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Sample records for genetic diversity increased

  1. Increased Mitochondrial Genetic Diversity in Persons Infected With Hepatitis C VirusSummary

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    David S. Campo

    2016-09-01

    Full Text Available Background & Aims: The host genetic environment contributes significantly to the outcomes of hepatitis C virus (HCV infection and therapy response, but little is known about any effects of HCV infection on the host beyond any changes related to adaptive immune responses. HCV persistence is associated strongly with mitochondrial dysfunction, with liver mitochondrial DNA (mtDNA genetic diversity linked to disease progression. Methods: We evaluated the genetic diversity of 2 mtDNA genomic regions (hypervariable segments 1 and 2 obtained from sera of 116 persons using next-generation sequencing. Results: Results were as follows: (1 the average diversity among cases with seronegative acute HCV infection was 4.2 times higher than among uninfected controls; (2 the diversity level among cases with chronic HCV infection was 96.1 times higher than among uninfected controls; and (3 the diversity was 23.1 times higher among chronic than acute cases. In 2 patients who were followed up during combined interferon and ribavirin therapy, mtDNA nucleotide diversity decreased dramatically after the completion of therapy in both patients: by 100% in patient A after 54 days and by 70.51% in patient B after 76 days. Conclusions: HCV infection strongly affects mtDNA genetic diversity. A rapid decrease in mtDNA genetic diversity observed after therapy-induced HCV clearance suggests that the effect is reversible, emphasizing dynamic genetic relationships between HCV and mitochondria. The level of mtDNA nucleotide diversity can be used to discriminate recent from past infections, which should facilitate the detection of recent transmission events and thus help identify modes of transmission. Keywords: Disease Biomarkers, mtDNA, Noninvasive

  2. Rapid Increase of Genetically Diverse Methicillin-Resistant Staphylococcus aureus, Copenhagen, Denmark

    DEFF Research Database (Denmark)

    Bartels, Mette Damkjær; Boye, Kit; Larsen, Anders Rhod

    2007-01-01

    In Copenhagen, methicillin-resistant Staphylococcus aureus (MRSA) accounted for <15 isolates per year during 1980-2002. However, since 2003 an epidemic increase has been observed, with 33 MRSA cases in 2003 and 110 in 2004. We analyzed these 143 cases epidemiologically and characterized isolates ...... and soft tissue infections dominated. CO-MRSA with diverse genetic backgrounds is rapidly emerging in a low MRSA prevalence area. Udgivelsesdato: October...

  3. Genetic diversity within honeybee colonies increases signal production by waggle-dancing foragers

    Science.gov (United States)

    Mattila, Heather R; Burke, Kelly M; Seeley, Thomas D

    2008-01-01

    Recent work has demonstrated considerable benefits of intracolonial genetic diversity for the productivity of honeybee colonies: single-patriline colonies have depressed foraging rates, smaller food stores and slower weight gain relative to multiple-patriline colonies. We explored whether differences in the use of foraging-related communication behaviour (waggle dances and shaking signals) underlie differences in foraging effort of genetically diverse and genetically uniform colonies. We created three pairs of colonies; each pair had one colony headed by a multiply mated queen (inseminated by 15 drones) and one colony headed by a singly mated queen. For each pair, we monitored the production of foraging-related signals over the course of 3 days. Foragers in genetically diverse colonies had substantially more information available to them about food resources than foragers in uniform colonies. On average, in genetically diverse colonies compared with genetically uniform colonies, 36% more waggle dances were identified daily, dancers performed 62% more waggle runs per dance, foragers reported food discoveries that were farther from the nest and 91% more shaking signals were exchanged among workers each morning prior to foraging. Extreme polyandry by honeybee queens enhances the production of worker–worker communication signals that facilitate the swift discovery and exploitation of food resources. PMID:18198143

  4. Population genetic diversity and fitness in multiple environments

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    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

  5. Investigation of wild species potential to increase genetic diversity useful for apple breeding

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    Dan Catalina

    2015-01-01

    Full Text Available The potential of testing new apple cultivars and the possibility to induce valuable traits is directly dependent on the availability of sufficient genetic diversity, while apple breeding has narrowed the genetic ground of commercial cultivars. Wild species were studied in regard to their influence upon progenies and their capacity to enlarge apple genetic diversity. The interspecific seedlings were framed in five biparental mating (paired crosses, in which Malus species were crossed with different cultivars, obtaining half-sib families. The number of F1 progenies per combination varied from 31 (Cluj 218/2 × M. floribunda up to 142 (Reinette Baumann × M. floribunda, with a total of 1650 hybrids F1. The influences upon vigour and juvenile period and possible correlation among fruit size and taste were analyzed. Juvenile period varied from 6.00 (M. zumi × Jonathan to 9.31 years (Cluj 218/2 × M. floribunda. Data based on correlation coefficient illustrated that the fructification year was not influenced by the vigour of trees. The highest value of correlation for fruit’s size and taste was obtained among M. coronaria hybrids. This result might suggest that once the fruit are larger, there is a high chance the taste is also more appreciative and fruit quality for mouth feels increase. Depending on the parental formula, additive effects may be inferior compared to genetic effects of dominance and epistasis. Although M. zumi and M. floribunda achieved the same genetic gain (0.31, M. zumi had a higher expected selection response for fruit size. The difficulty of obtaining seedlings with tasty and large fruit when wild Malus species are used as genitors is resulting from the values of expected selection response data, but in the same time results confirm that wild Malus species are suitable resources for genetic variability, both for dessert and ornamental apple cultivars.

  6. Increased extinction potential of insular fish populations with reduced life history variation and low genetic diversity.

    Science.gov (United States)

    Hellmair, Michael; Kinziger, Andrew P

    2014-01-01

    Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi), show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species.

  7. Increased extinction potential of insular fish populations with reduced life history variation and low genetic diversity.

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    Michael Hellmair

    Full Text Available Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi, show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species.

  8. High and distinct range-edge genetic diversity despite local bottlenecks.

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    Jorge Assis

    Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

  9. Human impacts on genetic diversity in forest ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Ledig, F T [Inst. of Forest Genetics, Southwest Forest and Range Experiment Station, USDA Forest Service, Berkeley (US)

    1992-01-01

    Humans have converted forest to agricultural and urban uses, exploited species, fragmented wildlands, changed the demographic structure of forests, altered habitat, degraded the environment with atmospheric and soil pollutants, introduced exotic pests and competitors, and domesticated favored species. None of these activities is new; perhaps with the exception of atmospheric pollution, they date back to prehistory. All have impacted genetic diversity by their influence on the evolutionary processes of extinction, selection, drift, gene flow, and mutation, sometimes increasing diversity, as int he case of domestication, but often reducing it. Even in the absence of changes in diversity, mating systems were altered, changing the genetic structure of populations. Demographic changes influenced selection by increasing the incidence of disease. Introduction of exotic diseases, insects, mammalian herbivores, and competing vegetation has had the best-documented effects on genetic diversity, reducing both species diversity and intraspecific diversity. Deforestation has operated on a vast scale to reduce diversity by direct elimination of locally-adapted populations. Atmospheric pollution and global warming will be a major threat in the near future, particularly because forests are fragmented and migration is impeded. Past impacts can be estimated with reference to expert knowledge, but hard data are often laching. Baselines are needed to quantify future impacts and provide an early warning of problems. Genetic inventories of indicator species can provide the baselines against which to measure changes in diversity. (author) (44 refs.).

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

    DEFF Research Database (Denmark)

    Hughes, William Owen Hamar; Boomsma, Jacobus Jan

    2006-01-01

    of host genetic diversity on parasite evolution by carrying out serial passages of a virulent fungal pathogen through leaf-cutting ant workers of known genotypes. Parasite virulence increased over the nine-generation span of the experiment while spore production decreased. The effect of host relatedness...... upon virulence appeared limited. However, parasites cycled through more genetically diverse hosts were more likely to go extinct during the experiment and parasites cycled through more genetically similar hosts had greater spore production. These results indicate that host genetic diversity may indeed...

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

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    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.

  12. Do species conservation assessments capture genetic diversity?

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    Malin C. Rivers

    2014-12-01

    Full Text Available The best known system for classifying threat status of species, the IUCN Red List, currently lacks explicit considerations of genetic diversity, and consequently may not account for potential adaptation of species to future environmental change. To address this gap, we integrate range-wide genetic analysis with IUCN Red List assessments.We calculated the loss of genetic diversity under simulated range loss for species of Delonix (Leguminosae. Simulated range loss involved random loss of populations and was intended to model ongoing habitat destruction. We found a strong relationship between loss of genetic diversity and range. Moreover, we found correspondence between levels of genetic diversity and thresholds for ‘non-threatened’ versus ‘threatened’ IUCN Red List categories.Our results support the view that current threat thresholds of the IUCN Red List criteria reflect genetic diversity, and hence evolutionary potential; although the genetic diversity distinction between threatened categories was less evident. Thus, by supplementing conventional conservation assessments with genetic data, new insights into the biological robustness of IUCN Red List assessments for targeted conservation initiatives can be achieved. Keywords: Conservation assessment, Conservation genetics, Extinction risk, Genetic diversity, IUCN Red List, Range

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

    Science.gov (United States)

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

    2009-01-01

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

  14. Personalized medicine and human genetic diversity.

    Science.gov (United States)

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

    2014-07-24

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

  15. Reduced Genetic Diversity and Increased Structure in American Mink on the Swedish Coast following Invasive Species Control.

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    Zalewski, Andrzej; Zalewska, Hanna; Lunneryd, Sven-Gunnar; André, Carl; Mikusiński, Grzegorz

    2016-01-01

    Eradication and population reductions are often used to mitigate the negative impacts of non-native invasive species on native biodiversity. However, monitoring the effectiveness of non-native species control programmes is necessary to evaluate the efficacy of these measures. Genetic monitoring could provide valuable insights into temporal changes in demographic, ecological, and evolutionary processes in invasive populations being subject to control programmes. Such programmes should cause a decrease in effective population size and/or in genetic diversity of the targeted non-native species and an increase in population genetic structuring over time. We used microsatellite DNA data from American mink (Neovison vison) to determine whether the removal of this predator on the Koster Islands archipelago and the nearby Swedish mainland affected genetic variation over six consecutive years of mink culling by trappers as part of a population control programme. We found that on Koster Islands allelic richness decreased (from on average 4.53 to 3.55), genetic structuring increased, and effective population size did not change. In contrast, the mink population from the Swedish coast showed no changes in genetic diversity or structure, suggesting the stability of this population over 6 years of culling. Effective population size did not change over time but was higher on the coast than on the islands across all years. Migration rates from the islands to the coast were almost two times higher than from the coast to the islands. Most migrants leaving the coast were localised on the southern edge of the archipelago, as expected from the direction of the sea current between the two sites. Genetic monitoring provided valuable information on temporal changes in the population of American mink suggesting that this approach can be used to evaluate and improve control programmes of invasive vertebrates.

  16. Reduced Genetic Diversity and Increased Structure in American Mink on the Swedish Coast following Invasive Species Control.

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    Andrzej Zalewski

    Full Text Available Eradication and population reductions are often used to mitigate the negative impacts of non-native invasive species on native biodiversity. However, monitoring the effectiveness of non-native species control programmes is necessary to evaluate the efficacy of these measures. Genetic monitoring could provide valuable insights into temporal changes in demographic, ecological, and evolutionary processes in invasive populations being subject to control programmes. Such programmes should cause a decrease in effective population size and/or in genetic diversity of the targeted non-native species and an increase in population genetic structuring over time. We used microsatellite DNA data from American mink (Neovison vison to determine whether the removal of this predator on the Koster Islands archipelago and the nearby Swedish mainland affected genetic variation over six consecutive years of mink culling by trappers as part of a population control programme. We found that on Koster Islands allelic richness decreased (from on average 4.53 to 3.55, genetic structuring increased, and effective population size did not change. In contrast, the mink population from the Swedish coast showed no changes in genetic diversity or structure, suggesting the stability of this population over 6 years of culling. Effective population size did not change over time but was higher on the coast than on the islands across all years. Migration rates from the islands to the coast were almost two times higher than from the coast to the islands. Most migrants leaving the coast were localised on the southern edge of the archipelago, as expected from the direction of the sea current between the two sites. Genetic monitoring provided valuable information on temporal changes in the population of American mink suggesting that this approach can be used to evaluate and improve control programmes of invasive vertebrates.

  17. 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

  18. Evaluating human genetic diversity

    National Research Council Canada - National Science Library

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

  19. Genetic diversity of a Daugava basin brown trout (Salmo trutta brood stock

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    Schmidt Thomas

    2017-01-01

    Full Text Available Genetics play an increasingly important role in the conservation of threatened fish populations. We have examined twelve microsatellite markers to determine the genetic diversity of a brood stock of brown trout from the Latvian Daugava river basin, used in a local supportive breeding program and compared diversity values to other Baltic populations. Allelic data was further inspected for indications of increased inbreeding. Additionally, we have analyzed the mitochondrial control region to classify the population within a broader phylogenetic framework. We found that the genetic diversity was comparatively low, but there was no strong evidence of high inbreeding. A newly detected mitochondrial haplotype indicates unnoticed genetic diversity of “Atlantic lineage” brown trout in the Daugava basin region. Our study provides first genetic details on resident brown trout from the Baltic Daugava river basin to improve the regional conservation management of this valuable genetic resource and contributes phylogeographically useful information.

  20. Genetic diversity among endangered rare Dalbergia cochinchinensis

    African Journals Online (AJOL)

    hocvan

    Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy for Science and ... Genetic diversity of the 35 genotypes of D. cochinchinensis species were evaluated by ...... Dalbergia genus at the population level of genetic .... Population genetic software for teaching and research.

  1. Increased Virulence in Sunflower Broomrape (Orobanche cumana Wallr.) Populations from Southern Spain Is Associated with Greater Genetic Diversity.

    Science.gov (United States)

    Martín-Sanz, Alberto; Malek, Jebri; Fernández-Martínez, José M; Pérez-Vich, Begoña; Velasco, Leonardo

    2016-01-01

    Orobanche cumana Wallr. (sunflower broomrape) is a holoparasitic weed that infects roots of sunflower in large areas of Europe and Asia. Two distant O. cumana gene pools have been identified in Spain, one in Cuenca province in the Center and another one in the Guadalquivir Valley in the South. Race F has been hypothesized to have arisen by separate mutational events in both gene pools. In the Guadalquivir Valley, race F spread in the middle 1990's to become predominant and contained so far with race F hybrids. Recently, enhanced virulent populations of O. cumana have been observed in commercial fields parasitizing race F resistant hybrids. From them, we collected four independent populations and conducted virulence and SSR marker-based genetic diversity analysis. Virulence essays confirmed that the four populations studied can parasitize most of the race F resistant hybrids tested, but they cannot parasitize the differential inbred lines DEB-2, carrying resistance to race F and G, and P-96, resistant to F but susceptible to races G from other countries. Accordingly, the new populations have been classified as race GGV to distinguish them from other races G. Cluster analysis with a set of populations from the two Spanish gene pools and from other areas, mainly Eastern Europe, confirmed that race GGV populations maintain close genetic relatedness with the Guadalquivir Valley gene pool. This suggested that increased virulence was not caused by new introductions from other countries. Genetic diversity parameters revealed that the four populations had much greater genetic diversity than conventional populations of the same area, containing only alleles present in the Guadalquivir Valley and Cuenca gene pools. The results suggested that increased virulence may have resulted from admixture of populations from the Guadalquivir Valley and Cuenca followed by recombination of avirulence genes.

  2. Increased Virulence in Sunflower Broomrape (Orobanche cumana Wallr. Populations from Southern Spain is Associated with Greater Genetic Diversity

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    Alberto eMartín-Sanz

    2016-05-01

    Full Text Available Orobanche cumana Wallr. (sunflower broomrape is a holoparasitic weed that infects roots of sunflower in large areas of Europe and Asia. Two distant O. cumana gene pools have been identified in Spain, one in Cuenca province in the Centre and another one in the Guadalquivir Valley in the South. Race F has been hypothesized to have arisen by separate mutational events in both gene pools. In the Guadalquivir Valley, race F spread in the middle 1990’s to become predominant and contained so far with race F hybrids. Recently, enhanced virulent populations of O. cumana have been observed in commercial fields parasitizing race F resistant hybrids. From them, we collected four independent populations and conducted virulence and SSR marker-based genetic diversity analysis. Virulence essays confirmed that the four populations studied can parasitize most of the race F resistant hybrids tested, but they cannot parasitize the differential inbred lines DEB-2, carrying resistance to race F and G and, and P-96, resistant to F but susceptible to races G from other countries. Accordingly, the new populations have been classified as race GGV to distinguish them from other races G. Cluster analysis with a set of populations from the two Spanish gene pools and from other areas, mainly Eastern Europe, confirmed that race GGV populations maintain close genetic relatedness with the Guadalquivir Valley gene pool. This suggested that increased virulence was not caused by new introductions from other countries. Genetic diversity parameters revealed that the four populations had much greater genetic diversity than conventional populations of the same area, containing only alleles present in the Guadalquivir Valley and Cuenca gene pools. The results suggested that increased virulence may have resulted from admixture of populations from the Guadalquivir Valley and Cuenca followed by recombination of avirulence genes.

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

    African Journals Online (AJOL)

    sunny t

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

  4. 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.

  5. Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection.

    Science.gov (United States)

    Daetwyler, Hans D; Hayden, Matthew J; Spangenberg, German C; Hayes, Ben J

    2015-08-01

    Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations. Copyright © 2015 by the Genetics Society of America.

  6. Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community.

    Science.gov (United States)

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species

  7. 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 ...

  8. 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.

  9. Assessing Genetic Diversity after Mangrove Restoration in Brazil: Why Is It So Important?

    Directory of Open Access Journals (Sweden)

    Renan Granado

    2018-04-01

    Full Text Available Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic diversity distribution among natural populations. Moreover, while restoration efforts have increased, few studies have analyzed how recently-planted areas impact the original mangrove genetic diversity. We analyzed the genetic diversity of two mangroves species (Laguncularia racemosa and Avicennia schaueriana in three areas in Brazil, using inter-simple sequence repeat (ISSR markers. Using the local approach, we identified the genetic diversity pool of a restored area compared to nearby areas, including the remnant plants inside the restored area, one well-conserved population at the shore of Guanabara Bay, and one impacted population in Araçá Bay. The results for L. racemosa showed that the introduced population has lost genetic diversity by drift, but remnant plants with high genetic diversity or incoming propagules could help improve overall genetic diversity. Avicennia schaueriana showed similar genetic diversity, indicating an efficient gene flow. The principal component analysis showing different connections between both species indicate differences in gene flow and dispersal efficiencies, highlighting the needed for further studies. Our results emphasize that genetic diversity knowledge and monitoring associated with restoration actions can help avoid bottlenecks and other pitfalls, especially for the mangrove ecosystem.

  10. The influence of recombination on human genetic diversity.

    Directory of Open Access Journals (Sweden)

    Chris C A Spencer

    2006-09-01

    Full Text Available In humans, the rate of recombination, as measured on the megabase scale, is positively associated with the level of genetic variation, as measured at the genic scale. Despite considerable debate, it is not clear whether these factors are causally linked or, if they are, whether this is driven by the repeated action of adaptive evolution or molecular processes such as double-strand break formation and mismatch repair. We introduce three innovations to the analysis of recombination and diversity: fine-scale genetic maps estimated from genotype experiments that identify recombination hotspots at the kilobase scale, analysis of an entire human chromosome, and the use of wavelet techniques to identify correlations acting at different scales. We show that recombination influences genetic diversity only at the level of recombination hotspots. Hotspots are also associated with local increases in GC content and the relative frequency of GC-increasing mutations but have no effect on substitution rates. Broad-scale association between recombination and diversity is explained through covariance of both factors with base composition. To our knowledge, these results are the first evidence of a direct and local influence of recombination hotspots on genetic variation and the fate of individual mutations. However, that hotspots have no influence on substitution rates suggests that they are too ephemeral on an evolutionary time scale to have a strong influence on broader scale patterns of base composition and long-term molecular evolution.

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

    Indian Academy of Sciences (India)

    Abdulhakeem B. Ajibike

    2017-12-11

    Dec 11, 2017 ... RESEARCH ARTICLE. Genetic diversity, phylogeographic ... chickens as genetic resources towards ensuring food security. Keywords. genetic diversity ... PCR product as template DNA, 3.2 pmol of primer and. 8 μL of Big Dye ...

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

    Science.gov (United States)

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

    2013-05-01

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

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

    International Nuclear Information System (INIS)

    Kumar, V.; Bhagwat, S.G.

    2011-01-01

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

  14. 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.

  15. 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.

  16. Global change and genetic diversity

    International Nuclear Information System (INIS)

    Kremer, Antoine

    2000-01-01

    Are there grounds for concern as to the impact of global change on the future of European forests? This question is approached from the genetic angle, considering the modifications produced by climate change on the diversity and adaptive potential of forest species. In the absence of experimental data, the answers are derived from a set of arguments based on knowledge of evolutionary mechanisms involved in genetic diversity, the post-glacial history of European forests and lessons drawn from recent introductions of foreign wood species. These arguments entail less pessimistic conclusions than those generally reached for consequences attributed to global change. Even if major changes in composition could occur, past events show that genetic erosion capable of challenging the adaptive potential of species is unlikely. (author)

  17. 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 ...

  18. Evaluating human genetic diversity

    National Research Council Canada - National Science Library

    ... into human evolution and origins and serving as a springboard for important medical research. It also addresses issues of confidentiality and individual privacy for participants in genetic diversity research studies.

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

    African Journals Online (AJOL)

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

  20. 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

  1. Paradox of Genetic Diversity in the Case of Prionic Diseases in Sheep Breeds from Romania

    Directory of Open Access Journals (Sweden)

    Gheorghe Hrinca

    2016-05-01

    Full Text Available The main target of this debate is the revaluation of the biodiversity concept and especially of its significance in the animal husbandry field. The paper analyzes the genetic diversity at the determinant locus of scrapie (PrP in the sheep breeds from Romania: Palas Merino, Tsigai, Tsurcana, Botosani Karakul, Palas Meat Breed and Palas Milk Breed. The prionic genetic diversity (d has been quantified by means of informational energy (e. This study highlights the impact of increasing the genetic diversity from the PrP locus level on the health status of ovine species and especially on human food safety. The informational statistics processing shows that the resistance / susceptibility to scrapie is in relation to the degree of prionic genetic diversity. The limitation of genetic diversity by selecting the individuals possessing the ARR allele in both homozygous status and in combination with alleles ARQ, ARH AHQ confers to sheep herds certain levels of resistance to contamination with scrapie disease. Instead, promoting to reproduction also individuals possessing the VRQ allele in all possible genotypic combinations (including ARR allele increases genetic diversity but also has as effect increasing the susceptibility of sheep to prion disease onset. From the point of view of morbid phenomenon, the Botosani Karakul breed is clearly advantaged compared to all other indigenous sheep breeds from Romania. For methodological coherency in the interpretative context of this issue, the genetic diversity was analyzed in association with the heterozygosity degree of breeds and their Hardy-Weinberg genetic equilibrium at the PrP locus level. Finally, the paper refers to decisions that the improvers must take to achieve the genetic prophylaxis in the scrapie case taking into account the polymorphism degree of prion protein.

  2. Genetic diversity in wheat germplasm collections from Balochistan province of Pakistan

    International Nuclear Information System (INIS)

    Khan, A.A.; Iqbal, A.; Awan, F.S.; Khan, I.A.

    2010-01-01

    Productivity of wheat varieties being bred for the last many years is stagnant in Pakistan, apparently because of the narrowed genetic base of their parental lines. As a part of the national wheat germplasm characterization programme, we examined genetic diversity among 75 accessions of wheat using RAPD markers and assessed the relationship and genetic distance between them. The accessions surveyed were comprised of land race populations of Triticum aestivum L., collected from various districts of the Balochistan province of Pakistan, which is considered a reservoir of genetic diversity, particularly for wheat. The genetic similarity revealed by RAPD markers among the wheat accessions was medium to high. The accessions collected from Sibi and Pishin districts had the greatest similarity. The polymorphism revealed in the wheat accessions, appeared to be distributed with the location of collections. The high degree of similarity even among the presumably land race material emphasizes the need for the expansion of germplasm resources and development of wheat varieties with diverse genetic background, which could substantiate the wheat breeding programmes to increase its productivity. (author)

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

    Science.gov (United States)

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

    2009-09-01

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

  4. Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes.

    Science.gov (United States)

    Osborne, Megan J; Perkin, Joshuah S; Gido, Keith B; Turner, Thomas F

    2014-12-01

    We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic-spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most tributary basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and in response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage. © 2014 John Wiley & Sons Ltd.

  5. Does genetic diversity predict health in humans?

    Directory of Open Access Journals (Sweden)

    Hanne C Lie

    2009-07-01

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

  6. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography.

    Directory of Open Access Journals (Sweden)

    Ruth Hershberg

    2008-12-01

    Full Text Available Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC. However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis.

  7. Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

    Science.gov (United States)

    Brekke, Thomas D.; Steele, Katherine A.; Mulley, John F.

    2017-01-01

    Nonmodel rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift; so they may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly “outbred” colonies of nonmodel rodents (gerbils, hamsters, house mice, deer mice, and rats) varies considerably from nearly no segregating diversity to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the “replication crisis.” In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other genetically distinct individuals to explore the genetic basis of a trait. PMID:29242387

  8. 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.

  9. 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

    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...

  10. The role of propagule pressure, genetic diversity and microsite availability for Senecio vernalis invasion.

    Directory of Open Access Journals (Sweden)

    Alexandra Erfmeier

    Full Text Available Genetic diversity is supposed to support the colonization success of expanding species, in particular in situations where microsite availability is constrained. Addressing the role of genetic diversity in plant invasion experimentally requires its manipulation independent of propagule pressure. To assess the relative importance of these components for the invasion of Senecio vernalis, we created propagule mixtures of four levels of genotype diversity by combining seeds across remote populations, across proximate populations, within single populations and within seed families. In a first container experiment with constant Festuca rupicola density as matrix, genotype diversity was crossed with three levels of seed density. In a second experiment, we tested for effects of establishment limitation and genotype diversity by manipulating Festuca densities. Increasing genetic diversity had no effects on abundance and biomass of S. vernalis but positively affected the proportion of large individuals to small individuals. Mixtures composed from proximate populations had a significantly higher proportion of large individuals than mixtures composed from within seed families only. High propagule pressure increased emergence and establishment of S. vernalis but had no effect on individual growth performance. Establishment was favoured in containers with Festuca, but performance of surviving seedlings was higher in open soil treatments. For S. vernalis invasion, we found a shift in driving factors from density dependence to effects of genetic diversity across life stages. While initial abundance was mostly linked to the amount of seed input, genetic diversity, in contrast, affected later stages of colonization probably via sampling effects and seemed to contribute to filtering the genotypes that finally grew up. In consequence, when disentangling the mechanistic relationships of genetic diversity, seed density and microsite limitation in colonization of

  11. The role of propagule pressure, genetic diversity and microsite availability for Senecio vernalis invasion.

    Science.gov (United States)

    Erfmeier, Alexandra; Hantsch, Lydia; Bruelheide, Helge

    2013-01-01

    Genetic diversity is supposed to support the colonization success of expanding species, in particular in situations where microsite availability is constrained. Addressing the role of genetic diversity in plant invasion experimentally requires its manipulation independent of propagule pressure. To assess the relative importance of these components for the invasion of Senecio vernalis, we created propagule mixtures of four levels of genotype diversity by combining seeds across remote populations, across proximate populations, within single populations and within seed families. In a first container experiment with constant Festuca rupicola density as matrix, genotype diversity was crossed with three levels of seed density. In a second experiment, we tested for effects of establishment limitation and genotype diversity by manipulating Festuca densities. Increasing genetic diversity had no effects on abundance and biomass of S. vernalis but positively affected the proportion of large individuals to small individuals. Mixtures composed from proximate populations had a significantly higher proportion of large individuals than mixtures composed from within seed families only. High propagule pressure increased emergence and establishment of S. vernalis but had no effect on individual growth performance. Establishment was favoured in containers with Festuca, but performance of surviving seedlings was higher in open soil treatments. For S. vernalis invasion, we found a shift in driving factors from density dependence to effects of genetic diversity across life stages. While initial abundance was mostly linked to the amount of seed input, genetic diversity, in contrast, affected later stages of colonization probably via sampling effects and seemed to contribute to filtering the genotypes that finally grew up. In consequence, when disentangling the mechanistic relationships of genetic diversity, seed density and microsite limitation in colonization of invasive plants, a clear

  12. Genetic diversity in wild populations of Paulownia fortune.

    Science.gov (United States)

    Li, H Y; Ru, G X; Zhang, J; Lu, Y Y

    2014-11-01

    The genetic diversities of 16 Paulownia fortunei populations involving 143 individuals collected from 6 provinces in China were analyzed using amplified fragment length polymorphism (AFLP). A total of 9 primer pairs with 1169 polymorphic loci were screened out, and each pair possessed 132 bands on average. The percentage of polymorphic bands (98.57%), the effective number of alleles (1.2138-1.2726), Nei's genetic diversity (0.1566-0.1887), and Shannon's information index (0.2692-0.3117) indicated a plentiful genetic diversity and different among Paulownia fortunei populations. The genetic differentiation coefficient between populations was 0.2386, while the gene flow was 1.0954, and the low gene exchange promoted genetic differentiation. Analysis of variance indicated that genetic variation mainly occurred within populations (81.62% of total variation) rather than among populations (18.38%). The 16 populations were divided by unweighted pair-group method with arithmetic means (UPGMA) into 4 groups with obvious regionalism, in which the populations with close geographical locations (latitude) were clustered together.

  13. Conserving genetic diversity in the honeybee: comments on Harpur et al. (2012).

    Science.gov (United States)

    De la Rúa, Pilar; Jaffé, Rodolfo; Muñoz, Irene; Serrano, José; Moritz, Robin F A; Kraus, F Bernhard

    2013-06-01

    The article by Harpur et al. (2012) 'Management increases genetic diversity of honey bees via admixture' concludes that '…honey bees do not suffer from reduced genetic diversity caused by management and, consequently, that reduced genetic diversity is probably not contributing to declines of managed Apis mellifera populations'. In the light of current honeybee and beekeeping declines and their consequences for honeybee conservation and the pollination services they provide, we would like to express our concern about the conclusions drawn from the results of Harpur et al. (2012). While many honeybee management practices do not imply admixture, we are convinced that the large-scale genetic homogenization of admixed populations could drive the loss of valuable local adaptations. We also point out that the authors did not account for the extensive gene flow that occurs between managed and wild/feral honeybee populations and raise concerns about the data set used. Finally, we caution against underestimating the importance of genetic diversity for honeybee colonies and highlight the importance of promoting the use of endemic honeybee subspecies in apiculture. © 2013 John Wiley & Sons Ltd.

  14. 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 ...

  15. Using genomic information to conserve genetic diversity in livestock

    NARCIS (Netherlands)

    Eynard, Sonia E.

    2018-01-01

    Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of

  16. Genetic diversity of Colombian sheep by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Ricardo Ocampo

    2016-03-01

    Full Text Available In Colombia the sheep production systems are managed under extensive conditions and mainly correspond to peasant production systems so their genetic management has led to increased homozygosity and hence productivity loss. The aim of this study was to determine the genetic diversity in 549 individuals corresponding to 13 sheep breeds in Colombia, using a panel of 11 microsatellite molecular markers. One hundred and fifty seven alleles were found (average of 14.27 alleles/locus, with a range of observed and expected heterozygosity from 0.44 to 0.84 and 0.67 to 0.86, respectively. Thirty-three of 143 Hardy Weinberg tests performed showed significant deviations (p < 0.05 due to a general lack of heterozygous individuals. The Fis ranged from 0.01 in Corriedale to 0.15 for the Persian Black Head breed, suggesting that there are presenting low to moderate levels of inbreeding. Overall, Colombian sheep showed high levels of genetic diversity which is very important for future selection and animal breeding programs.

  17. 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, ...

  18. SSR-based genetic diversity and structure of garlic accessions from Brazil.

    Science.gov (United States)

    da Cunha, Camila Pinto; Resende, Francisco Vilela; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2014-10-01

    Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

  19. 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.

  20. Implications of recurrent disturbance for genetic diversity.

    Science.gov (United States)

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

    2016-02-01

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

  1. Increase in density of genetically diverse invasive Asian shore crab (Hemigrapsus sanguineus) populations in the Gulf of Maine.

    Science.gov (United States)

    Lord, Joshua P; Williams, Larissa M

    2017-04-01

    Hemigrapsus sanguineus , the Asian shore crab, has rapidly replaced Carcinus maenas , the green crab, as the most abundant crab on rocky shores in the northwest Atlantic since its introduction to the United States (USA) in 1988. The northern edge of this progressing invasion is the Gulf of Maine, where Asian shore crabs are only abundant in the south. We compared H. sanguineus population densities to those from published 2005 surveys and quantified genetic variation using the cytochrome c oxidase subunit I gene. We found that the range of H. sanguineus had extended northward since 2005, that population density had increased substantially (at least 10-fold at all sites), and that Asian shore crabs had become the dominant intertidal crab species in New Hampshire and southern Maine. Despite the significant increase in population density of H. sanguineus , populations only increased by a factor of 14 in Maine compared to 70 in southern New England, possibly due to cooler temperatures in the Gulf of Maine. Genetically, populations were predominantly composed of a single haplotype of Japanese, Korean, or Taiwanese origin, although an additional seven haplotypes were found. Six of these haplotypes were of Asian origin, while two are newly described. Large increases in population sizes of genetically diverse individuals in Maine will likely have a large ecological impact, causing a reduction in populations of mussels, barnacles, snails, and other crabs, similar to what has occurred at southern sites with large populations of this invasive crab species.

  2. Assessment of the genetic diversity and pattern of relationship of ...

    African Journals Online (AJOL)

    An understanding of the extent, distribution and patterns of genetic variation is useful for estimation of any possible loss of genetic diversity and assessment of genetic variability and its potential use in breeding programs, including establishment of heterotic groups. This study assessed patterns of genetic diversity and ...

  3. 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 ...

  4. Catastrophic floods may pave the way for increased genetic diversity in endemic artesian spring snail populations.

    Directory of Open Access Journals (Sweden)

    Jessica Worthington Wilmer

    Full Text Available The role of disturbance in the promotion of biological heterogeneity is widely recognised and occurs at a variety of ecological and evolutionary scales. However, within species, the impact of disturbances that decimate populations are neither predicted nor known to result in conditions that promote genetic diversity. Directly examining the population genetic consequences of catastrophic disturbances however, is rarely possible, as it requires both longitudinal genetic data sets and serendipitous timing. Our long-term study of the endemic aquatic invertebrates of the artesian spring ecosystem of arid central Australia has presented such an opportunity. Here we show a catastrophic flood event, which caused a near total population crash in an aquatic snail species (Fonscochlea accepta endemic to this ecosystem, may have led to enhanced levels of within species genetic diversity. Analyses of individuals sampled and genotyped from the same springs sampled both pre (1988-1990 and post (1995, 2002-2006 a devastating flood event in 1992, revealed significantly higher allelic richness, reduced temporal population structuring and greater effective population sizes in nearly all post flood populations. Our results suggest that the response of individual species to disturbance and severe population bottlenecks is likely to be highly idiosyncratic and may depend on both their ecology (whether they are resilient or resistant to disturbance and the stability of the environmental conditions (i.e. frequency and intensity of disturbances in which they have evolved.

  5. sGD: software for estimating spatially explicit indices of genetic diversity.

    Science.gov (United States)

    Shirk, A J; Cushman, S A

    2011-09-01

    Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans. © 2011 Blackwell Publishing Ltd.

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

    African Journals Online (AJOL)

    Genetic diversity and population structure of maize landraces from Côte ... However, no study on the genetic diversity of the species has been performed to date. ... The cross between two individuals from different groups might help exploit the ...

  7. Genetic Diversity of Turf-Type Tall Fescue Using Diversity Arrays Technology

    Czech Academy of Sciences Publication Activity Database

    Baird, J. H.; Kopecký, David; Lukaszewski, A.J.; Green, R. J.; Bartoš, Jan; Doležel, Jaroslav

    2012-01-01

    Roč. 52, č. 1 (2012), s. 408-412 ISSN 0011-183X Institutional research plan: CEZ:AV0Z50380511 Keywords : Festuca arundinacea * Diversity Arrays Technology (DArT) * Low genetic polymorphism Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.513, year: 2012

  8. Genetic diversity, population structure, and traditional culture of Camellia reticulata.

    Science.gov (United States)

    Xin, Tong; Huang, Weijuan; De Riek, Jan; Zhang, Shuang; Ahmed, Selena; Van Huylenbroeck, Johan; Long, Chunlin

    2017-11-01

    Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material ( n  = 190 individuals) from five populations at study sites using single-dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species ( H sp  = 0.3397, I sp  = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop  = 0.2937, I pop  = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio-economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

  9. Bovine viral diarrhea virus (BVDV) genetic diversity in Spain: A review

    International Nuclear Information System (INIS)

    Diéguez, F.J.; Cerviño, M.; Yus, E.

    2017-01-01

    Bovine viral diarrhea virus (BVDV), a member of the genus Pestivirus of the family Flaviviridae, causes significant losses in cattle farming worldwide because of reduced milk production, increased mortality of young animals and reproductive, respiratory and intestinal problems. The virus is characterized by an important genetic, and consequently antigenic and pathogenic diversity. Knowing the variability of viral strains present in a population provides valuable information, particularly relevant for control programs development, vaccination recommendations and even identification of likely infection sources. Such information is therefore important at both local and regional levels. This review focuses on the genetic diversity of BVDV isolates infecting cattle in Spain over the last years. According to the published data, the most prevalent BVDV group in Spain was 1b, and to a lesser extent 1d, 1e and 1f. Besides, BVDV-2 has also been found in Spain with several ratified isolates. The studies carried out in Spain also showed increased genetic heterogeneity of BVDV strains, possibly due to a more intensive use of analytical tools available, presenting studies with increasingly greater sample sizes.

  10. Bovine viral diarrhea virus (BVDV) genetic diversity in Spain: A review

    Energy Technology Data Exchange (ETDEWEB)

    Diéguez, F.J.; Cerviño, M.; Yus, E.

    2017-07-01

    Bovine viral diarrhea virus (BVDV), a member of the genus Pestivirus of the family Flaviviridae, causes significant losses in cattle farming worldwide because of reduced milk production, increased mortality of young animals and reproductive, respiratory and intestinal problems. The virus is characterized by an important genetic, and consequently antigenic and pathogenic diversity. Knowing the variability of viral strains present in a population provides valuable information, particularly relevant for control programs development, vaccination recommendations and even identification of likely infection sources. Such information is therefore important at both local and regional levels. This review focuses on the genetic diversity of BVDV isolates infecting cattle in Spain over the last years. According to the published data, the most prevalent BVDV group in Spain was 1b, and to a lesser extent 1d, 1e and 1f. Besides, BVDV-2 has also been found in Spain with several ratified isolates. The studies carried out in Spain also showed increased genetic heterogeneity of BVDV strains, possibly due to a more intensive use of analytical tools available, presenting studies with increasingly greater sample sizes.

  11. Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources

    Science.gov (United States)

    The genetic diversity present in crop landraces represents a valuable genetic resource for breeding and genetic studies. Bottle gourd (Lagenaria siceraria) landraces in Turkey are highly genetically diverse. However, the limited genomic resources available for this crop hinder the molecular characte...

  12. Genetic diversity in Carthamus tinctorius (Asteraceae; safflower), an underutilized oilseed crop.

    Science.gov (United States)

    Pearl, Stephanie A; Burke, John M

    2014-10-01

    • Underutilized crops are potentially valuable resources for meeting increasing food demands. Safflower, an oilseed crop, is an example of one such underutilized crop that thrives in moisture-limited areas. Characterization of the genetic diversity maintained within the gene pools of underutilized crops such as safflower is an important step in their further development.• A total of 190 safflower individuals, including 134 USDA accessions, 48 breeding lines from two private North American safflower breeding companies, and eight wild safflower individuals, were genotyped using 133 single nucleotide polymorphism (SNP) markers. We then used the resulting data to assess the amount and distribution of genetic diversity within and among these collections of safflower.• Although just a modest reduction in gene diversity was observed in the commercial breeding lines (relative to the other safflower groupings), safflower domestication was accompanied by a significant decrease in allelic richness. Further, our results suggest that most safflower breeding lines originated from a single pool of diversity within the Old World safflower germplasm.• Taken together, our results suggest that both the safflower germplasm collection and related, wild species harbor previously undocumented genetic diversity that could help fuel future improvement efforts. Paired with analyses of functional diversity, the molecular resources described herein will be thus be useful in the continued development of safflower as an oilseed crop. © 2014 Botanical Society of America, Inc.

  13. 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.

  14. 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

  15. Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

    Science.gov (United States)

    Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

    2015-09-25

    In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

  16. Determination of genetic diversity among some almond accessions

    Directory of Open Access Journals (Sweden)

    Pinar Hasan

    2015-01-01

    Full Text Available More recently the use of different molecular markers in fruit species to determine particularly genetic diversity, genetic relationships and cultivar identification has been gained more importance. In the study, 13 randomly amplified polimorfic DNA (RAPD and 4 inter-simple sequence repeat (ISSR markers were used to evaluate genetic relationships among 95 almong accessions (26 foreign cultivars and 69 national cultivars and selections. The all plant material found in Almond Germplasm Repository in Gaziantep, Turkey. Both RAPD and ISSR markers distinguished the almond cultivars and selections in various levels. 17 RAPD and ISSR markers yielded a total of 73 scorable bands, which 51 are polymorphic. The two marker system exhibited variation with regard to average band sizes and polymorphism ratio. The average polymorphism was higher in ISSR (88% compared to RAPD (74%. RAPD and ISSR marker systems were found to be useful for determining genetic diversity among almong genotypes and cultivars. Combining of two dendrograms obtained through these markers show different clustering of 96 almond specimens without geographical isolation. These results supported that almonds in Turkey indicated considerable genetic diversity.

  17. 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 (H o ) ranged between 0.30 and 0.32, expected heterozygosity (H e ) between 0.30 and 0.31 and inbreeding coefficients (F is ) 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 (F st  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.

  18. 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.

  19. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...

  20. Global issues of genetic diversity.

    Science.gov (United States)

    Vida, G

    1994-01-01

    Genetic diversity within species is highly significant during their adaptation to environmental changes and, consequently, for their long-term survival. The genetic variability of species is also the basis for the evolution of higher levels of biodiversity, the evolution of species, and it might be an indispensible prerequisite for the functioning of our biosphere. Studies which promote understanding of the maintenance and the functional aspects of biodiversity at any level are therefore essential for the future welfare of mankind.

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

    Jane

    2011-06-03

    Jun 3, 2011 ... Genetic diversity of 73 local mulberry varieties from Shanxi Province were screened using ISSR ... number effective of alleles, Nei's genetic diversity index and Shannon's ...... resources conservation program of the Agriculture.

  3. WITHIN-POPULATION GENETIC DIVERSITY OF CLIMBING PLANTS AND TREES IN A TEMPERATE FOREST IN CENTRAL CHILE

    OpenAIRE

    Torres-Díaz, Cristian; Ruiz, Eduardo; Salgado-Luarte, Cristian; Molina-Montenegro, Marco A; Gianoli, Ernesto

    2013-01-01

    The climbing habit is a key innovation in angiosperm evolution: climbing plant taxa have greater species richness than their non-climbing sister groups. It is considered that highly diversified clades should show increased among-population genetic differentiation. Less clear is the expected pattern regarding within-population genetic diversity in speciose lineages. We tested the hypothesis of greater within-population genetic diversity in climbing plants compared to trees in a temperate fores...

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

    Indian Academy of Sciences (India)

    Unknown

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

  5. 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 ...

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

    Directory of Open Access Journals (Sweden)

    Guillermo Velo-Antón

    2011-04-01

    Full Text Available 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.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.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.

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

    Science.gov (United States)

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

    2016-11-01

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

  8. Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species.

    Science.gov (United States)

    McKee, Anna M; Maerz, John C; Smith, Lora L; Glenn, Travis C

    2017-08-01

    Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond-breeding amphibian species (Dwarf salamanders, Eurycea quadridigitata ; and Southern Leopard frogs, Lithobates sphenocephalus ) to understand how habitat characteristics and spatial scale affect genetic diversity across a landscape. Samples were collected from wetlands on a longleaf pine reserve in Georgia. We genotyped microsatellite loci for both species to assess population structures and determine which habitat features were most closely associated with observed heterozygosity and rarefied allelic richness. Both species exhibited significant population genetic structure; however, structure in Southern Leopard frogs was driven primarily by one outlier site. Dwarf salamander allelic richness was greater at sites with less surrounding road area within 0.5 km and more wetland area within 1.0 and 2.5 km, and heterozygosity was greater at sites with more wetland area within 0.5 km. In contrast, neither measure of Southern Leopard frog genetic diversity was associated with any habitat features at any scale we evaluated. Genetic diversity in the Dwarf salamander was strongly associated with land cover variables up to 2.5 km away from breeding wetlands, and/or results suggest that minimizing roads in wetland buffers may be beneficial to the maintenance of population genetic diversity. This study suggests that patterns of genetic differentiation and genetic diversity have associations with different habitat features across different spatial scales for two syntopic pond-breeding amphibian species.

  9. Genetic diversity of Colletotrichum gloeosporioides in Nigeria using ...

    African Journals Online (AJOL)

    fmodupe

    2012-04-24

    Apr 24, 2012 ... gloeosporioides isolates and was effective in establishing genetic relationships ... Key words: Anthracnose disease, pathotypes, genetic diversity, amplified ..... isolates to use in an anthracnose resistance screening program.

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

    African Journals Online (AJOL)

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

  11. 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 ...

  12. Genetic diversity study of common bean ( Phaseolus vulgaris L ...

    African Journals Online (AJOL)

    In PCoA, majority individuals of Metekel (L) tended to form separate group. The result of the study confirmed the presence of genetic diversity that can be exploited to improve the productivity. This calls for a conserted efforts in the collection, conservation and sustainable use of P. vulgaris. Keywords: Genetic diversity, ISSR, ...

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

    African Journals Online (AJOL)

    sandeep kaswan

    improvement of this crop (Dhar et al., 2005). Therefore, it is necessary to analyze or examine the genetic diversity provided by the gene pools and then harnessed for crop improvement. The concept of molecular marker is an ideal approach for this purpose. They are reliable indicator of genetic diversity because they are ...

  14. Bovine viral diarrhea virus (BVDV genetic diversity in Spain: A review

    Directory of Open Access Journals (Sweden)

    Francisco J. Diéguez

    2017-07-01

    Full Text Available Bovine viral diarrhea virus (BVDV, a member of the genus Pestivirus of the family Flaviviridae, causes significant losses in cattle farming worldwide because of reduced milk production, increased mortality of young animals and reproductive, respiratory and intestinal problems. The virus is characterized by an important genetic, and consequently antigenic and pathogenic diversity. Knowing the variability of viral strains present in a population provides valuable information, particularly relevant for control programs development, vaccination recommendations and even identification of likely infection sources. Such information is therefore important at both local and regional levels. This review focuses on the genetic diversity of BVDV isolates infecting cattle in Spain over the last years. According to the published data, the most prevalent BVDV group in Spain was 1b, and to a lesser extent 1d, 1e and 1f. Besides, BVDV-2 has also been found in Spain with several ratified isolates. The studies carried out in Spain also showed increased genetic heterogeneity of BVDV strains, possibly due to a more intensive use of analytical tools available, presenting studies with increasingly greater sample sizes.

  15. Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa.

    Science.gov (United States)

    Fuchs, Eric J; Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania; Arrieta-Espinoza, Griselda

    2016-01-01

    Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

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

    Science.gov (United States)

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

    2018-04-01

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

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

    African Journals Online (AJOL)

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

  18. Genetic diversity and demographic instability in Riftia pachyptila tubeworms from eastern Pacific hydrothermal vents

    Science.gov (United States)

    Coykendall, D.K.; Johnson, S.B.; Karl, S.A.; Lutz, R.A.; Vrijenhoek, R.C.

    2011-01-01

    Background: Deep-sea hydrothermal vent animals occupy patchy and ephemeral habitats supported by chemosynthetic primary production. Volcanic and tectonic activities controlling the turnover of these habitats contribute to demographic instability that erodes genetic variation within and among colonies of these animals. We examined DNA sequences from one mitochondrial and three nuclear gene loci to assess genetic diversity in the siboglinid tubeworm, Riftia pachyptila, a widely distributed constituent of vents along the East Pacific Rise and Galpagos Rift. Results: Genetic differentiation (FST) among populations increased with geographical distances, as expected under a linear stepping-stone model of dispersal. Low levels of DNA sequence diversity occurred at all four loci, allowing us to exclude the hypothesis that an idiosyncratic selective sweep eliminated mitochondrial diversity alone. Total gene diversity declined with tectonic spreading rates. The southernmost populations, which are subjected to superfast spreading rates and high probabilities of extinction, are relatively homogenous genetically. Conclusions: Compared to other vent species, DNA sequence diversity is extremely low in R. pachyptila. Though its dispersal abilities appear to be effective, the low diversity, particularly in southern hemisphere populations, is consistent with frequent local extinction and (re)colonization events. ?? 2011 Coykendall et al; licensee BioMed Central Ltd.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    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.

  1. 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.

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

    Indian Academy of Sciences (India)

    agricultural plant species, most or all genetic diversity in live- stock exists within ..... African cattle breeds (0.506–0.697; Ibeagha-Awemu et al. 2004). However .... relationships among populations of Asian goats (Capra hircus). J. Anim. Breed. ... 120,. 73–87. Kim K. S., Yeo J. S. and Choi C. B. 2002 Genetic diversity of north-.

  3. Effects of Habitat Fragmentation on Genetic Diversity in Cycas Balansae (Cycadaceae

    Directory of Open Access Journals (Sweden)

    Nguyen Minh Tam

    2017-11-01

    Full Text Available Habitat fragmentation is a serious threat to species survival. In Vietnam, Cycas balansae has been considered as threatened species because of the reduction and fragmentation of its habitats and over-exploitation. We assessed genetic variability and the pattern of population structure among six populations sampled in four provinces: Hoa Binh, Ha Nam, Ninh Binh and Quang Ninh. Polyacrylamide gel electrophoresis was performed on leaf tissues from 152 individuals representing 6 populations of C. balansae. Six of twelve enzyme systems were used to estimate genetic diversity at population and species levels. Eleven loci were examined. The allozyme data showed high levels of genetic diversity within all populations, ranging from 0.538 in Ba Sao to 0.628 in Tan Dan (average 0.576. The maintenance of high levels of expected heterozygosity (average 0.571 and low in observed heterozygosity (average 0.347 might be related to great heterozygote deficiency and increased frequencies of rare alleles. Genetic differentiation among populations was low (Dst = 0.036 and Gst = 0.064, indicating high level of gene flow (Nm = 3.22. Isolation by geographical distance was observed, however, no significant relationship between genetic distances and geographical distances was recorded. Our studies suggest small population sizes of cycads brought about by fragmentation of its habitats, over-exploitation, and increasing number of inbred individuals within populations.

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

    African Journals Online (AJOL)

    R Madhusudhana

    genetic diversity available at molecular level among a set of phenotypically different ... allele matching and cluster analysis based on unweighted neighbor- joining (Gascuel, 1997) ..... on isozyme data-a simulation study. Theor. Appl. Genet.

  5. 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.

  6. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

    Science.gov (United States)

    Huff, David D.; Miller, Loren M.; Vondracek, Bruce C.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.

  7. Genetic diversity of citrus bacterial canker pathogens preserved in herbarium specimens.

    Science.gov (United States)

    Li, Wenbin; Song, Qijian; Brlansky, Ronald H; Hartung, John S

    2007-11-20

    Citrus bacterial canker (CBC) caused by Xanthomonas axonopodis pv. citri (Xac) was first documented in India and Java in the mid 19th century. Since that time, the known distribution of the disease has steadily increased. Concurrent with the dispersion of the pathogen, the diversity of described strains continues to increase, with novel strains appearing in Saudi Arabia, Iran, and Florida in the last decade. Herbarium specimens of infected plants provide an historical record documenting both the geographic distribution and genetic diversity of the pathogen in the past. However, no method was available to assess the genetic diversity within these herbarium samples. We have developed a method, insertion event scanning (IES), and applied the method to characterize the diversity present within CBC populations documented as herbarium specimens over the past century. IES is based on the specific amplification of junction fragments that define insertion events. The potential for IES in current forensic applications is demonstrated by finding an exact match of pathogen genotypes preserved in herbarium specimens from Japan and Florida, demonstrating the source of the original outbreak of citrus canker in Florida in 1911. IES is a very sensitive technique for differentiating bacterial strains and can be applied to any of the several hundred bacteria for which full genomic sequence data are available.

  8. 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...

  9. Genetic diversity assessed by microsatellite markers in sweet corn cultivars

    Directory of Open Access Journals (Sweden)

    Ana Daniela Lopes

    2015-12-01

    Full Text Available Information on genetic diversity is essential to the characterization and utilization of germplasm. The genetic diversity of twenty-two sweet corn cultivars (seventeen open-pollinated varieties, OPV, and five hybrids, H was investigated by applying simple sequence repeat markers. A total of 257 primers were tested, of which 160 were found to be usable in terms of high reproducibility for all the samples tested; 45 were polymorphic loci, of which 30 were used to assess the genetic diversity of sweet corn cultivars. We detected a total of 86 alleles using 30 microsatellite primers. The mean polymorphism was 82 %. The highest heterozygosity values (Ho = 0.20 were found in the PR030-Doce Flor da Serra and BR427 III OPVs, whereas the lowest values (0.14 were recorded in the MG161-Branco Doce and Doce Cubano OPVs. The polymorphism information content ranged from 0.19 (Umc2319 to 0.71 (Umc2205. The analysis of molecular variance revealed that most of the genetic variability was concentrated within the cultivars of sweet corn (75 %, with less variability between them (25 %. The consensus tree derived from the neighbor-joining (NJ algorithm using 1,000 bootstrapping replicates revealed seven genetically different groups. Nei’s diversity values varied between 0.103 (Doce do Hawai × CNPH-1 cultivars and 0.645 (Amarelo Doce × Lili cultivars, indicating a narrow genetic basis. The Lili hybrid was the most distant cultivar, as revealed by Principal Coordinates Analysis and the NJ tree. This study on genetic diversity will be useful for planning future studies on sweet corn genetic resources and can complement the breeding programs for this crop.

  10. 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.

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

    African Journals Online (AJOL)

    joining method. Its topology reflects the general pattern of genetic differentiation among the four chicken breeds. The results also showed high genetic diversity and genetic variation among all the breeds. The information about the four local ...

  12. Genetic diversity of Ascaris in southwestern Uganda

    DEFF Research Database (Denmark)

    Betson, Martha; Nejsum, Peter; Llewellyn-Hughes, Julia

    2012-01-01

    . Microsatellite analysis using eight loci provided evidence for high gene flow between worm populations from the two villages but comparing these worms with others obtained in a prior study on Unguja, Zanzibar, confirmed little genetic exchange and mixing of worm populations between the two areas. By adding......Despite the common occurrence of ascariasis in southwestern Uganda, helminth control in the region has been limited. To gain further insights into the genetic diversity of Ascaris in this area, a parasitological survey in mothers (n=41) and children (n=74) living in two villages, Habutobere...... and Musezero, was carried out. Adult Ascaris worms were collected from infected individuals by chemo-expulsion using pyrantel pamoate treatment. Genetic diversity within these worms was assessed by inspection of DNA sequence variation in a mitochondrial marker and length polymorphism at microsatellite loci...

  13. Genetic diversity and relationships of Vietnamese and European pig breeds

    Energy Technology Data Exchange (ETDEWEB)

    Thuy, N T.D. [Department of Animal Breeding and Biotechnology, University of Hohenheim, Stuttgart (Germany); Institute of Biotechnology (IBT), National Center for Natural Science and Technology, Hanoi (Viet Nam); Melchinger, E; Kuss, A W; Peischl, T; Bartenschlager, H; Geldermann, H [Department of Animal Breeding and Biotechnology, University of Hohenheim, Stuttgart (Germany); Cuong, N V [Institute of Biotechnology (IBT), National Center for Natural Science and Technology, Hanoi (Viet Nam)

    2005-07-01

    Indigenous resources of the Asian pig population are less defined and only rarely compared with European breeds. In this study, five indigenous pig breeds from Viet Nam (Mong Cai, Muong Khuong, Co, Meo, Tap Na), two exotic breeds kept in Viet Nam (Large White, Landrace), three European commercial breeds (Pietrain, Landrace, Large White), and European Wild Boar were chosen for evaluation and comparison of genetic diversity. Samples and data from 317 animals were collected and ten polymorphic microsatellite loci were selected according to the recommendations of the FAO Domestic Animal Diversity Information System (DAD-IS; http://www.fao.org/dad-is/). Effective number of alleles, Polymorphism Information Content (PIC), within-breed diversity, estimated heterozygosities and tests for Hardy-Weinberg equilibrium were determined. Breed differentiation was evaluated using the fixation indices of Wright (1951). Genetic distances between breeds were estimated according to Nei (1972) and used for the construction of UPGMA dendrograms which were evaluated by bootstrapping. Heterozygosity was higher in indigenous Vietnamese breeds than in the other breeds. The Vietnamese indigenous breeds also showed higher genetic diversity than the European breeds and all genetic distances had a strong bootstrap support. The European commercial breeds, in contrast, were closely related and bootstrapping values for genetic distances among them were below 60%. European Wild Boar displayed closer relation with commercial breeds of European origin than with the native breeds from Viet Nam. This study is one of the first to contribute to a genetic characterization of autochthonous Vietnamese pig breeds and it clearly demonstrates that these breeds harbour a rich reservoir of genetic diversity. (author)

  14. Genetic diversity and relationships of Vietnamese and European pig breeds

    International Nuclear Information System (INIS)

    Thuy, N.T.D.; Melchinger, E.; Kuss, A.W.; Peischl, T.; Bartenschlager, H.; Geldermann, H.; Cuong, N.V.

    2005-01-01

    Indigenous resources of the Asian pig population are less defined and only rarely compared with European breeds. In this study, five indigenous pig breeds from Viet Nam (Mong Cai, Muong Khuong, Co, Meo, Tap Na), two exotic breeds kept in Viet Nam (Large White, Landrace), three European commercial breeds (Pietrain, Landrace, Large White), and European Wild Boar were chosen for evaluation and comparison of genetic diversity. Samples and data from 317 animals were collected and ten polymorphic microsatellite loci were selected according to the recommendations of the FAO Domestic Animal Diversity Information System (DAD-IS; http://www.fao.org/dad-is/). Effective number of alleles, Polymorphism Information Content (PIC), within-breed diversity, estimated heterozygosities and tests for Hardy-Weinberg equilibrium were determined. Breed differentiation was evaluated using the fixation indices of Wright (1951). Genetic distances between breeds were estimated according to Nei (1972) and used for the construction of UPGMA dendrograms which were evaluated by bootstrapping. Heterozygosity was higher in indigenous Vietnamese breeds than in the other breeds. The Vietnamese indigenous breeds also showed higher genetic diversity than the European breeds and all genetic distances had a strong bootstrap support. The European commercial breeds, in contrast, were closely related and bootstrapping values for genetic distances among them were below 60%. European Wild Boar displayed closer relation with commercial breeds of European origin than with the native breeds from Viet Nam. This study is one of the first to contribute to a genetic characterization of autochthonous Vietnamese pig breeds and it clearly demonstrates that these breeds harbour a rich reservoir of genetic diversity. (author)

  15. Study on genetic diversity of some Iranian Pistachio (Pistacia vera L ...

    African Journals Online (AJOL)

    hope&shola

    2010-11-08

    Nov 8, 2010 ... Keywords: Pistacia vera, genetic diversity, clustering, population parameters. .... used to detect DNA polymorphism and genetic diversity in ..... Project on Underutilized ... 2nd. nat. symp. of cellular and molecular biology.

  16. 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

  17. 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.

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

    African Journals Online (AJOL)

    ajl yemi

    2011-12-26

    Dec 26, 2011 ... relief, diuresis, blood pressure and lipid metabolism. (Kawasaki et al., 2000). ... Habitat. Longitude(N),. Latitude(E). Population size. Sample size. LY. Luoyang, Henan ..... Compared with the high genetic diversity at the species.

  19. Genetic diversity for fermentable carbohydrates production in alfalfa

    Energy Technology Data Exchange (ETDEWEB)

    Castonguay, Y.; Bertrand, A.; Duceppe, M.O.; Dube, M.P.; Michaud, R. [Agriculture and Agri-Food Canada, Quebec City, PQ (Canada)

    2009-07-01

    Alfalfa has many attributes that renders it suitable for bioethanol production, including its adaptability to diverse environmental conditions without any need for nitrogen fertilizer. However research is needed to develop biofuel-type alfalfa with improved biomass production and standability, increased persistence, and better cell wall degradability. The ethanol conversion rates from alfalfa biomass could be increased by genetically improving the accumulation of readily fermentable non-structural carbohydrates (NSC). This presentation reported on a screening project where genotypes with superior cell wall degradability were identified. NSC accumulation within 300 genotypes was randomly selected within six genetic backgrounds from Europe and North America. Biochemical analyses of dried stems revealed a large genetic variability for NSC content, with concentrations ranging from 20 to 100 mg per g DW. NSC variability was considerably higher in a genetic background of European origin compared to the other populations, therefore emphasizing the potential for genetic improvement for that trait. A modified commercial enzymatic cocktail known as AcceleraseTM 1000 Genencor is being developed to optimize the degradation of alfalfa biomass. DNA extracted from genotypes with the highest and lowest cell wall degradability or NSC accumulation will be pooled and used for bulk segregant analysis of DNA polymorphisms using the PCR-based sequence-related amplified polymorphism technique. It was concluded that the commercial release of biofuel-type alfalfa can be accelerated if the genetic markers associated with these traits can be identified.

  20. Genetic diversity of populations of the dioecious Myrsine coriacea (Primulaceae in the Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Roberta Pena da Paschoa

    2018-04-01

    Full Text Available ABSTRACT Although a species’ sexual system may influence the genetic diversity of its populations in their natural environment, there have been few such studies involving indigenous species of the Atlantic Forest. Here we study Myrsine coriacea, a dioecious tree widely used in reforestation programs despite a lack of information about its natural interpopulation genetic variation. To address this knowledge gap, intra- and interpopulation genetic diversity were measured for male and female individuals of ten natural populations using ISSR markers. Greater intrapopulation genetic diversity indicated interpopulation gene flow, regardless of isolation and distance between populations. Multivariate analyses detected significant differences in genetic diversity between populations, but not between males and females, which indicates that genetic diversity did not differ between the two sex morphs. Distance between populations was unrelated to genetic diversity. Myrsine coriacea has not experienced a loss of genetic variability despite the characteristic segregated spatial distribution of its populations. These results suggest that obligatory cross-pollination and dispersal by birds may be important mechanisms for the maintenance of genetic diversity in natural populations of M. coriacea.

  1. 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.

  2. 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.

  3. Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

    Directory of Open Access Journals (Sweden)

    Flávio de Oliveira Francisco

    2013-01-01

    Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

  4. Genetic diversity of Coccidioides posadasii from Brazil.

    Science.gov (United States)

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

    2013-05-01

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

  5. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  7. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

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

  8. Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia.

    Science.gov (United States)

    Assaeed, Abdulaziz M; Al-Faifi, Sulieman A; Migdadi, Hussein M; El-Bana, Magdy I; Al Qarawi, Abdulaziz A; Khan, Mohammad Altaf

    2018-01-01

    The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel's test showed that there was a significant correlation between the genetic and geographical distances ( r  = 0.35, P  < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum . The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity.

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

    African Journals Online (AJOL)

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

  10. 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 ...

  11. 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 ...

  12. Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina.

    Science.gov (United States)

    Diekmann, Onno E; Serrão, Ester A

    2012-04-01

    Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value. © 2012 Blackwell Publishing Ltd.

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

    Science.gov (United States)

    Melito, Sara; Sias, Angela; Petretto, Giacomo L; Chessa, Mario; Pintore, Giorgio; Porceddu, Andrea

    2013-01-01

    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. 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. 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. 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.

  14. 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.

  15. Genetic diversity and phylogenetic relationship in different genotypes of cotton for future breeding

    Directory of Open Access Journals (Sweden)

    Jehan

    2017-11-01

    Full Text Available Background: To make the plants well adapted and more resistant to diseases and other environmental stresses there is always a need to improve the quality of plant’s genome i.e. to increase its genetic diversity. Methods: In the present study six variety and six lines of cotton were investigated for their genetic diversity and phylogenetic relationship. For this purpose 35 different RAPD primers obtained from the Gene Link Technologies, USA were used. Results: Among 35 RAPD primers, 13 primers produced reproducible PCR bands while the rest failed to show any amplification product. Our results indicated that the total count of the reproducible bands was 670 and polymorphic loci were counted to be 442 which constitute 66% of total loci. Phylogenetic analysis revealed two major groups each consists of 7 and 5 genotypes respectively. Genotypes Lp1 and Tp4 were placed at maximum genetic distance and in separate groups and could be utilized for future cotton breeding. Conclusions: RAPD analysis is a cheaper and time saving technique for the determination of genetic diversity of different cotton genotypes. Cotton genotype Lp1 and Tp4 could be the best candidates for future breeding programs as both genotypes are genetically distant from each other.

  16. 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.

  17. 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 ...

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

    African Journals Online (AJOL)

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

  19. 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.

  20. Increasing diversity in radiologic technology.

    Science.gov (United States)

    Carwile, Laura

    2003-01-01

    Diversity is increasingly important in the radiologic technology workplace. For significant changes to occur in work force diversity, educators must first recruit and retain students from a wide variety of backgrounds. This article examines personality, race and gender as factors affecting career choice and how educators can use these factors to increase diversity in their programs. An overview of the ASRT's efforts to improve diversity within the profession is presented, along with suggestions for developing effective recruitment and retention plans to increase diversity.

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

    African Journals Online (AJOL)

    Assessment of genetic variability among the Hypericum perforatum populations is critical to the development of effective conservation strategies in the Kashmir valley. To obtain accurate estimates of genetic diversity among and within populations of H. perforatum, inter-simple sequence repeats (ISSR) markers were used.

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

    African Journals Online (AJOL)

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

  3. 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.

  4. Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras.

    Science.gov (United States)

    Lopez, Ana Cecilia; Ortiz, Andres; Coello, Jorge; Sosa-Ochoa, Wilfredo; Torres, Rosa E Mejia; Banegas, Engels I; Jovel, Irina; Fontecha, Gustavo A

    2012-11-26

    Understanding the population structure of Plasmodium species through genetic diversity studies can assist in the design of more effective malaria control strategies, particularly in vaccine development. Central America is an area where malaria is a public health problem, but little is known about the genetic diversity of the parasite's circulating species. This study aimed to investigate the allelic frequency and molecular diversity of five surface antigens in field isolates from Honduras. Five molecular markers were analysed to determine the genotypes of Plasmodium vivax and Plasmodium falciparum from endemic areas in Honduras. Genetic diversity of ama-1, msp-1 and csp was investigated for P. vivax, and msp-1 and msp-2 for P. falciparum. Allelic frequencies were calculated and sequence analysis performed. A high genetic diversity was observed within Plasmodium isolates from Honduras. A different number of genotypes were elucidated: 41 (n = 77) for pvama-1; 23 (n = 84) for pvcsp; and 23 (n = 35) for pfmsp-1. Pvcsp sequences showed VK210 as the only subtype present in Honduran isolates. Pvmsp-1 (F2) was the most polymorphic marker for P. vivax isolates while pvama-1 was least variable. All three allelic families described for pfmsp-1 (n = 30) block 2 (K1, MAD20, and RO33), and both allelic families described for the central domain of pfmsp-2 (n = 11) (3D7 and FC27) were detected. However, K1 and 3D7 allelic families were predominant. All markers were randomly distributed across the country and no geographic correlation was found. To date, this is the most complete report on molecular characterization of P. vivax and P. falciparum field isolates in Honduras with regards to genetic diversity. These results indicate that P. vivax and P. falciparum parasite populations are highly diverse in Honduras despite the low level of transmission.

  5. Assessment of genetic diversity within sour cherry clones

    DEFF Research Database (Denmark)

    Clausen, Sabine Karin; Andersen, Sven Bode; 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...

  6. Genetic diversity and connectivity in the East African giant mud crab Scylla serrata: Implications for fisheries management.

    Directory of Open Access Journals (Sweden)

    Cyrus Rumisha

    Full Text Available The giant mud crab Scylla serrata provides an important source of income and food to coastal communities in East Africa. However, increasing demand and exploitation due to the growing coastal population, export trade, and tourism industry are threatening the sustainability of the wild stock of this species. Because effective management requires a clear understanding of the connectivity among populations, this study was conducted to assess the genetic diversity and connectivity in the East African mangrove crab S. serrata. A section of 535 base pairs of the cytochrome oxidase subunit I (COI gene and eight microsatellite loci were analysed from 230 tissue samples of giant mud crabs collected from Kenya, Tanzania, Mozambique, Madagascar, and South Africa. Microsatellite genetic diversity (He ranged between 0.56 and 0.6. The COI sequences showed 57 different haplotypes associated with low nucleotide diversity (current nucleotide diversity = 0.29%. In addition, the current nucleotide diversity was lower than the historical nucleotide diversity, indicating overexploitation or historical bottlenecks in the recent history of the studied population. Considering that the coastal population is growing rapidly, East African countries should promote sustainable fishing practices and sustainable use of mangrove resources to protect mud crabs and other marine fauna from the increasing pressure of exploitation. While microsatellite loci did not show significant genetic differentiation (p > 0.05, COI sequences revealed significant genetic divergence between sites on the East coast of Madagascar (ECM and sites on the West coast of Madagascar, mainland East Africa, as well as the Seychelles. Since East African countries agreed to achieve the Convention on Biological Diversity (CBD target to protect over 10% of their marine areas by 2020, the observed pattern of connectivity and the measured genetic diversity can serve to provide useful information for designing

  7. Preservation of the genetic diversity of a local common carp in the agricultural heritage rice–fish system

    Science.gov (United States)

    Ren, Weizheng; Hu, Liangliang; Guo, Liang; Zhang, Jian; Tang, Lu; Zhang, Entao; Zhang, Jiaen; Luo, Shiming; Tang, Jianjun; Chen, Xin

    2018-01-01

    We examined how traditional farmers preserve the genetic diversity of a local common carp (Cyprinus carpio), which is locally referred to as “paddy field carp” (PF-carp), in a “globally important agricultural heritage system” (GIAHS), i.e., the 1,200-y-old rice–fish coculture system in Zhejiang Province, China. Our molecular and morphological analysis showed that the PF-carp has changed into a distinct local population with higher genetic diversity and diverse color types. Within this GIAHS region, PF-carps exist as a continuous metapopulation, although three genetic groups could be identified by microsatellite markers. Thousands of small farmer households interdependently obtained fry and parental carps for their own rice–fish production, resulting in a high gene flow and large numbers of parent carps distributing in a mosaic pattern in the region. Landscape genetic analysis indicated that farmers’ connectivity was one of the major factors that shaped this genetic pattern. Population viability analysis further revealed that the numbers of these interconnected small farmer households and their connection intensity affect the carps’ inherent genetic diversity. The practice of mixed culturing of carps with diverse color types helped to preserve a wide range of genetic resources in the paddy field. This widespread traditional practice increases fish yield and resource use, which, in return, encourages famers to continue their practice of selecting and conserving diverse color types of PF-carp. Our results suggested that traditional farmers secure the genetic diversity of PF-carp and its viability over generations in this region through interdependently incubating and mixed-culturing practices within the rice−fish system. PMID:29295926

  8. Molecular characterization of genetic diversity in some durum wheat ...

    African Journals Online (AJOL)

    Molecular characterization of genetic diversity in some durum wheat ... African Journal of Biotechnology ... Thus, RAPD offer a potentially simple, rapid and reliable method to evaluate genetic variation and relatedness among ten wheat ...

  9. Evaluation of genetic diversity in Piper spp using RAPD and SRAP markers.

    Science.gov (United States)

    Jiang, Y; Liu, J-P

    2011-11-29

    Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analysis were applied to 74 individual plants of Piper spp in Hainan Island. The results showed that the SRAP technique may be more informative and more efficient and effective for studying genetic diversity of Piper spp than the RAPD technique. The overall level of genetic diversity among Piper spp in Hainan was relatively high, with the mean Shannon diversity index being 0.2822 and 0.2909, and the mean Nei's genetic diversity being 0.1880 and 0.1947, calculated with RAPD and SRAP data, respectively. The ranges of the genetic similarity coefficient were 0.486-0.991 and 0.520-1.000 for 74 individual plants of Piper spp (the mean genetic distance was 0.505 and 0.480) and the within-species genetic distance ranged from 0.063 to 0.291 and from 0.096 to 0.234, estimated with RAPD and SRAP data, respectively. These genetic indices indicated that these species are closely related genetically. The dendrogram generated with the RAPD markers was topologically different from the dendrogram based on SRAP markers, but the SRAP technique clearly distinguished all Piper spp from each other. Evaluation of genetic variation levels of six populations showed that the effective number of alleles, Nei's gene diversity and the Shannon information index within Jianfengling and Diaoluoshan populations are higher than those elsewhere; consequently conservation of wild resources of Piper in these two regions should have priority.

  10. 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.

  11. 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.

  12. Genetic diversity of different accessions of Thymus kotschyanus using RAPD marker

    Directory of Open Access Journals (Sweden)

    Ahmad Ismaili

    2014-11-01

    Full Text Available Analysis of genetic diversity is a major step for understanding evolution and breeding applications. Recent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD technique has been successfully used in a variety of taxonomic and genetic diversity studies. The genetic diversity of 18 accessions of Thymus kotschyanus collected from different districts of Iran has been reported in this study, using 30 random amplified polymorphic DNA primers. Multivariate statistical analyses including principal coordinate analysis (PCOA and cluster analysis were used to group the accessions. From 29 primers, 385 bands were scored corresponding to an average of 13.27 bands per primer with 298 bands showing polymorphism (77.40%. A dendrogram constructed based on the UPGMA clustering method revealed three major clusters. The obtained results from grouping 18 accessions of T. kotschyanus with two studied methods indicated that in the most cases the applied methods produced similar grouping results. This study revealed nearly rich genetic diversity among T. kotschyanus accessions from different regions of Iran. The results showed RAPD marker was a useful marker for genetic diversity studies of T. kotschyanus and it was indicative of geographica variations.

  13. 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, ...

  14. 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.

  15. Genetic diversity of sweet potatoes collection from Northeastern Brazil

    African Journals Online (AJOL)

    Ana Veruska Cruz da Silva Muniz

    2014-02-24

    Feb 24, 2014 ... RAPD was efficient for the analysis of genetic diversity to identify groups and measure the genetic distance between ..... management program. We recommend ... The author(s) have not declared any conflict of interests.

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

    African Journals Online (AJOL)

    aghomotsegin

    In this work, cluster analysis and principal component analysis (PCA) were used to study the genetic ... Key words: Vitis vinifera L., simple sequence repeat (SSR), genetic diversity, .... The data were used for the following statistical analyses.

  17. 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.

  18. Pleistocene climatic oscillations rather than recent human disturbance influence genetic diversity in one of the world's highest treeline species.

    Science.gov (United States)

    Peng, Yanling; Lachmuth, Susanne; Gallegos, Silvia C; Kessler, Michael; Ramsay, Paul M; Renison, Daniel; Suarez, Ricardo; Hensen, Isabell

    2015-10-01

    Biological responses to climatic change usually leave imprints on the genetic diversity and structure of plants. Information on the current genetic diversity and structure of dominant tree species has facilitated our general understanding of phylogeographical patterns. Using amplified fragment length polymorphism (AFLPs), we compared genetic diversity and structure of 384 adults of P. tarapacana with those of 384 seedlings across 32 forest sites spanning a latitudinal gradient of 600 km occurring between 4100 m and 5000 m a.s.l. in Polylepis tarapacana (Rosaceae), one of the world's highest treeline species endemic to the central Andes. Moderate to high levels of genetic diversity and low genetic differentiation were detected in both adults and seedlings, with levels of genetic diversity and differentiation being almost identical. Four slightly genetically divergent clusters were identified that accorded to differing geographical regions. Genetic diversity decreased from south to north and with increasing precipitation for adults and seedlings, but there was no relationship to elevation. Our study shows that, unlike the case for other Andean treeline species, recent human activities have not affected the genetic structure of P. tarapacana, possibly because its inhospitable habitat is unsuitable for agriculture. The current genetic pattern of P. tarapacana points to a historically more widespread distribution at lower altitudes, which allowed considerable gene flow possibly during the glacial periods of the Pleistocene epoch, and also suggests that the northern Argentinean Andes may have served as a refugium for historical populations. © 2015 Botanical Society of America.

  19. Concordance between botanical groups and genetic diversity in peanut

    Directory of Open Access Journals (Sweden)

    Ingrid Pinheiro Machado

    Full Text Available ABSTRACT The aims of this study were to characterize peanut accessions of germplasm collection of the CCA/UFC and check consistency between the pre-existing botanical groups to estimates of genetic diversity. For this were conducted a trial with 43 accessions of peanut in a randomized block design with three replications. To characterization were used 21 morphological descriptors, where revealed large genetic variation. The mass hundred grains trait showed the main discriminating factors, with relative percentage of 22.1%. The cluster obtained with the linkage complete method, it was possible to view the dendrogram the formation of seven groups based on the Mahalanobis distance. By principal components analysis was identified phenotypic diversity among genotypes. The first three components explained 81% of the total variation. Subsequently, built a three-dimensional scatter chart for access of visualization, eight groups being formed. There was medium magnitude of agreement between the botanical groups and genetic diversity, both by the dendrogram and graphic dispersion proving the dissimilarity between genotypes of different botanic groups. Therefore, crossings between group access botanical Spanish or Valencia with those belonging to the Virginia group should generate segregating populations with high genetic potential.

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

    Indian Academy of Sciences (India)

    Thus, with this study, we intend to evaluate the genetic diversity, structure and relationships of ... Carlo (MCMC) iterations, and different values of K (number of populations). .... such as tree form diversity and forest stand condition. According to ...

  1. Supplementary data: Molecular assessment of genetic diversity in ...

    Indian Academy of Sciences (India)

    Molecular assessment of genetic diversity in cluster bean. (Cyamopsis tetragonoloba) genotypes. Rakesh Pathak, S. K. Singh, Manjit Singh and A. Henry. J. Genet. 89, 243–246. Figure 1. RAPD profile of 1–16 Cyamopsis tetragonoloba genotypes amplified with arbitrary primer OPA-16. Figure 2. RAPD profile of 17–32 ...

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

    African Journals Online (AJOL)

    JMwacharos

    2016-03-16

    Mar 16, 2016 ... diversity and (2) Investigate population structure and extent of admixture .... to estimate and partition genetic variation within and ... K between 1 and 40 and inferred its most optimal value ... populations of 0.84 ± 0.021 with the lowest mean in ..... on population stratification and the distribution of genetic.

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

    DEFF Research Database (Denmark)

    Schou, Mads F.; Loeschcke, Volker; Bechsgaard, Jesper

    2017-01-01

    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...

  4. ASSOCIATIONS BETWEEN GENETIC DIVERSITY AND ANTHROPOGENIC DISTURBANCE IN MIDWESTERN STREAM-DWELLING MINNOWS

    Science.gov (United States)

    Anthropogenic disturbances may leave imprints on patterns of intraspecific genetic diversity through their effects on population size, adaptation, migration, and mutation. We examined patterns of genetic diversity for a stream-dwelling minnow (the central stoneroller, Campostoma...

  5. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers.

    Science.gov (United States)

    Sharma, Rekha; Kishore, Amit; Mukesh, Manishi; Ahlawat, Sonika; Maitra, Avishek; Pandey, Ashwni Kumar; Tantia, Madhu Sudan

    2015-06-30

    Indian agriculture is an economic symbiosis of crop and livestock production with cattle as the foundation. Sadly, the population of indigenous cattle (Bos indicus) is declining (8.94% in last decade) and needs immediate scientific management. Genetic characterization is the first step in the development of proper management strategies for preserving genetic diversity and preventing undesirable loss of alleles. Thus, in this study we investigated genetic diversity and relationship among eleven Indian cattle breeds using 21 microsatellite markers and mitochondrial D loop sequence. The analysis of autosomal DNA was performed on 508 cattle which exhibited sufficient genetic diversity across all the breeds. Estimates of mean allele number and observed heterozygosity across all loci and population were 8.784 ± 0.25 and 0.653 ± 0.014, respectively. Differences among breeds accounted for 13.3% of total genetic variability. Despite high genetic diversity, significant inbreeding was also observed within eight populations. Genetic distances and cluster analysis showed a close relationship between breeds according to proximity in geographic distribution. The genetic distance, STRUCTURE and Principal Coordinate Analysis concluded that the Southern Indian Ongole cattle are the most distinct among the investigated cattle populations. Sequencing of hypervariable mitochondrial DNA region on a subset of 170 cattle revealed sixty haplotypes with haplotypic diversity of 0.90240, nucleotide diversity of 0.02688 and average number of nucleotide differences as 6.07407. Two major star clusters for haplotypes indicated population expansion for Indian cattle. Nuclear and mitochondrial genomes show a similar pattern of genetic variability and genetic differentiation. Various analyses concluded that the Southern breed 'Ongole' was distinct from breeds of Northern/ Central India. Overall these results provide basic information about genetic diversity and structure of Indian cattle which

  6. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

    Directory of Open Access Journals (Sweden)

    Yun Duan

    Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

  7. 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 ...

  8. Genetic diversity of Aspergillus fumigatus in indoor hospital environments.

    Science.gov (United States)

    Araujo, Ricardo; Amorim, António; Gusmão, Leonor

    2010-09-01

    Environmental isolates of Aspergillus fumigatus are less studied than those recovered from clinical sources. In the present study, the genetic diversity among such environmental isolates was assessed, as well as their dispersion ability and the acquisition of new strains in 19 medical units of the same hospital. A. fumigatus isolates were genotyped using a single multiplex PCR-based reaction with eight microsatellite markers and an insertion/deletion polymorphism. A total of 130 unique genotypes were found among a total of 250 A. fumigatus isolates. Genotypic diversity ranged from 0.86 to 1 in samples from hospital rooms, and there was no correlation between these samples and the presence of high-efficiency particulate air filters or any other air filtration system. Four of the six most prevalent A. fumigatus strains were recovered from water samples. The occurrence of microvariation was common among environmental isolates, which affected each of the microsatellite markers. The assessment of the genetic diversity of A. fumigatus is a useful tool for illustrating the presence or absence of specific clonal populations in a clinical setting. A. fumigatus populations were highly dynamic indoors, and new populations were found in just a few months. Due to the high indoor dispersion capability of A. fumigatus, more attention should be given to strains with increased pathogenic potential or reduced susceptibility to anti-fungal drugs.

  9. Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm.

    Science.gov (United States)

    Pyne, Robert M; Honig, Josh A; Vaiciunas, Jennifer; Wyenandt, Christian A; Simon, James E

    2018-04-23

    The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew. Results obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession 'MRI' representing the only source of DM resistance. High levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure

  10. 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...

  11. Genetic structure and diversity in Juniperus communis populations in Saxony, Germany

    Directory of Open Access Journals (Sweden)

    Reim Stefanie

    2016-06-01

    Full Text Available In recent years, land use changes led to a rapid decline and fragmentation of J. communis populations in Germany. Population isolation may lead to a restricted gene flow and, further, to negative effects on genetic variation. In this study, genetic diversity and population structure in seven fragmented J. communis populations in Saxony, Germany, were investigated using nuclear microsatellites (nSSR and chloroplast single nucleotide polymorphism (cpSNP. In all Saxony J. communis populations, a high genetic diversity was determined but no population differentiation could be detected whatever method was applied (Bayesian cluster analysis, F-statistics, AMOVA. The same was true for three J. communis out-group samples originating from Italy, Slovakia and Norway, which also showed high genetic diversity and low genetic differences regarding other J. communis populations. Low genetic differentiation among the J. communis populations ascertained with nuclear and chloroplast markers indicated high levels of gene flow by pollen and also by seeds between the sampled locations. Low genetic differentiation may also provide an indicator of Juniper survival during the last glacial maximum (LGM in Europe. The results of this study serve as a basis for the implementation of appropriate conservation measures in Saxony.

  12. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

    DEFF Research Database (Denmark)

    Miller, Webb; Hayes, Vanessa M.; Ratan, Aakrosh

    2011-01-01

    The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we...... that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations....

  13. Roads, interrupted dispersal, and genetic diversity in timber rattlesnakes.

    Science.gov (United States)

    Clark, Rulon W; Brown, William S; Stechert, Randy; Zamudio, Kelly R

    2010-08-01

    Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine-scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic-assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads.

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

    Science.gov (United States)

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

    2013-10-01

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

  15. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis

    Directory of Open Access Journals (Sweden)

    Rabinowicz Pablo D

    2010-01-01

    Full Text Available Abstract Background Castor bean (Ricinus communis is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale. We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs at 48 loci. Results Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74% followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ϕPT values, p Conclusion Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.

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

    African Journals Online (AJOL)

    aghomotsegin

    2014-01-08

    Jan 8, 2014 ... Xoconostle or acidic prickly pear is an important fruit in Mexico; it is produced by a ... study, we report for the first time the estimation of genetic diversity within a set ... demonstrates the high genetic variation among genotypes of .... O. leucotricha Salm-Dyck × O. joconostle F.A.C Weber Zacatecas Wild Stock.

  17. [Genetic diversity of wild Cynodon dactylon germplasm detected by SRAP markers].

    Science.gov (United States)

    Yi, Yang-Jie; Zhang, Xin-Quan; Huang, Lin-Kai; Ling, Yao; Ma, Xiao; Liu, Wei

    2008-01-01

    Sequence-related amplified polymorphism (SRAP) molecular markers were used to detect the genetic diversity of 32 wild accessions of Cynodon dactylon collected from Sichuan, Chongqing, Guizhou and Tibet, China. The following results were obtained. (1) Fourteen primer pairs produced 132 polymorphic bands, averaged 9.4 bands per primer pair. The percentage of polymorphic bands in average was 79.8%. The Nei's genetic similarity coefficient of the tested accessions ranged from 0.591 to 0.957, and the average Nei's coefficient was 0.759. These results suggested that there was rich genetic diversity among the wild resources of Cynodon dactylon tested. (2) Thirty two wild accessions were clustered into four groups. Moreover, the accessions from the same origin frequently clustered into one group. The findings implied that a correlation among the wild resources, geographical and ecological environment. (3) Genetic differentiation between and within six eco-geographical groups of C. dactylon was estimated by Shannon's diversity index, which showed that 65.56% genetic variance existed within group, and 34.44% genetic variance was among groups. (4) Based on Nei's unbiased measures of genetic identity, UPGMA cluster analysis measures of six eco-geographical groups of Cynodon dactylon, indicated that there was a correlation between genetic differentiation and eco-geographical habits among the groups.

  18. Genetic diversity of native potatoes (Solanumspp. conserved in landraces from Peru

    Directory of Open Access Journals (Sweden)

    Julián Soto

    2014-03-01

    Full Text Available This paper analyzes the genetic diversity of 79 accessions of native potato varieties (Solanum spp. using 18 microsatellite markers. A random sample from Ayacucho, Cajamarca, Cusco, Huancavelica and Puno from "chacras" of farmers who collaborated with the "In situ conservation of native crops and wild relatives" were used. 17 markers amplified one single polymorphic locus, the mean number of alleles per locus was 8.79. The mean similarity was 0.62 and clustering indexes varied between 0.41 and 0.98. 19 loci showed a total of 166 alleles. Cuzco had the highest number of alleles (130 alleles. Of the 166 characterized alleles, 72 alleles (43.37% were common or shared with 5 sampling sites. Puno had the highest number of exclusive alleles (8 alleles. The 42 varieties of S. tuberosum subsp. andigena showed a mean diversity of 0.74 and 18 varieties of S. x chauchaan average diversity of 0.70. Polymorphism (PIC = 0.55 to 0.85 and genetic diversity indices show that microsatellites evaluated can identify high levels of genetic diversity, but also are not sufficient to discriminate differentiated by origin or species groups. Our analyzes indicate a high genetic diversity and are consistent with inventories and morphological characterizations performed in situ, we can also conclude that there would be a common pool of genes would be found widely distributed among the regions studied.

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

    AJL

    genetic diversity of P. infestans and geographical origin. These results provided a foundation for making integrated control measures in the future. Key words: Phytophthora infestans, population genetics, simple-sequence repeat (SSR), potato late blight. INTRODUCTION. Phytophthora infestans (Mont.) de Bary, causing the ...

  1. Conservation implications of the genetic diversity of Gymnospermium microrrhynchum in Korea.

    Science.gov (United States)

    Lee, S H; Yeon, M H; Shim, J K

    2016-10-24

    Gymnospermium microrrhynchum (Berberidaceae) is an ephemeral perennial herb with a limited distributional range in the Baekdudaegan mountain areas of the Korean Peninsula, and is designated a rare plant by the Korean Forest Service. Information about its genetic variation and structure is important for developing successful conservation strategies. To investigate the genetic variation within and among seven G. microrrhynchum populations, random amplified polymorphic DNA data were obtained for 207 individuals. The populations exhibited relatively low genetic diversity: the percentage of polymorphic bands (PPB) ranged from 32.1 to 66.7% (mean = 51.4%) and Nei's gene diversity (H E ) ranged from 0.116 to 0.248 (mean = 0.188). However, genetic diversity at the species level was relatively high (PPB = 98.7%, H E = 0.349). An analysis of molecular variance revealed high differentiation among populations (Φ ST = 0.6818), but the low gene flow value (N m = 0.117) suggests a low level of gene exchange occurs among populations. Principal coordinates analysis revealed that individuals were separated according to population. The high level of genetic differentiation and restricted gene flow among G. microrrhynchum populations, which resulted from their isolation in alpine areas after the Ice Age, indicates that it is essential to protect and manage all populations, rather than focus on specific populations, in order to maintain the genetic diversity of this species.

  2. Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India.

    Science.gov (United States)

    Choudhury, Baharul; Khan, Mohamed Latif; Dayanandan, Selvadurai

    2013-12-01

    The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the

  3. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Directory of Open Access Journals (Sweden)

    Sajjad Ahmad

    2015-06-01

    Full Text Available Field pea (Pisum sativum L. is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM taking population structure (Q and relative kinship (K into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  4. How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination.

    Science.gov (United States)

    Frankham, R

    2012-03-01

    Levels of genetic diversity in finite populations are crucial in conservation and evolutionary biology. Genetic diversity is required for populations to evolve and its loss is related to inbreeding in random mating populations, and thus to reduced population fitness and increased extinction risk. Neutral theory is widely used to predict levels of genetic diversity. I review levels of genetic diversity in finite populations in relation to predictions of neutral theory. Positive associations between genetic diversity and population size, as predicted by neutral theory, are observed for microsatellites, allozymes, quantitative genetic variation and usually for mitochondrial DNA (mtDNA). However, there are frequently significant deviations from neutral theory owing to indirect selection at linked loci caused by balancing selection, selective sweeps and background selection. Substantially lower genetic diversity than predicted under neutrality was found for chromosomes with low recombination rates and high linkage disequilibrium (compared with 'normally' recombining chromosomes within species and adjusted for different copy numbers and mutation rates), including W (median 100% lower) and Y (89% lower) chromosomes, dot fourth chromosomes in Drosophila (94% lower) and mtDNA (67% lower). Further, microsatellite genetic and allelic diversity were lost at 12 and 33% faster rates than expected in populations adapting to captivity, owing to widespread selective sweeps. Overall, neither neutral theory nor most versions of the genetic draft hypothesis are compatible with all empirical results.

  5. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    Science.gov (United States)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

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

    Science.gov (United States)

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

    2009-08-01

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

  7. Genetic diversity among endangered rare Dalbergia ...

    African Journals Online (AJOL)

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

  8. Spatial and temporal genetic diversity of lake whitefish (Coregonus clupeaformis (Mitchill)) from Lake Huron and Lake Erie

    Science.gov (United States)

    Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Hartman, Travis; Johnson, Jim; Roseman, Edward F.

    2013-01-01

    Lake whitefish (Coregonus clupeaformis (Mitchill)) are important commercially, culturally, and ecologically in the Laurentian Great Lakes. Stocks of lake whitefish in the Great Lakes have recovered from low levels of abundance in the 1960s. Reductions in abundance, loss of habitat and environmental degradation can be accompanied by losses of genetic diversity and overall fitness that may persist even as populations recover demographically. Therefore, it is important to be able to identify stocks that have reduced levels of genetic diversity. In this study, we investigated patterns of genetic diversity at microsatellite DNA loci in lake whitefish collected between 1927 and 1929 (historical period) and between 1997 and 2005 (contemporary period) from Lake Huron and Lake Erie. Genetic analysis of lake whitefish from Lakes Huron and Erie shows that the amount of population structuring varies from lake to lake. Greater genetic divergences among collections from Lake Huron may be the result of sampling scale, migration patterns and demographic processes. Fluctuations in abundance of lake whitefish populations may have resulted in periods of increased genetic drift that have resulted in changes in allele frequencies over time, but periodic genetic drift was not severe enough to result in a significant loss of genetic diversity. Migration among stocks may have decreased levels of genetic differentiation while not completely obscuring stock boundaries. Recent changes in spatial boundaries to stocks, the number of stocks and life history characteristics of stocks further demonstrate the potential of coregonids for a swift and varied response to environmental change and emphasise the importance of incorporating both spatial and temporal considerations into management plans to ensure that diversity is preserved.

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

    African Journals Online (AJOL)

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

  10. Population Genetic Structure and Genetic Diversity in Twisted-Jaw Fish, Belodontichthys truncatus Kottelat & Ng, 1999 (Siluriformes: Siluridae, from Mekong Basin

    Directory of Open Access Journals (Sweden)

    Surapon Yodsiri

    2017-01-01

    Full Text Available The Mekong River and its tributaries possess the second highest diversity in fish species in the world. However, the fish biodiversity in this river is threatened by several human activities, such as hydropower plant construction. Understanding the genetic diversity and genetic structure of the species is important for natural resource management. Belodontichthys truncatus Kottelat & Ng is endemic to the Mekong River basin and is an important food source for people in this area. In this study, the genetic diversity, genetic structure, and demographic history of the twisted-jaw fish, B. truncatus, were investigated using mitochondrial cytochrome b gene sequences. A total of 124 fish specimens were collected from 10 locations in the Mekong and its tributaries. Relatively high genetic diversity was found in populations of B. truncatus compared to other catfish species in the Mekong River. The genetic structure analysis revealed that a population from the Chi River in Thailand was genetically significantly different from other populations, which is possibly due to the effect of genetic drift. Demographic history analysis indicated that B. truncatus has undergone recent demographic expansion dating back to the end of the Pleistocene glaciation.

  11. 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 ...

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

    African Journals Online (AJOL)

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

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

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    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

  14. Estimation of loss of genetic diversity in modern Japanese cultivars by comparison of diverse genetic resources in Asian pear (Pyrus spp.).

    Science.gov (United States)

    Nishio, Sogo; Takada, Norio; Saito, Toshihiro; Yamamoto, Toshiya; Iketani, Hiroyuki

    2016-06-14

    Pears (Pyrus spp.) are one of the most important fruit crops in temperate regions. Japanese pear breeding has been carried out for over 100 years, working to release new cultivars that have good fruit quality and other desirable traits. Local cultivar 'Nijisseiki' and its relatives, which have excellent fruit texture, have been repeatedly used as parents in the breeding program. This strategy has led to inbreeding within recent cultivars and selections. To avoid inbreeding depression, we need to clarify the degree of inbreeding among crossbred cultivars and to introgress genetic resources that are genetically different from modern cultivars and selections. The objective of the present study was to clarify the genetic relatedness between modern Japanese pear cultivars and diverse Asian pear genetic resources. We genotyped 207 diverse accessions by using 19 simple sequence repeat (SSR) markers. The heterozygosity and allelic richness of modern cultivars was obviously decreased compared with that of wild individuals, Chinese pear cultivars, and local cultivars. In analyses using Structure software, the 207 accessions were classified into four clusters (K = 4): one consisting primarily of wild individuals, one of Chinese pear cultivars, one of local cultivars from outside the Kanto region, and one containing both local cultivars from the Kanto region and crossbred cultivars. The results of principal coordinate analysis (PCoA) were similar to those from the Structure analysis. Wild individuals and Chinese pears appeared to be distinct from other groups, and crossbred cultivars became closer to 'Nijisseiki' as the year of release became more recent. Both Structure and PCoA results suggest that the modern Japanese pear cultivars are genetically close to local cultivars that originated in the Kanto region, and that the genotypes of the modern cultivars were markedly biased toward 'Nijisseiki'. Introgression of germplasm from Chinese pear and wild individuals that are

  15. Population genetic diversity and hybrid detection in captive zebras.

    Science.gov (United States)

    Ito, Hideyuki; Langenhorst, Tanya; Ogden, Rob; Inoue-Murayama, Miho

    2015-08-21

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy's zebra E. grevyi and the mountain zebra E. zebra. The Grevy's zebra and the mountain zebra are endangered, and hybridization between the Grevy's zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy's zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy's and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy's zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy's zebra.

  16. 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...

  17. Translating conservation genetics into management: Pan-European minimum requirements for dynamic conservation units of forest tree genetic diversity

    OpenAIRE

    Koskela, Jarkko; Lefèvre, François; Schueler, Silvio; Kraigher, Hojka; Olrik, Ditte C.; Hubert, Jason; Longauer, Roman; Bozzano, Michele; Yrjänä, Leena; Alizoti, Paraskevi; Rotach, Peter; Vietto, Lorenzo; Bordács, Sándor; Myking, Tor; Eysteinsson, Thröstur

    2013-01-01

    This paper provides a review of theoretical and practical aspects related to genetic management of forest trees. The implementation of international commitments on forest genetic diversity has been slow and partly neglected. Conservation of forest genetic diversity is still riddled with problems, and complexities of national legal and administrative structures. Europe is an example of a complex region where the dis- tribution ranges of tree species extend across large geographical areas with ...

  18. 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.

  19. Genetic diversity characterization of cassava cultivars (Manihot esculenta Crantz.: I RAPD markers

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    Colombo Carlos

    1998-01-01

    Full Text Available RAPD markers were used to investigate the genetic diversity of 31 Brazilian cassava clones. The results were compared with the genetic diversity revealed by botanical descriptors. Both sets of variates revealed identical relationships among the cultivars. Multivariate analysis of genetic similarities placed genotypes destinated for consumption "in nature" in one group, and cultivars useful for flour production in another. Brazil?s abundance of landraces presents a broad dispersion and is consequently an important resource of genetic variability. The botanical descriptors were not able to differentiate thirteen pairs of cultivars compared two-by-two, while only one was not differentiated by RAPD markers. These results showed the power of RAPD markers over botanical descriptors in studying genetic diversity, identifying duplicates, as well as validating, or improving a core collection. The latter is particularly important in this vegetatively propagated crop.

  20. 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.

  1. Genetic Diversity of Koala Retroviral Envelopes

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    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.

  2. Genetic diversity and paternal origin of domestic donkeys.

    Science.gov (United States)

    Han, H; Chen, N; Jordana, J; Li, C; Sun, T; Xia, X; Zhao, X; Ji, C; Shen, S; Yu, J; Ainhoa, F; Chen, H; Lei, C; Dang, R

    2017-12-01

    Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male-specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome-specific microsatellites (Y-STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y-STRs-EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4-were male specific and polymorphic, showing two to eight alleles in the donkeys studied. A total of 21 haplotypes corresponding to three haplogroups were identified, indicating three independent patrilines in domestic donkey. These markers are useful for the study the Y-chromosome diversity and population genetics of donkeys in Africa, Europe, South America and China. © 2017 Stichting International Foundation for Animal Genetics.

  3. 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.

  4. Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene.

    Science.gov (United States)

    Sheng, Gui-Lian; Barlow, Axel; Cooper, Alan; Hou, Xin-Dong; Ji, Xue-Ping; Jablonski, Nina G; Zhong, Bo-Jian; Liu, Hong; Flynn, Lawrence J; Yuan, Jun-Xia; Wang, Li-Rui; Basler, Nikolas; Westbury, Michael V; Hofreiter, Michael; Lai, Xu-Long

    2018-04-06

    The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cyt b and 12s rRNA, partial 16s rRNA and ND1 , and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

  5. Ancient DNA from Giant Panda (Ailuropoda melanoleuca of South-Western China Reveals Genetic Diversity Loss during the Holocene

    Directory of Open Access Journals (Sweden)

    Gui-Lian Sheng

    2018-04-01

    Full Text Available The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae. Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

  6. Genetic Diversity in Natural Populations of New World Leishmania

    Directory of Open Access Journals (Sweden)

    Cupolillo Elisa

    1998-01-01

    Full Text Available Our results have shown the wide diversity of parasites within New World Leishmania. Biochemical and molecular characterization of species within the genus has revealed that much of the population heterogeneity has a genetic basis. The source of genetic diversity among Leishmania appears to arise from predominantly asexual, clonal reproduction, although occasional bouts of sexual reproduction can not be ruled out. Genetic variation is extensive with some clones widely distributed and others seemingly unique and localized to a particular endemic focus. Epidemiological studies of leishmaniasis has been directed to the ecology and dynamics of transmission of Leishmania species/variants, particularly in localized areas. Future research using molecular techniques should aim to identify and follow Leishmania types in nature and correlate genetic typing with important clinical characteristics such as virulence, pathogenicity, drug resistance and antigenic variation. The epidemiological significance of such variation not only has important implications for the control of the leishmaniases, but would also help to elucidate the evolutionary biology of the causative agents.

  7. Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs

    Directory of Open Access Journals (Sweden)

    Sonia E. Eynard

    2018-01-01

    Full Text Available Genomic selection (GS is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.

  8. Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs.

    Science.gov (United States)

    Eynard, Sonia E; Croiseau, Pascal; Laloë, Denis; Fritz, Sebastien; Calus, Mario P L; Restoux, Gwendal

    2018-01-04

    Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations. Copyright © 2018 Eynard et al.

  9. Genetic diversity of tambaqui broodstocks in stock enhancement programs

    Directory of Open Access Journals (Sweden)

    Americo Moraes Neto

    2017-06-01

    Full Text Available Natural populations of tambaqui (Colossoma macropomum have significantly decreased in recent decades especially due to human extraction activities. So that the environmental impact may be reduced, the restocking of fish and increase in fish production are enhanced. Genetic evaluations using molecular markers are essential for this purpose. Current study evaluates the genetic variability of two tambaqui broodstocks used in restocking programs. Sixty-five samples (33 samples from broodstock A and 32 samples from broodstock B were collected. DNA was extracted from caudal fin samples, with the amplification of four microsatellite loci: Cm1A11 (EU685307 Cm1C8 (EU685308 Cm1F4 (EU685311 and Cm1H8 (EU685315. Fourteen alleles in the stock of broodstock A were produced, five alleles for Cm1A11 locus (230, 255, 260, 270 and 276 bp, three alleles Cm1C8 (239, 260, and 273 bp, two alleles Cm1F4 (211 and 245 bp, four alleles for Cm1H8 (275, 290, 320 and 331 bp and two unique alleles were found for Cm1A11 loci (alleles 270 and 276 bp and Cm1H8 (alleles 275 and 331 bp. In broodstock B, ten alleles were produced, the same alleles of the first stock except for alleles 270 and 276 bp in Cm1A11 locus and 275 and 331 bp in Cm1H8 locus. Broodstock A revealed low frequency alleles in Cm1A11 loci, Cm1C8, Cm1F4 and Cm1H8, whereas broodstock B had no locus with low allelic frequency. Loci Cm1A11, Cm1C8 and Cm1H8 exhibited significant deficit of heterozygotes in both broodstocks, revealing changes in Hardy-Weinberg equilibrium. Genetic diversity between stocks was 0.1120, whilst genetic similarity was 0.894, with FST rate = 0.05, and Nm = 3.93, indicating gene flow between the two broodstocks. Results show that broodstocks are genetically closely related, with no great genetic variability. Strategies such as a previous genetic analysis of breeding with its marking, use of a large Ne crossing between the most genetically divergent specimens, and the introduction of new

  10. Elm genetic diversity and hybridization in the presence of Dutch elm disease

    Science.gov (United States)

    Johanne Brunet; Raymond P. Guries

    2017-01-01

    The impact of Dutch elm disease (DED) on the genetic diversity of slippery elm (Ulmus rubra) is summarized and its potential impact on the genetic diversity of other North American native elms, American elm (U. americana), rock elm (U. thomasii), winged elm (U. alata), cedar elm (

  11. Use of SNP markers to conserve genome-wide genetic diversity in livestock

    NARCIS (Netherlands)

    Engelsma, K.A.

    2012-01-01

    Conservation of genetic diversity in livestock breeds is important since it is, both within and between breeds, under threat. The availability of large numbers of SNP markers has resulted in new opportunities to estimate genetic diversity in more detail, and to improve prioritization of animals

  12. Use of microsatellites for evaluation of genetic diversity in cherry tomato

    Directory of Open Access Journals (Sweden)

    Nelson Ceballos Aguirre

    Full Text Available ABSTRACT Much of the diversity of tomato is found in wild forms, the most important being the Solanum lycopersicum L. var. cerasiforme and S. pimpinellifolium. The objective of this research was to assess the genetic diversity of 30 introductions of cherry tomato with 36 microsatellite molecular markers. The study was conducted at the Plant Transformation Research Center (PTRC of the University of California. A dendrogram was built using the Dice-Nei and Li similarity index and the UPGMA clustering method, where introductions were differentiated without preserving a distribution pattern obeying the geographical area of origin. A coefficient of genetic differentiation was found (Fst = 0.3474, showing a high genetic differentiation of the introductions; those from Brazil, Ecuador, and Peru were the most genetically diverse, presenting 100% of polymorphic loci. The molecular variance analysis indicated a variation of 11% between the groups and 89% within the same. The broad genotypic variability of the evaluated introductions favors the possibility of selecting those for genetic improvement and sustainable use of the species.

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... 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.

  15. 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 ...

  16. 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 ...

  17. 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.

  18. Genetic diversity among old Portuguese bread wheat cultivars and ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 88; Issue 3. Genetic diversity among old Portuguese bread wheat cultivars and botanical varieties evaluated by ITS rDNA PCR-RFLP markers. A. Carvalho H. Guedes-Pinto J. Lima-Brito. Research Note Volume 88 Issue 3 December 2009 pp 363-367 ...

  19. Plasmodium vivax merozoite surface protein-3 alpha: a high-resolution marker for genetic diversity studies.

    Science.gov (United States)

    Prajapati, Surendra Kumar; Joshi, Hema; Valecha, Neena

    2010-06-01

    Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3 alpha (msp-3 alpha) and assessed its suitability as high-resolution genetic marker for population genetic studies. 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3 alpha. We observed three distinct PCR alleles at msp-3 alpha, and among them allele A showed significantly high frequency (53%, chi2 = 8.22, p = 0.001). PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3 alpha is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3 alpha in the field isolates. P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3 alpha could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

  20. 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.

  1. Low genetic diversity despite multiple introductions of the invasive plant species Impatiens glandulifera in Europe.

    Science.gov (United States)

    Hagenblad, Jenny; Hülskötter, Jennifer; Acharya, Kamal Prasad; Brunet, Jörg; Chabrerie, Olivier; Cousins, Sara A O; Dar, Pervaiz A; Diekmann, Martin; De Frenne, Pieter; Hermy, Martin; Jamoneau, Aurélien; Kolb, Annette; Lemke, Isgard; Plue, Jan; Reshi, Zafar A; Graae, Bente Jessen

    2015-08-20

    Invasive species can be a major threat to native biodiversity and the number of invasive plant species is increasing across the globe. Population genetic studies of invasive species can provide key insights into their invasion history and ensuing evolution, but also for their control. Here we genetically characterise populations of Impatiens glandulifera, an invasive plant in Europe that can have a major impact on native plant communities. We compared populations from the species' native range in Kashmir, India, to those in its invaded range, along a latitudinal gradient in Europe. For comparison, the results from 39 other studies of genetic diversity in invasive species were collated. Our results suggest that I. glandulifera was established in the wild in Europe at least twice, from an area outside of our Kashmir study area. Our results further revealed that the genetic diversity in invasive populations of I. glandulifera is unusually low compared to native populations, in particular when compared to other invasive species. Genetic drift rather than mutation seems to have played a role in differentiating populations in Europe. We find evidence of limitations to local gene flow after introduction to Europe, but somewhat less restrictions in the native range. I. glandulifera populations with significant inbreeding were only found in the species' native range and invasive species in general showed no increase in inbreeding upon leaving their native ranges. In Europe we detect cases of migration between distantly located populations. Human activities therefore seem to, at least partially, have facilitated not only introductions, but also further spread of I. glandulifera across Europe. Although multiple introductions will facilitate the retention of genetic diversity in invasive ranges, widespread invasive species can remain genetically relatively invariant also after multiple introductions. Phenotypic plasticity may therefore be an important component of the

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

    Directory of Open Access Journals (Sweden)

    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.

  3. 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

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

    African Journals Online (AJOL)

    Mwale

    2016-05-25

    May 25, 2016 ... the highest genetic diversity followed by genome B while genome D was the lowest diverse. Cluster ... and 95% of people in the developing countries eat wheat or maize in ... area for wheat production in China due to pressure from ...... hypertension in the stroke-prone spontaneously hypertensive rat. Cell.

  5. 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.

  6. 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 ...

  7. Genetic diversity and population structure of Miscanthus sinensis germplasm in China.

    Directory of Open Access Journals (Sweden)

    Hua Zhao

    Full Text Available Miscanthus is a perennial rhizomatous C4 grass native to East Asia. Endowed with great biomass yield, high ligno-cellulose composition, efficient use of radiation, nutrient and water, as well as tolerance to stress, Miscanthus has great potential as an excellent bioenergy crop. Despite of the high potential for biomass production of the allotriploid hybrid M. ×giganteus, derived from M. sacchariflorus and M. sinensis, other options need to be explored to improve the narrow genetic base of M. ×giganteus, and also to exploit other Miscanthus species, including M. sinensis (2n = 2x = 38, as bioenergy crops. In the present study, a large number of 459 M. sinensis accessions, collected from the wide geographical distribution regions in China, were genotyped using 23 SSR markers transferable from Brachypodium distachyon. Genetic diversity and population structure were assessed. High genetic diversity and differentiation of the germplasm were observed, with 115 alleles in total, a polymorphic rate of 0.77, Nei's genetic diversity index (He of 0.32 and polymorphism information content (PIC of 0.26. Clustering of germplasm accessions was primarily in agreement with the natural geographic distribution. AMOVA and genetic distance analyses confirmed the genetic differentiation in the M. sinensis germplasm and it was grouped into five clusters or subpopulations. Significant genetic variation among subpopulations indicated obvious genetic differentiation in the collections, but within-subpopulation variation (83% was substantially greater than the between-subpopulation variation (17%. Considerable phenotypic variation was observed for multiple traits among 300 M. sinensis accessions. Nine SSR markers were found to be associated with heading date and biomass yield. The diverse Chinese M. sinensis germplasm and newly identified SSR markers were proved to be valuable for breeding Miscanthus varieties with desired bioenergy traits.

  8. Managing genetic diversity and society needs

    Directory of Open Access Journals (Sweden)

    Arthur da Silva Mariante

    2008-07-01

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

  9. Genetic diversity of Trichomonas vaginalis reinfection in HIV-positive women.

    Science.gov (United States)

    Conrad, Melissa D; Kissinger, Patricia; Schmidt, Norine; Martin, David H; Carlton, Jane M

    2013-09-01

    Recently developed genotyping tools allow better understanding of Trichomonas vaginalis population genetics and epidemiology. These tools have yet to be applied to T vaginalis collected from HIV+ populations, where understanding the interaction between the pathogens is of great importance due to the correlation between T vaginalis infection and HIV transmission. The objectives of the study were twofold: first, to compare the genetic diversity and population structure of T vaginalis collected from HIV+ women with parasites from reference populations; second, to use the genetic markers to perform a case study demonstrating the usefulness of these techniques in investigating the mechanisms of repeat infections. Repository T vaginalis samples from a previously described treatment trial were genotyped at 11 microsatellite loci. Estimates of genetic diversity and population structure were determined using standard techniques and compared with previously reported estimates of global populations. Genotyping data were used in conjunction with behavioural data to evaluate mechanisms of repeat infections. T vaginalis from HIV+ women maintain many of the population genetic characteristics of parasites from global reference populations. Although there is evidence of reduced diversity and bias towards type 1 parasites in the HIV+ population, the populations share a two-type population structure and parasite haplotypes. Genotyping/behavioural data suggest that 36% (12/33) of repeat infections in HIV+ women can be attributed to treatment failure. T vaginalis infecting HIV+ women is not genetically distinct from T vaginalis infecting reference populations. Information from genotyping can be valuable for understanding mechanisms of repeat infections.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-20

    Jul 20, 2009 ... The presence of sufficient genetic diversity in the germplam is an important ..... Figure 1. PCR amplification profile of Elite-II SH Wheat using the primer OPG-2. .... genetic relationships among cowpea breeding lines and local.

  11. Genetic Diversity in Sub continental Land race cultivars

    African Journals Online (AJOL)

    M. shahbaz

    2012-05-31

    May 31, 2012 ... 1Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan. ... Narrowing genetic diversity is a limiting factor in wheat breeding. .... DNA was extracted following the modified.

  12. Evolution of increased phenotypic diversity enhances population performance by reducing sexual harassment in damselflies.

    Science.gov (United States)

    Takahashi, Yuma; Kagawa, Kotaro; Svensson, Erik I; Kawata, Masakado

    2014-07-18

    The effect of evolutionary changes in traits and phenotypic/genetic diversity on ecological dynamics has received much theoretical attention; however, the mechanisms and ecological consequences are usually unknown. Female-limited colour polymorphism in damselflies is a counter-adaptation to male mating harassment, and thus, is expected to alter population dynamics through relaxing sexual conflict. Here we show the side effect of the evolution of female morph diversity on population performance (for example, population productivity and sustainability) in damselflies. Our theoretical model incorporating key features of the sexual interaction predicts that the evolution of increased phenotypic diversity will reduce overall fitness costs to females from sexual conflict, which in turn will increase productivity, density and stability of a population. Field data and mesocosm experiments support these model predictions. Our study suggests that increased phenotypic diversity can enhance population performance that can potentially reduce extinction rates and thereby influence macroevolutionary processes.

  13. Genetic Diversity of Hibiscus tiliaceus (Malvaceae) in China Assessed using AFLP Markers

    Science.gov (United States)

    TANG, TIAN; ZHONG, YANG; JIAN, SHUGUANG; SHI, SUHUA

    2003-01-01

    Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variations within and among nine natural populations of Hibiscus tiliaceus in China. DNA from 145 individuals was amplified with eight primer pairs. No polymorphisms were found among the 20 samples of a marginal population of recent origin probably due to a founder effect. Across the other 125 individuals, 501 of 566 bands (88·5 %) were polymorphic, and 125 unique AFLP phenotypes were observed. Estimates of genetic diversity agreed with life history traits of H. tiliaceus and geographical distribution. AMOVA analysis revealed that most genetic diversity resided within populations (84·8 %), which corresponded to results reported for outcrossing plants. The indirect estimate of gene flow based on ϕST was moderate (Nm = 1·395). Long-distance dispersal of floating seeds and local environments may play an important role in shaping the genetic diversity of the population and the genetic structure of this species. PMID:12930729

  14. Inbreeding and Genetic Diversity in Three Imported Swine Breeds in China Using Pedigree Data

    Directory of Open Access Journals (Sweden)

    G. Q. Tang

    2013-06-01

    Full Text Available The accumulation of inbreeding and the loss of genetic diversity is a potential problem in the modern swine breeds in China. Therefore, the purpose of this study was to analyze the pedigrees of Chinese Duroc (CD, Landrace (CL and Yorkshire (CY swine to estimate the past and current rates of inbreeding, and to identify the main causes of genetic diversity loss. Pedigree files from CD, CL and CY containing, 4529, 16,776 and 22,600 records, respectively, were analyzed. Pedigree completeness indexes of the three breeds, accounting for one generation back, were 83.72, 93.93 and 93.59%, respectively. The estimated average annual inbreeding rates for CD, CL and CY in recent three years were 0.21, 0.19 and 0.13%, respectively. The estimated average percentage of genetic diversity loss within each breed in recent three years was about 8.92, 2.19, and 3.36%, respectively. The average relative proportion of genetic diversity loss due to unequal contributions of founders in CD, CL and CY was 69.09, 57.95 and 60.57%, and due to random genetic drift was 30.91, 42.05 and 39.43%, respectively. The estimated current effective population size for CD, CL and CY was 76, 117 and 202, respectively. Therefore, CD has been found to have lost considerable genetic diversity, demanding priority for optimizing the selection and mating to control future coancestry and inbreeding. Unequal contribution of founders was a major cause of genetic diversity loss in Chinese swine breeds and random genetic drift also showed substantial impact on the loss of diversity.

  15. Elm genetic diversity and hybridization in the presence of Dutch elm disease

    Science.gov (United States)

    Dutch elm disease (DED) has devastated native North American elm species for more than 75 years. The impact of DED on the genetic diversity of one native elm species, U. rubra or slippery elm, is summarized and its potential impact on the genetic diversity of the other four North American native elm...

  16. 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- ...

  17. 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

  18. 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

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

    Directory of Open Access Journals (Sweden)

    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

  20. Loss of genetic diversity in Maculinea populations over 10 years

    DEFF Research Database (Denmark)

    Nash, David Richard; Lomborg, Andreas Eg

    I will present the results of research on the population genetics of Maculinea alcon and M. arion in Southern scandinavia, which shows a strong decrease in genetic diversity in most populations, even if those populations are apparently otherwise healthy....

  1. Molecular Insights into the Genetic Diversity of Garcinia cambogia Germplasm Accessions

    Directory of Open Access Journals (Sweden)

    C Tharachand

    2015-10-01

    Full Text Available ABSTRACTIn this work, the genetic relationship among twelveGarcinia cambogia (Gaertn. Desr. accessions were evaluated using Random Amplified Polymorphic DNA markers. The samples were part of the germplasm collected and maintained at NBPGR Regional station, Thrissur, India. Out of thirty RAPD primers used for screening, seven primers produced a total of 128 polymorphic markers in twelve accessions. The Polymorphic Information Content (PIC ranged from 0.28 (OPA18 to 0.37 (OPA9 and Marker Index (MI ranged between 3.61 (OPA12 and 5.93 (OPA3 among the primers used. Jaccard's coefficient of genetic similarity ranged between 0.07 and 0.64. The dendrogram constructed based on the similarity matrix generated from the molecular and morphological data showed the genetic relationship among the sampled accessions. Mantel matrix test showed a positive correlation (r = 0.49 between the cluster analysis of RAPD data and morphological data. The clustering pattern in the molecular dendrogram and Principle Coordinate Analysis (PCoA showed that the genotypes were diverse, which was in congruence with the similarity index values and morphological dendrogram. High frequency of similarity values in the range of 0.11 to 0.17 suggested the existence of high genetic diversity among the accessions. The high level of genetic diversity among the studied accessions ofG.cambogia was also supported by the large variation in the morphological characters observed in the flowers, leaves, fruits and seeds of these sampled accessions. This is the first report for the molecular based genetic diversity studies for these accessions.

  2. 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.

  3. The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages.

    Science.gov (United States)

    Selkoe, Kimberly A; Gaggiotti, Oscar E; Treml, Eric A; Wren, Johanna L K; Donovan, Mary K; Toonen, Robert J

    2016-04-27

    Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbour the greatest genetic diversity on average. We found that a species's life history (e.g. depth range and herbivory) mediates response of genetic diversity to seascape drivers in logical ways. Furthermore, a metric of combined multi-species AR showed strong coupling to species richness and habitat area, quality and stability that few species showed individually. We hypothesize that macro-ecological forces and species interactions, by mediating species turnover and occupancy (and thus a site's mean effective population size), influence the aggregate genetic diversity of a site, potentially allowing it to behave as an apparent emergent trait that is shaped by the dominant seascape drivers. The results highlight inherent feedbacks between ecology and genetics, raise concern that genetic resilience of entire reef communities is compromised by factors that reduce coral cover or available habitat, including thermal stress, and provide a foundation for new strategies for monitoring and preserving biodiversity of entire reef ecosystems. © 2016 The Authors.

  4. Genetic diversity of high performance cultivars of upland and irrigated Brazilian rice.

    Science.gov (United States)

    Coelho, G R C; Brondani, C; Hoffmann, L V; Valdisser, P A M R; Borba, T C O; Mendonça, J A; Rodrigues, L A; de Menezes, I P P

    2017-09-21

    The objective of this study was to analyze the diversity and discrimination of high-performance Brazilian rice cultivars using microsatellite markers. Twenty-nine rice cultivars belonging to EMBRAPA Arroz e Feijão germplasm bank in Brazil were genotyped by 24 SSR markers to establish their structure and genetic discrimination. It was demonstrated that the analyzed germplasm of rice presents an expressive and significant genetic diversity with low heterogeneity among the cultivars. All 29 cultivars were differentiated genetically, and were organized into two groups related to their upland and irrigated cultivation systems. These groups showed a high genetic differentiation, with greater diversity within the group that includes the cultivars for irrigated system. The genotyping data of these cultivars, with the morphological e phenotypical data, are valuable information to be used by rice breeding programs to develop new improved cultivars.

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

    African Journals Online (AJOL)

    Jane

    2011-07-25

    Jul 25, 2011 ... The genetic diversity of 19 Arrhenatherum elatius accessions was analyzed ... can be used as novel DNA markers for genomic .... phylogenies and evolutionary biology. .... struction Project of the Beijing Academy of Agriculture.

  6. 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. ... program for Bambara groundnut, a thorough under- ..... na* = Observed number of alleles; ne* = Effective number of alleles ...

  7. Genetic diversity as assessed by morphological and microsatellite ...

    African Journals Online (AJOL)

    lap

    2012-10-18

    Oct 18, 2012 ... Genetic diversity in 20 elite greengram [Vigna radiata (L.) R. Wilczek] ... bean and cowpea were successfully amplified across 20 greengram genotypes of .... PCR amplified products were subjected to electrophoresis in a.

  8. Morphological classification of genetic diversity in cultivated okra ...

    African Journals Online (AJOL)

    Morphological classification of genetic diversity in cultivated okra, Abelmoschus esculentus (L) Moench using principal component analysis (PCA) and single linkage cluster analysis (SLCA). CC Nwangburuka, OB Kehinde, DK Ojo, OA Denton, AR Popoola ...

  9. The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico.

    Science.gov (United States)

    Rodelo-Urrego, Manuel; García-Arenal, Fernando; Pagán, Israel

    2015-01-01

    Current declines in biodiversity put at risk ecosystem services that are fundamental for human welfare. Increasing evidence indicates that one such service is the ability to reduce virus emergence. It has been proposed that the reduction of virus emergence occurs at two levels: through a reduction of virus prevalence/transmission and, as a result of these epidemiological changes, through a limitation of virus genetic diversity. Although the former mechanism has been studied in a few host-virus interactions, very little is known about the association between ecosystem biodiversity and virus genetic diversity. To address this subject, we estimated genetic diversity, synonymous and non-synonymous nucleotide substitution rates, selection pressures, and frequency of recombinants and re-assortants in populations of Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV) that infect chiltepin plants in Mexico. We then analyzed how these parameters varied according to the level of habitat anthropization, which is the major cause of biodiversity loss. Our results indicated that genetic diversity of PepGMV (but not of PHYVV) populations increased with the loss of biodiversity at higher levels of habitat anthropization. This was mostly the consequence of higher rates of synonymous nucleotide substitutions, rather than of adaptive selection. The frequency of recombinants and re-assortants was higher in PepGMV populations infecting wild chiltepin than in those infecting cultivated ones, suggesting that genetic exchange is not the main mechanism for generating genetic diversity in PepGMV populations. These findings provide evidence that biodiversity may modulate the genetic diversity of plant viruses, but it may differentially affect even two closely related viruses. Our analyses may contribute to understanding the factors involved in virus emergence.

  10. Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

    Directory of Open Access Journals (Sweden)

    Gregory W. Peterson

    2014-10-01

    Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

  11. Entropy and Information Approaches to Genetic Diversity and its Expression: Genomic Geography

    Directory of Open Access Journals (Sweden)

    William B. Sherwin

    2010-07-01

    Full Text Available This article highlights advantages of entropy-based genetic diversity measures, at levels from gene expression to landscapes. Shannon’s entropy-based diversity is the standard for ecological communities. The exponentials of Shannon’s and the related “mutual information” excel in their ability to express diversity intuitively, and provide a generalised method of considering microscopic behaviour to make macroscopic predictions, under given conditions. The hierarchical nature of entropy and information allows integrated modeling of diversity along one DNA sequence, and between different sequences within and among populations, species, etc. The aim is to identify the formal connections between genetic diversity and the flow of information to and from the environment.

  12. Lowered Diversity and Increased Inbreeding Depression within Peripheral Populations of Wild Rice Oryza rufipogon.

    Science.gov (United States)

    Gao, Li-Zhi; Gao, Cheng-Wen

    2016-01-01

    peripheral populations. Our results together suggest that historical contraction of geographical range, demographic changes, and environmental conditions near the northern and northeastern margins of O. rufipogon favor inbreeding and possibly selfing, leading to the rapidly decreased effective population size. Genetic drift, reduced gene flow, and possible local selection, consequently lead to lowered gene diversity, accelerated genetic divergence and increased inbreeding depression found in peripheral populations of O. rufipogon. Given these characteristics observed, northern and northeastern peripheral populations deserve relatively different conservation strategies for either germplasm sampling of ex situ conservation or setting in situ reserves for the adaptation to possible environmental changes and the future germplasm utilization of wild rice.

  13. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

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

  14. Genetic diversity in soybean genotypes using phenotypic characters and enzymatic markers.

    Science.gov (United States)

    Zambiazzi, E V; Bruzi, A T; Sales, A P; Borges, I M M; Guilherme, S R; Zuffo, A M; Lima, J G; Ribeiro, F O; Mendes, A E S; Godinho, S H M; Carvalho, M L M

    2017-09-21

    The objective of this study was to evaluate the genetic diversity of soybean cultivars by adopting phenotypic traits and enzymatic markers, the relative contribution of agronomic traits to diversity, as well as diversity between the level of technology used in soybean cultivars and genetic breeding programs in which cultivars were inserted. The experiments were conducted on the field at the Center for Scientific and Technological Development in crop-livestock production and the Electrophoresis Laboratory of Lavras Federal University. The agronomic traits adopted were grain yield, plant height, first legume insertion, plant lodging, the mass of one thousand seeds, and days for complete maturation, in which the Euclidean distance, grouped by Tocher and UPGMA criteria, was obtained. After electrophorese gels for enzymatic systems, dehydrogenase alcohol, esterase, superoxide dismutase, and peroxidase were performed. The genetic similarity estimative was also obtained between genotypes by the Jaccard coefficient with subsequent grouping by the UPGMA method. The formation of two groups was shown using phenotypic characters in the genetic diversity study and individually discriminating the cultivar 97R73 RR. The character with the greatest contribution to the genetic divergence was grain yield with contribution higher than 90.0%. To obtain six different groups, individually discriminating the cultivars CG 8166 RR, FPS Jupiter RR, and BRS MG 780 RR, enzymatic markers were used. Cultivars carrying the RR technology presented more divergence than conventional cultivars and IPRO cultivars.

  15. Genetic diversity of Pinus halepensis Mill. populations detected by RAPD loci

    OpenAIRE

    Gómez , Aránzazu; Alía , Ricardo; Bueno , María

    2001-01-01

    International audience; Genetic diversity of Pinus halepensis Mill. was analysed in nine populations (six Spanish populations and one each from Tunisia, France and Greece). Twenty four RAPD loci were amplified with 60 megagametophyte DNA samples from each population. Populations' contribution to Nei gene diversity and to allelic richness were calculated. Results showed higher within population genetic variation but also a $G_{{\\rm ST}} = 13.6\\%$ higher than those detected in previous studies ...

  16. Genetic diversity and population structure of a protected species: Polygala tenuifolia Willd.

    Science.gov (United States)

    Peng, Yan Qun; Fan, Ling Ling; Mao, Fu Ying; Zhao, Yun Sheng; Xu, Rui; Yin, Yu Jie; Chen, Xin; Wan, De Guang; Zhang, Xin Hui

    2018-03-01

    Polygala tenuifolia Willd. is an important protected species used in traditional Chinese medicine. In the present study, amplified fragment length polymorphism (AFLP) markers were employed to characterize the genetic diversity in wild and cultivated P. tenuifolia populations. Twelve primer combinations of AFLP produced 310 unambiguous and repetitious bands. Among these bands, 261 (84.2%) were polymorphic. The genetic diversity was high at the species level: percentage of polymorphic loci (PPL)=84.2%, Nei's gene diversity (h)=0.3296 and Shannon's information index (I)=0.4822. Between the two populations, the genetic differentiation of 0.1250 was low and the gene flow was relatively high, at 3.4989. The wild population (PPL=81.9%, h=0.3154, I=0.4635) showed a higher genetic diversity level than the cultivated population (PPL=63.9%, h=0.2507, I=0.3688). The results suggest that the major factors threatening the persistence of P. tenuifolia resources are ecological and human factors rather than genetic. These results will assist with the design of conservation and management programs, such as in natural habitat conservation, setting the excavation time interval for resource regeneration and the substitution of cultivated for wild plants. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  17. Genetic Diversity of the Black Mangrove Avicennia germinans (L. Stearn in Northwestern Mexico

    Directory of Open Access Journals (Sweden)

    Olivia Millán-Aguilar

    2016-09-01

    Full Text Available Mangrove forests of Mexico have been threatened by the effects of anthropogenic activities during the last decades, mostly related to aquaculture, agriculture, livestock and urban development. Genetic diversity and fine-scale genetic structure of two generations of the black mangrove Avicennia germinans (L. Stearn were investigated in perturbed and preserved sites from three lagoon systems in Sinaloa, Mexico. Genetic diversity and overall genetic structure were similar between perturbed and preserved sites. However, lower levels of fine-scale spatial genetic structure were observed in two of the younger (sapling generations. We attribute this to differences in local dynamics of each lagoon system, their status of conservation and levels of fragmentation. Also, low connectivity and the effects of disturbance could restrict the movement of pollinators and seed dispersal capabilities, resulting in low levels of genetic diversity and signs of inbreeding. Perturbed populations of A. germinans may play an important role in in situ conservation of this complex ecosystem.

  18. Genetic diversity of the cestode Echinococcus multilocularis in red foxes at a continental scale in Europe.

    Directory of Open Access Journals (Sweden)

    Jenny Knapp

    2009-06-01

    Full Text Available Alveolar echinococcosis (AE is a severe helminth disease affecting humans, which is caused by the fox tapeworm Echinococcus multilocularis. AE represents a serious public health issue in larger regions of China, Siberia, and other regions in Asia. In Europe, a significant increase in prevalence since the 1990s is not only affecting the historically documented endemic area north of the Alps but more recently also neighbouring regions previously not known to be endemic. The genetic diversity of the parasite population and respective distribution in Europe have now been investigated in view of generating a fine-tuned map of parasite variants occurring in Europe. This approach may serve as a model to study the parasite at a worldwide level.The genetic diversity of E. multilocularis was assessed based upon the tandemly repeated microsatellite marker EmsB in association with matching fox host geographical positions. Our study demonstrated a higher genetic diversity in the endemic areas north of the Alps when compared to other areas.The study of the spatial distribution of E. multilocularis in Europe, based on 32 genetic clusters, suggests that Europe can be considered as a unique global focus of E. multilocularis, which can be schematically drawn as a central core located in Switzerland and Jura Swabe flanked by neighbouring regions where the parasite exhibits a lower genetic diversity. The transmission of the parasite into peripheral regions is governed by a "mainland-island" system. Moreover, the presence of similar genetic profiles in both zones indicated a founder event.

  19. Genetic Diversity and Identification of Chinese-Grown Pecan Using ISSR and SSR Markers

    Directory of Open Access Journals (Sweden)

    Zhong-Ren Guo

    2011-12-01

    Full Text Available Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic in the range of 140–1,950 bp for the ISSR and 70 amplified bands (100% polymorphic in the range of 50–350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

  20. Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.

    Science.gov (United States)

    Jia, Xiao-Dong; Wang, Tao; Zhai, Min; Li, Yong-Rong; Guo, Zhong-Ren

    2011-12-06

    Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

  1. Genetic diversity enhances the resistance of a seagrass ecosystem to disturbance

    OpenAIRE

    Hughes, A. R.; Stachowicz, John J

    2004-01-01

    Motivated by recent global reductions in biodiversity, empirical and theoretical research suggests that more species-rich systems exhibit enhanced productivity, nutrient cycling, or resistance to disturbance or invasion relative to systems with fewer species. In contrast, few data are available to assess the potential ecosystem-level importance of genetic diversity within species known to play a major functional role. Using a manipulative field experiment, we show that increasing genotypic di...

  2. 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

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  4. Genetic diversity of Toxoplama gondii isolates from Ethiopian feral cats

    Science.gov (United States)

    Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioa...

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

    African Journals Online (AJOL)

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

  6. Genetic diversity in three morphological types of Astragalus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... high genetic diversity suggested that each type had a potential to develop new strains or cultivars and .... herbs and widespread distributed species (Yao et al.,. 2008) ... 1) A. membranaceus var. mongholicus is a cross-.

  7. Raps markers for genetic diversity analysis in rice (Oryza sativa L)

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez, A; Fuentes, Jorge L [Centro de Estudios Aplicados al Desarrollo Nuclear, La Habana (Cuba); Deus, Juan E [Instituto de Investigaciones del Arroz, Habana (Cuba); Duque, Maria C [Centro Internacional de la Agricultura Tropical. Proyecto de Arroz , Cali (Colombia)

    1999-07-01

    The establishment of relationships between genotypes existing in gene banks that may be used in new crosses, and about genetic diversity in available germplasm, is very useful for plant breeders. In this work, a genetic diversity analysis among 20 varieties of the Cuban rice germplasm bank was performed by using RAPD markers. Twenty four decamer primers were screened which produced 61 polymorphic bands out of 105 consistent and reproducible amplified fragments (58.1 %). The proportion of polymorphic bands varied for each primer, with an average of 3 polymorphic bands per primer, these results agreed with previous reports on RAPD polymorphism in rice germplasm. Depending on the primer, 1 to 7 distinct patterns were obtained among the screened genotypes. Pair-wise genetic distances between genotypes were computed based on Dice's coefficient. Three major, statistically robust groups were obtained in the UPGMA dendrogram (A, B and C) which clearly corresponded to different genetic pools. Additionally, more insight could be gained according to the sub-grouping pattern within group A, which included the principal semi-dwarf commercial varieties. The present study allowed to prove the efficiency of RAPD markers for genetic diversity analysis in closely related germplasm, particularly for the semi-dwarf Cuban commercial rice cultivars. Also, the existence of a narrow genetic base among these varieties has been confirmed, pointing at the urgent necessity of widen it.

  8. Raps markers for genetic diversity analysis in rice (Oryza sativa L)

    International Nuclear Information System (INIS)

    Alvarez, A.; Fuentes, Jorge L.; Deus, Juan E.; Duque, Maria C.

    1999-01-01

    The establishment of relationships between genotypes existing in gene banks that may be used in new crosses, and about genetic diversity in available germplasm, is very useful for plant breeders. In this work, a genetic diversity analysis among 20 varieties of the Cuban rice germplasm bank was performed by using RAPD markers. Twenty four decamer primers were screened which produced 61 polymorphic bands out of 105 consistent and reproducible amplified fragments (58.1 %). The proportion of polymorphic bands varied for each primer, with an average of 3 polymorphic bands per primer, these results agreed with previous reports on RAPD polymorphism in rice germplasm. Depending on the primer, 1 to 7 distinct patterns were obtained among the screened genotypes. Pair-wise genetic distances between genotypes were computed based on Dice's coefficient. Three major, statistically robust groups were obtained in the UPGMA dendrogram (A, B and C) which clearly corresponded to different genetic pools. Additionally, more insight could be gained according to the sub-grouping pattern within group A, which included the principal semi-dwarf commercial varieties. The present study allowed to prove the efficiency of RAPD markers for genetic diversity analysis in closely related germplasm, particularly for the semi-dwarf Cuban commercial rice cultivars. Also, the existence of a narrow genetic base among these varieties has been confirmed, pointing at the urgent necessity of widen it

  9. GENETIC DIVERSITY ANALYSIS OF MANGABA (Hancornia speciosa Gomes, AN EXOTIC BRAZILIAN TROPICAL SPECIES

    Directory of Open Access Journals (Sweden)

    Ana Veruska Cruz da Silva

    2012-05-01

    Full Text Available Twenty genotypes from natural population of mangaba located in Itaporanga D’Ajuda (Sergipe state - Brazil were subjected to analysis using RAPD markers. Polymorphism, genetic diversity and structure parameters were determined to characterize the differences between plants. 60 DNA fragments were generated by 10 primers, 85% of which were polymorphic. Results show a quantitative genetic diversity value of 0.35 and a Shannon index of 0.46 in the population. The similarity among the specimens according to Jaccard’s coefficient ranged from 0.36 to 0.87. Using cluster analysis it was possible to indentify five groups. Three individuals also stand out since they presented significant divergence from the groups. The PCoA formed four groups, with three of the groups isolated from the others. This investigation showed that genetic diversity was relatively large among these individuals. In addition, the results demonstrated that RAPD markers are a useful tool for evaluating the genetic diversity and relationships among mangaba.

  10. 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.

  11. 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.

    2016-01-01

    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 methods using genetic modification of populations. PMID:27671732

  12. 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...

  13. Probing genetic diversity to characterize red rot resistance in sugarcane

    Energy Technology Data Exchange (ETDEWEB)

    Mumtaz, A S; Dure-e-Nayab,; Iqbal, M J; Shinwari, Z.K., E-mail: asmumtaz@qau.edu.pk

    2011-10-15

    Genetic diversity was assessed in a set of twelve sugarcane genotypes using Random Amplified Polymorphic DNA (RAPD). A total of thirty-two oligo-primers were employed, sixteen of them revealed amplification at 149 loci, out of which 136 were polymorphic. The genotype SPSG-26 showed the highest number of polymorphic loci, followed by CSSG-668 and HSF-242. Pairwise genetic similarity ranged from 67.2% to 83.3%. The UPGMA cluster analysis resolved most of the accessions in two groups. The clustering pattern did not place all resistant varieties in one or related group which depict diverse resistance source in the present set of sugarcane varieties. Ten primers revealed genotype specific bands among which four primers (K07, H02, K10 and F01) produced multiple genotype specific bands that aid genotype identification especially those with red rot resistance. The present study not only provided information on the genetic diversity among the genotypes but also revealed the potential of RAPD-PCR markers for genotype identification and therefore could be utilized in marker assisted selection for red rot resistance in sugarcane. (author)

  14. Genetic diversity and environmental associations of sacsaoul ( Haloxylon ammodendron)

    Science.gov (United States)

    Zhang, Linjing; Zhao, Guifang; Yue, Ming; Pan, Xiaoling

    2003-07-01

    Random amplified polymorphic DNA (RAPD) markers were used to assess levels and patterns of genetic diversity in H. ammodendron (Chenopodiaceae). A total of 117 plants from 6 subpopulations on oasis-desert ecotone was analyzed by 16 arbitrarily chosen primers resulting in highly reproducible RAPD bands. The analysis of molecular variance (AMOVA) with distances among individuals showed that most of the variation (74%) occurred among individuals within subpopulations, which is expected for a crossing organism, and 26% of variation among subpopulations. Estimates of Shannon index and Nei"s index from allele frequencies corroborated AMOVA partitioning in H. ammodendron. UPGMA cluster analyses, based on genetic distance, do not revealed grouping of some geographically proximate populations. This is the first report of the partitioning of genetic variability within and between subpopulations of H. ammodendron and provides important baseline data for optimizing sampling strategies and for conserving the genetic resources of this species. The Percentage of polymorphic loci was as high as 96%, presumably being response to oasis-desert ecotone. There were gene flows (Nm=5.38 individuals/generation), based on gene differentiation coefficient (GST was 0.1567) between subpopulations, and strong habitat selection override the gene flow to maintain the subpopulation differentiation. Correlation analyses showed that there was significant relationship between genetic diversity and soil CL ion.

  15. EvoSNP-DB: A database of genetic diversity in East Asian populations.

    Science.gov (United States)

    Kim, Young Uk; Kim, Young Jin; Lee, Jong-Young; Park, Kiejung

    2013-08-01

    Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

  16. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity.

    Directory of Open Access Journals (Sweden)

    Nicolas Heslot

    Full Text Available Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L. genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.

  17. Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

    Science.gov (United States)

    Heslot, Nicolas; Rutkoski, Jessica; Poland, Jesse; Jannink, Jean-Luc; Sorrells, Mark E.

    2013-01-01

    Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis. PMID:24040295

  18. Estimating intraspecific genetic diversity from community DNA metabarcoding data

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    2018-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Saba Jasim Aljumaili

    2018-01-01

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

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

    Science.gov (United States)

    Jasim Aljumaili, Saba; Rafii, M Y; Latif, M A; Sakimin, Siti Zaharah; Arolu, Ibrahim Wasiu; Miah, Gous

    2018-01-01

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

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

    Science.gov (United States)

    Jasim Aljumaili, Saba; Sakimin, Siti Zaharah; Arolu, Ibrahim Wasiu; Miah, Gous

    2018-01-01

    Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon's information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei's gene diversity index of 0.36. The dendrogram based on UPGMA and Nei's genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development. PMID:29736396

  2. GENETIC DIVERSITY OF WINTER BREAD WHEAT (Triticum aestivum L. ssp. vulgare

    Directory of Open Access Journals (Sweden)

    Sonja Petrović

    2011-06-01

    Full Text Available Diversity was analyzed based on agronomic and morphologic traits and molecular data. The main objectives of this study were: 1. to estimate genetic diversity of wheat germplasm using agronomic and morphologic traits and molecular markers, 2. to investigate the existence of genetic erosion within tested wheat germplasm, 3. to explore potential utilization of combination of agronomic, morphologic and molecular markers in plant breeding. Forty winter bread wheat varieties were used originating from Croatia, Austria, France, Italy and Russia. Field trial was conducted during two vegetation years (2007/2008, 2008/2009 in three replications according to randomized block design. Ten traits were included in agronomic and morphologic analysis. Composition of high molecular weight glutenin subunits (HMW GS was evaluated for 16 varieties, whereas literature data are used for the rest. Starch composition analysis was based on amylose and amylopectin isolation, their quantity and ratio. For the SSR analysis 26 microsatellite primers were used, and for the AFLP analysis four primer combinations. Statistical analysis was performed using SAS Software 9.1.3, NTSYS ver.2.2., Arlequin ver2.0. and Powermarker ver.3.25. Analyzed varieties displayed highly significant differences (p<0,001 for all agronomic traits and for amylose/amylopectin ratio. High variability of HMW GS was found among varieties. Estimation of genetic diversity based on morphologic and molecular data were used to construct dendograms. AMOVA was used to evaluate variability based on molecular data. Genetic diversity was estimated among and within morphologic and molecular data. SSR and AFLP markers showed efficient discrimination power between highly related genotypes. Significant correlation was found out between two molecular methods which showed more accurate estimate of genetic diversity than by agronomic and morphologic data.

  3. Serpentine soils affect heavy metal tolerance but not genetic diversity in a common Mediterranean ant.

    Science.gov (United States)

    Frizzi, Filippo; Masoni, Alberto; Çelikkol, Mine; Palchetti, Enrico; Ciofi, Claudio; Chelazzi, Guido; Santini, Giacomo

    2017-08-01

    Natural habitats with serpentine soils are rich in heavy metal ions, which may significantly affect ecological communities. Exposure to metal pollutants results, for instance, in a reduction of population genetic diversity and a diffused higher tolerance towards heavy metals. In this study, we investigated whether chronic exposure to metals in serpentine soils affect accumulation patterns, tolerance towards metal pollutants, and genetic diversity in ants. In particular, we studied colonies of the common Mediterranean ant, Crematogaster scutellaris, along a contamination gradient consisting of two differently contaminated forests and a reference soil with no geogenic contamination. We first evaluated the metal content in both soil and ants' body. Then, we tested for tolerance towards metal pollutants by evaluating the mortality of ants fed with nickel (Ni) solutions of increasing concentrations. Finally, differences in genetic diversity among ants from different areas were assessed using eight microsatellite loci. Interestingly, a higher tolerance to nickel solutions was found in ants sampled in sites with intermediate levels of heavy metals. This may occur, because ants inhabiting strongly contaminated areas tend to accumulate higher amounts of contaminants. Additional ingestion of toxicants beyond the saturation threshold would lead to death. There was no difference in the genetic diversity among ant colonies sampled in different sites. This was probably the result of queen mediated gene flow during nuptial flights across uncontaminated and contaminated areas of limited geographical extent. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. 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, ...

  5. Loss and recovery of genetic diversity in adapting populations of HIV.

    Directory of Open Access Journals (Sweden)

    Pleuni S Pennings

    2014-01-01

    Full Text Available The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence data, we make four observations that shed a light on the underlying processes and allow us to infer the short-term effective population size of the viral population in a patient. Our first observation is that the evolution of drug resistance usually occurs by the fixation of one drug-resistance mutation at a time, as opposed to several changes simultaneously. Second, we find that these fixation events are accompanied by a reduction in genetic diversity in the region surrounding the fixed drug-resistance mutation, due to the hitchhiking effect. Third, we observe that the fixation of drug-resistance mutations involves both hard and soft selective sweeps. In a hard sweep, a resistance mutation arises in a single viral particle and drives all linked mutations with it when it spreads in the viral population, which dramatically reduces genetic diversity. On the other hand, in a soft sweep, a resistance mutation occurs multiple times on different genetic backgrounds, and the reduction of diversity is weak. Using the frequency of occurrence of hard and soft sweeps we estimate the effective population size of HIV to be 1.5 x 10(5 (95% confidence interval [0.8 x 10(5,4.8 x 10(5]. This number is much lower than the actual number of infected cells, but much larger than previous population size estimates based on synonymous diversity. We propose several explanations for the observed discrepancies. Finally, our fourth observation is that genetic diversity at non-synonymous sites recovers to its pre-fixation value within 18 months, whereas diversity at synonymous sites remains depressed after this time period. These results improve our understanding of HIV evolution and have potential implications for treatment strategies.

  6. 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

  7. Genetic Diversity in Commercial Rapeseed (Brassica napus L.) Varieties from Turkey as Revealed by RAPD

    OpenAIRE

    Özlem ÖZBEK; Betül Uçar GIDIK

    2013-01-01

    In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as Brassica napus L. should be evaluated and the genotypes, which have higher genetic diversity index, should be addressed as potential parental cross materials in breeding programs. In this study, the genetic diversity was analysed by using randomly amplified polymorphic DNA analysis (RAPD) technique in nine Turkish com...

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

    African Journals Online (AJOL)

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

  9. Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

    Science.gov (United States)

    Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

    2013-01-01

    In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

  10. High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae uncovered by microsatellite loci.

    Directory of Open Access Journals (Sweden)

    Chris D Lowe

    2010-12-01

    Full Text Available Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST values indicated weak to moderate population sub-division (0.01-0.12, but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.

  11. 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

    -monitoring schemes. Here, we provide a review and an assessment of the different attempts made to provide such indicators for tree genetic diversity from the global level down to the level of the management unit. So far, no generally accepted indicators have been provided as international standards, nor tested...... for their possible use in practice. We suggest that indicators for monitoring genetic diversity and dynamics should be based on ecological and demographic surrogates of adaptive diversity as well as genetic markers capable of identifying genetic erosion and gene flow. A comparison of past and present genecological...... 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...

  12. Study of human genetic diversity : inferences on population origin and history

    OpenAIRE

    Haber, Marc, 1980-

    2013-01-01

    Patterns of human genetic diversity suggest that all modern humans originated from a small population in Africa that expanded rapidly 50,000 years ago to occupy the whole world. While moving into new environments, genetic drift and natural selection affected populations differently, creating genetic structure. By understanding the genetic structure of human populations, we can reconstruct human history and understand the genetic basis of diseases. The work presented here contributes to the on...

  13. 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...

  14. Genetic Diversity Analysis in 27 Tomato Accessions Using Morphological and Molecular Markers

    Directory of Open Access Journals (Sweden)

    Catur Herison

    2018-02-01

    Full Text Available Genetic diversity is the most important aspect in tomato breeding activities. Better assessment on the diversity of the collected accessions will come up with better result of the cultivar development. This study aimed at analyzing the genetic diversity of 27 tomato accessions by morphological and molecular markers. Twenty seven accessions collected from various regions of Indonesia were planted in the field and evaluated for their morphological traits, and RAPD analyzed for their molecular markers. The UPGMA clustering analyzes, elaborating the combination of morphological and molecular data, indicated that the tomato accessions could be grouped into 5 major groups with 70 % genetic similarity levels. Current study indicated that although many accessions came from different locations, they congregated into the same group. Cherry, Kudamati 1 and Lombok 3 were the farthest genetic distant accessions to the others. Those three genotypes will be the most valuable accessions, when they were crossed with other accessions, for designing a prospective breeding program in the future.

  15. Low genetic diversity and intrapopulation spatial genetic structure of the Atlantic Forest tree, Esenbeckia leiocarpa Engl. (Rutaceae

    Directory of Open Access Journals (Sweden)

    G. Forti

    2014-12-01

    Full Text Available Studies on population genetics are the key to designing effective in situ management plans for tree species, in particular, those subjected to pressure from anthropogenic processes, such as forest fragmentation and logging. To investigate genetic diversity, inbreeding and intrapopulation spatial genetic structure (SGS in a fragmented population of the insect-pollinated tropical tree, Esenbeckia leiocarpa, we developed specific microsatellite markers for this species and mapped and sampled 100 individuals in a forest plot. Two issues were addressed in particular: (i the level of genetic diversity, inbreeding and effective population size, (ii whether intrapopulation spatial genetic structure exists. Among the 14 loci developed, we only used the three that presented polymorphism to estimate the genetic parameters. Genetic diversity was low, whereby the average number of alleles per locus (A was 3.3 and observed (H0 and expected heterozygosities (He were 0.336 and 0.298, respectively. The average fixation index was significantly higher than zero (F = 0.112, suggesting inbreeding. Significant SGS was found up to 7 m and between 31 to 38 m, indicating that trees growing within these distances may be related. Estimates of the effective population size indicated that the 100 sampled trees correspond to 14 individuals that are neither related nor inbred. Our results suggest that the microsatellite markers developed in this study are suitable for studies on geneticdiversity and structure, mating systems, gene flow and SGS in this species.

  16. 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 ...

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

    African Journals Online (AJOL)

    USER

    2010-08-02

    Aug 2, 2010 ... The average genetic diversity index of wild soybeans and landraces was 1.5421 and ... genetic identity (0.5265) and gene flow (1.8338) between wild soybeans and cultivars ..... The project was financed by the National Natural Science .... Biology and Biotechnology Centre, University of Alberta, Alberta.

  18. Study of genetic diversity in Sudanese sesame (Sesamum indicum L ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-17

    Dec 17, 2008 ... Study of genetic diversity in Sudanese sesame. (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers. E. Abdellatef 1*, R. Sirelkhatem 1, M. M. Mohamed Ahmed1, K. H. Radwan2 and. M. M. Khalafalla1. 1Commission for Biotechnology and Genetic Engineering, ...

  19. Gene flow and maintenance of genetic diversity in invasive mosquitofish (Gambusia holbrooki.

    Directory of Open Access Journals (Sweden)

    David Díez-del-Molino

    Full Text Available Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations.

  20. Genetic diversity and variation of mitochondrial DNA in native and introduced bighead carp

    Science.gov (United States)

    Li, Si-Fa; Yang, Qin-Ling; Xu, Jia-Wei; Wang, Cheng-Hui; Chapman, Duane C.; Lu, Guoping

    2010-01-01

    The bighead carp Hypophthalmichthys nobilis is native to China but has been introduced to over 70 countries and is established in many large river systems. Genetic diversity and variation in introduced bighead carp have not previously been evaluated, and a systematic comparison among fish from different river systems was unavailable. In this study, 190 bighead carp specimens were sampled from five river systems in three countries (Yangtze, Pearl, and Amur rivers, China; Danube River, Hungary; Mississippi River basin, USA) and their mitochondrial 16S ribosomal RNA gene and D-loop region were sequenced (around 1,345 base pairs). Moderate genetic diversity was found in bighead carp, ranging from 0.0014 to 0.0043 for nucleotide diversity and from 0.6879 to 0.9333 for haplotype diversity. Haplotype analysis provided evidence that (1) multiple haplotype groups might be present among bighead carp, (2) bighead carp probably originated from the Yangtze River, and (3) bighead carp in the Mississippi River basin may have some genetic ancestry in the Danube River. The analysis of molecular variance showed significant genetic differentiation among these five populations but also revealed limited differentiation between the Yangtze and Amur River bighead carp. This large-scale study of bighead carp genetic diversity and variation provides the first global perspective of bighead carp in the context of biodiversity conservation as well as invasive species control and management.

  1. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    Science.gov (United States)

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

  2. Genetic diversity among and within cultured cyanobionts of diverse species of Azolla.

    Science.gov (United States)

    Sood, A; Prasanna, R; Prasanna, B M; Singh, P K

    2008-01-01

    The cyanobionts isolated from 10 Azolla accessions belonging to 6 species (Azolla mexicana, A. microphylla, A. rubra, A. caroliniana, A. filiculoides, A. pinnata) were cultured under laboratory conditions and analyzed on the basis of whole cell protein profiles and molecular marker dataset generated using repeat sequence primers (STRR(mod) and HipTG). The biochemical and molecular marker profiles of the cyanobionts were compared with those of the free-living cyanobacteria and symbiotic Nostoc strains from Anthoceros sp., Cycas sp. and Gunnera monoika. Cluster analysis revealed the genetic diversity among the selected strains, and identified 3 distinct clusters. Group 1 included cyanobionts from all the 10 accessions of Azolla, group 2 comprised all the symbiotic Nostoc strains, while group 3 included the free-living cyanobacteria belonging to the genera Nostoc and Anabaena. The interrelationships among the Azolla cyanobionts were further revealed by principal component analysis. Cyanobionts from A. caroliniana-A. microphylla grouped together while cyanobionts associated with A. mexicana-A. filiculoides along with A. pinnata formed another group. A. rubra cyanobionts had intermediate relationship with both the subgroups. This is the first study analyzing the diversity existing among the cultured cyanobionts of diverse Azolla species through the use of biochemical and molecular profiles and also the genetic distinctness of these free-living cyanobionts as compared to cyanobacterial strains of the genera Anabaena and Nostoc.

  3. 1 Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    2015-04-14

    Apr 14, 2015 ... Study of genetic diversity is the process by which variation ... diversity tree is available, a core collection can be selected by .... are numerous natural factors, such as hybridization and clinical .... to develop a deeper understanding of the topic .... This can be detected by southern hybridization after running ...

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

    African Journals Online (AJOL)

    HP-PROBOOK

    2016-10-05

    Oct 5, 2016 ... Genetic diversity and relationship among 48 coconut individuals (Cocos nucifera L.) collections from ... Cluster analysis was constructed using DARwin program version 6.0. ... effective crop improvement programme.

  5. Genetic diversity study of common bean (Phaseolus vulgaris L ...

    African Journals Online (AJOL)

    SAM

    2014-09-03

    Sep 3, 2014 ... Key words: Genetic diversity, ISSR, Phaseolus vulgaris. INTRODUCTION ..... effective germplasm conservation and for setting germ- plasm collection ... conservation and research programs of the species. Furthermore, the ...

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... Common wheat (Triticum aestivum L.) is a grass species, cultivated world wide. Globally, it is ... A high degree of genetic polymorphism was observed among the wheat varieties with average ... cold, heat, soil salinization and water logging and (ii) ... and to find genetically most diverse genotypes of wheat.

  7. 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 ...

  8. Genetic Diversity of Tick-Borne Rickettsial Pathogens; Insights Gained from Distant Strains

    Directory of Open Access Journals (Sweden)

    Sebastián Aguilar Pierlé

    2014-01-01

    Full Text Available The ability to capture genetic variation with unprecedented resolution improves our understanding of bacterial populations and their ability to cause disease. The goal of the pathogenomics era is to define genetic diversity that results in disease. Despite the economic losses caused by vector-borne bacteria in the Order Rickettsiales, little is known about the genetic variants responsible for observed phenotypes. The tick-transmitted rickettsial pathogen Anaplasma marginale infects cattle in tropical and subtropical regions worldwide, including Australia. Genomic analysis of North American A. marginale strains reveals a closed core genome defined by high levels of Single Nucleotide Polymorphisms (SNPs. Here we report the first genome sequences and comparative analysis for Australian strains that differ in virulence and transmissibility. A list of genetic differences that segregate with phenotype was evaluated for the ability to distinguish the attenuated strain from virulent field strains. Phylogenetic analyses of the Australian strains revealed a marked evolutionary distance from all previously sequenced strains. SNP analysis showed a strikingly reduced genetic diversity between these strains, with the smallest number of SNPs detected between any two A. marginale strains. The low diversity between these phenotypically distinct bacteria presents a unique opportunity to identify the genetic determinants of virulence and transmission.

  9. The genetic diversity of the mangrove kandelia obovata in China revealed by ISSR analysis

    International Nuclear Information System (INIS)

    Chen, Shao-Bo; Ding, When-Young; Qiu, Jia-Biao; Wang, Guang-Yin; Zhou, Zhi-Min; Chen- Jiao-Fei; Ai, Wewi-ming; Wang, Cheng-Yi; Xie, Qi-Lang

    2010-01-01

    The genetic diversity of 7 populations of Kandelia obovata in China was characterized using inter simple sequence repeats (ISSR) technique. A total of 50 primers were screened, of which 9 polymorphic and informative patterns were selected to determine genetic relationships. ISSR amplification was conducted on 140 individuals from 7 populations, and 88 polymorphic loci were detected from 106 total loci. The total percentage of polymorphic loci (PPL) was 83.02%. The percentage of PPL at the population level ranged from 32.08% to 47.17%, with an average of 39.89%. Nei's gene diversity (H) and Shannon's information index (I) of K. obovata at the species level were 0.3631 and 0.5203, respectively. The genetic differentiation coefficient (Gst) among populations was 0.5548. Among populations component accounted for 55.48% of the total variation, whereas the within populations component accounted for 44.52%, suggesting that genetic differentiation among K. obovata populations was relatively high. The gene flow among populations was 0.4012, indicating that gene flow was low among geographically diverse populations of K. obovata. The results of the genetic diversity and cluster analysis suggest that geographical isolation of K. obovata populations mainly results in low gene flow and random genetic drift, leading to genetic differentiation. (author)

  10. Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata

    Science.gov (United States)

    Aplasca, Andrea C.; Iverson, John B.; Welch, Mark E.; Colosimo, Giuliano

    2016-01-01

    The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations. PMID:26989628

  11. Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata

    Directory of Open Access Journals (Sweden)

    Andrea C. Aplasca

    2016-03-01

    Full Text Available The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each. However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations.

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

    Science.gov (United States)

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

    2016-11-14

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

  13. Genetic diversity and breeding of larch (Larix decidua Mill. in Romania

    Directory of Open Access Journals (Sweden)

    Georgeta Mihai

    2009-12-01

    Full Text Available Although it is one of the most important coniferous species, the larch (Larix decidua Mill. covers a restricted area in Romania, only 0.3% of the forest area, most being represented by artificial stands. The natural area of the larch is fragmented, being concentrated into five genetic centers: Ceahlău, Ciucas, Bucegi, Lotru and Apuseni. The speed of growth, high productivity, high wood quality and resistance to adversities resulted in initiating research on the genetic variability of the larch. In 1978 and 1982 respectively, by means of international collaboration, two series of comparative trials were installed, with Romanian and foreign provenances of larch, totalizing 6 experimental areas. Selection of seed stands followed, and among them, more than 300 plus trees. There have been installed 26 orchards (134 hectares of which 3 (15 hectares are interspecific seed orchards (Larix x eurolepis. This paper presents the results obtained over the last years, regarding the continuing larch breeding program; genetic variation of the main characters in multisite provenances comparative trials planted in 1982, evaluation of the genetic parameters in a clonal seed orchard in order to advance to the second generation seed orchard, and a study of the genetic diversity by means of primary biochemical markers. The provenance tests include 24 populations of larch, 13 Romanian and 11 from the following countries: Germany (4, Austria (2, Belgium (1 and the Czech Republic (4. The studied characters are total height, diameter at 1.30 meters, volume/tree, branches characters, stem straightness and survival. At the age of 25 years from planting, the variance analysis reveals significant interpopulation genetic variation for all the studied characters. The expected genetic gain and the genetic parameters, estimated in the Adâncata larch seed orchard, shows that selection on the clones level, in the first generation seed orchard, can be successfully applied, being

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

    African Journals Online (AJOL)

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

  15. The effect of multiple paternity on genetic diversity of small populations during and after colonisation.

    Directory of Open Access Journals (Sweden)

    Marina Rafajlović

    Full Text Available Genetic variation within and among populations is influenced by the genetic content of the founders and the migrants following establishment. This is particularly true if populations are small, migration rate low and habitats arranged in a stepping-stone fashion. Under these circumstances the level of multiple paternity is critical since multiply mated females bring more genetic variation into founder groups than single mated females. One such example is the marine snail Littorina saxatilis that during postglacial times has invaded mainland refuge areas and thereafter small islands emerging due to isostatic uplift by occasional rafting of multiply mated females. We modelled effects of varying degrees of multiple paternity on the genetic variation of island populations colonised by the founders spreading from the mainland, by quantifying the population heterozygosity during both the transient colonisation process, and after a steady state (with migration has been reached. During colonisation, multiple mating by [Formula: see text] males increased the heterozygosity by [Formula: see text] in comparison with single paternity, while in the steady state the increase was [Formula: see text] compared with single paternity. In the steady state the increase of heterozygosity due to multiple paternity is determined by a corresponding increase in effective population size. During colonisation, by contrast, the increase in heterozygosity is larger and it cannot be explained in terms of the effective population size alone. During the steady-state phase bursts of high genetic variation spread through the system, and far from the mainland this led to short periods of high diversity separated by long periods of low diversity. The size of these fluctuations was boosted by multiple paternity. We conclude that following glacial periods of extirpation, recolonization of isolated habitats by this species has been supported by its high level of multiple paternity.

  16. The Effect of Multiple Paternity on Genetic Diversity of Small Populations during and after Colonisation

    KAUST Repository

    Rafajlović, Marina

    2013-10-28

    Genetic variation within and among populations is influenced by the genetic content of the founders and the migrants following establishment. This is particularly true if populations are small, migration rate low and habitats arranged in a stepping-stone fashion. Under these circumstances the level of multiple paternity is critical since multiply mated females bring more genetic variation into founder groups than single mated females. One such example is the marine snail Littorina saxatilis that during postglacial times has invaded mainland refuge areas and thereafter small islands emerging due to isostatic uplift by occasional rafting of multiply mated females. We modelled effects of varying degrees of multiple paternity on the genetic variation of island populations colonised by the founders spreading from the mainland, by quantifying the population heterozygosity during both the transient colonisation process, and after a steady state (with migration) has been reached. During colonisation, multiple mating by 2-10 males increased the heterozygosity by 10-300% in comparison with single paternity, while in the steady state the increase was 10-50% compared with single paternity. In the steady state the increase of heterozygosity due to multiple paternity is determined by a corresponding increase in effective population size. During colonisation, by contrast, the increase in heterozygosity is larger and it cannot be explained in terms of the effective population size alone. During the steady-state phase bursts of high genetic variation spread through the system, and far from the mainland this led to short periods of high diversity separated by long periods of low diversity. The size of these fluctuations was boosted by multiple paternity. We conclude that following glacial periods of extirpation, recolonization of isolated habitats by this species has been supported by its high level of multiple paternity. 2013 Rafajlovi? et al.

  17. Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil

    DEFF Research Database (Denmark)

    Rasmussen, Lasse Dam; Sørensen, S. J.

    2001-01-01

    This study investigates the effect of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. The changes in diversity were monitored in soil microcosms, enriched with 25 mug Hg(II) g(-1) soil, over a period of 3 months...... by purification of total soil DNA and amplification of bacterial 16S rDNA fragments by polymerase chain reaction. Concentrations of bioavailable and total mercury were measured throughout the experiment. The effect on the culturable heterotrophic and genetic diversity was very similar, showing an immediate...... decrease after mercury addition but then slowly increasing throughout the entire experimental period. Pre-exposure levels were not reached within the time span of this investigation. The DGGE band pattern indicated that a shift in the community structure was responsible for recovered diversity. When...

  18. 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

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

    Directory of Open Access Journals (Sweden)

    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,

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

    African Journals Online (AJOL)

    SERVER

    2008-02-05

    Feb 5, 2008 ... Keywords: Conservation, genetic diversity, Oroxylum indicum, RAPD (Random Amplified Polymorphic DNA). ... Srilanka, Philippines and Indonesia. In India it is distri- .... indicum since pollination occurs by bats and black ...

  1. Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

    Science.gov (United States)

    Eltaher, Shamseldeen; Sallam, Ahmed; Belamkar, Vikas; Emara, Hamdy A; Nower, Ahmed A; Salem, Khaled F M; Poland, Jesse; Baenziger, Peter S

    2018-01-01

    The availability of information on the genetic diversity and population structure in wheat ( Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F 3:6 ) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon's information index ( I ) = 0.494, diversity index ( h ) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity ( I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.

  2. Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

    Science.gov (United States)

    van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  3. 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 ...

  4. A simple ssr analysis for genetic diversity estimation of maize landraces

    Directory of Open Access Journals (Sweden)

    Ignjatovic-Micic Dragana

    2015-01-01

    Full Text Available collection of 2217 landraces from western Balkan (former Yugoslavia is maintained at Maize Research Institute Zemun Polje gene bank. Nine flint and nine dent accessions from six agro-ecological groups (races, chosen on the basis of diverse pedigrees, were analyzed for genetic relatedness using phenotypic and simple sequence repeat (SSR markers. One of the aims was to establish a reliable set of SSR markers for a rapid diversity analysis using polyacrilamide gels and ethidium bromide staining. In the principal component analysis (PCA the first three principal components accounted for 80.86% of total variation and separated most of the flint from dent landraces. Ten SSR primers revealed a total of 56 and 63 alleles in flint and dent landraces, respectively, with low stuttering and good allele resolution on the gels. High average PIC value (0.822 also supports informativeness and utility of the markers used in this study. Higher genetic variation was observed among flint genotypes, as genetic distances between flint landraces covered a larger range of values (0.11- 0.38 than between dent (0.22 - 0.33 genotypes. Both phenotypic and SSR analyses distinguished flint and dent landraces, but neither of them could abstract agro-ecological groups. The SSR method used gave clear, easy to read band patterns that could be used for reliable allele frequency determination. Genetic diversity revealed for both markers indicated that the landraces were highly adapted to specific environmental conditions and purposes and could be valuable sources of genetic variability. [Projekat Ministarstva nauke Republike Srbije, br. TR31028: Exploitation of maize diversity to improve grain quality and drought tolerance

  5. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

    Science.gov (United States)

    2009-01-01

    The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds. PMID:19284689

  6. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

    International Nuclear Information System (INIS)

    Vahidi, S.M.F.; Faruque, M.O.; Falahati Anbaran, M.; Afraz, F.; Mousavi, S.M.; Boettcher, P.; Joost, S.; Han, J.L.; Colli, L.; Periasamy, K.; Negrini, R.; Ajmone-Marsan, P.

    2016-01-01

    Full text: Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7–22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72–0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes are discussed. (author)

  7. A neutral theory for interpreting correlations between species and genetic diversity in communities.

    Science.gov (United States)

    Laroche, Fabien; Jarne, Philippe; Lamy, Thomas; David, Patrice; Massol, Francois

    2015-01-01

    Spatial patterns of biological diversity have been extensively studied in ecology and population genetics, because they reflect the forces acting on biodiversity. A growing number of studies have found that genetic (within-species) and species diversity can be correlated in space (the so-called species-gene diversity correlation [SGDC]), which suggests that they are controlled by nonindependent processes. Positive SGDCs are generally assumed to arise from parallel responses of genetic and species diversity to variation in site size and connectivity. However, this argument implicitly assumes a neutral model that has yet to be developed. Here, we build such a model to predict SGDC in a metacommunity. We describe how SGDC emerges from competition within sites and variation in connectivity and carrying capacity among sites. We then introduce the formerly ignored mutation process, which affects genetic but not species diversity. When mutation rate is low, our model confirms that variation in the number of migrants among sites creates positive SGDCs. However, when considering high mutation rates, interactions between mutation, migration, and competition can produce negative SGDCs. Neutral processes thus do not always contribute positively to SGDCs. Our approach provides empirical guidelines for interpreting these novel patterns in natura with respect to evolutionary and ecological forces shaping metacommunities.

  8. Genetic diversity analysis among collected purslane (Portulaca oleracea L.) accessions using ISSR markers.

    Science.gov (United States)

    Alam, M Amirul; Juraimi, Abdul Shukor; Rafii, Mohd Yusop; Hamid, Azizah Abdul; Arolu, Ibrahim Wasiu; Abdul Latif, M

    2015-01-01

    Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Boris Briñez R.

    2011-05-01

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

  10. Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission.

    Directory of Open Access Journals (Sweden)

    Shuzhen Sim

    Full Text Available Dengue virus (DENV infection of an individual human or mosquito host produces a dynamic population of closely-related sequences. This intra-host genetic diversity is thought to offer an advantage for arboviruses to adapt as they cycle between two very different host species, but it remains poorly characterized. To track changes in viral intra-host genetic diversity during horizontal transmission, we infected Aedes aegypti mosquitoes by allowing them to feed on DENV2-infected patients. We then performed whole-genome deep-sequencing of human- and matched mosquito-derived DENV samples on the Illumina platform and used a sensitive variant-caller to detect single nucleotide variants (SNVs within each sample. >90% of SNVs were lost upon transition from human to mosquito, as well as from mosquito abdomen to salivary glands. Levels of viral diversity were maintained, however, by the regeneration of new SNVs at each stage of transmission. We further show that SNVs maintained across transmission stages were transmitted as a unit of two at maximum, suggesting the presence of numerous variant genomes carrying only one or two SNVs each. We also present evidence for differences in selection pressures between human and mosquito hosts, particularly on the structural and NS1 genes. This analysis provides insights into how population drops during transmission shape RNA virus genetic diversity, has direct implications for virus evolution, and illustrates the value of high-coverage, whole-genome next-generation sequencing for understanding viral intra-host genetic diversity.

  11. Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

    Science.gov (United States)

    Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

    2016-06-17

    In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

  12. Investigating Genetic Diversity Among Cotton Genotypes Available in the Iranian Gene Bank (Gossypium sp. Using ISSR Molecular Marker

    Directory of Open Access Journals (Sweden)

    F Shahriari Ahmadi

    2013-04-01

    Full Text Available Cotton is one of the most important world crops and is considered as a major cash crop in the North East of Iran. All selections in plant breeding are based on diversity and an increase in genetic diversity determines the range of selection. In the present study, 24 cultivars of cotton available at the research station for cotton in the East of Iran -Kashmar- were studied using the ISSR marker. A total number of 13 primers, with repeated simple sequences, were used for the amplification of genomic DNA. Overall, 128 bands were obtained, 109 of which showed polymorphism. To evaluate genetic similarity between cultivars, cluster analysis accompanied by the similarity coefficient developed by Jaccard and Nee (1972, were applied using the UPGMA method. Dendrogram analysis showed a high diversity in the cotton cultivars and two main groups with 70 percent genetic similarity dividing the cotton cultivars into two main groups; namely, tetraploid and diploid. The highest polymorphism percentage was related to 5' (CT8RC3' (100% and the lowest belonged to 5' (AG8YA3' and 5' (TC8G3' (25% primers. Based on the similarity matrix, the highest genetic similarity was found in Varamin and Khordad and the lowest in Avangard and Bakhtegan cultivars. Based on the obtained results, ISSR markers can be efficiently used for the investigation of genetic diversity among cotton cultivars.

  13. Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data.

    Science.gov (United States)

    Ai, XianTao; Liang, YaJun; Wang, JunDuo; Zheng, JuYun; Gong, ZhaoLong; Guo, JiangPing; Li, XueYuan; Qu, YanYing

    2017-10-01

    Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0.25, indicating a relatively low degree of genetic diversity. Population structure analysis revealed extensive admixture and identified three subgroups. Phylogenetic analysis supported the subgroups identified by STRUCTURE. The results from both population structure and phylogenetic analysis were, for the most part, in agreement with pedigree information. Analysis of molecular variance revealed a larger amount of variation was due to diversity within the groups. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton.

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

    OpenAIRE

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

    2009-01-01

    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 dive...

  15. Genetic Diversity in Commercial Rapeseed (Brassica napus L. Varieties from Turkey as Revealed by RAPD

    Directory of Open Access Journals (Sweden)

    Özlem ÖZBEK

    2013-02-01

    Full Text Available In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as Brassica napus L. should be evaluated and the genotypes, which have higher genetic diversity index, should be addressed as potential parental cross materials in breeding programs. In this study, the genetic diversity was analysed by using randomly amplified polymorphic DNA analysis (RAPD technique in nine Turkish commercial rapeseed varieties. The RAPD primers (10-mer oligonucleotides produced 51 scorable loci, 31 loci of which were polymorphic (60.78% and 20 loci (39.22% were monomorphic The RAPD bands were scored as binary matrix data and were analysed using POPGENE version 1.32. At locus level, the values of genetic diversity within population (Hs and total (HT were 0.15 and 0.19 respectively. The genetic differentiation (GST and the gene flow (Nm values between the populations were 0.20 and 2.05 respectively. The mean number of alleles (na, the mean number of effective alleles (nae, and the mean value of genetic diversity (He were 2.00, 1.26, and 0.19 respectively. According to Pearson’s correlation, multiple regression and principal component analyses, eco-geographical conditions in combination had significant effect on genetic indices of commercial B. napus L. varieties were discussed.

  16. Analysis of genetic diversity in chickpea ( Cicer arietinum L ...

    African Journals Online (AJOL)

    Genetic diversity of seven chickpea (Cicer arietinum L.) cultivars of Pakistani origin ... effective method to determine the variations among the chickpea cultivars. ... to broaden the germplasm base in the future for chickpea breeding programs.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2010-01-18

    Jan 18, 2010 ... Key words: Genetic diversity, microsatellite markers, Caspian horse breed. INTRODUCTION ... heterozygosity, observed and effective number of alleles at each ... computer program version 1.31 (Yeh et al., 1999). Based on ...

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

    African Journals Online (AJOL)

    Genetic diversity, classification and comparative study on the larval phenotypic ... B. mori showed different performance based on larval phenotypic data. The analysis of variance regarding the studied traits showed that different strains have ...

  19. Marine reserves help preserve genetic diversity after impacts derived from climate variability: Lessons from the pink abalone in Baja California

    Directory of Open Access Journals (Sweden)

    Adrián Munguía-Vega

    2015-07-01

    Full Text Available Genetic diversity is crucial for the adaptation of exploited species like the pink abalone (Haliotis corrugata, faced with threats from climate change, overfishing and impacts associated with aquaculture production. While marine reserves are commonly used to mitigate risks to marine populations, the duration, size, location and larval connectivity needed for a reserve to help conserve genetic resources is still poorly understood. Here, we examine the effects of fishing, reserves, and restocking on the genetic diversity of 10 populations from central Baja California, Mexico, and Southern California, USA. We demonstrate that each population shows characteristic genetic signatures according to recent management decisions. We found high allelic diversity, particularly rare alleles, a larger effective population size and a lack of a recent genetic bottleneck in pink abalones within a small (0.8 km2, recently established (5 years reserve in Baja California, compared to other fished sites after a climatic bottleneck. Higher diversity may result from the presence of older animals in the reserve. Due to its location, the reserve may also act as an important hub connecting distant populations via larval dispersal. In contrast, a population from California showed genetic isolation, loss of allelic diversity and high relatedness, consistent with the collapse of fisheries in the 1990s and their lack of recovery thereafter. In addition, a fished area in Baja California with a history of restocking for over a decade showed an increase in frequency of related individuals and high genetic differentiation from nearby sites that were consistent with the production of larvae from a few adults in the laboratory. A network of strategically placed small marine reserves that considers ocean circulation patterns could help to maintain genetic diversity and connectivity of exploited populations.

  20. Genetic diversity of Cryptosporidium spp. in captive reptiles

    Czech Academy of Sciences Publication Activity Database

    Xiao, L.; Ryan, U. M.; Graczyk, T. K.; Limor, J.; Li, L.; Kombert, M.; Junge, R.; Sulaiman, I. M.; Zhou, L.; Arrowood, M. J.; Koudela, Břetislav; Modrý, David; Lal, A. A.

    2004-01-01

    Roč. 70, č. 2 (2004), s. 891-899 ISSN 0099-2240 R&D Projects: GA ČR GA524/00/P015 Institutional research plan: CEZ:AV0Z6022909 Keywords : Cryptosporidium * reptiles * genetic diversity Subject RIV: EG - Zoology Impact factor: 3.810, year: 2004

  1. Increasing global participation in genetics research through DNA barcoding.

    Science.gov (United States)

    Adamowicz, Sarah J; Steinke, Dirk

    2015-12-01

    DNA barcoding--the sequencing of short, standardized DNA regions for specimen identification and species discovery--has promised to facilitate rapid access to biodiversity knowledge by diverse users. Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003-2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources.

  2. Characterisation of adaptive genetic diversity in environmentally contrasted populations of Eucalyptus camaldulensis Dehnh. (river red gum.

    Directory of Open Access Journals (Sweden)

    Shannon Dillon

    Full Text Available As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh. is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F(ST = 17%, exceeding previous estimates based on neutral markers. Complementary statistical approaches identified 6 SNP loci in four genes (COMT, Dehydrin, ERECTA and PIP2 which, after accounting for demographic effects, exhibited higher than expected levels of genetic differentiation among populations and whose allelic variation was associated with local environment. While this study employs but a small proportion of available diversity in the eucalyptus genome, it draws our attention to the potential for application of wide spread eucalypt species to test adaptive hypotheses.

  3. Ancient Male Recombination Shaped Genetic Diversity of Neo-Y Chromosome in Drosophila albomicans.

    Science.gov (United States)

    Satomura, Kazuhiro; Tamura, Koichiro

    2016-02-01

    Researchers studying Y chromosome evolution have drawn attention to neo-Y chromosomes in Drosophila species due to their resembling the initial stage of Y chromosome evolution. In the studies of neo-Y chromosome of Drosophila miranda, the extremely low genetic diversity observed suggested various modes of natural selection acting on the nonrecombining genome. However, alternative possibility may come from its peculiar origin from a single chromosomal fusion event with male achiasmy, which potentially caused and maintained the low genetic diversity of the neo-Y chromosome. Here, we report a real case where a neo-Y chromosome is in transition from an autosome to a typical Y chromosome. The neo-Y chromosome of Drosophila albomicans harbored a rich genetic diversity comparable to its gametologous neo-X chromosome and an autosome in the same genome. Analyzing sequence variations in 53 genes and measuring recombination rates between pairs of loci by cross experiments, we elucidated the evolutionary scenario of the neo-Y chromosome of D. albomicans having high genetic diversity without assuming selective force, i.e., it originated from a single chromosomal fusion event, experienced meiotic recombination during the initial stage of evolution and diverged from neo-X chromosome by the suppression of recombination tens or a few hundreds of thousand years ago. Consequently, the observed high genetic diversity on the neo-Y chromosome suggested a strong effect of meiotic recombination to introduce genetic variations into the newly arisen sex chromosome. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis as Revealed by Mitochondrial and Microsatellite DNA

    Directory of Open Access Journals (Sweden)

    Minmin Chen

    2014-06-01

    Full Text Available Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS, and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY and Tongling (TL and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP.

  5. Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis) as Revealed by Mitochondrial and Microsatellite DNA

    Science.gov (United States)

    Chen, Minmin; Zheng, Jinsong; Wu, Min; Ruan, Rui; Zhao, Qingzhong; Wang, Ding

    2014-01-01

    Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis) is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA) control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS), and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY) and Tongling (TL)) and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP. PMID:24968271

  6. Patterns of genetic diversity in three plant lineages endemic to the Cape Verde Islands.

    Science.gov (United States)

    Romeiras, Maria M; Monteiro, Filipa; Duarte, M Cristina; Schaefer, Hanno; Carine, Mark

    2015-05-15

    Conservation of plant diversity on islands relies on a good knowledge of the taxonomy, distribution and genetic diversity of species. In recent decades, a combination of morphology- and DNA-based approaches has become the standard for investigating island plant lineages and this has led, in some cases, to the discovery of previously overlooked diversity, including 'cryptic species'. The flora of the Cape Verde archipelago in the North Atlantic is currently thought to comprise ∼740 vascular plant species, 92 of them endemics. Despite the fact that it is considered relatively well known, there has been a 12 % increase in the number of endemics in the last two decades. Relatively few of the Cape Verde plant lineages have been included in genetic studies so far and little is known about the patterns of diversification in the archipelago. Here we present an updated list for the endemic Cape Verde flora and analyse diversity patterns for three endemic plant lineages (Cynanchum, Globularia and Umbilicus) based on one nuclear (ITS) and four plastid DNA regions. In all three lineages, we find genetic variation. In Cynanchum, we find two distinct haplotypes with no clear geographical pattern, possibly reflecting different ploidy levels. In Globularia and Umbilicus, differentiation is evident between populations from northern and southern islands. Isolation and drift resulting from the small and fragmented distributions, coupled with the significant distances separating the northern and southern islands, could explain this pattern. Overall, our study suggests that the diversity in the endemic vascular flora of Cape Verde is higher than previously thought and further work is necessary to characterize the flora. Published by Oxford University Press on behalf of the Annals of Botany Company.

  7. 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.

  8. 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.

  9. Assessment of genetic diversity and variation of acer mono max seedlings after spaceflight

    International Nuclear Information System (INIS)

    Long, C.; Li, Y.; Zhang, Y.; Yang, M.

    2015-01-01

    Genetic diversity and variation of Acer Mono Maxim seedlings sampled from space-mutated (sm) populations were compared to seedlings from parallel control (ck) ones using molecular markers. RAMP analysis showed that the percentage of polymorphic band, Shannon diversity index and Nei gene diversity index of the space-mutated populations were higher than those of the control ones, which indicated that genetic variation increased after spaceflight in populations of Acer Mono Maxim. By using un-weighted pair group method with arithmetic mean (UPGMA) method, three space-mutated repeats (populations) were clustered together, and control groups clustered separately, which further indicated that there was difference between the space-mutated ones and the control ones, which may be caused by space mutation. Further analysis of genomic inconsistency between the root and leaf samples from the same tree showed that a total variation rate of 6.3% and 1.7% were obtained in ten space-mutated individuals by using RAMP and SSR markers, respectively, however, the variation rate was zero in control ones. It provided that space mutation may be caused the individual variation of Acer Mono Maxim. (author)

  10. Diversity and genetic structure of the Mexican endemic epiphyte Tillandsia achyrostachys E. Morr. ex Baker var. achyrostachys (Bromeliaceae).

    Science.gov (United States)

    González-Astorga, Jorge; Cruz-Angón, Andrea; Flores-Palacios, Alejandro; Vovides, Andrew P

    2004-10-01

    The monoecious, bird-pollinated epiphytic Tillandsia achyrostachys E. Morr. ex Baker var. achyrostachys is an endemic bromeliad of the tropical dry forests of Mexico with clonal growth. In the Sierra de Huautla Natural Reserve this species shows a host preference for Bursera copallifera (Sessé & Moc ex. DC) Bullock. As a result of deforestation in the study area, B. copallifera has become a rare tree species in the remaining forest patches. This human-induced disturbance has directly affected the population densities of T. achyrostachys. In this study the genetic consequences of habitat fragmentation were assessed by comparing the genetic diversity, gene flow and genetic differentiation in six populations of T. achyrostachys in the Sierra de Huautla Natural Reserve, Mexico. Allozyme electrophoresis of sixteen loci (eleven polymorphic and five monomorphic) were used. The data were analysed with standard statistical approximations for obtaining diversity, genetic structure and gene flow. Genetic diversity and allelic richness were: HE = 0.21 +/- 0.02, A = 1.86 +/- 0.08, respectively. F-statistics revealed a deficiency of heterozygous plants in all populations (Fit = 0.65 +/- 0.02 and Fis = 0.43 +/- 0.06). Significant genetic differentiation between populations was detected (Fst = 0.39 +/- 0.07). Average gene flow between pairs of populations was relatively low and had high variation (Nm = 0.46 +/- 0.21), which denotes a pattern of isolation by distance. The genetic structure of populations of T. achyrostachys suggests that habitat fragmentation has reduced allelic richness and genetic diversity, and increased significant genetic differentiation (by approx. 40 %) between populations. The F-statistic values (>0) and the level of gene flow found suggest that habitat fragmentation has broken up the former population structure. In this context, it is proposed that the host trees of T. achyrostachys should be considered as a conservation priority, since they represent the

  11. Genetic diversity of sweet potatoes collection from Northeastern Brazil

    African Journals Online (AJOL)

    Ana Veruska Cruz da Silva Muniz

    2014-02-24

    Feb 24, 2014 ... RAPD was efficient for the analysis of genetic diversity to identify groups and measure the .... the molecular characterization of accessions using RAPD ..... clusters of individuals using the software Structure: a simulation study.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... RFLP, RAPD, AFLP, and micro-satellites have been beneficial by being ... List of pepper genotypes used in the experiment. Genotype. Type. Source. Classification of ..... Artificial selection might decrease the genetic diversity ...

  13. Molecular Identification and Genetic Diversity of Acropora hyacinthus from Boo and Deer Island, Raja Ampat, West Papua

    Science.gov (United States)

    Wijayanti, DP; Indrayanti, E.; Nuryadi, H.; Dewi, RA; Sabdono, A.

    2018-02-01

    Indonesia lies at the centre of biodiversity for corals. However, the reefs suffered from extensive human exploitation. Marine Protected Areas is thought to be best solution to protect coral reefs ecosystem. Understanding genetic diversity is crucial for effective management of the MPAs, however genetic diversity is rarely been corporate in designing an MPA. Moreover, many MPAs are uneffectively manage due to poor designated and demarcated.Raja Ampat which is located in western tip of West Papua, was designated as a park to mitigatethreatsand protect the valuable marine resources.Scleractinian corals in the genus Acropora are among the most dominant distributed in Raja Ampat waters, including the species of Acroporahyacinthus. The research aimed to analyze genetic diversity and to describe the kinship relationship of Acroporahyacinthus between 2 populations: Boo Island and Deer Island, Raja Ampat. Genetic marker Cytochrome Oxidase I (CO I) of the mitochondrial genome DNA (mtDNA) was used to analyze genetic diversity. Reconstruction of phylogenetic tree and genetic diversity were made by usingsoftware MEGA 5.05 (Moleculer Evolutionary Genetics Analysis). The results of this research indicatecorals A. hyacinthus from Boo Island and Deer Island Raja Ampat are in the low category of genetic diversity and overall had a close genetic relationship of kinship. This is likely due to the small size of the population and few numbers of samples that may not represent the population.

  14. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Directory of Open Access Journals (Sweden)

    Melissa D Conrad

    Full Text Available Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes.Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2 differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages.Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  15. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Science.gov (United States)

    Conrad, Melissa D; Gorman, Andrew W; Schillinger, Julia A; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E; Carlton, Jane M

    2012-01-01

    Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  16. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Mériaux Jean-Claude

    2009-01-01

    Full Text Available Abstract The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099. Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds.

  17. Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

    Science.gov (United States)

    Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

    2016-01-01

    The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

  18. Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

    Science.gov (United States)

    2011-01-01

    Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine

  19. Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus

    Directory of Open Access Journals (Sweden)

    Timms Peter

    2011-04-01

    Full Text Available Abstract Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58, we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of

  20. Curcumin profiing and genetic diversity of different accessions of Curcuma longa L.

    Directory of Open Access Journals (Sweden)

    Neelam Arya

    2016-01-01

    Full Text Available Objective: To investigate the genetic diversity and variation in active compound of turmeric rhizomes collected from different niches of Uttarakhand. Methods: Genetic diversity and relationship of Curcuma longa accessions was evaluated by random amplification polymorphism DNA analysis and curcumin profiling was evaluated by high performance liquid chromatography method. Results: The curcumin contents in 20 accessions of turmeric rhizomes were found to be in the range of 0.90% to 3.26%. All accessions were separated into six groups (92% genetic similarity by using 10 decamer oligonucleotide primers for the amplification of genomic DNA. Conclusions: The results indicated the possibility of selecting high quality clones for large scale production.

  1. Genetic diversity and domestication origin of tea plant Camellia taliensis (Theaceae) as revealed by microsatellite markers.

    Science.gov (United States)

    Zhao, Dong-Wei; Yang, Jun-Bo; Yang, Shi-Xiong; Kato, Kenji; Luo, Jian-Ping

    2014-01-09

    Tea is one of the most popular beverages in the world. Many species in the Thea section of the Camellia genus can be processed for drinking and have been domesticated. However, few investigations have focused on the genetic consequence of domestication and geographic origin of landraces on tea plants using credible wild and planted populations of a single species. Here, C. taliensis provides us with a unique opportunity to explore these issues. Fourteen nuclear microsatellite loci were employed to determine the genetic diversity and domestication origin of C. taliensis, which were represented by 587 individuals from 25 wild, planted and recently domesticated populations. C. taliensis showed a moderate high level of overall genetic diversity. The greater reduction of genetic diversity and stronger genetic drift were detected in the wild group than in the recently domesticated group, indicating the loss of genetic diversity of wild populations due to overexploitation and habitat fragmentation. Instead of the endangered wild trees, recently domesticated individuals were used to compare with the planted trees for detecting the genetic consequence of domestication. A little and non-significant reduction in genetic diversity was found during domestication. The long life cycle, selection for leaf traits and gene flow between populations will delay the emergence of bottleneck in planted trees. Both phylogenetic and assignment analyses suggested that planted trees may have been domesticated from the adjacent central forest of western Yunnan and dispersed artificially to distant places. This study contributes to the knowledge about levels and distribution of genetic diversity of C. taliensis and provides new insights into genetic consequence of domestication and geographic origin of planted trees of this species. As an endemic tea source plant, wild, planted and recently domesticated C. taliensis trees should all be protected for their unique genetic characteristics, which

  2. Geographic distribution of genetic diversity in populations of Rio Grande Chub Gila pandora

    Science.gov (United States)

    Galindo, Rene; Wilson, Wade; Caldwell, Colleen A.

    2016-01-01

    In the southwestern United States (US), the Rio Grande chub (Gila pandora) is state-listed as a fish species of greatest conservation need and federally listed as sensitive due to habitat alterations and competition with non-native fishes. Characterizing genetic diversity, genetic population structure, and effective number of breeders will assist with conservation efforts by providing a baseline of genetic metrics. Genetic relatedness within and among G. pandora populations throughout New Mexico was characterized using 11 microsatellite loci among 15 populations in three drainage basins (Rio Grande, Pecos, Canadian). Observed heterozygosity (HO) ranged from 0.71–0.87 and was similar to expected heterozygosity (0.75–0.87). Rio Ojo Caliente (Rio Grande) had the highest allelic richness (AR = 15.09), while Upper Rio Bonito (Pecos) had the lowest allelic richness (AR = 6.75). Genetic differentiation existed among all populations with the lowest genetic variation occurring within the Pecos drainage. STRUCTURE analysis revealed seven genetic clusters. Populations of G. pandora within the upper Rio Grande drainage (Rio Ojo Caliente, Rio Vallecitos, Rio Pueblo de Taos) had high levels of admixture with Q-values ranging from 0.30–0.50. In contrast, populations within the Pecos drainage (Pecos River and Upper Rio Bonito) had low levels of admixture (Q = 0.94 and 0.87, respectively). Estimates of effective number of breeders (N b ) varied from 6.1 (Pecos: Upper Rio Bonito) to 109.7 (Rio Grande: Rio Peñasco) indicating that populations in the Pecos drainage are at risk of extirpation. In the event that management actions are deemed necessary to preserve or increase genetic diversity of G. pandora, consideration must be given as to which populations are selected for translocation.

  3. Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil.

    Science.gov (United States)

    Góes, Luiz Gustavo Bentim; Campos, Angélica Cristine de Almeida; Carvalho, Cristiano de; Ambar, Guilherme; Queiroz, Luzia Helena; Cruz-Neto, Ariovaldo Pereira; Munir, Muhammad; Durigon, Edison Luiz

    2016-10-01

    Bats are notorious reservoirs of genetically-diverse and high-profile pathogens, and are playing crucial roles in the emergence and re-emergence of viruses, both in human and in animals. In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. These results highlight the virus richness of bats and their possible roles in the public health. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    African Journals Online (AJOL)

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

  5. 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 ...

  6. Genetic diversity in coastal and inland desert populations of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-14

    Nov 14, 2011 ... 0.00196 showed low degree of differentiation among populations. .... number of amplification products per primer varied from 6 to 14, and these ..... strategies on genetic diversity estimates obtained with RAPD markers in ...

  7. Assessing the genetic diversity of 48 groundnut ( Arachis hypogaea ...

    African Journals Online (AJOL)

    Assessing the genetic diversity of 48 groundnut ( Arachis hypogaea L. ) ... both at the phenotypic and molecular level is important in all plant breeding programs. ... other and could therefore serve as effective parental material for future work.

  8. Genetic diversity analysis of brassica napus/brassica campestris progenies using microsatellite markers

    International Nuclear Information System (INIS)

    Fayyaz, L.; Farhatullah, A.; Iqbal, S.; Kanwal, M.; Nawaz, I.

    2014-01-01

    Genetic diversity and relationship of F2 segregating progenies of interspecific crosses between B. napus N-501/B. campestris C-118 were studied. A set of 90 genotypes (2 parental lines and their 88 F2 progenies) was characterized separately using 24 microsatellite or SSR markers to cover the diversity as broadly as possibly present in them. In initial screening only 12 out of 24 SSR primers combination amplified DNA fragments, while the remaining 12 SSR primers did not amplify DNA fragment therefore those 12 SSR molecular markers were not used for further analysis. The 12 SSR primer combinations generated a total of 33 alleles, of that 32 were polymorphic loci, whereas only one was monomorphic locus. Primers BRMS-19 and BRMS-40 were highly polymorphic producing 4 bands each. Primer Ra2-D04 was less polymorphic and it produced only one band. The proportion of polymorphic loci was 95.83% which indicates high genetic diversity among the progenies. The average number of polymorphic alleles per locus was 2.66. The PIC values ranged from 0.395 for primer Ra2-E03 to 0.726 for primer BRMS-019 with an average genetic diversity (PIC value) of 0.584 per locus. Seven primers showed PIC values above 0.5 (50%) indicating high genetic diversity in the studied plant materials. Pair-wise similarity indices among 90 genotypes ranged from 0.3 to 0.95. Dendrogram obtained through UPGMA clustering of F2 progenies depicted eight main groups using similarity coefficient of 0.70. The progenies could be similar to their parents if they have the same banding patterns as that of the parents and could be distinguished from each other by the combination of fragments which are repeatedly present in one progeny and absent in the other. Considerable genetic diversity has been found among the F2 segregating progenies and their parents using SSR markers thus, SSR analysis proved to be a useful tool. (author)

  9. Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data.

    Science.gov (United States)

    Zanella, Ricardo; Peixoto, Jane O; Cardoso, Fernando F; Cardoso, Leandro L; Biegelmeyer, Patrícia; Cantão, Maurício E; Otaviano, Antonio; Freitas, Marcelo S; Caetano, Alexandre R; Ledur, Mônica C

    2016-03-30

    Genetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (F x) and genomic information using runs of homozygosity (F ROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (F SNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (N e ) were also estimated. Estimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller N e . Estimates of N e based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed. The use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding

  10. Genetic diversity and pectinolytic activity of epiphytic yeasts from grape carposphere.

    Science.gov (United States)

    Filho, M Cilião; Bertéli, M B D; Valle, J S; Paccola-Meirelles, L D; Linde, G A; Barcellos, F G; Colauto, N B

    2017-06-20

    The genetic diversity of epiphytic yeasts from grape carposphere is susceptible to environmental variations that determine the predominant carposphere microbiota. Understanding the diversity of yeasts that inhabit grape carposphere in different environments and their pectinolytic activity is a way to understand the biotechnological potential that surrounds us and help improve winemaking. Therefore, this study aimed to evaluate the pectinolytic activity and characterize the genetic diversity of isolated epiphytic yeasts from grape carposphere. Grapes of the Bordeaux cultivar were collected from different regions of Paraná and Rio Grande do Sul States, in Brazil, and the yeasts were isolated from these grape carpospheres. Monosporic isolates were morphologically and genetically characterized on potato dextrose agar medium and by PCR-RFLP and rep-PCR (BOX-PCR) in the ITS1-5.8S-ITS2 region of rDNA. The index of pectinolytic activity of isolates was also evaluated estimating the ratio between the halo diameter of enzymatic degradation and the diameter of the colony when the isolates were grown in cultivation medium containing 10 g/L pectin, 5 g/L yeast extract, 15 g/L agar, 0.12% (w/v) Congo red, and pH 6.2. We observed that the grape carposphere is an environment with a great genetic diversity of epiphytic yeasts of the following genera: Cryptococcus (31.25%), Pichia (25.0%), Candida (25.0%), Dekkera (12.5%), and Saccharomyces (6.25%). The PCR-RFLP technique allowed analyzing existing polymorphism among individuals of a population based on a more restrict and evolutionarily preserved region, mostly utilized to differentiate isolates at the genus level. Approximately 33% of yeast isolates presented pectinolytic activity with potential biotechnological for wine and fruit juice production. This great genetic variability found indicated that it is a potential reservoir of genes to be applied in viniculture improvement programs.

  11. Appraisal of biochemical and genetic diversity of mango cultivars ...

    African Journals Online (AJOL)

    Appraisal of biochemical and genetic diversity of mango cultivars using molecular markers. ... Mango (Mangifera indica L.) is one of the oldest fruit crops and is broadly cultivated worldwide. To determine the level of ... HOW TO USE AJOL.

  12. Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers.

    Science.gov (United States)

    Korir, N K; Diao, W; Tao, R; Li, X; Kayesh, E; Li, A; Zhen, W; Wang, S

    2014-01-08

    The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties.

  13. Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae.

    Directory of Open Access Journals (Sweden)

    Jiali Zhao

    Full Text Available We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1 determine the level of genetic diversity across the studied regions; (2 explore the likely origins of invasive populations in China; and (3 investigate whether there is the evidence of multiple introductions into China.We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China.We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (F IS or population differentiation (F ST. Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China.

  14. Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs.

    Science.gov (United States)

    Gillies, A C; Navarro, C; Lowe, A J; Newton, A C; Hernández, M; Wilson, J; Cornelius, J P

    1999-12-01

    Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P = 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica.

  15. 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.

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

    African Journals Online (AJOL)

    ajl

    2013-02-27

    Feb 27, 2013 ... 2Department of Plant Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil. ... primers were used to characterize toxicity alleles, and none of the accessions presented patterns ... accessions from India (Gupta et al., 2008; Gohil and. Pandya .... ISSR primers, generally low genetic diversity was.

  17. Conserving genetic diversity in Ponderosa Pine ecosystem restoration

    Science.gov (United States)

    L.E. DeWald

    2017-01-01

    Restoration treatments in the ponderosa pine (Pinus ponderosa P. & C. Lawson) ecosystems of the southwestern United States often include removing over 80 percent of post-EuroAmerican settlement-aged trees to create healthier forest structural conditions. These types of stand density reductions can have negative effects on genetic diversity. Allozyme analyses...

  18. 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 ...

  19. Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Sangwon Suh

    2014-11-01

    Full Text Available Four Korean native cattle (KNC breeds—Hanwoo, Chikso, Heugu, and Jeju black—are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO. The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120 and exotic breeds (Holstein and Charolais, n = 56. Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

  20. Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa

    Science.gov (United States)

    Duque-Lazo, Joaquín; Durka, Walter; Hauenschild, Frank; Schnitzler, Jan; Michalak, Ingo; Ogundipe, Oluwatoyin Temitayo; Muellner-Riehl, Alexandra Nora

    2018-01-01

    Climate change is predicted to impact species’ genetic diversity and distribution. We used Senegalia senegal (L.) Britton, an economically important species distributed in the Sudano-Sahelian savannah belt of West Africa, to investigate the impact of climate change on intraspecific genetic diversity and distribution. We used ten nuclear and two plastid microsatellite markers to assess genetic variation, population structure and differentiation across thirteen sites in West Africa. We projected suitable range, and potential impact of climate change on genetic diversity using a maximum entropy approach, under four different climate change scenarios. We found higher genetic and haplotype diversity at both nuclear and plastid markers than previously reported. Genetic differentiation was strong for chloroplast and moderate for the nuclear genome. Both genomes indicated three spatially structured genetic groups. The distribution of Senegalia senegal is strongly correlated with extractable nitrogen, coarse fragments, soil organic carbon stock, precipitation of warmest and coldest quarter and mean temperature of driest quarter. We predicted 40.96 to 6.34 per cent of the current distribution to favourably support the species’ ecological requirements under future climate scenarios. Our results suggest that climate change is going to affect the population genetic structure of Senegalia senegal, and that patterns of genetic diversity are going to influence the species’ adaptive response to climate change. Our study contributes to the growing evidence predicting the loss of economically relevant plants in West Africa in the next decades due to climate change. PMID:29659603

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

    Directory of Open Access Journals (Sweden)

    Dong Hwan Lee

    2014-06-01

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

  2. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    Science.gov (United States)

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  3. AFLP analysis of genetic diversity and phylogenetic relationships of Brassica oleracea in Ireland.

    Science.gov (United States)

    El-Esawi, Mohamed A; Germaine, Kieran; Bourke, Paula; Malone, Renee

    2016-01-01

    Brassica oleracea L. is one of the most economically important vegetable crop species of the genus Brassica L. This species is threatened in Ireland, without any prior reported genetic studies. The use of this species is being very limited due to its imprecise phylogeny and uncompleted genetic characterisation. The main objective of this study was to assess the genetic diversity and phylogenetic relationships of a set of 25 Irish B. oleracea accessions using the powerful amplified fragment length polymorphism (AFLP) technique. A total of 471 fragments were scored across all the 11 AFLP primer sets used, out of which 423 (89.8%) were polymorphic and could differentiate the accessions analysed. The dendrogram showed that cauliflowers were more closely related to cabbages than kales were, and accessions of some cabbage types were distributed among different clusters within cabbage subgroups. Approximately 33.7% of the total genetic variation was found among accessions, and 66.3% of the variation resided within accessions. The total genetic diversity (HT) and the intra-accessional genetic diversity (HS) were 0.251 and 0.156, respectively. This high level of variation demonstrates that the Irish B. oleracea accessions studied should be managed and conserved for future utilisation and exploitation in food and agriculture. In conclusion, this study addressed important phylogenetic questions within this species, and provided a new insight into the inclusion of four accessions of cabbages and kales in future breeding programs for improving varieties. AFLP markers were efficient for assessing genetic diversity and phylogenetic relationships in Irish B. oleracea species. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  4. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation

    Science.gov (United States)

    Tucker, Kimberly Pause; Hunter, Margaret E.; Bonde, Robert K.; Austin, James D.; Clark, Ann Marie; Beck, Cathy A.; McGuire, Peter M.; Oli, Madan K.

    2012-01-01

    Species of management concern that have been affected by human activities typically are characterized by low genetic diversity, which can adversely affect their ability to adapt to environmental changes. We used 18 microsatellite markers to genotype 362 Florida manatees (Trichechus manatus latirostris), and investigated genetic diversity, population structure, and estimated genetically effective population size (Ne). The observed and expected heterozygosity and average number of alleles were 0.455 ± 0.04, 0.479 ± 0.04, and 4.77 ± 0.51, respectively. All measures of Florida manatee genetic diversity were less than averages reported for placental mammals, including fragmented or nonideal populations. Overall estimates of differentiation were low, though significantly greater than zero, and analysis of molecular variance revealed that over 95% of the total variance was among individuals within predefined management units or among individuals along the coastal subpopulations, with only minor portions of variance explained by between group variance. Although genetic issues, as inferred by neutral genetic markers, appear not to be critical at present, the Florida manatee continues to face demographic challenges due to anthropogenic activities and stochastic factors such as red tides, oil spills, and disease outbreaks; these can further reduce genetic diversity of the manatee population.

  5. Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp.

    Science.gov (United States)

    Zhang, Jinxiu; Fernando, W G Dilantha; Remphrey, William R

    2005-08-01

    ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow

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

    Directory of Open Access Journals (Sweden)

    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].

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... Effects of landscape fragmentation on genetic diversity of Stipa krylovii ..... nation plant tends to anemophily, this pollination mode enable it to have the .... sity on newly isolated tropical islands: a test of a null hypothesis and.

  8. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands.

    Science.gov (United States)

    Sun, Ye; Vargas-Mendoza, Carlos F

    2017-01-01

    Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  9. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae on the Canary Islands

    Directory of Open Access Journals (Sweden)

    Ye Sun

    2017-06-01

    Full Text Available Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat. The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote and western islands (EI Hierro, La Palma, La Gomera, Tenerife, this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  10. Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse.

    Directory of Open Access Journals (Sweden)

    Heather R Mattila

    Full Text Available Recent losses of honey bee colonies have led to increased interest in the microbial communities that are associated with these important pollinators. A critical function that bacteria perform for their honey bee hosts, but one that is poorly understood, is the transformation of worker-collected pollen into bee bread, a nutritious food product that can be stored for long periods in colonies. We used 16S rRNA pyrosequencing to comprehensively characterize in genetically diverse and genetically uniform colonies the active bacterial communities that are found on honey bees, in their digestive tracts, and in bee bread. This method provided insights that have not been revealed by past studies into the content and benefits of honey bee-associated microbial communities. Colony microbiotas differed substantially between sampling environments and were dominated by several anaerobic bacterial genera never before associated with honey bees, but renowned for their use by humans to ferment food. Colonies with genetically diverse populations of workers, a result of the highly promiscuous mating behavior of queens, benefited from greater microbial diversity, reduced pathogen loads, and increased abundance of putatively helpful bacteria, particularly species from the potentially probiotic genus Bifidobacterium. Across all colonies, Bifidobacterium activity was negatively correlated with the activity of genera that include pathogenic microbes; this relationship suggests a possible target for understanding whether microbes provide protective benefits to honey bees. Within-colony diversity shapes microbiotas associated with honey bees in ways that may have important repercussions for colony function and health. Our findings illuminate the importance of honey bee-bacteria symbioses and examine their intersection with nutrition, pathogen load, and genetic diversity, factors that are considered key to understanding honey bee decline.

  11. Genetic Diversity in Jatropha curcas L. Assessed with SSR and SNP Markers

    Directory of Open Access Journals (Sweden)

    Juan M. Montes

    2014-08-01

    Full Text Available Jatropha curcas L. (jatropha is an undomesticated plant that has recently received great attention for its utilization in biofuel production, rehabilitation of wasteland, and rural development. Knowledge of genetic diversity and marker-trait associations is urgently needed for the design of breeding strategies. The main goal of this study was to assess the genetic structure and diversity in jatropha germplasm with co-dominant markers (Simple Sequence Repeats (SSR and Single Nucleotide Polymorphism (SNP in a diverse, worldwide, germplasm panel of 70 accessions. We found a high level of homozygosis in the germplasm that does not correspond to the purely outcrossing mating system assumed to be present in jatropha. We hypothesize that the prevalent mating system of jatropha comprise a high level of self-fertilization and that the outcrossing rate is low. Genetic diversity in accessions from Central America and Mexico was higher than in accession from Africa, Asia, and South America. We identified makers associated with the presence of phorbol esters. We think that the utilization of molecular markers in breeding of jatropha will significantly accelerate the development of improved cultivars.

  12. Genetic structure and diversity of the black and rufous sengiin Tanzanian coastal forests

    Czech Academy of Sciences Publication Activity Database

    Sabuni, C. A.; Van Houtte, N.; Gryseels, S.; Maganga, S. L. S.; Makundi, R. H.; Leirs, H.; Goüy de Bellocq, Joëlle

    2016-01-01

    Roč. 300, č. 4 (2016), s. 305-313 ISSN 0952-8369 Institutional support: RVO:68081766 Keywords : Rhynchocyon petersi * vulnerable * conservation genetics * coastal forests * Beamys hindei * genetic structure * genetic diversity * habitat fragmentation Subject RIV: EH - Ecology, Behaviour Impact factor: 2.186, year: 2016

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

    African Journals Online (AJOL)

    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 obtained from 30 primers. The value of Jaccard coefficient ranged from 0.66 to ...

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

    African Journals Online (AJOL)

    Vostro 2520

    Generally, Tigray and Amhara regions showed moderate to high diversity in ISSR analysis. ... other crops. The main purpose of its cultivation in. Ethiopia is to use it as a medicinal plant. It is used for human abdominal ache and diarrhea. Moreover, L. ... of 10 primers were obtained from the Genetic Research Laboratory.

  15. Genetic diversity of Diaphorina citri and its endosymbionts across east and south-east Asia.

    Science.gov (United States)

    Wang, Yanjing; Xu, Changbao; Tian, Mingyi; Deng, Xiaoling; Cen, Yijing; He, Yurong

    2017-10-01

    Diaphorina citri is the vector of 'Candidatus Liberibacter asiaticus', the most widespread pathogen associated huanglongbing, the most serious disease of citrus. To enhance our understanding of the distribution and origin of the psyllid, we investigated the genetic diversity and population structures of 24 populations in Asia and one from Florida based on the mtCOI gene. Simultaneously, genetic diversity and population structures of the primary endosymbiont (P-endosymbiont) 'Candidatus Carsonella ruddii' and secondary endosymbiont (S-endosymbiont) 'Candidatus Profftella armatura' of D. citri were determined with the housekeeping genes. AMOVA analysis indicated that populations of D. citri and its endosymbionts in east and south-east Asia were genetically distinct from populations in Pakistan and Florida. Furthermore, P-endosymbiont populations displayed a strong geographical structure across east and south-east Asia, while low genetic diversity indicated the absence of genetic structure among the populations of D. citri and its S-endosymbiont across these regions. The 'Ca. C. ruddii' is more diverse and structured than the D. citri and the 'Ca. P. armatura' across east and south-east Asia. Multiple introductions of the psyllid have occurred in China. Management application for controlling the pest is proposed based on the genetic information of D. citri and its endosymbionts. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  16. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  17. A genetic code alteration is a phenotype diversity generator in the human pathogen Candida albicans.

    Directory of Open Access Journals (Sweden)

    Isabel Miranda

    Full Text Available BACKGROUND: The discovery of genetic code alterations and expansions in both prokaryotes and eukaryotes abolished the hypothesis of a frozen and universal genetic code and exposed unanticipated flexibility in codon and amino acid assignments. It is now clear that codon identity alterations involve sense and non-sense codons and can occur in organisms with complex genomes and proteomes. However, the biological functions, the molecular mechanisms of evolution and the diversity of genetic code alterations remain largely unknown. In various species of the genus Candida, the leucine CUG codon is decoded as serine by a unique serine tRNA that contains a leucine 5'-CAG-3'anticodon (tRNA(CAG(Ser. We are using this codon identity redefinition as a model system to elucidate the evolution of genetic code alterations. METHODOLOGY/PRINCIPAL FINDINGS: We have reconstructed the early stages of the Candida genetic code alteration by engineering tRNAs that partially reverted the identity of serine CUG codons back to their standard leucine meaning. Such genetic code manipulation had profound cellular consequences as it exposed important morphological variation, altered gene expression, re-arranged the karyotype, increased cell-cell adhesion and secretion of hydrolytic enzymes. CONCLUSION/SIGNIFICANCE: Our study provides the first experimental evidence for an important role of genetic code alterations as generators of phenotypic diversity of high selective potential and supports the hypothesis that they speed up evolution of new phenotypes.

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

    Indian Academy of Sciences (India)

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

  19. Gene flow from North Africa contributes to differential human genetic diversity in southern Europe

    Science.gov (United States)

    Botigué, Laura R.; Henn, Brenna M.; Gravel, Simon; Maples, Brian K.; Gignoux, Christopher R.; Corona, Erik; Atzmon, Gil; Burns, Edward; Ostrer, Harry; Flores, Carlos; Bertranpetit, Jaume; Comas, David; Bustamante, Carlos D.

    2013-01-01

    Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis. PMID:23733930

  20. Interspecific sex in grass smuts and the genetic diversity of their pheromone-receptor system.

    Directory of Open Access Journals (Sweden)

    Ronny Kellner

    2011-12-01

    Full Text Available The grass smuts comprise a speciose group of biotrophic plant parasites, so-called Ustilaginaceae, which are specifically adapted to hosts of sweet grasses, the Poaceae family. Mating takes a central role in their life cycle, as it initiates parasitism by a morphological and physiological transition from saprobic yeast cells to pathogenic filaments. As in other fungi, sexual identity is determined by specific genomic regions encoding allelic variants of a pheromone-receptor (PR system and heterodimerising transcription factors. Both operate in a biphasic mating process that starts with PR-triggered recognition, directed growth of conjugation hyphae, and plasmogamy of compatible mating partners. So far, studies on the PR system of grass smuts revealed diverse interspecific compatibility and mating type determination. However, many questions concerning the specificity and evolutionary origin of the PR system remain unanswered. Combining comparative genetics and biological approaches, we report on the specificity of the PR system and its genetic diversity in 10 species spanning about 100 million years of mating type evolution. We show that three highly syntenic PR alleles are prevalent among members of the Ustilaginaceae, favouring a triallelic determination as the plesiomorphic characteristic of this group. Furthermore, the analysis of PR loci revealed increased genetic diversity of single PR locus genes compared to genes of flanking regions. Performing interspecies sex tests, we detected a high potential for hybridisation that is directly linked to pheromone signalling as known from intraspecies sex. Although the PR system seems to be optimised for intraspecific compatibility, the observed functional plasticity of the PR system increases the potential for interspecific sex, which might allow the hybrid-based genesis of newly combined host specificities.

  1. An analysis of genetic diversity and inbreeding in Wuchereria bancrofti: implications for the spread and detection of drug resistance.

    Directory of Open Access Journals (Sweden)

    Thomas S Churcher

    2008-04-01

    Full Text Available Estimates of genetic diversity in helminth infections of humans often have to rely on genotyping (immature parasite transmission stages instead of adult worms. Here we analyse the results of one such study investigating a single polymorphic locus (a change at position 200 of the beta-tubulin gene in microfilariae of the lymphatic filarial parasite Wuchereria bancrofti. The presence of this genetic change has been implicated in benzimidazole resistance in parasitic nematodes of farmed ruminants. Microfilariae were obtained from patients of three West African villages, two of which were sampled prior to the introduction of mass drug administration. An individual-based stochastic model was developed showing that a wide range of allele frequencies in the adult worm populations could have generated the observed microfilarial genetic diversity. This suggests that appropriate theoretical null models are required in order to interpret studies that genotype transmission stages. Wright's hierarchical F-statistic was used to investigate the population structure in W. bancrofti microfilariae and showed significant deficiency of heterozygotes compared to the Hardy-Weinberg equilibrium; this may be partially caused by a high degree of parasite genetic differentiation between hosts. Studies seeking to quantify accurately the genetic diversity of helminth populations by analysing transmission stages should increase their sample size to account for the variability in allele frequency between different parasite life-stages. Helminth genetic differentiation between hosts and non-random mating will also increase the number of hosts (and the number of samples per host that need to be genotyped, and could enhance the rate of spread of anthelmintic resistance.

  2. SCoT marker for the assessment of genetic diversity in saudi arabian date palm cultivars

    International Nuclear Information System (INIS)

    Qurainy, F.A.; Tarroum, M.

    2015-01-01

    Different types of molecular markers based on DNA have been used for the assessment of genetic diversity in the plant species. Start Codon Targeted Polymorphism (SCoT) marker has recently become the marker of choice in genetic diversity studies. SCoT marker was used for the assessment of genetic diversity in Saudi Arabian date palm cultivars. The percentage of polymorphic loci (PPL) at population level ranged from 3.28 to 13.11 with an average of 7.10. The Neis gene diversity (h) and Shannons Information index (I) were 0.033 and 0.046, respectively. However, at cultivar level, PPL, Neis gene diversity (h) and Shannons Information index (I) were 42.62, 0.090 and 0.155, respectively. Analysis of molecular variance (AMOVA) showed 48% of variation within the populations, whereas 52% was found among the populations. A hierarchical analysis of molecular variance revealed level of genetic differentiation among populations (52% of total variance, P = 0.001), consistent with the gene differentiation coefficient (Gst = 0.631). Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the six cultivars and their populations into five main clusters at 0.95 genetic similarity coefficient level. (author)

  3. Genetic diversity and selection gain in the physic nut (Jatropha curcas).

    Science.gov (United States)

    Brasileiro, B P; Silva, S A; Souza, D R; Santos, P A; Oliveira, R S; Lyra, D H

    2013-07-08

    The use of efficient breeding methods depends on knowledge of genetic control of traits to be improved. We estimated genetic parameters, selection gain, and genetic diversity in physic nut half-sib families, in order to provide information for breeding programs of this important biofuel species. The progeny test included 20 half-sib families in 4 blocks and 10 plants per plot. The mean progeny heritability values were: 50% for number of bunches, 47% for number of fruits, 35% for number of seeds, 6% for stem diameter, 26% for number of primary branches, 14% for number of secondary branches, 66% for plant height, and 25% for survival of the plants, demonstrating good potential for early selection in plant height, number of branches, and number of fruits per plant. In the analysis of genetic diversity, genotypes were divided into 4 groups. Genotypes 18, 19, 20, and 8 clustered together and presented the highest means for the vegetative and production. Lower means were observed in the 17, 12, 13, and 9 genotypes from the same group. We detected genetic variability in this population, with high heritability estimates and accuracy, demonstrating the possibility of obtaining genetic gains for vegetative characters and production at 24 months after planting.

  4. Exploiting a wheat EST database to assess genetic diversity.

    Science.gov (United States)

    Karakas, Ozge; Gurel, Filiz; Uncuoglu, Ahu Altinkut

    2010-10-01

    Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F(2) individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01.

  5. Exploiting a wheat EST database to assess genetic diversity

    Directory of Open Access Journals (Sweden)

    Ozge Karakas

    2010-01-01

    Full Text Available Expressed sequence tag (EST markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum. In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29% contigs and 96 (10% singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs and metabolism and energy (singletons. EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725 being between Harmankaya99 and Sönmez2001, and the lowest (0.622 between Aytin98 and Izgi01.

  6. Analysis of genetic diversity in Brown Swiss, Jersey and Holstein populations using genome-wide single nucleotide polymorphism markers

    Directory of Open Access Journals (Sweden)

    Melka Melkaye G

    2012-03-01

    Full Text Available Abstract Background Studies of genetic diversity are essential in understanding the extent of differentiation between breeds, and in designing successful diversity conservation strategies. The objective of this study was to evaluate the level of genetic diversity within and between North American Brown Swiss (BS, n = 900, Jersey (JE, n = 2,922 and Holstein (HO, n = 3,535 cattle, using genotyped bulls. GENEPOP and FSTAT software were used to evaluate the level of genetic diversity within each breed and between each pair of the three breeds based on genome-wide SNP markers (n = 50,972. Results Hardy-Weinberg equilibrium (HWE exact test within breeds showed a significant deviation from equilibrium within each population (P st indicated that the combination of BS and HO in an ideally amalgamated population had higher genetic diversity than the other pairs of breeds. Conclusion Results suggest that the three bull populations have substantially different gene pools. BS and HO show the largest gene differentiation and jointly the highest total expected gene diversity compared to when JE is considered. If the loss of genetic diversity within breeds worsens in the future, the use of crossbreeding might be an option to recover genetic diversity, especially for the breeds with small population size.

  7. Genetic diversity of three surface protein genes in Plasmodium malariae from three Asian countries.

    Science.gov (United States)

    Srisutham, Suttipat; Saralamba, Naowarat; Sriprawat, Kanlaya; Mayxay, Mayfong; Smithuis, Frank; Nosten, Francois; Pukrittayakamee, Sasithon; Day, Nicholas P J; Dondorp, Arjen M; Imwong, Mallika

    2018-01-11

    Genetic diversity of the three important antigenic proteins, namely thrombospondin-related anonymous protein (TRAP), apical membrane antigen 1 (AMA1), and 6-cysteine protein (P48/45), all of which are found in various developmental stages of Plasmodium parasites is crucial for targeted vaccine development. While studies related to the genetic diversity of these proteins are available for Plasmodium falciparum and Plasmodium vivax, barely enough information exists regarding Plasmodium malariae. The present study aims to demonstrate the genetic variations existing among these three genes in P. malariae by analysing their diversity at nucleotide and protein levels. Three surface protein genes were isolated from 45 samples collected in Thailand (N = 33), Myanmar (N = 8), and Lao PDR (N = 4), using conventional polymerase chain reaction (PCR) assay. Then, the PCR products were sequenced and analysed using BioEdit, MEGA6, and DnaSP programs. The average pairwise nucleotide diversities (π) of P. malariae trap, ama1, and p48/45 were 0.00169, 0.00413, and 0.00029, respectively. The haplotype diversities (Hd) of P. malariae trap, ama1, and p48/45 were 0.919, 0.946, and 0.130, respectively. Most of the nucleotide substitutions were non-synonymous, which indicated that the genetic variations of these genes were maintained by positive diversifying selection, thus, suggesting their role as a potential target of protective immune response. Amino acid substitutions of P. malariae TRAP, AMA1, and P48/45 could be categorized to 17, 20, and 2 unique amino-acid variants, respectively. For further vaccine development, carboxyl terminal of P48/45 would be a good candidate according to conserved amino acid at low genetic diversity (π = 0.2-0.3). High mutational diversity was observed in P. malariae trap and ama1 as compared to p48/45 in P. malariae samples isolated from Thailand, Myanmar, and Lao PDR. Taken together, these results suggest that P48/45 might be a good vaccine

  8. Optimizing Conservation Strategies for a Threatened Tree Species: In Situ Conservation of White Ash (Fraxinus americana L. Genetic Diversity through Insecticide Treatment

    Directory of Open Access Journals (Sweden)

    Charles E. Flower

    2018-04-01

    Full Text Available Forest resources face numerous threats that require costly management. Hence, there is an increasing need for data-informed strategies to guide conservation practices. The introduction of the emerald ash borer to North America has caused rapid declines in ash populations (Fraxinus spp. L.. Natural resource managers are faced with a choice of either allowing ash trees to die, risking forest degradation and reduced functional resilience, or investing in conserving trees to preserve ecosystem structure and standing genetic diversity. The information needed to guide these decisions is not always readily available. Therefore, to address this concern, we used eight microsatellites to genotype 352 white ash trees (Fraxinus americana L. across 17 populations in the Allegheny National Forest; a subset of individuals sampled are part of an insecticide treatment regimen. Genetic diversity (number of alleles and He was equivalent in treated and untreated trees, with little evidence of differentiation or inbreeding, suggesting current insecticidal treatment is conserving local, neutral genetic diversity. Using simulations, we demonstrated that best practice is treating more populations rather than more trees in fewer populations. Furthermore, through genetic screening, conservation practitioners can select highly diverse and unique populations to maximize diversity and reduce expenditures (by up to 21%. These findings will help practitioners develop cost-effective strategies to conserve genetic diversity.

  9. 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

  10. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

    2011-01-01

    Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprisin...

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

    African Journals Online (AJOL)

    Assessment of genetic diversity among maize accessions using inter simple sequence repeats (ISSR) markers. AT do Amaral Júnior, EC de Oliveira, LSA Gonçalves, CA Scapim, LS Candido, TR da Conceição Silva, C Vittorazzi, KS da Cunha ...

  12. 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 ...

  13. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    Directory of Open Access Journals (Sweden)

    Steeves Buckland

    Full Text Available Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko, is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA markers in 13 subpopulations to: (i assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii estimate effective population sizes and migration rates of subpopulations; and (iii examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable

  14. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    Directory of Open Access Journals (Sweden)

    Annika M E Noreen

    Full Text Available Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter, 193 saplings (>1 yr, and 1,822 seedlings (<1 yr of the canopy tree Koompassia malaccensis (Fabaceae. We tested hypotheses relevant to the genetic consequences of habitat loss: (1 that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2 K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854, high allelic richness (R = 16.7-19.5, low inbreeding co-efficients (FIS = 0.013-0.076, and a large proportion (30.1% of rare alleles (i.e. frequency <1%. However, spatial genetic structure (SGS analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961, calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

  15. [Genetic diversity analysis of Andrographis paniculata in China based on SRAP and SNP].

    Science.gov (United States)

    Chen, Rong; Wang, Xiao-Yun; Song, Yu-Ning; Zhu, Yun-feng; Wang, Peng-liang; Li, Min; Zhong, Guo-Yue

    2014-12-01

    In order to reveal genetic diversity of domestic Andrographis paniculata and its impact on quality, genetic backgrounds of 103 samples from 7 provinces in China were analyzed using SRAP marker and SNP marker. Genetic structures of the A. paniculata populations were estimated with Powermarker V 3.25 and Mega 6.0 software, and polymorphic SNPs were identified with CodonCode Aligner software. The results showed that the genetic distances of domestic A. paniculata germplasm ranged from 0. 01 to 0.09, and no polymorphic SNPs were discovered in coding sequence fragments of ent-copalyl diphosphate synthase. A. paniculata germplasm from various regions in China had poor genetic diversity. This phenomenon was closely related to strict self-fertilization and earlier introduction from the same origin. Therefore, genetic background had little impact on variable qualities of A. paniculata in domestic market. Mutation breeding, polyploid breeding and molecular breeding were proposed as promising strategies in germplasm innovation.

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

    Directory of Open Access Journals (Sweden)

    Hamid Khazaei

    2016-07-01

    Full Text Available 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 countries to estimate genetic diversity and genetic structure using 1194 polymorphic single nucleotide polymorphism (SNP markers which span the lentil genome. Using principal coordinate analysis, population structure analysis and UPGMA cluster analysis, the accessions were categorized into three major groups that prominently reflected geographical origin (world’s agro-ecological zones. The three clusters complemented the origins, pedigrees and breeding histories of the germplasm. The three groups were a South Asia (sub-tropical savannah, b Mediterranean and c northern temperate. Based on the results from this study, it is also clear that breeding programs still have considerable genetic diversity to mine within the cultivated lentil, however, surveyed South Asian and Canadian germplasm revealed narrow genetic diversity.

  17. Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management.

    Science.gov (United States)

    Wultsch, Claudia; Caragiulo, Anthony; Dias-Freedman, Isabela; Quigley, Howard; Rabinowitz, Salisa; Amato, George

    2016-01-01

    Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of

  18. Genetic health and population monitoring of two small black bear (Ursus americanus populations in Alabama, with a regional perspective of genetic diversity and exchange.

    Directory of Open Access Journals (Sweden)

    John P Draper

    Full Text Available One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76-124, 95% C.I., the lowest genetic diversity of compared populations (richness = 2.33, Ho and He = 0.33, and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26-43, 95% C.I., relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho = 0.53, He = 0.65, and showed a high level of genetic connectivity with surrounding populations.

  19. Genetic health and population monitoring of two small black bear (Ursus americanus) populations in Alabama, with a regional perspective of genetic diversity and exchange.

    Science.gov (United States)

    Draper, John P; Waits, Lisette P; Adams, Jennifer R; Seals, Christopher L; Steury, Todd D

    2017-01-01

    One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76-124, 95% C.I.), the lowest genetic diversity of compared populations (richness = 2.33, Ho and He = 0.33), and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26-43, 95% C.I.), relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho = 0.53, He = 0.65), and showed a high level of genetic connectivity with surrounding populations.

  20. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

    DEFF Research Database (Denmark)

    Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine

    2011-01-01

    insight into consequences of population declines in a broader conservation context. The harbour seal population at Svalbard is the world's northernmost harbour seal population. Nothing is known about the genetic diversity, distinctiveness or origin of this small, marginalized mammalian population. Thus......  It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... microsatellites and variation in the D-loop. Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size and showed an indication of having...

  1. 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...

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

    African Journals Online (AJOL)

    DR TONUKARI NYEROVWO

    2011-06-06

    Jun 6, 2011 ... Fax: +86. 29 87082604. Abbreviations: NEsp, Northeastern spring .... the present study, genetic diversity of this primary core .... spectroscopy DA7200 (Sweden Perten instruments Company). ... All primers were synthesized ..... 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 MS. SSR Locus. G e n e tic d.

  3. Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers

    Science.gov (United States)

    Arnau, Gemma; MN, Sheela; Chair, Hana; Lebot, Vincent; K, Abraham; Perrier, Xavier; Petro, Dalila; Penet, Laurent; Pavis, Claudie

    2017-01-01

    Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods. PMID:28355293

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

    African Journals Online (AJOL)

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

  5. Genetic calibration of species diversity among North America's freshwater fishes.

    Science.gov (United States)

    April, Julien; Mayden, Richard L; Hanner, Robert H; Bernatchez, Louis

    2011-06-28

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.

  6. Genetic diversity in some tunisian barley land races based on raped markers

    International Nuclear Information System (INIS)

    Abdellaos, R.; Kadir, K.; Naceur, M.B.; Kaab, L.B.B.

    2010-01-01

    The genetic diversity analysis of 15 barley land races was carried out using RAPD markers.These land races were collected from various bio climatic Tunisian zones. The amplification products varied from 4 to 11 bands ranging between 250 pb and 3000 pb. On 698 fragments counted, 578 are polymorphic showing a high level of polymorphism (82.8%). The relationship between the studied land races was evaluated according to (UPGMA) method that classified barley land races in 4 homogeneous groups. Among which, the group D included the majority of the land races with the introduced variety 'Martin'. The genetic distance between these land races is reduced, may be because of the presence of a common ancestor which led to a narrow genetic diversity. (author)

  7. Genetic diversity in some tunisian barley land races based on raped markers

    Energy Technology Data Exchange (ETDEWEB)

    Abdellaos, R; Kadir, K; Naceur, M B; Kaab, L B.B.,

    2010-12-15

    The genetic diversity analysis of 15 barley land races was carried out using RAPD markers.These land races were collected from various bio climatic Tunisian zones. The amplification products varied from 4 to 11 bands ranging between 250 pb and 3000 pb. On 698 fragments counted, 578 are polymorphic showing a high level of polymorphism (82.8%). The relationship between the studied land races was evaluated according to (UPGMA) method that classified barley land races in 4 homogeneous groups. Among which, the group D included the majority of the land races with the introduced variety 'Martin'. The genetic distance between these land races is reduced, may be because of the presence of a common ancestor which led to a narrow genetic diversity. (author)

  8. Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

    Science.gov (United States)

    Herrera, C M; Pozo, M I; Bazaga, P

    2011-11-01

    Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

  9. 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 ...

  10. Genetic diversity of Plasmodium falciparum populations in southeast and western Myanmar.

    Science.gov (United States)

    Soe, Than Naing; Wu, Yanrui; Tun, Myo Win; Xu, Xin; Hu, Yue; Ruan, Yonghua; Win, Aung Ye Naung; Nyunt, Myat Htut; Mon, Nan Cho Nwe; Han, Kay Thwe; Aye, Khin Myo; Morris, James; Su, Pincan; Yang, Zhaoqing; Kyaw, Myat Phone; Cui, Liwang

    2017-07-04

    The genetic diversity of malaria parasites reflects the complexity and size of the parasite populations. This study was designed to explore the genetic diversity of Plasmodium falciparum populations collected from two southeastern areas (Shwekyin and Myawaddy bordering Thailand) and one western area (Kyauktaw bordering Bangladesh) of Myanmar. A total of 267 blood samples collected from patients with acute P. falciparum infections during 2009 and 2010 were used for genotyping at the merozoite surface protein 1 (Msp1), Msp2 and glutamate-rich protein (Glurp) loci. One hundred and eighty four samples were successfully genotyped at three genes. The allelic distributions of the three genes were all significantly different among three areas. MAD20 and 3D7 were the most prevalent alleles in three areas for Msp1 and Msp2, respectively. The Glurp allele with a bin size of 700-750 bp was the most prevalent both in Shwekyin and Myawaddy, whereas two alleles with bin sizes of 800-850 bp and 900-1000 bp were the most prevalent in the western site Kyauktaw. Overall, 73.91% of samples contained multiclonal infections, resulting in a mean multiplicity of infection (MOI) of 1.94. Interestingly, the MOI level presented a rising trend with the order of Myawaddy, Kyauktaw and Shwekyin, which also paralleled with the increasing frequencies of Msp1 RO33 and Msp2 FC27 200-250 bp alleles. Msp1 and Msp2 genes displayed higher levels of diversity and higher MOI rates than Glurp. PCR revealed four samples (two from Shwekyin and two from Myawaddy) with mixed infections of P. falciparum and P. vivax. This study genotyped parasite clinical samples from two southeast regions and one western state of Myanmar at the Msp1, Msp2 and Glurp loci, which revealed high levels of genetic diversity and mixed-strain infections of P. falciparum populations at these sites. The results indicated that malaria transmission intensity in these regions remained high and more strengthened control efforts are

  11. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

    Directory of Open Access Journals (Sweden)

    Niko eBeerenwinkel

    2012-09-01

    Full Text Available Many viruses, including the clinically relevant RNA viruses HIV and HCV, exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different next-generation sequencing platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of next-generation sequencing to estimate viral diversity.

  12. How and how much does RAD-seq bias genetic diversity estimates?

    Science.gov (United States)

    Cariou, Marie; Duret, Laurent; Charlat, Sylvain

    2016-11-08

    RAD-seq is a powerful tool, increasingly used in population genomics. However, earlier studies have raised red flags regarding possible biases associated with this technique. In particular, polymorphism on restriction sites results in preferential sampling of closely related haplotypes, so that RAD data tends to underestimate genetic diversity. Here we (1) clarify the theoretical basis of this bias, highlighting the potential confounding effects of population structure and selection, (2) confront predictions to real data from in silico digestion of full genomes and (3) provide a proof of concept toward an ABC-based correction of the RAD-seq bias. Under a neutral and panmictic model, we confirm the previously established relationship between the true polymorphism and its RAD-based estimation, showing a more pronounced bias when polymorphism is high. Using more elaborate models, we show that selection, resulting in heterogeneous levels of polymorphism along the genome, exacerbates the bias and leads to a more pronounced underestimation. On the contrary, spatial genetic structure tends to reduce the bias. We confront the neutral and panmictic model to "ideal" empirical data (in silico RAD-sequencing) using full genomes from natural populations of the fruit fly Drosophila melanogaster and the fungus Shizophyllum commune, harbouring respectively moderate and high genetic diversity. In D. melanogaster, predictions fit the model, but the small difference between the true and RAD polymorphism makes this comparison insensitive to deviations from the model. In the highly polymorphic fungus, the model captures a large part of the bias but makes inaccurate predictions. Accordingly, ABC corrections based on this model improve the estimations, albeit with some imprecisions. The RAD-seq underestimation of genetic diversity associated with polymorphism in restriction sites becomes more pronounced when polymorphism is high. In practice, this means that in many systems where

  13. Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis)

    Czech Academy of Sciences Publication Activity Database

    Phalen, D. N.; Hall, J.; Ganesh, G.; Hartigan, Ashlie; Smith, C.; De Jong, C.; Field, H.; Rose, K.

    2017-01-01

    Roč. 98, č. 2 (2017), s. 428-437 ISSN 0022-2372 Institutional support: RVO:60077344 Keywords : diversity * flying fox * mitochondrial DNA * phylogeny * Pteropus melanotus natalis Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 1.630, year: 2016

  14. Genetic diversity and relationship analysis of Gossypium arboreum accessions.

    Science.gov (United States)

    Liu, F; Zhou, Z L; Wang, C Y; Wang, Y H; Cai, X Y; Wang, X X; Zhang, Z S; Wang, K B

    2015-11-19

    Simple sequence repeat techniques were used to identify the genetic diversity of 101 Gossypium arboreum accessions collected from India, Vietnam, and the southwest of China (Guizhou, Guangxi, and Yunnan provinces). Twenty-six pairs of SSR primers produced a total of 103 polymorphic loci with an average of 3.96 polymorphic loci per primer. The average of the effective number of alleles, Nei's gene diversity, and Shannon's information index were 0.59, 0.2835, and 0.4361, respectively. The diversity varied among different geographic regions. The result of principal component analysis was consistent with that of unweighted pair group method with arithmetic mean clustering analysis. The 101 G. arboreum accessions were clustered into 2 groups.

  15. Genetic diversity among five T4-like bacteriophages

    Directory of Open Access Journals (Sweden)

    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

  16. Evaluation of genetic diversity in different Pakistani wheat land races

    International Nuclear Information System (INIS)

    Mahmood, T.; Siddiqua, A.; Rasheed, A.; Nazar, N.

    2011-01-01

    Wheat is one of the main sources of nutrition worldwide. Genetic improvement of the seed makes wheat a source of high quality flour for human consumption and for other industrial uses. With the help of molecular markers, the available germplasm of wheat can be assessed for future breeding programs. Therefore, the aim of the present work was to analyze the genetic diversity among 15 Pakistani wheat land races based on Random Amplified Polymorphism DNA (RAPD) markers. A total of 284 DNA fragments were amplified, ranging in size from 200bp to 1100bp by using six primers. The number of DNA fragments for each primer varied from 2 (OPC-6) to 9 (OPC-8) with an average of 6 fragments per primer. Out of 284 amplified products, 120 were monomorphic and 137 were polymorphic showing an average of 7.8% polymorphism per primer. One specific marker was detected both for OPC-1 and OPC-8, two for OPC-5, while no RAPD specific marker was detected for the remaining primers. The genetic similarity index values ranged from 0.36 to 0.93, with an average of 0.64. Maximum genetic similarity (91%) was observed between Sur bej and Khushkawa. On the contrary, minimum genetic similarity (32%) was observed in Khushkaba-1 and Khushkawa. The dendrogram resulting from the NTSYS cluster analysis showed that the studied genotypes are divided into two main clusters from the same node. The first cluster contained 13 land races, while the second cluster contained only 2 land races. The dendrogram clustered the genotypes into 5 groups and showed efficiency in identifying genetic variability. These results indicated the usefulness of RAPD technique in estimating the genetic diversity among wheat genetic resources. (author)

  17. Analysis of genetic diversity in mango ( Mangifera indica L.) using ...

    African Journals Online (AJOL)

    Analysis of genetic diversity in mango ( Mangifera indica L.) using isozymetic polymorphism. ... All the isozymes, used in the present study showed polymorphism for mango. A total of 25 different electrophoretic ... HOW TO USE AJOL.

  18. Analysis of genetic diversity of Piper spp. in Hainan Island (China ...

    African Journals Online (AJOL)

    Inter-simple sequence repeat (ISSR) analysis was used to evaluate the genetic variation of Piper spp. from Hainan, China. 247 polymorphic bands out of a total of 248 (99.60%) were generated from 74 individual plants of Piper spp. The overall level of genetic diversity among Piper spp. in Hainan was high, with the mean ...

  19. Diversity and genetic structure of jenipapo (Genipa americana L. Brazilian accessions

    Directory of Open Access Journals (Sweden)

    Ana Veruska Cruz da Silva

    2014-10-01

    Full Text Available Usually known as jenipapo, Genipa americana L. is a Rubiaceae Brazilian native species. It is an important species in the restoration of Brazilian riparian forests and is one of the most promising fruit trees for sustainable harvesting programs. In this study we provide the first data on the genetic diversity and structure of a Jenipapo Germplasm Bank using inter simple sequence repeat (ISSR markers. We evaluated 160 accessions from wild populations, and the data generated from 12 ISSR primers were used to determine genetic variability via a model-based Bayesian procedure (Structure and molecular variance analysis. In addition, Shannon index, genetic diversity and Jaccard coefficients were estimated. A total of 12 primers were used, which generated 123 polymorphic fragments. Four groups were formed from the analysis of the fragments, and the CR1-2 genotype was isolated, being more divergent than the other genotypes.

  20. The study of genetic diversity of Daemonorops draco (Palmae using ISSR markers

    Directory of Open Access Journals (Sweden)

    REVIS ASRA

    2014-10-01

    Full Text Available Asra R, Syamsuardi, Mansyurdin, Witono JR. 2014. The study of genetic diversity of Daemonorops draco (Palmae using ISSR markers. Biodiversitas 15: 109-114. The genetic diversity in five populations of Daemonorops draco(Willd. Blume (Jernang: in Bahasa Indonesia was analyzed using Inter Simple Sequence Repeat (ISSR markers. The screening results from using 15 ISSR primers showed that only 5 of ISSR primers had clear and reproducible bands. Based on the data from the matrix binary analyzed using POPGENE version 3.2, the highest genetic diversity was found in the Sepintun population at 0.0969 average heterozygosis (H and 0.146 average Shannon Index (I. The heterozygosis calculation of the total population (HT was 0.2571. The heterozygosis value within a population (HS=0.0704 was smaller than that between populations (DST=0.1867. Using the clustering analysis program Past version 32 on 43 individuals of D. draco, we found that there were three groups of D. draco. Group A consisted of 8 individuals in the Bengayoan population, group B consisted of 9 units in the Nunusan population and group C consisted of three populations; Tebo, Sepintun and Mandiangin consisted of 10, 8 and 8 individuals. The genetic similarity varied among all populations withthe values between 0.07-0.93.

  1. Males and females contribute unequally to offspring genetic diversity in the polygynandrous mating system of wild boar.

    Directory of Open Access Journals (Sweden)

    Javier Pérez-González

    Full Text Available The maintenance of genetic diversity across generations depends on both the number of reproducing males and females. Variance in reproductive success, multiple paternity and litter size can all affect the relative contributions of male and female parents to genetic variation of progeny. The mating system of the wild boar (Sus scrofa has been described as polygynous, although evidence of multiple paternity in litters has been found. Using 14 microsatellite markers, we evaluated the contribution of males and females to genetic variation in the next generation in independent wild boar populations from the Iberian Peninsula and Hungary. Genetic contributions of males and females were obtained by distinguishing the paternal and maternal genetic component inherited by the progeny. We found that the paternally inherited genetic component of progeny was more diverse than the maternally inherited component. Simulations showed that this finding might be due to a sampling bias. However, after controlling for the bias by fitting both the genetic diversity in the adult population and the number of reproductive individuals in the models, paternally inherited genotypes remained more diverse than those inherited maternally. Our results suggest new insights into how promiscuous mating systems can help maintain genetic variation.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  3. Genetic diversity of sesame (sesamum indicum L.) germplasm from Pakistan using RAPD markers

    Energy Technology Data Exchange (ETDEWEB)

    Akbar, F; Rabbani, M A; Masood, M S; Shinwari, Z.K., E-mail: shinwari@qau.edu.p

    2011-08-15

    Genetic diversity among 20 sesame (Sesamum indicum L.) accessions was examined at DNA level by means of random amplified polymorphic DNA (RAPD) analysis. Ten primers used produced a total of 93 RAPD fragments, of which 70 (75%) were polymorphic. Each primer generated 5 to 17 amplified fragments with an average of 9.3 bands per primer. Based on pair-wise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were computed to assess the associations among the accessions. Pair-wise similarity indices varied from 0.65 to 0.91. A UPGMA cluster analysis based on these genetic similarities located most of the accessions far apart from one another, showing a high level of polymorphism. Genetically, all the genotypes were classified into two major groups and six subgroups or clusters. A single accession (22243) was relatively distinct from rest of the accessions and created independent cluster. In conclusion, even with the use of a limited set of primers, RAPD technique revealed a high level of genetic variation among sesame accessions collected from diverse ecologies of Pakistan. This high level of genetic diversity among the genotypes suggested that RAPD technique is valuable for sesame systematic, and can be helpful for the upholding of germplasm banks and the competent choice of parents in breeding programs. (author)

  4. Identification of genetically diverse genotypes for photoperiod insensitivity in soybean using RAPD markers.

    Science.gov (United States)

    Singh, R K; Bhatia, V S; Yadav, Sanjeev; Athale, Rashmi; Lakshmi, N; Guruprasad, K N; Chauhan, G S

    2008-10-01

    Most of the Indian soybean varieties were found to be highly sensitive to photoperiod, which limits their cultivation in only localized area. Identification of genetically diverse source of photoperiod insensitive would help to broaden the genetic base for this trait. Present study was undertaken with RAPD markers for genetic diversity estimation in 44 accessions of soybean differing in response to photoperiod sensitivity. The selected twenty-five RAPD primers produced a total of 199 amplicons, which generated 89.9 % polymorphism. The number of amplification products ranged from 2 to 13 for different primers. The polymorphism information content ranged from 0.0 for monomorphic loci to 0.5 with an average of 0.289. Genetic diversity between pairs of genotypes was 37.7% with a range of 3.9 to 71.6%. UPGMA cluster analysis placed all the accessions of soybean into four major clusters. No discernable geographical patterns were observed in clustering however; the smaller groups corresponded well with pedigree. Mantel's test (r = 0.915) indicates very good fit for clustering pattern. Two genotypes, MACS 330 and 111/2/1939 made a very divergent group from other accessions of soybean and highly photoperiod insensitive that may be potential source for broadening the genetic base of soybean for this trait.

  5. Genetic diversity of sesame (sesamum indicum L.) germplasm from Pakistan using RAPD markers

    International Nuclear Information System (INIS)

    Akbar, F; Rabbani, M.A.; Masood, M.S.; Shinwari, Z.K.

    2011-01-01

    Genetic diversity among 20 sesame (Sesamum indicum L.) accessions was examined at DNA level by means of random amplified polymorphic DNA (RAPD) analysis. Ten primers used produced a total of 93 RAPD fragments, of which 70 (75%) were polymorphic. Each primer generated 5 to 17 amplified fragments with an average of 9.3 bands per primer. Based on pair-wise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were computed to assess the associations among the accessions. Pair-wise similarity indices varied from 0.65 to 0.91. A UPGMA cluster analysis based on these genetic similarities located most of the accessions far apart from one another, showing a high level of polymorphism. Genetically, all the genotypes were classified into two major groups and six subgroups or clusters. A single accession (22243) was relatively distinct from rest of the accessions and created independent cluster. In conclusion, even with the use of a limited set of primers, RAPD technique revealed a high level of genetic variation among sesame accessions collected from diverse ecologies of Pakistan. This high level of genetic diversity among the genotypes suggested that RAPD technique is valuable for sesame systematic, and can be helpful for the upholding of germplasm banks and the competent choice of parents in breeding programs. (author)

  6. Genetic Diversity Analysis of Iranian Jujube Ecotypes (Ziziphus spp. Using RAPD Molecular Marker

    Directory of Open Access Journals (Sweden)

    S Abbasi

    2012-12-01

    Full Text Available Jujube (Ziziphus jujuba Mill. is a valuable medicinal plant which is important in Iranian traditional medicines. Although the regional plants such as jujube play an important role in our economy, but they are forgotten in research and technology. Considering the economic and medicinal importance of jujube, the first step in breeding programs is determination of the genetic diversity among the individuals. 34 ecotypes of jujube, which have been collected from eight provinces of Iran, were used in this study. The genetic relationships of Iranian jujube ecotypes were analyzed using Random Amplified Polymorphic DNA (RAPD marker. Six out of 15 random decamer primers applied for RAPD analysis, showed an informative polymorphism. According to clustering analysis using UPGMA's methods, the ecotypes were classified into two major groups at the 0.81 level of genetic similarity. The highest value of similarity coefficient (0.92 was detected between Mazandaran and Golestan ecotypes and the most genetic diversity was observed in ecotypes of Khorasan-Jonoubi. The affinity of Khorasan-Jonoubi and Esfahan ecotypes indicated a possible common origin for the variation in these areas. Results indicated that RAPD analysis could be successfully used for the estimation of genetic diversity among Ziziphus ecotypes and it can be useful for further investigations.

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

    Directory of Open Access Journals (Sweden)

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

    African Journals Online (AJOL)

    This study was therefore conducted to estimate the genetic diversity of 114 Sweet potato [Ipomoea batatas (L.) Lam] accessions obtained from Nigeria, Asia, Latin America and Local collections along with two improved varieties. Accessions were planted in 2012/13 cropping season at Haramaya University, eastern Ethiopia ...

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

    Indian Academy of Sciences (India)

    In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination ...

  10. Low genetic diversity and recent demographic expansion in the red starfish Echinaster sepositus (Retzius 1816).

    Science.gov (United States)

    Garcia-Cisneros, Alex; Palacín, Creu; Ben Khadra, Yousra; Pérez-Portela, Rocío

    2016-09-15

    Understanding the phylogeography and genetic structure of populations and the processes responsible of patterns therein is crucial for evaluating the vulnerability of marine species and developing management strategies. In this study, we explore how past climatic events and ongoing oceanographic and demographic processes have shaped the genetic structure and diversity of the Atlanto-Mediterranean red starfish Echinaster sepositus. The species is relatively abundant in some areas of the Mediterranean Sea, but some populations have dramatically decreased over recent years due to direct extraction for ornamental aquariums and souvenir industries. Analyses across most of the distribution range of the species based on the mitochondrial cytochrome c oxidase subunit I gene and eight microsatellite loci revealed very low intraspecific genetic diversity. The species showed a weak genetic structure within marine basins despite the a priori low dispersal potential of its lecithotrophic larva. Our results also revealed a very recent demographic expansion across the distribution range of the species. The genetic data presented here indicate that the species might be highly vulnerable, due to its low intraspecific genetic diversity.

  11. The effects of riverine physical complexity on anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss around the Pacific Rim.

    Science.gov (United States)

    McPhee, M V; Whited, D C; Kuzishchin, K V; Stanford, J A

    2014-07-01

    This study explored the relationship between riverine physical complexity, as determined from remotely sensed metrics, and anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss. The proportion of anadromy (estimated fraction of individuals within a drainage that are anadromous) was correlated with riverine complexity, but this correlation appeared to be driven largely by a confounding negative relationship between drainage area and the proportion of anadromy. Genetic diversity decreased with latitude, was lower in rivers with only non-anadromous individuals and also decreased with an increasing ratio of floodplain area to total drainage area. Anadromy may be less frequent in larger drainages due to the higher cost of migration associated with reaches farther from the ocean, and the negative relationship between genetic diversity and floodplain area may be due to lower effective population size resulting from greater population fluctuations associated with higher rates of habitat turnover. Ultimately, the relationships between riverine physical complexity and migratory life history or genetic diversity probably depend on the spatial scale of analysis. © 2014 The Fisheries Society of the British Isles.

  12. Genetic diversity and relatedness among seven red deer (Cervus elaphus populations

    Directory of Open Access Journals (Sweden)

    Lenka Maršálková

    2014-02-01

    Full Text Available Deer (Cervidae recently belongs to the most important species. The aim of presenting study was evaluation of genetic diversity and relationship within and among seven red deer populations from different origins - Czech Republic, Hungary, hybrids Hungary x New Zealand, Lithuania, New Zealand, Poland and Slovak Republic. This study was conducted to determine the levels of genetic variability and relationships among deer populations from a total of 637 animals originating from seven countries Czech Republic (50, Hungary (35, Hungary x New Zealand hybrids (67, Lithuania (26, New Zealand (82, Poland (347 and Slovak Republic (30.  We used the hair bulbs as a source of DNA.  In total, 213 alleles were observed from the 10 loci surveyed. The number of alleles per locus ranged from 11 (IOBT965 to 35 (T156, RT13. Genetic diversity and relatedness among red deer populations has been performed on a total of 637 animals. A panel of 10 microsatellite markers used in deer were optimized. On the basis of this panel of microsatellites we were investigated genetic variability and relationships by using statistical and graphical programmes. We evaluated how close populations are to each other and their genetic admixture. Molecular genetic data combined with evaluation in statistical programmes could lead to a complex view of populations. 

  13. Genetic diversity in India and the inference of Eurasian population expansion.

    Science.gov (United States)

    Xing, Jinchuan; Watkins, W Scott; Hu, Ya; Huff, Chad D; Sabo, Aniko; Muzny, Donna M; Bamshad, Michael J; Gibbs, Richard A; Jorde, Lynn B; Yu, Fuli

    2010-01-01

    Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored. To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans. Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia. © 2010 Xing et al.; licensee BioMed Central Ltd.

  14. Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species.

    Science.gov (United States)

    Lima, Jacqueline S; Ballesteros-Mejia, Liliana; Lima-Ribeiro, Matheus S; Collevatti, Rosane G

    2017-11-01

    The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long-lived, they may not be able to cope with ongoing climatic changes. Here, we coupled ecological niche modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters. Genetic simulations were conditioned to climatic variables and restricted to plant dispersal and establishment. We used a Neotropical savanna tree as species model that shows a preference for hot and drier climates, but with low temperature seasonality. The ENM predicts a decreasing range size along the more severe future climatic scenario. Additionally, genetic diversity and allelic richness also decrease with range retraction and climatic genetic clusters are lost for both future scenarios, which will lead genetic variability to homogenize throughout the landscape. Besides, climatic genetic clusters will spatially reconfigure on the landscape following displacements of climatic conditions. Our findings indicate that climate change effects will challenge population adaptation to new environmental conditions because of the displacement of genetic ancestry clusters from their optimal conditions. © 2017 John Wiley & Sons Ltd.

  15. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    Science.gov (United States)

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  16. Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature.

    Directory of Open Access Journals (Sweden)

    Monika Sharma

    Full Text Available The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA. Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes. Further the nucleotide sequences (retrieved from GenBank for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima's D test and Fu's FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia, indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.

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

    Science.gov (United States)

    Ort, Brian S; Cohen, C Sarah; Boyer, Katharyn E; Reynolds, Laura K; Tam, Sheh May; Wyllie-Echeverria, Sandy

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Brian S Ort

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

  19. Assessment of Genetic Diversity in Opuntia spp. Portuguese Populations Using SSR Molecular Markers

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    Carlos M. G. Reis

    2018-04-01

    Full Text Available The Opuntia spp., most likely few individuals, were introduced in the Iberian Peninsula in the beginning of the 16th century, after the discovery of America, spreading afterwards throughout the Mediterranean basin. We analysed, for the first time, the genetic diversity in a set of 19 Portuguese Opuntia spp. populations from the species O. ficus-indica, O. elata, O. dillenii and O. robusta using nuclear microsatellite (nuSSR markers. The Italian cultivars ‘Bianca’, ‘Gialla’ and ‘Rossa’ were included in the study for comparison purposes. The nuSSR amplifications produced from five to 16 alleles, with an average of 9.2 alleles per primer pair, and average polymorphism information content of 0.71. The estimated Dice coefficient among populations varied from 0.26 to 1.0, indicating high interspecific genetic diversity but low genetic diversity at the intraspecific level. The hierarchical clustering analysis revealed four major groups that clearly separated the four Opuntia species. Among the O. ficus-indica populations, two sub-clusters were found, one including the white pulp fruits (with cv. Bianca and the other with the orange pulp ones and including the cv. Gialla, the cv. Rossa, and one pale yellow pulp population. No genetic differences were found between the inermis form, O. ficus-indica f. ficus-indica, and the rewilded spiny one, O. ficus-indica f. amyclaea. The dendrogram indicated that the clustering pattern was unrelated to geographical origin. The results revealed a low level of genetic diversity among the Portuguese populations of O. ficus-indica.

  20. Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea.

    Science.gov (United States)

    Kim, Hye Ri; Park, Yung Chul

    2015-11-10

    The aim of this study was to investigate the genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae in Korea. The Korean A. a. coreae is characterized by high levels of haplotype diversity (Hd=0.967) and low levels of nucleotide diversity (π=0.00683). Haplogroup 1 is well separated from the haplotypes of the neighboring regions of the Korean Peninsula, while the other haplogroups are closely related to those from the Russian Far East. Thus, further investigations are required to confirm the validity of the subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations present in the Korean Peninsula and its neighboring countries. Haplogroup 1 includes most Korean haplotypes and forms a star-like haplotype network structure, which reveals relatively low levels of sequence divergence and high frequency of unique mutations (only few mutations are shared in most of the haplotype nodes). The results indicate that the haplotypes of Haplogroup 1 might have experienced population expansion since their migration into Korea, which was further corroborated with negative results of neutrality tests for Korean population of A. a. coreae. Copyright © 2015. Published by Elsevier B.V.

  1. Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation

    Science.gov (United States)

    Nourisson, C.; Morales-Vela, B.; Padilla-Saldivar, J.; Tucker, K.P.; Clark, A.; Olivera-Gomez, L. D.; Bonde, R.; McGuire, P.

    2011-01-01

    The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: NA=2.69; HE=0.41 and ChB: NA=3.0; HE=0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx. ?? 2011 Springer Science+Business Media B.V.

  2. Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation.

    Science.gov (United States)

    Nourisson, Coralie; Morales-Vela, Benjamín; Padilla-Saldívar, Janneth; Tucker, Kimberly Pause; Clark, Annmarie; Olivera-Gómez, Leon David; Bonde, Robert; McGuire, Peter

    2011-07-01

    The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: N(A) = 2.69; H(E) = 0.41 and ChB: N(A) = 3.0; H(E) = 0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx.

  3. Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation

    Science.gov (United States)

    Nourisson, Coralie; Morales-Vela, Benjamin; Padilla-Saldivar, Janneth; Tucker, Kimberly Pause; Clark, Ann Marie; Olivera-Gomez, Leon David; Bonde, Robert; McGuire, Peter

    2011-01-01

    The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: NA = 2.69; HE = 0.41 and ChB: NA = 3.0; HE = 0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx.

  4. Genetic diversity in different populations of sloths assessed by DNA fingerprinting

    Directory of Open Access Journals (Sweden)

    MORAES N.

    2002-01-01

    Full Text Available In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 ± 0.07 to 0.87 ± 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations.

  5. Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel

    Directory of Open Access Journals (Sweden)

    Sithembile Olga Makina

    2014-09-01

    Full Text Available Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA including Afrikaner (n=44, Nguni (n=54, Drakensberger (n=47, Bonsmara (n=44, Angus (n=31 and Holstein (n=29. Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR, expected heterozygosity (He and inbreeding coefficient (f. Genetic distances between breed pairs were evaluated using Nei’s genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE. Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner to 1.73 (Nguni. Afrikaner cattle had the lowest level of genetic diversity (He=0.24 and the Drakensberger cattle (He=0.30 had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of South African cattle breeds.

  6. Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?

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    Daniela Lazo-Cancino

    2017-09-01

    Full Text Available Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA, we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i Isolation by Distance (IBD as null model, (ii Least-cost Path (LCP where genetic distances between patch pairs increase with cost-weighted distances, and (iii Isolation by Resistance (IBR where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05, with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that

  7. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Science.gov (United States)

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

  8. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  9. Unexpected pattern of pearl millet genetic diversity among ethno-linguistic groups in the Lake Chad Basin.

    Science.gov (United States)

    Naino Jika, A K; Dussert, Y; Raimond, C; Garine, E; Luxereau, A; Takvorian, N; Djermakoye, R S; Adam, T; Robert, T

    2017-05-01

    Despite of a growing interest in considering the role of sociological factors in seed exchanges and their consequences on the evolutionary dynamics of agro-biodiversity, very few studies assessed the link between ethno-linguistic diversity and genetic diversity patterns in small-holder farming systems. This is key for optimal improvement and conservation of crop genetic resources. Here, we investigated genetic diversity at 17 SSR markers of pearl millet landraces (varieties named by farmers) in the Lake Chad Basin. 69 pearl millet populations, representing 27 landraces collected in eight ethno-linguistic farmer groups, were analyzed. We found that the farmers' local taxonomy was not a good proxy for population's genetic differentiation as previously shown at smaller scales. Our results show the existence of a genetic structure of pearl millet mainly associated with ethno-linguistic diversity in the western side of the lake Chad. It suggests there is a limit to gene flow between landraces grown by different ethno-linguistic groups. This result was rather unexpected, because of the highly outcrossing mating system of pearl millet, the high density of pearl millet fields all along the green belt of this Sahelian area and the fact that seed exchanges among ethno-linguistic groups are known to occur. In the eastern side of the Lake, the pattern of genetic diversity suggests a larger efficient circulation of pearl millet genes between ethno-linguistic groups that are less numerous, spatially intermixed and, for some of them, more prone to exogamy. Finally, other historical and environmental factors which may contribute to the observed diversity patterns are discussed.

  10. Genetic structure and genetic diversity of Swietenia macrophylla in areas subjected to selective logging in Quintana Roo, Mexico

    OpenAIRE

    Alcalá, Raúl Ernesto; Cruz, Silvia De la; Gutiérrez-Granados, Gabriel

    2015-01-01

    The hypothesis that selective logging has a negative effect by altering the genetic parameters of tropical tree species was evaluated. The genetic diversity and genetic structure between adult trees (N = 47) and saplings (N = 50) of Swietenia macrophylla were contrasted within an area subjected to selective logging in the Mayan zone. Although differences in the number of alleles and in their frequencies were detected between both groups, the observed and expected heterozygosity and the coeffi...

  11. Preliminary molecular analysis of the genetic diversity of some ...

    African Journals Online (AJOL)

    In the arid and semi arid areas, salt bush (Atriplex) represents an important forage resource. The characterization of the genetic diversity of these species is useful for their classification, their conservation and their improvement. In this context, we used the random amplified polymorphic DNA-polymerase chain reaction ...

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

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    M. Grema

    2017-11-01

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

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

    African Journals Online (AJOL)

    PROGMANAGER

    2013-04-24

    Apr 24, 2013 ... objective of this study was to determine the genetic diversity of HIV-1 and the prevalence of antiretroviral (ARV) ... individuals in resource limited settings. Key words: ... management of HIV infection even as antiretroviral (ARV).

  14. Digital phenotyping for quantification of genetic diversity in inbred guava (Psidium guajava) families.

    Science.gov (United States)

    Krause, W; Viana, A P; Cavalcante, N R; Ambrósio, M; Santos, E A; Vieira, H D

    2017-03-22

    Digital image analysis of seeds has been used for the identification of cultivars, determination of seed color and mechanical damage, and classification of different seed sizes. The aim of the present study was to evaluate the efficiency of digital image analysis of seeds for the quantification of genetic diversity among genotypes of inbred guava (Psidium guajava L.) families. The SAS Mini equipment, which consists of a capture module and a software program for analysis, was employed for the capture and analysis of the seed images. Different genetic diversity quantification strategies were tested using the Ward-Modified Location Model method. The set of variables related to geometry of the seeds was the largest contributor to divergence among the guava genotypes. The use of seed descriptors obtained by digital image analysis via the SAS system was efficient at quantifying the genetic diversity among genotypes of inbred guava families associated with the use of the Ward-Modified Location Model method.

  15. Genetic diversity and apple leaf spot disease resistance characterization assessed by SSR markers

    Directory of Open Access Journals (Sweden)

    Gustavo H.F. Klabunde

    2016-09-01

    Full Text Available Among the cultivation problems of apple production in Brazil, Apple Leaf Spot (ALS disease represents one of the main breeding challenges. This study aims at analyzing the genetic diversity among 152 apple scion accessions available at the Apple Gene Bank of EPAGRI, located in Caçador, Santa Catarina/ Brazil. Eleven genomic SSR loci were analyzed to assess genetic diversity of ALS resistant and susceptible accessions. Results revealed high genetic diversity of the studied accessions, being 120 exclusive alleles (67 unique from scion accessions resistant to ALS, and a mean PIC of 0.823. The locus Probability of Identity (I ranged from 0.017 to 0.089. The combined I was 4.11 x 10-16, and the Power of Exclusion was 99.99999259%. In addition, the DNA fingerprint patterns will contribute as additional descriptors to select parental for crosses and early identification of apple accessions for breeding purposes, and also for cultivar protection.

  16. Genetic Diversity in Jatropha curcas Populations in the State of Chiapas, Mexico

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    Miguel Salvador-Figueroa

    2011-10-01

    Full Text Available Jatropha curcas L. has become an important source of oil production for biodiesel fuel. Most genetic studies of this plant have been conducted with Asian and African accessions, where low diversity was encountered. There are no studies of this kind focusing in the postulated region of origin. Therefore, five populations of J. curcas were studied in the state of Chiapas, Mexico, using amplified fragment length polymorphism (AFLP markers. One hundred and fifty-two useful markers were obtained: overall polymorphism = 81.18% and overall Nei’s genetic diversity (He = 0.192. The most diverse population was the Border population [He: 0.245, Shanon’s information index (I: 0.378]. A cluster analysis revealed the highest dissimilarity coefficient (0.893 yet to be reported among accessions. An analysis of molecular variance (AMOVA revealed that the greatest variation is within populations (87.8%, followed by the variation among populations (7.88%. The PhiST value (0.121 indicated moderate differentiation between populations. However, a spatial AMOVA (SAMOVA detected a stronger genetic structure of populations, with a PhiST value of 0.176. To understand the fine structure of populations, an analysis of data with Bayesian statistics was conducted with software Structure©. The number of genetic populations (K was five, with mixed ancestry in most individuals (genetic migrants, except in the Soconusco, where there was a tiny fraction of fragments from other populations. In contrast, SAMOVA grouped populations in four units. To corroborate the above findings, we searched for possible genetic barriers, determining as the main barrier that separating the Border from the rest of the populations. The results are discussed based on the possible ancestry of populations.

  17. Genetic Diversity Analysis of Medicinally Important Horticultural Crop Aegle marmelos by ISSR Markers.

    Science.gov (United States)

    Mujeeb, Farina; Bajpai, Preeti; Pathak, Neelam; Verma, Smita Rastogi

    2017-01-01

    Inter simple sequence repeat (ISSR) markers help in identifying and determining the extent of genetic diversity in cultivars. Here, we describe their application in determining the genetic diversity of bael (Aegle marmelos Corr.). Universal ISSR primers are selected and their marker characteristics such as polymorphism information content, effective multiplex ratio and marker index have been evaluated. ISSR-PCR is then performed using universal ISSR primers to generate polymorphic bands. This information is used to determine the degree of genetic similarity among the bael varieties/accessions by cluster analysis using unweighted pair-group method with arithmetic averages (UPGMA). This technology is valuable for biodiversity conservation and for making an efficient choice of parents in breeding programs.

  18. Honey bee nest thermoregulation: diversity promotes stability.

    Science.gov (United States)

    Jones, Julia C; Myerscough, Mary R; Graham, Sonia; Oldroyd, Benjamin P

    2004-07-16

    A honey bee colony is characterized by high genetic diversity among its workers, generated by high levels of multiple mating by its queen. Few clear benefits of this genetic diversity are known. Here we show that brood nest temperatures in genetically diverse colonies (i.e., those sired by several males) tend to be more stable than in genetically uniform ones (i.e., those sired by one male). One reason this increased stability arises is because genetically determined diversity in workers' temperature response thresholds modulates the hive-ventilating behavior of individual workers, preventing excessive colony-level responses to temperature fluctuations.

  19. Climatic niche and neutral genetic diversity of the six Iberian pine species: a retrospective and prospective view.

    Science.gov (United States)

    Soto, A; Robledo-Arnuncio, J J; González-Martínez, S C; Smouse, P E; Alía, R

    2010-04-01

    Quaternary climatic fluctuations have left contrasting historical footprints on the neutral genetic diversity patterns of existing populations of different tree species. We should expect the demography, and consequently the neutral genetic structure, of taxa less tolerant to particular climatic extremes to be more sensitive to long-term climate fluctuations. We explore this hypothesis here by sampling all six pine species found in the Iberian Peninsula (2464 individuals, 105 populations), using a common set of chloroplast microsatellite markers, and by looking at the association between neutral genetic diversity and species-specific climatic requirements. We found large variation in neutral genetic diversity and structure among Iberian pines, with cold-enduring mountain species (Pinus uncinata, P. sylvestris and P. nigra) showing substantially greater diversity than thermophilous taxa (P. pinea and P. halepensis). Within species, we observed a significant positive correlation between population genetic diversity and summer precipitation for some of the mountain pines. The observed pattern is consistent with the hypotheses that: (i) more thermophilous species have been subjected to stronger demographic fluctuations in the past, as a consequence of their maladaptation to recurrent glacial cold stages; and (ii) altitudinal migrations have allowed the maintenance of large effective population sizes and genetic variation in cold-tolerant species, especially in more humid regions. In the light of these results and hypotheses, we discuss some potential genetic consequences of impending climate change.

  20. Population genetic diversity and genetic structure of Spodoptera exigua around the Bohai Gulf area of China based on mitochondrial DNA signatures.

    Science.gov (United States)

    Zhou, L-H; Wang, X-Y; Lei, J-J

    2016-09-30

    The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae), is an economically important pest that causes major losses in some main crop-producing areas of China. To control this pest effectively, it is necessary to investigate its population genetic diversity and genetic structure around the Bohai Gulf area of China. In this study, we used two mitochondrial genes, COI (578 bp) and Cytb (724 bp), to investigate its genetic diversity. We obtained 622 COI sequences and 462 Cytb sequences from 23 populations, and 28 and 73 haplotypes, respectively, were identified. Low to moderate levels of genetic diversity (COI: Hd = 0.267 ± 0.023, Pi = 0.00082 ± 0.00010; Cytb: Hd = 0.689 ± 0.018, Pi = 0.00255 ± 0.00029) for the total populations were observed. Phylogenetic and median-joining network analyses indicated no distinct geographical distribution pattern among the haplotypes. Overall, this study revealed that there was significant differentiation among the populations (COI: F ST = 0.158, P neutrality test results, showed a recent population expansion of the beet armyworm around the Bohai Gulf area of China.

  1. Neonicotinoid pesticides can reduce honeybee colony genetic diversity.

    Directory of Open Access Journals (Sweden)

    Nadège Forfert

    Full Text Available 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.

  2. Genetic diversity for nutritional traits in the leaves of baobab ...

    African Journals Online (AJOL)

    User

    Key words: Adansonia digitata, Genetic variability, diversity, populations, and clusters. INTRODUCTION ... competition with the crops for nutrient, water, and sunlight, more ... (11° 11'N, 07° 38'E, attitude 688 m above sea level). The experiment ...

  3. Effects of space flight factors on genetic diversity of Buchloe ...

    African Journals Online (AJOL)

    Jane

    2011-10-05

    Oct 5, 2011 ... results for wheat coleoptiles, lettuce hypocotyls, and garden-cress ... space radiation dose for plant seeds at linear energy transfer (LET) space was 4.79 ... information content (PIC), total genetic diversity of materials i and j.

  4. Genetic diversity of maize genotypes on the basis of morpho ...

    African Journals Online (AJOL)

    Genetic diversity of maize genotypes on the basis of morpho-physiological and simple sequence repeat (SSR) markers. Ashish Kumar, Arunita Rakshit, Naresh K Mangilipelli, Y Varalaxmi, T Vijayalakshmi, Jainender M Vanaja, SK Yadav, B Venkateswarlu, M Maheswari ...

  5. Intra-specific genetic diversity in wild olives (Olea europaea ssp cuspidata) in Hormozgan Province, Iran.

    Science.gov (United States)

    Noormohammadi, Z; Samadi-Molayousefi, H; Sheidai, M

    2012-03-19

    Wild olive (O. europaea ssp cuspidata) plants grow in various regions of Iran and are expected to have considerable genetic diversity due to adaptation to the various environmental conditions. We examined the genetic diversity of four populations of wild olive growing in Hormozgan Province located in southern Iran by using 30 RAPDs and 10 ISSR markers. The mean value of polymorphism for RAPD loci was 73.71%, while the value for ISSR loci was 81.74%. The Keshar population had the highest value of intra-population polymorphism for both RAPD and ISSR loci (66.86 and 62.71%, respectively), while the Tudar population had the lowest values (20.35 and 28.81%, respectively). Similarly, the highest and lowest number of effective alleles, Shannon index and Nei's genetic diversity were also found for these two populations. The highest value of H(pop)/H(sp) within population genetic diversity for RAPD and ISSR loci was found for the Keshar population (H(pop) = 0.85 and H(sp) = 0.90). OPA04-750, OPA13-650 and OPA02-350 RAPD bands were specific for Tudar, Bondon and Keshar populations, respectively, while no specific ISSR bands were observed. Analysis of molecular variance as well as the pairwise F(ST) test showed significant differences for RAPD and ISSR markers among the populations. The NJ and UPGMA trees also separated the wild olive populations from each other, indicating their genetic distinctness. UPGMA clustering of the four wild olive populations placed the Tudar population far from the other populations; Keshar and Bokhoon population samples revealed more similarity and were grouped together. We conclude that there is high genetic diversity among O. europaea ssp cuspidata populations located in southern Iran. We also found RAPD and ISSR markers to be useful molecular tools to discriminate and evaluate genetic variations in wild olive trees.

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

    Science.gov (United States)

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

    2015-01-01

    Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon–Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range. PMID:26311734

  7. Analysis of genetic diversity of certain species of Piper using RAPD-based molecular markers.

    Science.gov (United States)

    Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj

    2014-09-01

    The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.

  8. High Levels of Genetic Diversity of Plasmodium falciparum Populations in Papua New Guinea despite Variable Infection Prevalence

    Science.gov (United States)

    Barry, Alyssa E.; Schultz, Lee; Senn, Nicholas; Nale, Joe; Kiniboro, Benson; Siba, Peter M.; Mueller, Ivo; Reeder, John C.

    2013-01-01

    High levels of genetic diversity in Plasmodium falciparum populations are an obstacle to malaria control. Here, we investigate the relationship between local variation in malaria epidemiology and parasite genetic diversity in Papua New Guinea (PNG). Cross-sectional malaria surveys were performed in 14 villages spanning four distinct malaria-endemic areas on the north coast, including one area that was sampled during the dry season. High-resolution msp2 genotyping of 2,147 blood samples identified 761 P. falciparum infections containing a total of 1,392 clones whose genotypes were used to measure genetic diversity. Considerable variability in infection prevalence and mean multiplicity of infection was observed at all of the study sites, with the area sampled during the dry season showing particularly striking local variability. Genetic diversity was strongly associated with multiplicity of infection but not with infection prevalence. In highly endemic areas, differences in infection prevalence may not translate into a decrease in parasite population diversity. PMID:23400571

  9. Genetic diversity patterns of arbuscular mycorrhizal fungi associated with the mycoheterotroph Arachnitis uniflora Phil. (Corsiaceae).

    Science.gov (United States)

    Renny, Mauricio; Acosta, M Cristina; Cofré, Noelia; Domínguez, Laura S; Bidartondo, Martin I; Sérsic, Alicia N

    2017-06-01

    Arachnitis uniflora is a mycoheterotrophic plant that exploits arbuscular mycorrhizal fungi of neighbouring plants. We tested A. uniflora 's specificity towards fungi across its large latitudinal range, as well as the role of historical events and current environmental, geographical and altitudinal variables on fungal genetic diversity. Arachnitis uniflora mycorrhizas were sampled at 25 sites. Fungal phylogenetic relationships were reconstructed, genetic diversity was calculated and the main divergent lineages were dated. Phylogeographical analysis was performed with the main fungal clade. Fungal diversity correlations with environmental factors were investigated. Glomeraceae fungi dominated, with a main clade that likely originated in the Upper Cretaceous and diversified in the Miocene. Two other arbuscular mycorrhizal fungal families not previously known to be targeted by A. uniflora were detected rarely and appear to be facultative associations. High genetic diversity, found in Bolivia and both northern and southern Patagonia, was correlated with temperature, rainfall and soil features. Fungal genetic diversity and its distribution can be explained by the ancient evolutionary history of the target fungi and by micro-scale environmental conditions with a geographical mosaic pattern. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  10. Genetic diversity and population structure of leafy kale and Brassica rupestris Raf. in south Italy.

    Science.gov (United States)

    Maggioni, Lorenzo; von Bothmer, Roland; Poulsen, Gert; Branca, Ferdinando; Bagger Jørgensen, Rikke

    2014-12-01

    Local varieties of leafy kales (Brassica oleracea L.) are grown in home gardens in Calabria and Sicily for self-consumption, in the same area where the wild relative Brassica rupestris Raf. also grows. With the use of AFLP markers, comparisons were made of the genetic diversity and population structure of ten wild and 22 cultivated populations, as well as of a hybrid population and of four commercial cultivars of different B. oleracea crops. The level of genetic diversity was higher in leafy kales than in wild populations and this diversity was mainly distributed within populations. Wild populations remained distinct from cultivated material. Additionally, most wild populations were distinctively isolated from each other. On the other hand, it was not possible to molecularly distinguish even geographically distant leafy kale populations from each other or from different B. oleracea crops. It was possible to detect inter-crossing between leafy kales and B. rupestris. Findings from this study illustrate the existing level of genetic diversity in the B. oleracea gene pool. Individual populations (either wild or leafy kales) with higher levels of genetic diversity have been identified and suggestions are given for an informed conservation strategy. Domestication hypotheses are also discussed. © 2015 The Authors.

  11. Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean.

    Science.gov (United States)

    Davies, S W; Treml, E A; Kenkel, C D; Matz, M V

    2015-01-01

    Understanding how genetic diversity is maintained across patchy marine environments remains a fundamental problem in marine biology. The Coral Triangle, located in the Indo-West Pacific, is the centre of marine biodiversity and has been proposed as an important source of genetic diversity for remote Pacific reefs. Several studies highlight Micronesia, a scattering of hundreds of small islands situated within the North Equatorial Counter Current, as a potentially important migration corridor. To test this hypothesis, we characterized the population genetic structure of two ecologically important congeneric species of reef-building corals across greater Micronesia, from Palau to the Marshall Islands. Genetic divergences between islands followed an isolation-by-distance pattern, with Acropora hyacinthus exhibiting greater genetic divergences than A. digitifera, suggesting different migration capabilities or different effective population sizes for these closely related species. We inferred dispersal distance using a biophysical larval transport model, which explained an additional 15-21% of the observed genetic variation compared to between-island geographical distance alone. For both species, genetic divergence accumulates and genetic diversity diminishes with distance from the Coral Triangle, supporting the hypothesis that Micronesian islands act as important stepping stones connecting the central Pacific with the species-rich Coral Triangle. However, for A. hyacinthus, the species with lower genetic connectivity, immigration from the subequatorial Pacific begins to play a larger role in shaping diversity than input from the Coral Triangle. This work highlights the enormous dispersal potential of broadcast-spawning corals and identifies the biological and physical drivers that influence coral genetic diversity on a regional scale. © 2014 John Wiley & Sons Ltd.

  12. Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers.

    Science.gov (United States)

    Zhang, Xiao; Zhang, Hua; Li, Lujiang; Lan, Hai; Ren, Zhiyong; Liu, Dan; Wu, Ling; Liu, Hailan; Jaqueth, Jennifer; Li, Bailin; Pan, Guangtang; Gao, Shibin

    2016-08-31

    Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area. In this study, the population structure, genetic diversity, and linkage disequilibrium decay distance of 362 important inbred lines collected from the breeding program of Southwest China were characterized using the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs). With respect to population structure, two (Tropical and Temperate), three (Tropical, Stiff Stalk and non-Stiff Stalk), four [Tropical, group A germplasm derived from modern U.S. hybrids (PA), group B germplasm derived from modern U.S. hybrids (PB) and Reid] and six (Tropical, PB, Reid, Iowa Stiff Stalk Synthetic, PA and North) subgroups were identified. With increasing K value, the Temperate group showed pronounced hierarchical structure with division into further subgroups. The Genetic Diversity of each group was also estimated, and the Tropical group was more diverse than the Temperate group. Seven low-genetic-diversity and one high-genetic-diversity regions were collectively identified in the Temperate, Tropical groups, and the entire panel. SNPs with significant variation in allele frequency between the Tropical and Temperate groups were also evaluated. Among them, a region located at 130 Mb on Chromosome 2 showed the highest genetic diversity, including both number of SNPs with significant variation and the ratio of significant SNPs to total SNPs. Linkage disequilibrium decay distance in the Temperate group was greater (2.5-3 Mb) than that in the entire panel (0.5-0.75 Mb) and the Tropical group (0.25-0.5 Mb). A large region at 30-120 Mb of Chromosome 7 was concluded to be a region conserved during the breeding process by comparison between S37, which was considered a representative tropical line in Southwest China, and its 30 most similar derived lines. For the panel covered most of widely used inbred lines in Southwest China, this work

  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. 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 ...

  15. 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 ...

  16. Optimal diversity: Increasing returns versus recombinant innovation

    NARCIS (Netherlands)

    van den Bergh, J.C.J.M.; Zeppini Rossi, P.

    2008-01-01

    Choices regarding diversity play an important role in economics and innovation management, but often remain implicit. Once made explicit, the objectives of efficiency and diversity are usually posed as in conflict, as efficiency relates positively and diversity negatively to various increasing

  17. Assessment of the genetic diversity and pattern of relationship of ...

    African Journals Online (AJOL)

    SAM

    2014-04-02

    Apr 2, 2014 ... Cluster and principal coordinate analysis of the 30 ... The FST value (0.63) indicated a very high genetic differentiation as expected for ..... diversity) using Markov chain method showed that the ..... WL, Lee M, Porter K (2000).

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

    Directory of Open Access Journals (Sweden)

    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

  19. Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity.

    Science.gov (United States)

    Eidesen, Pernille Bronken; Ehrich, Dorothee; Bakkestuen, Vegar; Alsos, Inger Greve; Gilg, Oliver; Taberlet, Pierre; Brochmann, Christian

    2013-11-01

    We provide the first comparative multispecies analysis of spatial genetic structure and diversity in the circumpolar Arctic using a common strategy for sampling and genetic analyses. We aimed to identify and explain potential general patterns of genetic discontinuity/connectivity and diversity, and to compare our findings with previously published hypotheses. We collected and analyzed 7707 samples of 17 widespread arctic-alpine plant species for amplified fragment length polymorphisms (AFLPs). Genetic structure, diversity and distinctiveness were analyzed for each species, and extrapolated to cover the geographic range of each species. The resulting maps were overlaid to produce metamaps. The Arctic and Atlantic Oceans, the Greenlandic ice cap, the Urals, and lowland areas between southern mountain ranges and the Arctic were the strongest barriers against gene flow. Diversity was highest in Beringia and gradually decreased into formerly glaciated areas. The highest degrees of distinctiveness were observed in Siberia. We conclude that large-scale general patterns exist in the Arctic, shaped by the Pleistocene glaciations combined with long-standing physical barriers against gene flow. Beringia served as both refugium and source for interglacial (re)colonization, whereas areas further west in Siberia served as refugia, but less as sources for (re)colonization. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  20. Water-level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species.

    Science.gov (United States)

    Nevado, B; Mautner, S; Sturmbauer, C; Verheyen, E

    2013-08-01

    Understanding how genetic variation is generated and maintained in natural populations, and how this process unfolds in a changing environment, remains a central issue in biological research. In this work, we analysed patterns of genetic diversity from several populations of three cichlid species from Lake Tanganyika in parallel, using the mitochondrial DNA control region. We sampled populations inhabiting the littoral rocky habitats in both very deep and very shallow areas of the lake. We hypothesized that the former would constitute relatively older, more stable and genetically more diverse populations, because they should have been less severely affected by the well-documented episodes of dramatic water-level fluctuations. In agreement with our predictions, populations of all three species sampled in very shallow shorelines showed traces of stronger population growth than populations of the same species inhabiting deep shorelines. However, contrary to our working hypothesis, we found a significant trend towards increased genetic diversity in the younger, demographically less stable populations inhabiting shallow areas, in comparison with the older and more stable populations inhabiting the deep shorelines. We interpret this finding as the result of the establishment of metapopulation dynamics in the former shorelines, by the frequent perturbation and reshuffling of individuals between populations due to the lake-level fluctuations. The repeated succession of periods of allopatric separation and secondary contact is likely to have further increased the rapid pace of speciation in lacustrine cichlids. © 2013 John Wiley & Sons Ltd.