowledge of genetic diversity and strain distribution within wine and winery-related environments. In this study, amplified fragment length polymorphism (AFLP) analysis was conducted on 244 Dekkera bruxellensis isolates from red wine made in 31 winemaking regions of Australia. The results indicated there were eight genotypes among the isolates, and three of these were commonly found across multiple winemaking regions. Analysis of 26S rRNA gene sequences provided further evidence of three common, conserved groups, whereas a phylogeny based upon the AFLP data demonstrated that the most common D. bruxellensis genotype (I) in Australian red wine was highly divergent from the D. bruxellensis type strain (CBS 74).

  16. Italian Common Bean Landraces: History, Genetic Diversity and Seed Quality

    Directory of Open Access Journals (Sweden)

    Angela R. Piergiovanni

    2010-05-01

    Full Text Available The long tradition of common bean cultivation in Italy has allowed the evolution of many landraces adapted to restricted areas. Nowadays, in response to market demands, old landraces are gradually being replaced by improved cultivars. However, landraces still survive in marginal areas of several Italian regions. Most of them appear severely endangered with risk of extinction due to the advanced age of the farmers and the socio-cultural context where they are cultivated. The present contribution is an overview of the state of the art about the knowledge of Italian common bean germplasm, describing the most important and recent progresses made in its characterization, including genetic diversity and nutritional aspects.

  17. A decade of norovirus genetic diversity in Belgium.

    Science.gov (United States)

    Wollants, Elke; De Coster, Sarah; Van Ranst, Marc; Maes, Piet

    2015-03-01

    Outbreaks of norovirus-associated gastroenteritis occur during all seasons and in various locations, and are recognized as one of the most common causes of nonbacterial food-borne infections. The molecular epidemiology of norovirus infections has not been well characterized in Belgium. To study the incidence of norovirus infections and the nature of the circulating genotypes, 3080 specimens were collected from patients with acute gastroenteritis between 2004 and 2014. Norovirus was detected with RT-PCR in 554 samples (18%). The circulating strains were genotyped based on the variability in the 5' end of the capsid gene (region C). The GII.4 genotype, which is detected predominantly worldwide, was also the most prevalent genotype in our study (87%). This study shows a high frequency and genetic diversity of norovirus in patients with acute gastroenteritis in health care facilities in Flanders, Belgium. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Genetic Diversity of Cryptosporidium spp. in Captive Reptiles

    Science.gov (United States)

    Xiao, Lihua; Ryan, Una M.; Graczyk, Thaddeus K.; Limor, Josef; Li, Lixia; Kombert, Mark; Junge, Randy; Sulaiman, Irshad M.; Zhou, Ling; Arrowood, Michael J.; Koudela, Břetislav; Modrý, David; Lal, Altaf A.

    2004-01-01

    The genetic diversity of Cryptosporidium in reptiles was analyzed by PCR-restriction fragment length polymorphism and sequence analysis of the small subunit rRNA gene. A total of 123 samples were analyzed, of which 48 snake samples, 24 lizard samples, and 3 tortoise samples were positive for Cryptosporidium. Nine different types of Cryptosporidium were found, including Cryptosporidium serpentis, Cryptosporidium desert monitor genotype, Cryptosporidium muris, Cryptosporidium parvum bovine and mouse genotypes, one C. serpentis-like parasite in a lizard, two new Cryptosporidium spp. in snakes, and one new Cryptosporidium sp. in tortoises. C. serpentis and the desert monitor genotype were the most common parasites and were found in both snakes and lizards, whereas the C. muris and C. parvum parasites detected were probably the result of ingestion of infected rodents. Sequence and biologic characterizations indicated that the desert monitor genotype was Cryptosporidium saurophilum. Two host-adapted C. serpentis genotypes were found in snakes and lizards. PMID:14766569

  19. Chemical and genetic diversity of two Mediterranean subspecies of Teucrium polium L

    OpenAIRE

    DJABOU, Nassim; MUSELLI, Alain; ALLALI, Hocine; DIB, Mohammed El Amine; TABTI, Boufeldja; VARESI, Laurent; COSTA, Jean

    2013-01-01

    Chemical and genetic diversity of Teucrium polium L. subsp. polium from western Algeria and T. polium L. subsp. capitatum from Corsica were investigated. Diversity within and among the two populations of subspecies was assessed according to the chemical composition of their essential oils and the genetic diversity. Chemical analysis was performed using a combination of capillary GC-RI and GC/MS after fractionation using column chromatography. Genetic structures were mapped usin...

  20. 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...... major groups. This is the first report of the genetic diversity and structure of Eritrean bread wheat....

  1. Assessing the functional diversity of herbivorous reef fishes using a compound-specific stable isotope approach

    KAUST Repository

    Tietbohl, Matthew

    2016-12-01

    Herbivorous coral reef fishes play an important role in helping to structure their environment directly by consuming algae and indirectly by promoting coral health and growth. These fishes are generally separated into three broad groups: browsers, grazers, and excavators/scrapers, with these groupings often thought to have a fixed general function and all fishes within a group thought to have similar ecological roles. This categorization assumes a high level of functional redundancy within herbivorous fishes. However, recent evidence questions the use of this broad classification scheme, and posits that there may actually be more resource partitioning within these functional groupings. Here, I use a compound-specific stable isotope approach (CSIA) to show there appears to be a greater diversity of functional roles than previously assumed within broad functional groups. The δ13C signatures from essential amino acids of reef end-members (coral, macroalgae, detritus, and phytoplankton) and fish muscle were analyzed to investigate differences in resource use between fishes. Most end-members displayed clear isotopic differences, and most fishes within functional groups were dissimilar in their isotopic signature, implying differences in the resources they target. No grazers closely resembled each other isotopically, implying a much lower level of functional redundancy within this group; scraping parrotfish were also distinct from excavating parrotfish and to a lesser degree distinct between scrapers. This study highlights the potential of CSIA to help distinguish fine-scale ecological differences within other groups of reef organisms as well. These results question the utility of lumping nominally herbivorous fishes into broad groups with assumed similar roles. Given the apparent functional differences between nominally herbivorous reef fishes, it is important for managers to incorporate the diversity of functional roles these fish play.

  2. Diversity of the definition of stable vital sign in trauma patients: results of a nationwide survey.

    Science.gov (United States)

    Mun, Seongpyo

    2015-12-01

    Hemodynamic stability (HS) based on vital sign (VS) is thought to be the most useful criteria for successful non-operative management (NOM) of blunt spleen injury (BSI). However, a consistent definition of HS has not been established. We wanted to evaluate the definition of HS through conducting a nationwide survey and find the factors affectting diversity. The questionnaire regarding the definition of HS was sent to the department of trauma surgery and emergency medicine of level I trauma center between October 2012 and November 2012. Data was compared using analysis of variance, t-test, χ2 test and logistic regression. Among five hundred and sixty-three doctors, 507 responded (90%). Forty-eight responses were incomplete, and hence, 459 (81.5%) responses were analyzed. There was a significant diversity in the definition of HS on the subject of type of blood pressure (BP), cut off value of hypotension, measuring technique of BP, duration of hypotension, whether or not using heart rate (HR) as a determinant of HS, cut off value of hypotension when the patient has comorbidity or when the patient is a pediatric patient. 91.5% replied that they were confused defining HS and felt the need to have more objective determinants. Nevertheless, 90% of the responders were not using laboratory test to define HS. Many trauma doctors are using only VS to define HS. This is why there is a confusion regarding how to define which patient is hemodynamically stable. More objective determinants such as base deficit or lactate can be useful adjuncts.

  3. High local genetic diversity of canine parvovirus from Ecuador.

    Science.gov (United States)

    Aldaz, Jaime; García-Díaz, Juan; Calleros, Lucía; Sosa, Katia; Iraola, Gregorio; Marandino, Ana; Hernández, Martín; Panzera, Yanina; Pérez, Ruben

    2013-09-27

    Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Epidemiology and genetic diversity of Taenia asiatica: a systematic review.

    Science.gov (United States)

    Ale, Anita; Victor, Bjorn; Praet, Nicolas; Gabriël, Sarah; Speybroeck, Niko; Dorny, Pierre; Devleesschauwer, Brecht

    2014-01-22

    Taenia asiatica has made a remarkable journey through the scientific literature of the past 50 years, starting with the paradoxical observation of high prevalences of T. saginata-like tapeworms in non-beef consuming populations, to the full description of its mitochondrial genome. Experimental studies conducted in the 1980s and 1990s have made it clear that the life cycle of T. asiatica is comparable to that of T. saginata, except for pigs being the preferential intermediate host and liver the preferential location of the cysts. Whether or not T. asiatica can cause human cysticercosis, as is the case for Taenia solium, remains unclear. Given the specific conditions needed to complete its life cycle, in particular the consumption of raw or poorly cooked pig liver, the transmission of T. asiatica shows an important ethno-geographical association. So far, T. asiatica has been identified in Taiwan, South Korea, Indonesia, the Philippines, Thailand, south-central China, Vietnam, Japan and Nepal. Especially this last observation indicates that its distribution is not restricted to South-East-Asia, as was thought so far. Indeed, the molecular tools developed over the last 20 years have made it increasingly possible to differentiate T. asiatica from other taeniids. Such tools also indicated that T. asiatica is related more closely to T. saginata than to T. solium, feeding the debate on its taxonomic status as a separate species versus a subspecies of T. saginata. Furthermore, the genetic diversity within T. asiatica appears to be very minimal, indicating that this parasite may be on the verge of extinction. However, recent studies have identified potential hybrids between T. asiatica and T. saginata, reopening the debate on the genetic diversity of T. asiatica and its status as a separate species.

  5. GENETIC DIVERSITY IN ACCESSIONS OF Stylosanthes spp. USING MORPHOAGRONOMIC DESCRIPTORS

    Directory of Open Access Journals (Sweden)

    RONALDO SIMÃO DE OLIVEIRA

    2016-01-01

    Full Text Available The great diversity of plants in the Brazilian Semiarid environment represents a vital natural resource for the human populations of these areas. Many of these plants have been subject to extractivism and among these, the species of the genus Stylosanthes , which have occurrence in this region, show great potential, however, studies on this topic are limited, and little is known about the existing variability among these plants. Therefore, further study is necessary, to facilitate the development of cultivars. This might reduce the scarcity of fodder supply in this region, but to commence a plant breeding programme, it is essential to identify genetic variability. Therefore, this study evaluated 25 accessions of Stylosanthes spp., to identify the most suitable candidates to be parents in a plant breeding programme for the semiarid region of the state of Bahia. Two experiments were carried out in different sites in an experimental design of randomized blocks with four replicates, with a spacing of 3.0 × 8.0 m. A large amount of genetic diversity was observed among accessions and the genotypes BGF 08 - 007, BGF 08 - 016, BGF 08 - 015 and BGF 08 - 021 were the most divergent in the overall evaluation. For the structuring of segregating populations, it is recommended to combine the genotypes BGF 08 - 016, BGF 08 - 015, BGF 08 - 007 and BGF 08 - 006, and for the interspecific crosses, a hybrid from the accession BGF - 024 with the accessions BGF 08 - 016 or BGF 08 - 015. This might generate superior individuals for mass descriptors, which are the most important for animal forage breeding.

  6. Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

    NARCIS (Netherlands)

    Cascante-Marín, A.; Oostermeijer, G.; Wolf, J.; Fuchs, E.J.

    2014-01-01

    Information on genetic variation and its distribution in tropical plant populations relies mainly on studies of ground-rooted species, while genetic information of epiphytic plants is still limited. Particularly, the effect of forest successional condition on genetic diversity and structure of

  7. The impact of global climate change on genetic diversity within populations and species.

    Science.gov (United States)

    Pauls, Steffen U; Nowak, Carsten; Bálint, Miklós; Pfenninger, Markus

    2013-02-01

    Genetic diversity provides the basic substrate for evolution, yet few studies assess the impacts of global climate change (GCC) on intraspecific genetic variation. In this review, we highlight the importance of incorporating neutral and non-neutral genetic diversity when assessing the impacts of GCC, for example, in studies that aim to predict the future distribution and fate of a species or ecological community. Specifically, we address the following questions: Why study the effects of GCC on intraspecific genetic diversity? How does GCC affect genetic diversity? How is the effect of GCC on genetic diversity currently studied? Where is potential for future research? For each of these questions, we provide a general background and highlight case studies across the animal, plant and microbial kingdoms. We further discuss how cryptic diversity can affect GCC assessments, how genetic diversity can be integrated into studies that aim to predict species' responses on GCC and how conservation efforts related to GCC can incorporate and profit from inclusion of genetic diversity assessments. We argue that studying the fate of intraspecifc genetic diversity is an indispensable and logical venture if we are to fully understand the consequences of GCC on biodiversity on all levels. © 2012 Blackwell Publishing Ltd.

  8. Genetic diversity and germplasm conservation of three minor Andean tuber crop species

    Directory of Open Access Journals (Sweden)

    Malice M.

    2009-01-01

    Full Text Available In traditional Andean agrosystems, three minor tuber crop species are of regional or local importance: oca (Oxalis tuberosa Molina, ulluco (Ullucus tuberosus Caldas and mashua (Tropaeolum tuberosum Ruiz and Pav.. Genetic diversity within these species is very large and could result from the high ecological and cultural variability that characterizes the Andean area. Nowadays, many anthropic or ecological factors cause the loss of diversity and contribute to genetic erosion. The development of conservation strategies for genetic resources of Andean tubers, in situ as well as ex situ, includes a better knowledge of diversity in addition to the study of Andean farming strategies linked to this genetic diversity.

  9. Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide

    Science.gov (United States)

    Lam, Joseph S.; Taylor, Véronique L.; Islam, Salim T.; Hao, Youai; Kocíncová, Dana

    2011-01-01

    Lipopolysccharide (LPS) is an integral component of the Pseudomonas aeruginosa cell envelope, occupying the outer leaflet of the outer membrane in this Gram-negative opportunistic pathogen. It is important for bacterium–host interactions and has been shown to be a major virulence factor for this organism. Structurally, P. aeruginosa LPS is composed of three domains, namely, lipid A, core oligosaccharide, and the distal O antigen (O-Ag). Most P. aeruginosa strains produce two distinct forms of O-Ag, one a homopolymer of D-rhamnose that is a common polysaccharide antigen (CPA, formerly termed A band), and the other a heteropolymer of three to five distinct (and often unique dideoxy) sugars in its repeat units, known as O-specific antigen (OSA, formerly termed B band). Compositional differences in the O units among the OSA from different strains form the basis of the International Antigenic Typing Scheme for classification via serotyping of different strains of P. aeruginosa. The focus of this review is to provide state-of-the-art knowledge on the genetic and resultant functional diversity of LPS produced by P. aeruginosa. The underlying factors contributing to this diversity will be thoroughly discussed and presented in the context of its contributions to host–pathogen interactions and the control/prevention of infection. PMID:21687428

  10. Internal lattice reconfiguration for diversity tuning in Cellular Genetic Algorithms.

    Science.gov (United States)

    Morales-Reyes, Alicia; Erdogan, Ahmet T

    2012-01-01

    Cellular Genetic Algorithms (cGAs) have attracted the attention of researchers due to their high performance, ease of implementation and massive parallelism. Maintaining an adequate balance between exploitative and explorative search is essential when studying evolutionary optimization techniques. In this respect, cGAs inherently possess a number of structural configuration parameters that are able to sustain diversity during evolution. In this study, the internal reconfiguration of the lattice is proposed to constantly or adaptively control the exploration-exploitation trade-off. Genetic operators are characterized in their simplest form since algorithmic performance is assessed on implemented reconfiguration mechanisms. Moreover, internal reconfiguration allows the adjacency of individuals to be maintained. Hence, any improvement in performance is only a consequence of topological changes. Two local selection methods presenting opposite selection pressures are used in order to evaluate the influence of the proposed techniques. Problems ranging from continuous to real world and combinatorial are tackled. Empirical results are supported statistically in terms of efficiency and efficacy.

  11. Adapting populations in space: clonal interference and genetic diversity

    Science.gov (United States)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  12. [Genetic diversity of a rare hepatitis A virus genotype].

    Science.gov (United States)

    Desbois, D; Couturier, E; Graube, A; Letort, M-J; Dussaix, E; Roque-Afonso, A-M

    2011-02-01

    Very few is known on genotype II hepatitis A virus (HAV) since it is rarely isolated. From 2002 to 2007, the French observatory of HAV identified six sub-genotype IIA strains of which one from a patient having travelled to West Africa. To investigate the possible African origin of sub-genotype IIA, we determined its prevalence among French travellers in 2008 and characterised its genetic variability. The 2008 mandatory notification records were screened for travel to Africa. Viral genotype was determined on the nucleotide sequencing of the VP1/2A junction region. The P1 region coding for capsid proteins was used to compare the genetic diversity of IIA isolates to those of other genotypes. In 2008, five out of 54 patients returning from West Africa were infected by IIA strains and an additional "autochthonous" case was identified. Two more African cases were identified in 2009. A total of 14 IIA isolates (eight African and six "autochthonous") were analysed. Nucleotide and amino-acid variability of IIA sequences was lower than that of the other genotypes. Phylogenetic analysis revealed the clustering of two "autochthonous" cases with African isolates whereas the other ones belonged to a different lineage. Most IIA strains isolated in France are imported by travellers returning from West Africa. However, the unexplained contamination mode of some "autochthonous" cases suggests another geographical origin to discover or a French reservoir to explore. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  13. Genetic diversity of human blastocystis isolates in khorramabad, central iran.

    Directory of Open Access Journals (Sweden)

    Ebrahim Badparva

    2014-03-01

    Full Text Available There are some genetic differences in Blastocystis that show the existence of species or genotypes. One of these genes that help in identifying Blastocystis is SSUrRNA. The aim of this study was assessment of genetic diversity of Blastocystis by PCR with seven pairs of STS primers.This study was done on 511 stool samples collected from patients referred to the health care centers of Khorramabad, Central Iran, in 2012. Genomic DNA was extracted and in order to determine the Blastocystis subtype in contaminated samples, seven pairs of primers STS (subtype specific sequence-tagged site were used.Out of 511 samples, 33 (6.5% samples were infected with Blastocystis. Subtype (ST of 30 samples was identified and three subtypes 2, 3 and 4 were determined. Mix infection was reported 10% which 3.33% of the infection was for the mixture of ST 3 and ST5 and 6.67% was for the mixture of ST 2 and ST 3.The predominant subtype was ST3 that is the main human subtype. The dominance of ST2 and 5 are important in this study. This superiority has been reported in some of the studies in ST 2 which is different from the studies in other countries, because they have announced priorities of the ST1 and ST6 after ST3.

  14. The genetic diversity of Mesodinium and associated cryptophytes

    Directory of Open Access Journals (Sweden)

    Matthew David Johnson

    2016-12-01

    Full Text Available Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the M. major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides. Here we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (8 globally dispersed habitats including 5 Mesodinium blooms, using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL. In addition, 22 new cryptophyte and 4 new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all 4 blooms were dominated by T. amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic M. chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.

  15. Diversity of Five Anaerobic Toluene-Degrading Microbial Communities Investigated Using Stable Isotope Probing

    Science.gov (United States)

    Sun, Weimin

    2012-01-01

    Time-series DNA-stable isotope probing (SIP) was used to identify the microbes assimilating carbon from [13C]toluene under nitrate- or sulfate-amended conditions in a range of inoculum sources, including uncontaminated and contaminated soil and wastewater treatment samples. In all, five different phylotypes were found to be responsible for toluene degradation, and these included previously identified toluene degraders as well as novel toluene-degrading microorganisms. In microcosms constructed from granular sludge and amended with nitrate, the putative toluene degraders were classified in the genus Thauera, whereas in nitrate-amended microcosms constructed from a different source (agricultural soil), microorganisms in the family Comamonadaceae (genus unclassified) were the key putative degraders. In one set of sulfate-amended microcosms (agricultural soil), the putative toluene degraders were identified as belonging to the class Clostridia (genus Desulfosporosinus), while in other sulfate-amended microcosms, the putative degraders were in the class Deltaproteobacteria, within the family Syntrophobacteraceae (digester sludge) or Desulfobulbaceae (contaminated soil) (genus unclassified for both). Partial benzylsuccinate synthase gene (bssA, the functional gene for anaerobic toluene degradation) sequences were obtained for some samples, and quantitative PCR targeting this gene, along with SIP, was further used to confirm anaerobic toluene degradation by the identified species. The study illustrates the diversity of toluene degraders across different environments and highlights the utility of ribosomal and functional gene-based SIP for linking function with identity in microbial communities. PMID:22156434

  16. Molecular and genetic diversity in the metastatic process of melanoma.

    Science.gov (United States)

    Harbst, Katja; Lauss, Martin; Cirenajwis, Helena; Winter, Christof; Howlin, Jillian; Törngren, Therese; Kvist, Anders; Nodin, Björn; Olsson, Eleonor; Häkkinen, Jari; Jirström, Karin; Staaf, Johan; Lundgren, Lotta; Olsson, Håkan; Ingvar, Christian; Gruvberger-Saal, Sofia K; Saal, Lao H; Jönsson, Göran

    2014-05-01

    Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. © 2014 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

  17. Evaluation of Genetic Diversity of Candida spp. and Klebsiella spp. Isolated from the Denture Plaque of COPD Patients.

    Science.gov (United States)

    Przybyłowska, D; Piskorska, K; Gołaś, M; Sikora, M; Swoboda-Kopeć, E; Kostrzewa-Janicka, J; Mierzwińska-Nastalska, E

    2017-01-01

    Yeast-like fungi and gram-negative bacilli are the most frequent potential pathogens of the respiratory tract isolated from the denture plaque of patients with chronic obstructive pulmonary disease (COPD). Dominant species among yeast-like fungi are Candida albicans and Candida tropicalis. Significant frequency is also exhibited by Klebsiella pneumoniae and Klebsiella oxytoca. The purpose of this study was to analyze genetic diversity of the strains of C. albicans, C. tropicalis, and Klebsiella spp. present in patients in stable phases of COPD. The analysis was conducted by the random amplified polymorphic DNA (RAPD) method on clinical strains isolated from patients with COPD and control patients in overall good health. Forty one strains of Candida albicans, 12 of Candida tropicalis, as well as 9 strains of K. pneumoniae and 7 of K. oxytoca were scrutinized. The dominant species in clinical material from COPD patients was Candida albicans with a substantial degree of variations of genetic profiles. On the basis of affinity analysis, 19 genetic types were identified within this strain. An analysis of the banding patterns among C. tropicalis strains indicated the existence of 6 genetic types. A considerable diversity of genetic profiles among Klebsiella spp. also was established. The genotype diversity of Klebsiella spp. strains may indicate the endogenic character of the majority of infections, regardless of the therapy applied for the underlying condition.

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

    Science.gov (United States)

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

    2007-02-01

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

  19. Low genetic diversity and strong but shallow population differentiation suggests genetic homogenization by metapopulation dynamics in a social spider.

    Science.gov (United States)

    Settepani, V; Bechsgaard, J; Bilde, T

    2014-12-01

    Mating systems and population dynamics influence genetic diversity and structure. Species that experience inbreeding and limited gene flow are expected to evolve isolated, divergent genetic lineages. Metapopulation dynamics with frequent extinctions and colonizations may, on the other hand, deplete and homogenize genetic variation, if extinction rate is sufficiently high compared to the effect of drift in local demes. We investigated these theoretical predictions empirically in social spiders that are highly inbred. Social spiders show intranest mating, female-biased sex ratio, and frequent extinction and colonization events, factors that deplete genetic diversity within nests and populations and limit gene flow. We characterized population genetic structure in Stegodyphus sarasinorum, a social spider distributed across the Indian subcontinent. Species-wide genetic diversity was estimated over approximately 2800 km from Sri Lanka to Himalayas, by sequencing 16 protein-coding nuclear loci. We found 13 SNPs in 6592 bp (π = 0.00045) indicating low species-wide nucleotide diversity. Three genetic lineages were strongly differentiated; however, only one fixed difference among them suggests recent divergence. This is consistent with a scenario of metapopulation dynamics that homogenizes genetic diversity across the species' range. Ultimately, low standing genetic variation may hamper a species' ability to track environmental change and render social inbreeding spiders 'evolutionary dead-ends'. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  20. Genetic diversity of pheasants from natural habitat and farm ...

    African Journals Online (AJOL)

    The original source of the pheasants living in the natural habitat is the farm, and the present genetic variation between the two groups of birds can be interpreted as an effect of natural selection. Keywords: Common pheasant (Phasianus colchicus), genetic distance, genetic polymorphism, genetic similarities, genetic ...

  1. Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

    Directory of Open Access Journals (Sweden)

    Ming-Cheng Luo

    2013-03-01

    Full Text Available Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.

  2. Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

    Science.gov (United States)

    Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

    2013-01-01

    Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

  3. Moderate Genetic Diversity and Genetic Differentiation in the Relict Tree Liquidambar formosana Hance Revealed by Genic Simple Sequence Repeat Markers

    Science.gov (United States)

    Sun, Rongxi; Lin, Furong; Huang, Ping; Zheng, Yongqi

    2016-01-01

    Chinese sweetgum (Liquidambar formosana) is a relatively fast-growing ecological pioneer species. It is widely used for multiple purposes. To assess the genetic diversity and genetic differentiation of the species, genic SSR markers were mined from transcriptome data for subsequent analysis of the genetic diversity and population structure of natural populations. A total of 10645 potential genic SSR loci were identified in 80482 unigenes. The average frequency was one SSR per 5.12 kb, and the dinucleotide unit was the most abundant motif. A total of 67 alleles were found, with a mean of 6.091 alleles per locus and a mean polymorphism information content of 0.390. Moreover, the species exhibited a relatively moderate level of genetic diversity (He = 0.399), with the highest was found in population XY (He = 0.469). At the regional level, the southwestern region displayed the highest genetic diversity (He = 0.435) and the largest number of private alleles (n = 5), which indicated that the Southwestern region may be the diversity hot spot of L. formosana. The AMOVA results showed that variation within populations (94.02%) was significantly higher than among populations (5.98%), which was in agreement with the coefficient of genetic differentiation (Fst = 0.076). According to the UPGMA analysis and principal coordinate analysis and confirmed by the assignment test, 25 populations could be divided into three groups, and there were different degrees of introgression among populations. No correlation was found between genetic distance and geographic distance (P > 0.05). These results provided further evidence that geographic isolation was not the primary factor leading to the moderate genetic differentiation of L. formosana. As most of the genetic diversity of L. formosana exists among individuals within a population, individual plant selection would be an effective way to use natural variation in genetic improvement programs. This would be helpful to not only protect the

  4. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    assist with maintaining genetic diversity for long-term selection gains and to plan future breeding programs.

  5. Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains

    Energy Technology Data Exchange (ETDEWEB)

    Hill, K K; Smith, T J; Helma, C H; Ticknor, L O; Foley, B T; Svennson, R T; Brown, J L; Johnson, E A; Smith, L A; Okinaka, R T; Jackson, P J; Marks, J D

    2006-07-06

    Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and even death in humans and various other animal species. A collection of 174 C. botulinum strains were examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT A-G). Analysis of the16S rRNA sequences confirmed earlier reports of at least four distinct genomic backgrounds (Groups I-IV) each of which has independently acquired one or more BoNT serotypes through horizontal gene transfer. AFLP analysis provided higher resolution, and can be used to further subdivide the four groups into sub-groups. Sequencing of the BoNT genes from serotypes A, B and E in multiple strains confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes, and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven serotypes of BoNT were compared and show varying degrees of interrelatedness and recombination as has been previously noted for the NTNH gene which is linked to BoNT. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for treatment of botulism.

  6. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

    Science.gov (United States)

    Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

    2016-01-01

    Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  7. Genetic diversity of Phytophthora infestans in the Northern Andean region

    Directory of Open Access Journals (Sweden)

    Grünwald Niklaus J

    2011-02-01

    Full Text Available Abstract Background Phytophthora infestans (Mont. de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana and tree tomato (Solanum betaceum, all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, β-tubulin and Avr3a and one mitochondrial (Cox1 region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. Results Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. Conclusions The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a.

  8. Genetic Diversity as Consequence of a Microaerobic and Neutrophilic Lifestyle.

    Directory of Open Access Journals (Sweden)

    Nora-Johanna Krüger

    2016-05-01

    Full Text Available As a neutrophilic bacterium, Helicobacter pylori is growth deficient under extreme acidic conditions. The gastric pathogen is equipped with an acid survival kit, regulating urease activity by a pH-gated urea channel, opening below pH 6.5. After overcoming acid stress, the bacterium's multiplication site is situated at the gastric mucosa with near neutral pH. The pathogen exhibits exceptional genetic variability, mainly due to its capability of natural transformation, termed competence. Using single cell analysis, we show here that competence is highly regulated in H. pylori. DNA uptake complex activity was reversibly shut down below pH 6.5. pH values above 6.5 opened a competence window, in which competence development was triggered by the combination of pH increase and oxidative stress. In contrast, addition of sublethal concentrations of the DNA-damaging agents ciprofloxacin or mitomycin C did not trigger competence development under our conditions. An oxygen-sensitive mutant lacking superoxide dismutase (sodB displayed a higher competent fraction of cells than the wild type under comparable conditions. In addition, the sodB mutant was dependent on adenine for growth in broth and turned into non-cultivable coccoid forms in its absence, indicating that adenine had radical quenching capacity. Quantification of periplasmically located DNA in competent wild type cells revealed outstanding median imported DNA amounts of around 350 kb per cell within 10 min of import, with maximally a chromosomal equivalent (1.6 Mb in individual cells, far exceeding previous amounts detected in other Gram-negative bacteria. We conclude that the pathogen's high genetic diversity is a consequence of its enormous DNA uptake capacity, triggered by intrinsic and extrinsic oxidative stress once a neutral pH at the site of chronic host colonization allows competence development.

  9. Is there a positive relationship between naturalness and genetic diversity in forest tree communities?

    Energy Technology Data Exchange (ETDEWEB)

    Wehenkel, C.; Corral-Rivas, J. J.; Castellanos-Bocaz, H. A.; Pinedo-Alvarez, A.

    2009-07-01

    Abstract The concepts of genetic diversity and naturalness are well known as measures of conservation values and as descriptors of state or condition. A lack of research evaluating the relationship between genetic diversity and naturalness in biological communities, along with the possible implications in terms of evolutionary aspects and conservation management, make this subject particularly important as regards forest tree communities.We therefore examined the following hypothesis: the genetic diversity of a central-European tree stand averaged over species increases with the naturalness of the stand, as defined by the Potential Natural Vegetation (PNV). The results obtained show that the hypothesis is unsustainable because differences between the averaged genetic diversities of the unnatural and semi-natural stand classes (69 cases) were mostly non-significant. Moreover in three cases, the average genetic diversity of unnatural stand classes was significantly higher than the average genetic diversity of the semi-natural stand classes. A significantly lower average genetic diversity of unnatural stand class was not detected in the statistical analysis. Thus, the naturalness of a tree species community, as inferred from PNV, does not serve as a straightforward indicator of ecological stability when the genetic diversity and the adaptability of tree species are unknown. (Author) 30 refs.

  10. Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep

    NARCIS (Netherlands)

    Epps, CW; Palsboll, PJ; Wehausen, JD; Roderick, GK; Ramey, RR; McCullough, DR

    2005-01-01

    The rapid expansion of road networks has reduced connectivity among populations of flora and fauna. The resulting isolation is assumed to increase population extinction rates, in part because of the loss of genetic diversity. However, there are few cases where loss of genetic diversity has been

  11. Past climate-driven range shifts and population genetic diversity in arctic plants

    DEFF Research Database (Denmark)

    Pellissier, Loïc; Eidesen, Pernille Bronken; Ehrich, Dorothee

    2016-01-01

    High intra-specific genetic diversity is necessary for species adaptation to novel environments under climate change, but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here, we investigated the relationship between range shift since ...... the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses...

  12. Do Farmers reduce genetic diversity when they domesticate tropical trees? a case study from Amazonia.

    NARCIS (Netherlands)

    Hollingsworth, P.M.; Dawson, I.K.; Goodall-Copestake, W.P.; Richardson, J.E.; Weber, J.C.; Sotelo Montes, C.; Pennington, R.T.

    2005-01-01

    Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity

  13. Environmental factors influence both abundance and genetic diversity in a widespread bird species

    NARCIS (Netherlands)

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-01-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors

  14. Conservation of biodiversity in sugar pine: effects of the blister rust epidemic on genetic diversity

    Science.gov (United States)

    Constance I. Millar; Bohun B. Kinloch; Robert D. Westfall

    1992-01-01

    Genetic diversity in sugar plne will be severely reduced by the blister rust pandemic predicted within the next 50 to 75 years. We model effects of the epidemic on genetic diversity at the stand and landscape levels for both natural and artificial regeneration. In natural stands, because natural frequencies of the dominant gene (R) for resistance are low, the most...

  15. Recloned transgenic pigs possess normal reproductive performance and stable genetic transmission capacity.

    Science.gov (United States)

    Cao, Zubing; Li, Yan; Wen, Xiao; Li, Zhiyuan; Mi, Changsheng; Zhang, Zaihu; Li, Ning; Li, Qiuyan

    2014-02-01

    The present study investigated whether a recloning procedure would affect the reproductive performance or the germline transmission capacity of recloned transgenic pigs. This study has also laid the foundation for the development of elite transgenic swine breeds in the future. Recloned transgenic pigs were developed from ear tissue fibroblasts of primary transgenic cloned pigs using a recloning procedure, and their reproductive performance and exogenous gene transmission were analyzed. Two transgenic cell lines with different genetic backgrounds (derived from a female miniature pig and a male Landrace pig) with stable expression of green fluorescent protein (GFP) were established successfully. Furthermore, recloned transgenic embryos were developed to full term successfully. One female Chinese experimental miniature piglet (CEMP) (GFP+) and three male Landrace piglets (GFP+) were delivered naturally. Furthermore, the index values for the reproductive characteristics of the recloned transgenic pigs, such as puberty, gestation period, sperm volume and sperm concentration, were not significantly different from those of conventionally bred pigs. In addition, 53% of the F1 offspring of the recloned transgenic pigs were GFP positive. These results demonstrate that ear tissue fibroblasts from primary transgenic cloned pigs efficiently support the full-term development of recloned transgenic embryos. Furthermore, recloned transgenic pigs maintain normal reproductive performance and stable germline (genetic) transmission capacities.

  16. Agrobacterium-mediated stable genetic transformation of Populus angustifolia and Populus balsamifera

    Directory of Open Access Journals (Sweden)

    Priti eMaheshwari

    2016-03-01

    Full Text Available The present study demonstrates Agrobacterium tumefaciens-mediated stable genetic transformation of two species of Poplar - Populus angustifolia and Populus balsamifera. The binary vector pCAMBIA-Npro-long-Luc containing the luciferase reporter gene was used to transform stem internode and axillary bud explants. Putative transformants were regenerated on selection-free medium using our previously established in vitro regeneration method. Explant type, genotype, effect of pre-culture, Agrobacterium concentration, a time period of infection and varying periods of co-culture with bacteria were tested for the transformation frequency. The highest frequency of transformation was obtained with stem internode explants pre-cultured for 2 days, infected with Agrobacterium culture at the concentration of OD600=0.5 for 10 min and co-cultivated with Agrobacterium for 48 h. Out of the two genotypes tested, P. balsamifera exhibited a higher transformation rate in comparison to P. angustifolia. The primary transformants that exhibited luciferase activity in a bioluminescence assay under the CCD camera when subjected to PCR and southern blot analysis revealed a stable single-copy integration of luc in their genomes. The reported protocol is highly reproducible and can be applied to other species of poplar; it will also be useful for future genetic engineering of one of the most important families of woody plants for sustainable development.

  17. Patterns in genetic diversity of Trifolium pallescens populations do not reflect chronosequence on alpine glacier forelands.

    Science.gov (United States)

    Raffl, C; Holderegger, R; Parson, W; Erschbamer, B

    2008-05-01

    How does genetic diversity within populations of plants develop during primary succession on alpine glacier forelands? Theory predicts that pioneer populations are characterized by low genetic diversity due to founder effects and that genetic diversity increases within populations as they mature and recurrent gene flow occurs. However, few genetic studies have so far been carried out on plants on glacier forelands. In this study, we analysed the development of genetic diversity with time for populations of Trifolium pallescens along successional series (chronosequences) on three parallel glacier forelands in the European Alps, using neutral amplified fragment length polymorphism. No general trend in the development of genetic diversity was observed with increasing population age: even pioneer populations harboured substantial genetic diversity. Assignment tests showed that the latter consist of a genetic sub-sample from several source areas, and not just from other populations on the glacier forelands. We also detected some long distances-that is, inter-valley gene flow events. However, gene flow was not spatially unrestricted, as shown by a weak isolation by distance pattern within glacier valleys. The actual patterns of genetic diversity along the chronosequences are a result of the combination of factors, such as gene flow and growth rate, influenced by site- and species-specific attributes.

  18. Genetic variation between populations of the stable fly, Stomoxys calcitrans (L.)(Diptera: Muscidae) from Nebraska, Denmark and Australia

    Science.gov (United States)

    The stable fly, Stomoxys calcitrans L., is a cosmopolitan, major pest of livestock. Previous studies on this insect, from samples within the United States, suggested a large amount of gene flow; more genetic variation was detected within populations than between populations. To compare the genetic v...

  19. Genetic Diversity of Acacia mangium Seed Orchard in Wonogiri Indonesia Using Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    VIVI YUSKIANTI

    2012-09-01

    Full Text Available Genetic diversity is important in tree improvement programs. To evaluate levels of genetic diversity of first generation Acacia mangium seedling seed orchard in Wonogiri, Central Java, Indonesia, three populations from each region of Papua New Guinea (PNG and Queensland, Australia (QLD were selected and analyzed using 25 microsatellite markers. Statistical analysis showed that PNG populations have higher number of detected alleles and level of genetic diversity than QLD populations. This study provides a basic information about the genetic background of the populations used in the development of an A. mangium seed orchard in Indonesia.

  20. Loss of Genetic Diversity of Jatropha curcas L. through Domestication: Implications for Its Genetic Improvement

    DEFF Research Database (Denmark)

    Sanou, Haby; Angel Angulo-Escalante, Miguel; Martinez-Herrera, Jorge

    2015-01-01

    between 0.34 and 0.54. Bayesian analysis showed differentiation according to geographic locations, which was confirmed by principal coordinate analysis and neighbor-joining tree. Estimations of outcrossing rate of individual families from Chiapas showed that some mother trees were mainly outcrossing......Jatropha curcas L. has been promoted as a “miracle” tree in many parts of the world, but recent studies have indicated very low levels of genetic diversity in various landraces. In this study, the genetic diversity of landrace collections of J. curcas was compared with the genetic diversity...... of the species from its native range, and the mating system was analyzed on the basis of microsatellite markers. The genetic diversity parameters were estimated, and analysis of molecular variance, principal coordinate analysis, and unrooted neighbor-joining tree were used to describe the relationship among...

  1. A preliminary examination of genetic diversity in the Indian false vampire bat Megaderma lyra

    Directory of Open Access Journals (Sweden)

    Emmanuvel Rajan, K.

    2006-12-01

    Full Text Available Habitat loss and fragmentation have serious consequences for species extinction as well as genetic diversity within a species. Random Amplified Polymorphic DNA (RAPD analysis was employed to assess the genetic diversity within and between four natural populations of M. lyra. Our results suggest that the genetic diversity varied from 0.21 to 0.26 with a mean of 0.11 to 0.13 (± SD. The mean Gst value of 0.15 was obtained from all four populations and estimated average Nm (1.41 showing gene flow between the populations. AMOVA analysis showed 88.96% within and 11.04% among the studied populations. Cluster analyses of RAPD phenotypes showed that specimens were not grouped by geographical origin. The genetic diversity found in the M. lyra population may be explained by its breeding behaviors. Though preliminary, the results indicate that all four populations should be considered to maintain the genetic diversity.

  2. Genetic Diversity of Some Capparis L. Species Growing in Syria

    Directory of Open Access Journals (Sweden)

    Bassam Al- Safadi

    2014-12-01

    Full Text Available This work investigated the genetic diversity and relationships among Capparis species growing in Syria using IRAP and ISSR techniques. Forty-seven samples of three Capparis species genotypes were collected from 21 different locations in Syria. The genotypes were morphologically identified based on the descriptions available in the literature. When IRAP technique was used, an average of 71.5% of the amplified fragments were polymorphic compared to 82.04% in ISSR. Morphological characterization along with the cluster and PCoA analyses of the data divided the studied genotypes into three groups. The groups included genotypes identified as Capparis spinosa L, C. sicula Duh., and C. aegyptia Lam. Based on the morphological description, molecular studies and statistical analyses of this study, C. aegyptia could be suggested as a separate species and not a varietal rank of C. spinosa(C. spinosa var. aegyptia (Lam.. Two samples (Alep1 and Idl were not placed in any of the three distinctive groups, despite their closeness morphologically to C. spinosa. In PCoA analysis, sample Alep1 came between C. sicula and C. spinosa and Idl was placed between C. sicula and C. aegyptia. Although hybridization between Capparis species could occur, it was not clear from the present study if these two genotypes were hybrids.

  3. Genetic diversity of some chili (Capsicum annuum L. genotypes

    Directory of Open Access Journals (Sweden)

    M.J. Hasan

    2014-06-01

    Full Text Available A study on genetic diversity was conducted with 54 Chili (Capsicum annuum L. genotypes through Mohalanobis’s D2 and principal component analysis for twelve quantitative characters viz. plant height, number of secondary branch/plant, canopy breadth , days to first flowering, days to 50% flowering, fruits/plant, 5 fruits weight, fruit length, fruit diameter, seeds/fruit, 1000 seed weight and yield/plant were taken into consideration. Cluster analysis was used for grouping of 54 chili genotypes and the genotypes were fallen into seven clusters. Cluster II had maximum (13 and cluster III had the minimum number (1 of genotypes. The highest inter-cluster distance was observed between cluster I and III and the lowest between cluster II and VII. The characters yield/plant, canopy breadth, secondary branches/plant, plant height and seeds/fruit contributed most for divergence in the studied genotypes. Considering group distance, mean performance and variability the inter genotypic crosses between cluster I and cluster III, cluster III and cluster VI, cluster II and cluster III and cluster III and cluster VII may be suggested to use for future hybridization program.

  4. Genetic diversity of hepatitis B virus (HBV) in Madagascar.

    Science.gov (United States)

    Andriamandimby, Soa Fy; Lo Presti, Alessandra; Lai, Alessia; Olive, Marie-Marie; Angeletti, Silvia; De Florio, Lucia; Cella, Eleonora; Razafindramparany, Minoharimbola; Ravalohery, Jean-Piere; Andriamamonjy, Seta; Gioffrè, Sonia; Zehender, Gianguglielmo; Mottini, Giovanni; Ciccozzi, Massimo; Heraud, Jean-Michel

    2016-12-01

    Hepatitis B virus (HBV) is a DNA virus belonging to Hepadnaviridae family. Chronic infection with HBV is one major risk factor of hepatic disease. In Madagascar, former studies classified the country as part of high endemic area, as HBV prevalence can reach 23% in general population. However, this prevalence differs largely between urban and rural areas and is estimated to be, respectively, 5% and 26%. The aims of the present study were to describe the genetic diversity of HBV strains from different regions of Madagascar, and to describe the viral gene flow throughout the country by using phylogenetic analysis. This is the first large-scale molecular and phylogenetic study analyzing HBV sequences from 28 different Malagasy areas, never sampled in the past. In this study, the most prevalent genotype/sub-genotypes was E. Migration analysis showed a gene flow from zone 3 (rural) to zone 2 (suburban), and a greater gene flow from the middle part of Madagascar to the north than to the south. It is important to study the HBV infections in Madagascar and to monitor the potential spread of this viral strain inside this country. J. Med. Virol. 88:2138-2144, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese......) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean FIS=0.05) and genetic differentiation (mean FST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected...... of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic...

  6. Environmental and Climatic Determinants of Molecular Diversity and Genetic Population Structure in a Coenagrionid Damselfly

    OpenAIRE

    Maren Wellenreuther; Sánchez-Guillén, Rosa A.; Adolfo Cordero-Rivera; Svensson, Erik I.; Bengt Hansson

    2011-01-01

    Identifying environmental factors that structure intraspecific genetic diversity is of interest for both habitat preservation and biodiversity conservation. Recent advances in statistical and geographical genetics make it possible to investigate how environmental factors affect geographic organisation and population structure of molecular genetic diversity within species. Here we present a study on a common and wide ranging insect, the blue tailed damselfly Ischnuraelegans, which has been the...

  7. Genetic Diversity of Andean Tuber Crop Species in the in situ Microcenter of Huanuco, Peru

    OpenAIRE

    Malice, Marie; Bizoux, Jean-Philippe; Blas, Raul; Baudoin, Jean-Pierre

    2010-01-01

    Andean tuber crop species oca (Oxalis tuberosa Molina), ulluco (Ullucus tuberosus Caldas), and mashua (Tropaeolum tuberosum Ruiz & Pav.) play major roles in Andean communities. These species show high variability but are threatened with genetic erosion. To study the management of genetic resources of neglected vegetatively propagated crop species, we studied genetic diversity and structure of these species in an in situ diversity microcenter (Huanuco, Peru). A sample of 15 varieties of oca, 1...

  8. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    National Research Council Canada - National Science Library

    Emanuelli, Francesco; Lorenzi, Silvia; Grzeskowiak, Lukasz; Catalano, Valentina; Stefanini, Marco; Troggio, Michela; Myles, Sean; Martinez-Zapater, José M; Zyprian, Eva; Moreira, Flavia M; Grando, M Stella

    2013-01-01

    ... on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections...

  9. Analysis of genetic diversity in a close population of Zandi sheep ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 89; Issue 4. Analysis of genetic diversity in a close population of Zandi sheep using ... Author Affiliations. Farhad Ghafouri-Kesbi1. Department of Animal Breeding and Genetics, Animal Science Research Institute of Iran (ASRI), P. O. Box 1483, Karaj 3146618361, Iran ...

  10. Application of SRAP in the genetic diversity of Pinus koraiensis of ...

    African Journals Online (AJOL)

    It indicated that no close relationship can be well established between genetic diversity and the location of provenance. The genetic variation mainly caused by the variation of intra population, accounting for 92.35% of the total genetic variation. Moreover, the gene flow of P. koraiensis between the provenances was 2.905, ...

  11. Genetic diversity and drivers of genetic differentiation of Reaumuria soongorica of the Inner Mongolia plateau in China

    Science.gov (United States)

    Jiuyan Yang; Samuel A. Cushman; Xuemei Song; Jie Yang; Pujin Zhang

    2015-01-01

    We quantified genetic diversity and gene flow among eight populations of Reaumuria soongorica in Inner Mongolia, China. Our results showed that genetic differentiation of R. soongorica across the Inner Mongolian plateau is primarily clinal in nature and is driven primarily by differential landscape resistance across areas with changing patterns of seasonal...

  12. Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

    Science.gov (United States)

    Kovach, Ryan; Muhlfeld, Clint C.; Wade, Alisa A.; Hand, Brian K.; Whited, Diane C.; DeHaan, Patrick W.; Al-Chokhachy, Robert K.; Luikart, Gordon

    2015-01-01

    Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = −0.77;P bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

  13. Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat.

    Science.gov (United States)

    Bertin, Angeline; Gouin, Nicolas; Baumel, Alex; Gianoli, Ernesto; Serratosa, Juan; Osorio, Rodomiro; Manel, Stephanie

    2017-01-01

    Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species-genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species-genetic diversity relationships. © 2016 John Wiley & Sons Ltd.

  14. Genetic diversity of Halla horses using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Joo-Hee Seo

    2016-11-01

    Full Text Available Abstract Background Currently about 26,000 horses are breeding in Korea and 57.2% (14,776 horses of them are breeding in Jeju island. According to the statistics published in 2010, the horses breeding in Jeju island are subdivided into Jeju horse (6.1%, Thoroughbred (18.8% and Halla horse (75.1%. Halla horses are defined as a crossbreed between Jeju and Thoroughbred horses and are used for horse racing, horse riding and horse meat production. However, little research has been conducted on Halla horses because of the perception of crossbreed and people’s weighted interest toward Jeju horses. Method Using 17 Microsatellite (MS Markers recommended by International Society for Animal Genetics (ISAG, genomic DNAs were extracted from the hair roots of 3,880 Halla horses breeding in Korea and genetic diversity was identified by genotyping after PCR was performed. Results and conclusion In average, 10.41 alleles (from 6 alleles in HTG7 to 17 alleles in ASB17 were identified after the analysis using 17 MS Markers. The mean value of Hobs was 0.749 with a range from 0.612(HMS1 to 0.857(ASB2. Also, it was found that Hexp and PIC values were lowest in HMS1 (0.607 and 0.548, respectively, and highest in LEX3(0.859 and 0.843, respectively, and the mean value of Hexp was 0.760 and that of PIC was 0.728. 17 MS markers used in this studies were considered as appropriate markers for the polymorphism analysis of Halla horses. The frequency for the appearance of identical individuals was 5.90 × 10−20 when assumed as random mating population and when assumed as half-sib and full-sib population, frequencies were 4.08 × 10−15 and 3.56 × 10−8, respectively. Based on these results, the 17 MS markers can be used adequately for the Individual Identification and Parentage Verification of Halla horses. Remarkably, allele M and Q of ASB23 marker, G of HMS2 marker, H and L of HTG6 marker, L of HTG7 marker, E of LEX3 marker were the specific alleles

  15. Simulation of Invertebrate Aggregation Shows the Importance of Stable Personality over Diversity in Consensus Decision-Making.

    Science.gov (United States)

    Pogson, Mark

    2016-01-01

    Aggregation of many species of invertebrate is an example of a consensus decision, the success of which is central to survival. Personality is a stable form of behavioural diversity which has been observed in the aggregation process, but neither the reasons for its stability nor its effects on consensus decisions are well understood. By using an agent-based model of invertebrate aggregation, it is found that diverse personalities have only limited benefits to the experimental consensus decision-making process, but may have a more valuable role in natural settings. Importantly, although certain personalities may ostensibly have potential drawbacks at the individual level, such as choosing to rest in unfavourable places, all individuals are likely to benefit from maintaining a constant personality, which promotes group stability. These findings help to improve understanding of consensus decision-making and the prevalence of stable personality.

  16. High genetic variation in leopards indicates large and long-term stable effective population size.

    Science.gov (United States)

    Spong, G; Johansson, M; Björklund, M

    2000-11-01

    In this paper we employ recently developed statistical and molecular tools to analyse the population history of the Tanzanian leopard (Panthera pardus), a large solitary felid. Because of their solitary lifestyle little is known of their past or present population dynamics. Eighty-one individuals were scored at 18 microsatellite loci. Overall, levels of heterozygosity were high (0.77 +/- 0.03), with a small heterozygote deficiency (0.06 +/- 0.03). Effective population size (Ne) was calculated to be 38 000-48 000. A Ne:N ratio of 0.42 (average from four cat studies) gives a present population size of about 100 000 leopards in Tanzania. Four different bottleneck tests indicated that this population has been large and stable for a minimum of several thousand years. FST values were low and no significant genetic structuring of the population could be detected. This concurs well with the large migration values (Nm) obtained (>3.3 individuals/generation). Our analysis reveals that ecological factors (e.g. disease), which are known to have had major impact on other carnivore populations, are unlikely to have impacted strongly on the population dynamics of Tanzanian leopards. The explanation may be found in their solitary life-style, their often nonconfrontational behaviour toward interspecific competitors, or that any bottlenecks have been of limited size, localized, or too short to have affected genetic variation to any measurable degree. Since the genetic structuring is weak, gene flow is not restricted to within protected areas. Local loss of genetic variation is therefore not of immediate concern.

  17. Concordance between vocal and genetic diversity in crested gibbons

    Directory of Open Access Journals (Sweden)

    Roos Christian

    2011-02-01

    Full Text Available Abstract Background Gibbons or small apes are, next to great apes, our closest living relatives, and form the most diverse group of contemporary hominoids. A characteristic trait of gibbons is their species-specific song structure, which, however, exhibits a certain amount of inter- and intra-individual variation. Although differences in gibbon song structure are routinely applied as taxonomic tool to identify subspecies and species, it remains unclear to which degree acoustic and phylogenetic differences are correlated. To trace this issue, we comparatively analyse song recordings and mitochondrial cytochrome b gene sequence data from 22 gibbon populations representing six of the seven crested gibbon species (genus Nomascus. In addition, we address whether song similarity and geographic distribution can support a recent hypothesis about the biogeographic history of crested gibbons. Results The acoustic analysis of 92 gibbon duets confirms the hypothesised concordance between song structure and phylogeny. Based on features of male and female songs, we can not only distinguish between N. nasutus, N. concolor and the four southern species (N. leucogenys, N. siki, N. annamensis, N. gabriellae, but also between the latter by applying more detailed analysis. In addition to the significant correlation between song structure and genetic similarity, we find a similar high correlation between song similarity and geographic distance. Conclusions The results show that the structure of crested gibbon songs is not only a reliable tool to verify phylogenetic relatedness, but also to unravel geographic origins. As vocal production in other nonhuman primate species appears to be evolutionarily based, it is likely that loud calls produced by other species can serve as characters to elucidate phylogenetic relationships.

  18. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

    Directory of Open Access Journals (Sweden)

    Suping Feng

    2013-01-01

    Full Text Available Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8% of the 94 Simple Sequence Repeat (SSR loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp., and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus. Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

  19. Morphological Characteristics, Genetic Diversity and Classification of Chrysanthemum Genotypes

    Directory of Open Access Journals (Sweden)

    Z. Roein

    2015-09-01

    Full Text Available Chrysanthemum is one of the most important ornamental plants. The genus chrysanthemum is a popular cut flower, medicinal and pot plant. Morphological traits such as cut rooting and leaf characteristics and genetic diversity among 50 genotypes of chrysanthemum morifolium were analyzed. Based on analysis of variance of data all traits in the studied genotypes showed significant differences at 1% level. The results of correlation coefficient indicated a positive and significant correlation between stem length, leaf length, leaf width and leaf serration number.The leaf length showed the highest correlation (r = +0.90** with leaf width. Results showed that stem length and petiole length had the highest (h2>80% heritability. Cluster analysis according to the morphological traits using the Ward method classified all the genotypes into six groups. In this classification, two genotypes (‘Takapo’ and ‘Poloneh’ were classified into one cluster that was characterized by tall stem and low branch number. In this study, canonical discriminant analysis of 20 morphological traits revealed that 3 canonical discriminant variables explained 89.6% of the total variation among genotypes. Results revealed that among the studied traits, number of cutting root, leaf size, petiol length, stem length, number of branches and number of offsets were the most important traits for discriminating among chrysanthemum genotypes. The results of this study indicate that these traits are useful for selecting and identify superior genotypes of chrysanthemum germplasm. Using some of the genotypes belonging to cluster A (with a small size of plant and genotypes belonging to cluster E (with a large size of plant as parents can be practiced as a criteria for breeding programs.

  20. 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.

  1. A genetic risk score predicts cardiovascular events in patients with stable coronary artery disease

    DEFF Research Database (Denmark)

    Christiansen, Morten Krogh; Nyegaard, Mette; Larsen, Sanne Bøjet

    Background. Genetic risk scores (GRSs) may predict cardiovascular risk in community-based populations. However, studies investigating the association with recurrent cardiovascular events in patients with established coronary artery disease (CAD) are conflicting. Methods. We genotyped 879 patients...... with high-risk stable CAD and created a GRS based on 45 single nucleotide polymorphisms previously reported to be associated with CAD in genome-wide association studies. Patients were categorised into high or low GRS according to the median GRS and followed for recurrent cardiovascular events using national...... Danish registries. The primary endpoint was a composite of myocardial infarction, coronary revascularisation, and cardiovascular death. Results. Median (interquartile range) follow-up time was 2.8 (2.4–3.8) years. The cumulative incidence proportions of the primary endpoint at 1 and 3 years were 6...

  2. Genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world’s agro-ecological zones

    Science.gov (United States)

    Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countrie...

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

    African Journals Online (AJOL)

    Aghomotsegin

    2015-10-14

    Oct 14, 2015 ... 1Faculty of Art and Science Raniah Branch, University of Taif, Raniah, Kingdom of Saudi Arabia. 2Comission for Biotechnology and Genetic Engineering, ... The cluster analysis shows that Najdi breed is genetically different from both Harri and Awassi and that some Harri individuals showed genetic ...

  4. Genetic diversity study of important Indian rice genotypes using ...

    African Journals Online (AJOL)

    Rice is a staple food for 90% of the world. Genetic characterization of natural resources is an essential step to understand genetic resources. In the present study, commonly using 25 Indian rice genotypes were collected / procured from four different states of India. Genetic variation was assessed using isozyme and RAPD ...

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

    African Journals Online (AJOL)

    Genetic variation among and within five generations of an inbred commercial captive line of Litopenaeus vannamei and genetic distance among them were evaluated by random amplified polymorphic DNA (RAPD), using descriptive and genetic similarity analyses for dominant markers at single- and multi-populational level ...

  6. analysis of genetic diversity in linseed using aflp markers

    African Journals Online (AJOL)

    ADMIN

    characters (Adugna Wakjira and Labuschagne,. 2004). However, expression of traits, such as days to flowering and maturity, plant height, number of branches and seed yield is ..... genetic makeup of the accessions. The presence of a wide range of genetic variation between the accessions is a good basis for future genetic.

  7. Genetic diversity of Pakistani common myna (Acridotheres tristis ...

    African Journals Online (AJOL)

    Jane

    2011-08-01

    Aug 1, 2011 ... Acridotheres tristis is a widely distributed species of Pakistan but no genetic data of this species is available in the literature. ... protection programs, the genetic structure of species at population level has received ..... the Genetic Polymorphism in Duck: Differences among Breeds. Genetika, 36: 682-687.

  8. Diversity and general student scholarship recipient essays: 2010 National Society of Genetic Counselors Membership Committee.

    Science.gov (United States)

    Liu, Tina; Patek, Kyla; Schneider, Kami Wolfe

    2011-12-01

    In an effort to increase the diversity of the membership of the National Society of Genetic Counselors (NSGC), the Membership Committee provided two $500 scholarships to genetic counseling students planning to attend the NSGC AEC meeting in Dallas, Texas in October 2010. Requirements for applicants of both scholarships included enrollment in the fall of 2010, good standing at an accredited genetic counseling training program, and NSGC membership or plans to join in 2011. Students who are from communities underrepresented in the NSGC, including, but not limited to, those of minority cultural/ethnic backgrounds and those with disabilities were eligible to apply for the "Diversity" scholarship. Students from all backgrounds who have an interest in diversity issues were eligible to apply for the "General" scholarship. Applicants wrote essays 1000 words or less answering the following questions: How has your identity as a member of a group underrepresented in the genetic counseling profession affected your pursuit of this career? What do you feel is lacking in genetic counseling to address the issues of underrepresented groups? What strategies do you recommend for addressing these issues and/or increasing diversity? Why do you think diversity is an important issue for the field of genetic counseling? What strategies do you recommend to attract and retain students, especially those from underrepresented populations, into the field of genetic counseling? How do you envision contributing to these strategies? The essays by the award recipients elucidated interesting perspectives and ideas for increasing diversity in the genetic counseling profession.

  9. Mapping genetic and phylogenetic diversity of a temperate forest using remote sensing based upscaling methods

    Science.gov (United States)

    Escriba, C. G.; Yamasaki, E.; Leiterer, R.; Tedder, A.; Shimizu, K.; Morsdorf, F.; Schaepman, M. E.

    2015-12-01

    Functioning and resilience of forest ecosystems under environmental pressures increases when biodiversity at genetic, species, canopy and ecosystem level is higher. Therefore mapping and monitoring diversity becomes a necessity to assess changes in ecosystems and understanding their consequences. Diversity can be assessed by using different metrics, such as diversity of functional traits or genetic diversity amongst others. In-situ approaches have provided useful, but usually spatially constrained information, often dependent on expert knowledge. We propose using remote sensing in combination with in-situ sampling at different spatial scales. We map phylogenetic and genetic diversity using airborne imaging spectroscopy in combination with terrestrial and airborne laser scanning, as well as exhaustive in-situ sampling schemes. To this end, we propose to link leaf optical properties using a taxonomic approach (spectranomics) to genetic and phylogenetic diversity. The test site is a managed mixed temperate forest on the south-facing slope of Laegern Mountain, Switzerland (47°28'42.0" N, 8°21'51.8" E, 682 m.a.s.l.). The intensive sampling area is roughly 300m x 300m and dominant species are European beech (Fagus sylvatica) and Ash (Fraxinus excelsior). We perform phylogenetic and intraspecific genetic variation analyses for the five most dominant tree species at the test site. For these species, information on functional biochemical and architectural plant traits diversity is retrieved from imaging spectroscopy and laser scanning data and validated with laboratory and in-situ measurements. To assess regional-scale genetic diversity, the phylogenetic and genetic signals are quantified using the remote sensing data, resulting in spatially distributed intra-specific genetic variation. We discuss the usefulness of combined remote sensing and in-situ sampling, to bridge diversity scales from genetic to canopy level.

  10. Genomic patterns in Acropora cervicornis show 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.

  11. Environmental factors influence both abundance and genetic diversity in a widespread bird species.

    Science.gov (United States)

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-11-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations.

  12. Environmental factors influence both abundance and genetic diversity in a widespread bird species

    Science.gov (United States)

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-01-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations. PMID:24363897

  13. Development of STS and CAPS markers for variety identification and genetic diversity analysis of tea germplasm in Taiwan.

    Science.gov (United States)

    Hu, Chih-Yi; Tsai, You-Zen; Lin, Shun-Fu

    2014-12-01

    Tea (Camellia sinensis) is an important economic crop in Taiwan. Particularly, two major commercial types of tea (Paochong tea and Oolong tea) which are produced in Taiwan are famous around the world, and they must be manufactured with specific cultivars. Nevertheless, many elite cultivars have been illegally introduced to foreign countries. Because of the lower cost, large amount of "Taiwan-type tea" are produced and imported to Taiwan, causing a dramatic damage in the tea industry. It is very urgent to develop the stable, fast and reliable DNA markers for fingerprinting tea cultivars in Taiwan and protecting intellectual property rights for breeders. Furthermore, genetic diversity and phylogenetic relationship evaluations of tea germplasm in Taiwan are imperative for parental selection in the cross-breeding program and avoidance of genetic vulnerability. Two STS and 37 CAPS markers derived from cytoplasmic genome and ESTs of tea have been developed in this study providing a useful tool for distinguishing all investigated germplasm. For identifying 12 prevailing tea cultivars in Taiwan, five core markers, including each one of mitochondria and chloroplast, and three nuclear markers, were developed. Based on principal coordinate analysis and cluster analysis, 55 tea germplasm in Taiwan were divided into three groups: sinensis type (C. sinensis var. sinensis), assamica type (C. sinensis var. assamica) and Taiwan wild species (C. formosensis). The result of genetic diversity analysis revealed that both sinensis (0.44) and assamica (0.41) types had higher genetic diversity than wild species (0.25). The close genetic distance between the first (Chin-Shin-Oolong) and the third (Shy-Jih-Chuen) prevailing cultivars was found, and many recently released varieties are the descents of Chin-Shin-Oolong. This implies the potential risk of genetic vulnerability for tea cultivation in Taiwan. We have successfully developed a tool for tea germplasm discrimination and genetic

  14. Fire Increases Genetic Diversity of Populations of Six-Lined Racerunner.

    Science.gov (United States)

    Ragsdale, Alexandria K; Frederick, Bridget M; Dukes, David W; Liebl, Andrea L; Ashton, Kyle G; McCoy, Earl D; Mushinsky, Henry R; Schrey, Aaron W

    2016-01-01

    Wildfires are highly variable and can disturb habitats, leading to direct and indirect effects on the genetic characteristics of local populations. Florida scrub is a fire-dependent, highly fragmented, and severely threatened habitat. Understanding the effect of fire on genetic characteristics of the species that use this habitat is critically important. We investigated one such lizard, the Six-lined Racerunner (Aspidoscelis sexlineata), which has a strong preference for open areas. We collected Six-lined Racerunners (n = 154) from 11 sites in Highlands County, FL, and defined 2 time-since-last-fire (TSF) categories: recently burned and long unburned. We screened genetic variation at 6 microsatellites to estimate genetic differentiation and compare genetic diversity among sites to determine the relationship with TSF. A clear pattern exists between genetic diversity and TSF in the absence of strong genetic differentiation. Genetic diversity was greater and inbreeding was lower in sites with more recent TSF, and genetic characteristics had significantly larger variance in long unburned sites compared with more recently burned sites. Our results suggest that fire suppression increases variance in genetic characteristics of the Six-lined Racerunner. More generally, fire may benefit genetic characteristics of some species that use fire-dependent habitats and management efforts for such severely fragmented habitat will be challenged by the presence of multiple species with incompatible fire preferences. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Relationships among walleye population characteristics and genetic diversity in northern Wisconsin Lakes

    Science.gov (United States)

    Waterhouse, Matthew D.; Sloss, Brian L.; Isermann, Daniel A.

    2014-01-01

    The maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age-0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density-dependent factors. An isolation-by-distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic

  16. Heritability and genetic and phenotypic correlations of apple (Malus x domestica) fruit volatiles in a genetically diverse breeding population.

    Science.gov (United States)

    Rowan, Daryl D; Hunt, Martin B; Alspach, Peter A; Whitworth, Claire J; Oraguzie, Nnadozie C

    2009-09-09

    Flavor is an important quality trait of fruit and a target for improvement through plant breeding. Eighty-nine flavor volatiles from 240 apple (Malus domestica) genotypes from a highly diverse breeding population were measured by headspace gas chromatography-mass spectrometry (GC-MS) over 2 years. Heritabilities and phenotypic and genetic correlations were calculated for 23 flavor volatiles. Genetic correlations showed coinheritance of five groups of volatiles, ethyl esters, alcohols and alpha-farnesene, propyl and butyl esters, propanoate and 2-methylbutanoate esters, and acetate esters, consistent with our knowledge of volatile biosynthesis in apple. This work demonstrates a genetic structure underlying the highly variable volatile profiles observed for apple fruit and the potential of GC-MS volatile profiling for the genetic analysis of aroma volatiles in genetically diverse populations.

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

    Directory of Open Access Journals (Sweden)

    Pereira Albano

    2001-05-01

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

  18. Reduction of Genetic Diversity of the Harpy Eagle in Brazilian Tropical Forests.

    Directory of Open Access Journals (Sweden)

    Aureo Banhos

    Full Text Available Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest.

  19. The effect and relative importance of neutral genetic diversity for predicting parasitism varies across parasite taxa.

    Directory of Open Access Journals (Sweden)

    María José Ruiz-López

    Full Text Available Understanding factors that determine heterogeneity in levels of parasitism across individuals is a major challenge in disease ecology. It is known that genetic makeup plays an important role in infection likelihood, but the mechanism remains unclear as does its relative importance when compared to other factors. We analyzed relationships between genetic diversity and macroparasites in outbred, free-ranging populations of raccoons (Procyon lotor. We measured heterozygosity at 14 microsatellite loci and modeled the effects of both multi-locus and single-locus heterozygosity on parasitism using an information theoretic approach and including non-genetic factors that are known to influence the likelihood of parasitism. The association of genetic diversity and parasitism, as well as the relative importance of genetic diversity, differed by parasitic group. Endoparasite species richness was better predicted by a model that included genetic diversity, with the more heterozygous hosts harboring fewer endoparasite species. Genetic diversity was also important in predicting abundance of replete ticks (Dermacentor variabilis. This association fit a curvilinear trend, with hosts that had either high or low levels of heterozygosity harboring fewer parasites than those with intermediate levels. In contrast, genetic diversity was not important in predicting abundance of non-replete ticks and lice (Trichodectes octomaculatus. No strong single-locus effects were observed for either endoparasites or replete ticks. Our results suggest that in outbred populations multi-locus diversity might be important for coping with parasitism. The differences in the relationships between heterozygosity and parasitism for the different parasites suggest that the role of genetic diversity varies with parasite-mediated selective pressures.

  20. Genetic and Epigenetic Changes in Chromosomally Stable and Unstable Progeny of Irradiated Cells

    Energy Technology Data Exchange (ETDEWEB)

    Baulch, Janet E.; Aypar, Umut; Waters, Katrina M.; Yang, Austin; Morgan, William F.

    2014-09-24

    Radiation induced genomic instability is a well-studied phenomenon, the underlying mechanisms of which are poorly understood. Persistent oxidative stress, mitochondrial dysfunction, elevated cytokine levels and epigenetic changes are among the mechanisms invoked in the perpetuation of the phenotype. To determine whether epigenetic aberrations affect genomic instability we measured DNA methylation, mRNA and microRNA (miR) levels in well characterized chromosomally stable and unstable clonally expanded single cell survivors of irradiation. While no changes in DNA methylation were observed for the gene promoters evaluated, increased LINE-1 methylation was observed for two unstable clones (LS12, CS9) and decreased Alu element methylation was observed for the other two unstable clones (115, Fe5.0-8). These relationships also manifested for mRNA and miR expression. mRNA identified for the LS12 and CS9 clones were most similar to each other (261 mRNA), while the 115 and Fe5.0-8 clones were more similar to each other, and surprisingly also similar to the two stable clones, 114 and 118 (286 mRNA among these four clones). Pathway analysis showed enrichment for pathways involved in mitochondrial function and cellular redox, themes routinely invoked in genomic instability. The commonalities between the two subgroups of clones were also observed for miR. The number of miR for which anti-correlated mRNA were identified suggests that these miR exert functional effects in each clone. The results of this study demonstrate significant genetic and epigenetic changes in unstable cells, but similar changes almost equally common in chromosomally stable cells. Possible conclusions might be that the chromosomally stable clones have some other form of instability, or that some of the observed changes represent a sort of radiation signature for and that other changes are related to genomic instability. Irrespective, these findings again suggest that a spectrum of changes both drive genomic