WorldWideScience

Sample records for genetic diversity mining

  1. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4 for classification, population genetics and epidemiology

    Directory of Open Access Journals (Sweden)

    Sajduda Anna

    2006-03-01

    Full Text Available Abstract Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1 Unique Events Polymorphism (UEP (2 Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.

  2. Genetic diversity in populations.

    Czech Academy of Sciences Publication Activity Database

    Martínková, Natália; Zemanová, Barbora

    Brno : Akademické nakladatelství CERM, 2011 - (Jarkovský, J.), s. 21-27 ISBN 978-80-7204-756-7. [International Summer School on Computational Biology /7./. Lednice (CZ), 15.09.2011-17.09.2011] Institutional research plan: CEZ:AV0Z60930519 Keywords : nucleotide diversity * haplotype diversity * heterozygosity * Hardy-Weinberg equilibrium Subject RIV: EB - Genetics ; Molecular Biology

  3. Recombination and Genetic Diversity

    Scientific Electronic Library Online (English)

    T. C., Coutinho; T.T.da, Silva; G.L., Toledo.

    2012-12-01

    Full Text Available In this paper we present a spatial stochastic model for genetic recombination, that answers if diversity is preserved in an infinite population of recombinat-ing individuals distributed spatially. We show that, for finite times, recombination may maintain all the various potential different types, b [...] ut when time grows infinitely, the diversity of individuals extinguishes off. So under the model premisses, recombination and spatial localization alone are not enough to explain diversity in a population. Further we discuss an application of the model to a controversy regarding the diversity of "Major Histocompatibility Complex" (MHC).

  4. Imposing genetic diversity.

    Science.gov (United States)

    Sparrow, Robert

    2015-06-01

    The idea that a world in which everyone was born "perfect" would be a world in which something valuable was missing often comes up in debates about the ethics of technologies of prenatal testing and preimplantation genetic diagnosis (PGD). This thought plays an important role in the "disability critique" of prenatal testing. However, the idea that human genetic variation is an important good with significant benefits for society at large is also embraced by a wide range of figures writing in the bioethics literature, including some who are notoriously hostile to the idea that we should not select against disability. By developing a number of thought experiments wherein we are to contemplate increasing genetic diversity from a lower baseline in order to secure this value, I argue that this powerful intuition is more problematic than is generally recognized, especially where the price of diversity is the well-being of particular individuals. PMID:26030484

  5. XML Mining Using Genetic Algorithm

    OpenAIRE

    Amitava Nag

    2011-01-01

    In recent years XML documents have became very popular for representing semi-structured data and a standard for data exchange over the web. Mining XML data from the web is becoming increasingly important as well. In general frequent item sets are generated from large data sets by applying association rule mining algorithms like Apriori, Partition, Pincer-Search, Incremental, Border algorithm etc., which take too much computer time to compute all the frequent item sets. By using Genetic Algori...

  6. Genetic diversity in European Pisum germplasm collections

    OpenAIRE

    Jing, R.; Ambrose, M. A.; Knox, M. R.; Smykal, P.; Hybl, M.; Ramos, A?; Caminero, C.; Burstin, J.; Duc, G.; Soest, L. J. M.; S?wie?cicki, W. K.; Pereira, M. G.; Vishnyakova, M.; Davenport, G. F.; Flavell, A. J.

    2012-01-01

    The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analys...

  7. Does Genetic Diversity Predict Health in Humans?

    OpenAIRE

    Lie, Hanne C.; Simmons, Leigh W.; Rhodes, Gillian

    2009-01-01

    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 d2) at MHC and nonMHC mic...

  8. Human genetic diversity and comparative economic development

    OpenAIRE

    Ashraf, Quamrul; Galor, Oded

    2008-01-01

    This research contributes to the understanding of human genetic diversity within a society as a significant determinant of its economic development. The hypothesis advanced and empirically examined in this paper suggests that there are socioeconomic trade-offs associated with genetic diversity within a given society. The investigation exploits an exogenous source of cross-country variation in genetic diversity by appealing to the 'out of Africa' hypothesis of human origins to empirically esta...

  9. Genetic diversity in European Pisum germplasm collections.

    Science.gov (United States)

    Jing, R; Ambrose, M A; Knox, M R; Smykal, P; Hybl, M; Ramos, Á; Caminero, C; Burstin, J; Duc, G; van Soest, L J M; ?wi?cicki, W K; Pereira, M G; Vishnyakova, M; Davenport, G F; Flavell, A J; Ellis, T H N

    2012-07-01

    The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analysis was based upon the presence/absence of polymorphism of retrotransposon insertions scored by a high-throughput microarray and SSAP approaches. We conclude that the diversity of Pisum constitutes a broad continuum, with graded differentiation into sub-populations which display various degrees of distinctness. The most distinct genetic groups correspond to the named taxa while the cultivars and landraces of Pisum sativum can be divided into two broad types, one of which is strongly enriched for modern cultivars. The addition of germplasm sets from six European Genebanks, chosen to represent high diversity, to a single collection previously studied with these markers resulted in modest additions to the overall diversity observed, suggesting that the great majority of the total genetic diversity collected for the Pisum genus has now been described. Two interesting sources of novel genetic variation have been identified. Finally, we have proposed reference sets of core accessions with a range of sample sizes to represent Pisum diversity for the future study and exploitation by researchers and breeders. PMID:22466957

  10. Mining Frequent Itemsets Using Genetic Algorithm

    CERN Document Server

    Ghosh, Soumadip; Sarkar, Debasree; Sarkar, Partha Pratim; 10.5121/ijaia.2010.1411

    2010-01-01

    In general frequent itemsets are generated from large data sets by applying association rule mining algorithms like Apriori, Partition, Pincer-Search, Incremental, Border algorithm etc., which take too much computer time to compute all the frequent itemsets. By using Genetic Algorithm (GA) we can improve the scenario. The major advantage of using GA in the discovery of frequent itemsets is that they perform global search and its time complexity is less compared to other algorithms as the genetic algorithm is based on the greedy approach. The main aim of this paper is to find all the frequent itemsets from given data sets using genetic algorithm.

  11. Evolution and genetic diversity of Theileria.

    Science.gov (United States)

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

    2014-10-01

    Theileria parasites infect a wide range of domestic and wild ruminants worldwide, causing diseases with varying degrees of severity. A broad classification, based on the parasite's ability to transform the leukocytes of host animals, divides Theileria into two groups, consisting of transforming and non-transforming species. The evolution of transforming Theileria has been accompanied by drastic changes in its genetic makeup, such as acquisition or expansion of gene families, which are thought to play critical roles in the transformation of host cells. Genetic variation among Theileria parasites is sometimes linked with host specificity and virulence in the parasites. Immunity against Theileria parasites primarily involves cell-mediated immune responses in the host. Immunodominance and major histocompatibility complex class I phenotype-specificity result in a host immunity that is tightly focused and strain-specific. Immune escape in Theileria is facilitated by genetic diversity in its antigenic determinants, which potentially results in a loss of T cell receptor recognition in its host. In the recent past, several reviews have focused on genetic diversity in the transforming species, Theileriaparva and Theileriaannulata. In contrast, genetic diversity in Theileriaorientalis, a benign non-transforming parasite, which occasionally causes disease outbreaks in cattle, has not been extensively examined. In this review, therefore, we provide an outline of the evolution of Theileria, which includes T. orientalis, and discuss the possible mechanisms generating genetic diversity among parasite populations. Additionally, we discuss the potential implications of a genetically diverse parasite population in the context of Theileria vaccine development. PMID:25102031

  12. Mining Frequent Itemsets Using Genetic Algorithm

    OpenAIRE

    Soumadip Ghosh; Sushanta Biswas; Debasree Sarkar; Partha Pratim Sarkar

    2010-01-01

    In general frequent itemsets are generated from large data sets by applying association rule mining algorithms like Apriori, Partition, Pincer-Search, Incremental, Border algorithm etc., which take too much computer time to compute all the frequent itemsets. By using Genetic Algorithm (GA) we can improve the scenario. The major advantage of using GA in the discovery of frequent itemsets is that they perform global search and its time complexity is less compared to other algo...

  13. The Genetic Algorithm for Truck Dispatching Problems in Surface Mine

    Directory of Open Access Journals (Sweden)

    Xin- Ming Lu

    2010-01-01

    Full Text Available At first, this study described the characteristics of truck transport in surface mine, then construct the model of truck dispatching and expound working principle and application of genetic algorithm. Finally, the typical experiment, by using the MATLAB genetic algorithm toolbox for calculation, showed that using genetic algorithm to optimize mine vehicle dispatching is feasible and effective.

  14. The Genetic Algorithm for Truck Dispatching Problems in Surface Mine

    OpenAIRE

    Xin- Ming Lu; Jiu- Chuan Wei; Ming- Xiang He; Bao-Xiang Huang

    2010-01-01

    At first, this study described the characteristics of truck transport in surface mine, then construct the model of truck dispatching and expound working principle and application of genetic algorithm. Finally, the typical experiment, by using the MATLAB genetic algorithm toolbox for calculation, showed that using genetic algorithm to optimize mine vehicle dispatching is feasible and effective.

  15. Application of bio-diversity indices to mined land reclamation

    Energy Technology Data Exchange (ETDEWEB)

    Bian, Z.; Zhang, G. [China University of Mining and Technology, Xuzhou (China)

    2000-02-01

    Restoration of ecological balance of mine areas is one of the objectives of mined land reclamation. Diversity of reclaimed land use structure is employed for evaluating the effectiveness of restoration in this paper. An experimental study was carried out at Xuzhou Coal Mine area, in which four treatments, including backfilling mining wastes into subsidence basin with nothing covered, with soil covered, with cow dung covered, with cottonseed cake covered, were designed for planting Crotalaria Juncea L, Tell Featucearundonacea, Lolium perenne, Medicago Satica L, Coronilla Varia L and Trifolium Pratense L. Bio-diversity indices were employed for selecting reclamation alternatives and plant variety in this paper, and it is proved to be feasible by practice. 5 refs., 5 tabs.

  16. Genetic Diversity among Enterococcus faecalis

    OpenAIRE

    McBride, Shonna M.; Fischetti, Vincent A; LeBlanc, Donald J.; Moellering, Robert Charles; Gilmore, Michael S.

    2007-01-01

    Enterococcus faecalis, a ubiquitous member of mammalian gastrointestinal flora, is a leading cause of nosocomial infections and a growing public health concern. The enterococci responsible for these infections are often resistant to multiple antibiotics and have become notorious for their ability to acquire and disseminate antibiotic resistances. In the current study, we examined genetic relationships among 106 strains of E. faecalis isolated over the past 100 years, including strains identif...

  17. Effect of diversity and missing data on genetic assignment with RAD-Seq markers

    OpenAIRE

    Chattopadhyay, Balaji; Garg, Kritika M; Ramakrishnan, Uma

    2014-01-01

    Reduced representation libraries are being used as a preferred source of markers to address population genetic questions. However, libraries of RAD-Seq variants often suffer from significant percentage of missing data. In addition, algorithms used to mine SNPs from the raw data may also underscore biological variation. We investigate the effect of biological diversity in mining SNPs from the program STACKS and the effect of missing data on individual assignment implemented in STRUCTURE. We ob...

  18. Cotton genetic diversity study by AFLP markers

    Scientific Electronic Library Online (English)

    Naveed, Murtaza.

    2006-07-15

    Full Text Available Amplified fragmentlength polymorphism (AFLP) markers have been used to ascertain the intensity of inherent diversity and relatedness in cotton (Gossypium spp.) plants. The effectiveness of this method to distinguish inter and intra specific difference in cotton could be handy in cultivar recognition [...] and in marker assisted parental selection tool for plant breeders. Twenty cotton cultivars belonging to Gossypium hirsutum L., and G. arborium L. from the Pakistan and US origin were used for AFLP based genetic diversity estimates. The objective of this study was to assess the level of genetic variation among some cotton cultivars belonging to the old and new world species of cotton. Four EcoRI-MseI primer-pair combinations were used forthe AFLP analysis. The AFLP data assigned the genotypes into groups that corresponded with their origin and lineage relationships and showed a narrow genetic base among these cultivars.

  19. Genetic diversity of Ascaris in southwestern Uganda.

    Science.gov (United States)

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

    2012-02-01

    Despite the common occurrence of ascariasis in southwestern Uganda, helminth control in the region has been limited. To gain further insights into the genetic diversity of Ascaris in this area, a parasitological survey in mothers (n=41) and children (n=74) living in two villages, Habutobere and Musezero, was carried out. Adult Ascaris worms were collected from infected individuals by chemo-expulsion using pyrantel pamoate treatment. Genetic diversity within these worms was assessed by inspection of DNA sequence variation in a mitochondrial marker and length polymorphism at microsatellite loci. Overall prevalence of ascariasis was 42.5% in mothers and 30.4% in their children and a total of 98 worms was examined from 18 hosts. Sequence analysis of a portion of the mitochondrial cytochrome c oxidase subunit 1 gene revealed 19 different haplotypes, 13 of which had not been previously encountered. Microsatellite analysis using eight loci provided evidence for high gene flow between worm populations from the two villages but comparing these worms with others obtained in a prior study on Unguja, Zanzibar, confirmed little genetic exchange and mixing of worm populations between the two areas. By adding to our understanding of the genetic diversity of Ascaris in Africa, this study provides useful information for monitoring changes in parasite population structure in the face of ongoing and future control. PMID:22192492

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

    OpenAIRE

    Richards, Zoe T.; van Oppen, Madeleine J.H

    2012-01-01

    Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo–Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a...

  1. Genetic diversity in two Italian almond collections

    Scientific Electronic Library Online (English)

    Maria Pia, Rigoldi; Emma, Rapposelli; Donato, De Giorgio; Paolo, Resta; Andrea, Porceddu.

    2015-01-01

    Full Text Available Background Sweet-seeded domesticated almonds were brought to the Mediterranean Basin from central Asia about 4000 years ago. In Italy, most of the almonds produced are cultivated in the southern part of the country. Local populations of the tree in Sardinia are largely seed-derived and mostly self-i [...] ncompatible, so have developed extensive genetic diversity. The need to protect biodiversity has prompted a revived interest in local genetic materials in almond. Two Italian collections have been established, one in Sardinia and the other in Apulia. These collections were the focus of the present evaluation of genetic diversity. Results Eleven SSRs (microsatellites) were used for fingerprinting. The Sardinian germplasm was highly polymorphic, revealing a mean of 14.5 alleles per locus and a mean heterozygosity of 0.71. Using a model-based clustering approach, two genetic clusters were distinguished: one included all the commercial varieties and most of the Sardinian accessions, and the other most of the Apulian accessions. A similar structure was produced using a distance-based cluster analysis. The Sardinian accessions could still be distinguished from the commercial germplasm with few exceptions. Conclusion The extensive genetic variability present in the Sardinian and Apulian almond germplasm indicates that these materials represent an important source of genes for the improvement of the crop.

  2. Limited Genetic Diversity of Brucella spp.

    OpenAIRE

    Ga?ndara, Benjami?n; Merino, Ahide? Lo?pez; Rogel, Marco Antonio; Marti?nez-romero, Esperanza

    2001-01-01

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

  3. Effect of diversity and missing data on genetic assignment with RAD-Seq markers.

    Science.gov (United States)

    Chattopadhyay, Balaji; Garg, Kritika M; Ramakrishnan, Uma

    2014-01-01

    Reduced representation libraries are being used as a preferred source of markers to address population genetic questions. However, libraries of RAD-Seq variants often suffer from significant percentage of missing data. In addition, algorithms used to mine SNPs from the raw data may also underscore biological variation. We investigate the effect of biological diversity in mining SNPs from the program STACKS and the effect of missing data on individual assignment implemented in STRUCTURE. We observed that changing diversity parameters in STACKS significantly alters the number of SNPs discovered and allowing for higher percentage of missing data retrieves more loci and possibly more power for individual assignment. PMID:25424532

  4. Genetic diversity of American wild rice species

    Scientific Electronic Library Online (English)

    Elizabeth Ann, Veasey; Eduardo de Andrade, Bressan; Maria Imaculada, Zucchi; Roland, Vencovsky; Daruska Cavalcante, Cardim; Rainério Meireles da, Silva.

    2011-08-01

    Full Text Available Studies on genetic diversity and genetic structure of natural populations are important in order to define strategies for in situ and ex situ conservation actions and for plant pre-breeding programs. Aiming to assess the genetic diversity and genetic structure of three wild American Oryza species wi [...] th isozyme markers, 14 populations of the diploid O. glumaepatula (AglAgl), 11 populations of the tetraploid O. grandiglumis (CCDD) and five populations of the also tetraploid O. latifolia (CCDD) were studied. They were all originated from Rio Paraguay hydrographic basin and the Amazon. Four enzymes were used and they gave 40 polymorphic bands. The most polymorphic species was O. glumaepatula, followed by O. latifolia and O. grandiglumis. A cluster analysis with the Jaccard similarity coefficient separated the diploid from the two tetraploid species, and also the two tetraploid species. This separation was also evident on a scatter plot from a principal component analysis, suggesting that they should be treated as two separate species, although further studies are necessary to provide support for this affirmative. The AMOVA analyses showed a high intrapopulational variability for O. latifolia (67.6%) and O. grandiglumis (52.2%), when compared to their interpopulational variability (32.4% and 47.8%, respectively), which suggests the hypothesis of a higher degree of outcrossing events within these species. When studying the correlation between the Jaccard dissimilarity coefficient and geographic distances, a spatial genetic structure was observed for O. glumaepatula only. These results are important for defining strategies of both in situ and ex situ conservation.

  5. A Survey: Web Log Mining using Genetic Algorithm .

    OpenAIRE

    Ranu Singhal; NirupamaTiwari

    2013-01-01

    Web mining has become a vast area of Research in last few years. Web Mining Which deals with the extraction of interesting knowledge from logging information produced by web server. In this paper we present a survey generate clusters using a multi objective genetic algorithm. Genetic algorithm is also a very hot area of research. In this paper we will compare the error value between FCM(Fuzzy c-means) and FCM-MOGA(Fuzzy CMeans multi objective Genetic algorithm). Genetic algorithm follows some...

  6. Great ape genetic diversity and population history

    DEFF Research Database (Denmark)

    Prado-Martinez, Javier; Sudmant, Peter H.

    2013-01-01

    Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8?million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

  7. Genetic Diversity of Koala Retroviral Envelopes

    Directory of Open Access Journals (Sweden)

    Wenqin Xu

    2015-03-01

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

  8. Benefits of host genetic diversity for resistance to infection depend on parasite diversity

    OpenAIRE

    Ganz, Holly H.; Ebert, Dieter

    2010-01-01

    Host populations with high genetic diversity are predicted to have lower levels of infection prevalence. This theory assumes that host genetic diversity results in variation in susceptibility and that parasites exhibit variation in infectivity. Empirical studies on the effects of host heterogeneity typically neglect the role of parasite diversity. We conducted three laboratory experiments designed to test if genetic variation in Daphnia magna populations and genetic variation in its parasites...

  9. Beauveria bassiana: Quercetinase production and genetic diversity

    OpenAIRE

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

    2011-01-01

    Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detecte...

  10. A Survey of Association Rule Mining Using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Anubha Sharma

    2012-08-01

    Full Text Available Data mining is the analysis step of the "Knowledge Discovery in Databases" process, or KDD. It is the process that results in the discovery of new patterns in large data sets. It utilizes methods at the intersection of artificial intelligence, machine learning, statistics, and database systems. The overall goal of the data mining process is to extract knowledge from an existing data set and transform it into a human-understandable structure. In data mining, association rule learning is a popular and well researched method for discovering interesting relations between variables in large databases. Association rules are usually required to satisfy a user-specified minimum support and a user-specified minimum confidence at the same time. Genetic algorithm (GA is a search heuristic that mimics the process of natural evolution. This heuristic is routinely used to generate useful solutions to optimization and search problems. Genetic algorithms belong to the larger class of evolutionary algorithms, which generate solutions to optimization problems using techniques inspired by natural evolution, such as inheritance, mutation, selection, and crossover. In previous, many researchers have proposed Genetic Algorithms for mining interesting association rules from quantitative data. In this paper we represent a survey of Association Rule Mining Using Genetic Algorithm. The techniques are categorized based upon different approaches. This paper provides the major advancement in the approaches for association rule mining using genetic algorithms.

  11. Genetic Diversity Increases Insect Herbivory on Oak Saplings

    OpenAIRE

    Castagneyrol, Bastien; Lagache, Lélia; Giffard, Brice; Kremer, Antoine; Jactel, Hervé

    2012-01-01

    A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Qu...

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

    OpenAIRE

    Premo, L. S.; Hublin, Jean-jacques

    2008-01-01

    Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage ...

  13. Conservation of Genetic Diversity in Culture Plants

    Directory of Open Access Journals (Sweden)

    MAXIM A.

    2010-08-01

    Full Text Available The most important international document relating to the conservation of biodiversity is one adopted by theUN in Rio de Janeiro (1992 that "Convention on Biodiversity". Based on this agreement, the EU has taken a series ofmeasures to reduce genetic erosion in agriculture, which grew with the expansion of industrialized agriculture.Throughout its existence, mankind has used some 10,000 growing plant species. According to FAO statistics, today,90% of food production is ensured by some 120 growing plant species. In addition to drastic reduction in specificdiversity, the advent of industrialized agriculture has generated a process of strong genetic erosion. Old varieties andlocal varieties of crops have mostly been affected, in favour of "modern" varieties. Landraces are characterized by highheterogenity. They have the advantage of being much better adapted to biotic and abiotic stress conditions (diseases,pests, drought, low in nutrients, etc. and have excellent taste qualities, which can justify a higher price recovery thancommercial varieties. Thanks to these features, these crops need small inputs, which correspond to the concept ofsustainable development. Landraces are an invaluable genetic potential for obtaining new varieties of plants and are bestsuited for crop cultivation in ecological systems, becoming more common. Also, for long term food security in thecontext of global warming, rich genetic diversity will be require. “In situ” and “ex situ” conservation are the two majorstrategies used in the conservation of plant genetic resources. There is a fundamental difference between these twostrategies: “ex situ” conservation involves sampling, transfer and storage of a particular species population away fromthe original location, while “in situ” conservation (in their natural habitat implies that the varieties of interest,management and monitoring their place of origin takes place in the community to which they belong. These twostrategies should not be viewed as alternatives or in opposition, but a complementary approach is required. Obviously,only the on farm preservation, with traditional technologies, allows a sustainable management of the varieties, becausethese, in their natural habitat, can continue their evolutionary processes under the pressures of the environment, man,and technology. Romania, with an agricultural area of 14,722 millions Ha, still has a very rich diversity of conservationvarieties in plants growing, but they risk losing if appropriate action is taken.

  14. Data Quality Mining using Genetic Algorithm

    OpenAIRE

    Sufal Das

    2009-01-01

    Data quality mining (DQM) as a new and promising data mining approach from the academic and the business point of view. Data quality is important to organizations. People use information attributes as a tool for assessing data quality. The goal of DQM is to employ data mining methods in order to detect, quantify, explain and correct data quality deficiencies in very large databases. Data quality is crucial for many applications of knowledge discovery in databases (KDD). In this work, we have ...

  15. Population genetic diversity and fitness in multiple environments

    Directory of Open Access Journals (Sweden)

    McGreevy Thomas J

    2010-07-01

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

  16. Microbial diversity and metabolic networks in acid mine drainage habitats

    Science.gov (United States)

    Méndez-García, Celia; Peláez, Ana I.; Mesa, Victoria; Sánchez, Jesús; Golyshina, Olga V.; Ferrer, Manuel

    2015-01-01

    Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.

  17. Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity.

    Science.gov (United States)

    Vandergast, Amy G.; Perry, William M.; Lugo, Roberto V.; Hathaway, Stacie A.

    2011-01-01

    The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS, to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.

  18. Pyrosequencing and genetic diversity of microeukaryotes

    DEFF Research Database (Denmark)

    Harder, Christoffer Bugge

    2013-01-01

    Free-living, heterotrophic protozoa have an important ecological role in most terrestrial ecosystems by their grazing of bacteria as one of the first links in food chains and webs. Furthermore, some of them serve as reservoirs for disease-causing bacteria and /or as occasional opportunistic pathogens themselves. Protozoa is a morphological group which occurs in many different eukaryotic phyla, and many apparently morphologically similar types are very different from each others genetically. This complicates the development of good primers for analysis of their diversity with modern DNA based methods. Compared to other microorganisms such as fungi, algae and bacteria, much less is known about protozoa. It has been an essential element of this thesis to to advance our knowledge of protozoa by developing new primers for DNA-based studies of protozoa impact on ecosystems or as indicators of environmental conditions. The ribosomal 18S region is the only marker that is sufficiently well known in a broad range of eukaryotic microorganisms to be widely applicable in protozoa, and this defined the frame for the work. Pyrosequencing of environmental DNA from environmental DNA has revolutionised microbiology, as it enables the exploration and description of diversity (also the one that is not cultivable) on a hitherto unprecedented scale. In the bacterial microbiogy the technique is standardized and well established, and this was used in a study of bacterial diversity in sand filters at 11 Danish carefully selected waterworks (Article IV), where the bacterial metabolic diversity and its important for water purification was described. Building on this, the most important part of the thesis consists of two pyrosequencing analyses of protozoa with newly developed 18S primers. One specifically targets Cercozoa, a particularly abundant phylum of protozoa (Article III), on heath land that had been subjected to prolonged artificially induced drought in a Danish free-air climate-manipulation experiment (CLIMAITE). Article III showed that the testate cercozoan forms responded negatively to prolonged drought, and that on just on this one biotope, an unknown diversity of cercozoans is present, far exceeding the number of described cercozoan species. The other applied general eukaryotic 18S primers on the aforementioned 11 waterworks (Article V). Their eukaryotic community was dominated by protozoa, and when we compared it to the bacterial dataset from Article IV, we found that unlike the bacterial community composition, the eukaryotic community composition was not primarily driven by ecological conditions, but by geographical distances. Pyrosequencing analyses are highly dependent on existing DNA libraries that can be used to identify the thousands of DNA sequences, and Article II contributes to this by a morphological and phylogenetic characterization and naming of two new genera of flagellates found in Danish soil. The fact that it is possible to find two unknown and genetically divergent lineages in a few grams of soil froma well-studied country is an illustration of the limited knowledge of the microbial diversity. Finally, Article I separates a group of closely related fungi that could not be determined by morphology by using a phylogenetic analysis combining three marker genes. Using multiple markers makes it possible to evaluate the explanatory power of individual genes and their mutual consistency. The fact that ITS, the most widely used marker in fungi, did not show the best taxonomic resolution serves to put the heavy reliance upon a single marker (18S) in protozoology into perspective.

  19. A genetic programming based business process mining approach

    OpenAIRE

    Turner, Christopher James

    2009-01-01

    As business processes become ever more complex there is a need for companies to understand the processes they already have in place. To undertake this manually would be time consuming. The practice of process mining attempts to automatically construct the correct representation of a process based on a set of process execution logs. The aim of this research is to develop a genetic programming based approach for business process mining. The focus of this research is on automated/semi automat...

  20. High genetic diversity is not essential for successful introduction

    OpenAIRE

    Rollins, Lee A.; Moles, Angela T.; Lam, Serena; Buitenwerf, Robert; Joanna M. Buswell; Brandenburger, Claire R; Flores-Moreno, Habacuc; Nielsen, Knud B; Couchman, Ellen; Brown, Gordon S; Thomson, Fiona J; Hemmings, Frank; Frankham, Richard; Sherwin, William B

    2013-01-01

    Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduce...

  1. Genetic Diversity and Genetic Structure in Natural Populations of Prunus davidiana Germplasm by SSR Markers

    Directory of Open Access Journals (Sweden)

    Zhongping Cheng

    2011-11-01

    Full Text Available Prunus davidiana, which is a wild species, can be used as rootstocks for cultivation of fruit trees, breeding germplasm for improving resistance to diseases and insects, pioneer trees for recovering vegetation in arid areas, decoration trees for parks and gardens, and a potential medicinal plant for human health. Despite the valuable characteristics of P. davidiana, the genetic variations of resources of P. davidiana remain unclear. In this study, we used seven natural populations (GE; GH; ST; SF; SJ; SY; NX short for Heshui, Gansu; Huating Gansu; Taibai, Shaanxi; Fuxian, Shaanxi; Jiaocheng, Shanxi; Yangquan, Shanxi; Xiji, Ningxia, respectively of P. davidiana collected at distribution center in China to generate a fingerprint using 15 SSR markers by multifluorophore fragment analysis to assess transportability of the markers, genetic diversity and genetic structure within and among populations. Our data show that a 92% transportability rate was found from closely related species of P. davidiana based on SSR markers developed, and DNA polymorphisms were also detected among accessions by the selected SSR markers. The SSR markers amplified 137 alleles in total for all accessions with an average value of 9.13 alleles, ranging from the highest value of 15 alleles for UDP96-013 to the lowest value of 3 alleles for CPPCT017. Rare alleles, present at less than or equal to 5% of all accessions by marker, showed the highest value in BPPCT 020. By analyzing all accessions, the majority of the 192 accessions from seven populations were found to cluster together according to the given populations, while the minority from the given populations was distributed within clusters. The SY population appeared to have the most diversity among populations, followed by the NX population according to comprehensive analysis of all indices. The seven populations analyzed by unweighted parsimony and principal coordinate analysis were divided into two groups: ST, SY and SF; NX, GE, SJ and GH. A stark difference was found in the genetic variation—with 16% among populations and 84% within populations. Our results from this study imply that most SSR markers developed from related species can be used for genetic analyses of P. davidiana; some markers have more relevant applications for genetic analyses such as UDP96-013 for diversity evaluation and BPPCT 020 for mining rare alleles in P. davidiana; SY and NX are preferred when considering conservation and agronomic utilization.

  2. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    Science.gov (United States)

    Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structu...

  3. Genetic diversity studies of Papaya meleira virus

    Scientific Electronic Library Online (English)

    Cleidiane B., Daltro; Emanuel Felipe Medeiros, Abreu; Francisco Jose Lima, Aragão; Eduardo C., Andrade.

    2014-02-01

    Full Text Available Papaya (Carica papaya) is a fruit crop of great economic and social importance for Brazil and other papaya-producing countries. Brazil is the second largest producer in the world. The papaya sticky disease, caused by Papaya meleira virus (PMeV), has caused great losses in the major Brazilian papaya- [...] producing states. In order to estimate the genetic diversity of PMeV, latex samples were collected from papaya plants in the states of Bahia, Espírito Santo, Pernambuco, Ceará and Rio Grande do Norte, and total RNA was extracted. Specific primer for the replicase region allowed the amplification, by RT-PCR, of a fragment of approximately 560 bp from 31 isolates. The sequence analysis indicated a level of conservation greater than 88% among isolates. Furthermore, comparative analyzes indicated that PMeV has similarity with mycoviruses of the family Totiviridae. This phylogenetic relationship was reinforced by the presence of conserved motifs within in the RdRp regions from mycoviruses.

  4. Beauveria bassiana: quercetinase production and genetic diversity

    Directory of Open Access Journals (Sweden)

    Eula Maria de M. B Costa

    2011-03-01

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

  5. Beauveria bassiana: quercetinase production and genetic diversity

    Scientific Electronic Library Online (English)

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

    2011-03-01

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

  6. Genetic Research: Mining for Medical Treasures

    Science.gov (United States)

    Cathryn M. Delude (The Writing Group)

    2010-07-12

    FASEB Breakthroughs in Bioscience article. "Knock-out" mice, in which specific genes have been inactivated, have been tremendously useful in helping researchers understand the genetic basis of disease. Moreover, "knock out" mice also serve as animal models for human diseases, allowing researchers to develop treatments and diagnostic tests for genetic diseases.

  7. Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations.

    Science.gov (United States)

    Paris, Josephine R; King, R Andrew; Stevens, Jamie R

    2015-07-01

    Humans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal-impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal-impacted trout populations have low genetic diversity and have experienced severe population declines. Metal-river trout populations are genetically distinct from clean-river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal-impacted populations from clean-river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human-altered landscapes can change the genetic makeup of a species. PMID:26136823

  8. Genetic diversity in soybean genotypes with resistance to Heterodera glycines

    Directory of Open Access Journals (Sweden)

    Ana Paula Oliveira Nogueira

    2011-01-01

    Full Text Available The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variabilitywas maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode

  9. Nested core collections maximizing genetic diversity in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    McKhann, Heather I; Camilleri, Christine

    2004-01-01

    The successful exploitation of natural genetic diversity requires a basic knowledge of the extent of the variation present in a species. To study natural variation in Arabidopsis thaliana, we defined nested core collections maximizing the diversity present among a worldwide set of 265 accessions. The core collections were generated based on DNA sequence data from a limited number of fragments evenly distributed in the genome and were shown to successfully capture the molecular diversity in other loci as well as the morphological diversity. The core collections are available to the scientific community and thus provide an important resource for the study of genetic variation and its functional consequences in Arabidopsis. Moreover, this strategy can be used in other species to provide a rational framework for undertaking diversity surveys, including single nucleotide polymorphism (SNP) discovery and phenotyping, allowing the utilization of genetic variation for the study of complex traits.

  10. Genetic diversity of canine olfactory receptors

    Science.gov (United States)

    Robin, Stéphanie; Tacher, Sandrine; Rimbault, Maud; Vaysse, Amaury; Dréano, Stéphane; André, Catherine; Hitte, Christophe; Galibert, Francis

    2009-01-01

    Background Evolution has resulted in large repertoires of olfactory receptor (OR) genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations. Results We sequenced 109 OR genes considered representative of the whole OR canine repertoire, which consists of more than 800 genes, in a cohort of 48 dogs of six different breeds. SNP frequency showed the overall level of polymorphism to be high. However, the distribution of SNP was highly heterogeneous among OR genes. More than 50% of OR genes were found to harbour a large number of SNP, whereas the rest were devoid of SNP or only slightly polymorphic. Heterogeneity was also observed across breeds, with 25% of the SNP breed-specific. Linkage disequilibrium within OR genes and OR clusters suggested a gene conversion process, consistent with a mean level of polymorphism higher than that observed for introns and intergenic sequences. A large proportion (47%) of SNP induced amino-acid changes and the Ka/Ks ratio calculated for all alleles with a complete ORF indicated a low selective constraint with respect to the high level of redundancy of the olfactory combinatory code and an ongoing pseudogenisation process, which affects dog breeds differently. Conclusion Our demonstration of a high overall level of polymorphism, likely to modify the ligand-binding capacity of receptors distributed differently within the six breeds tested, is the first step towards understanding why Labrador Retrievers and German Shepherd Dogs have a much greater potential for use as sniffer dogs than Pekingese dogs or Greyhounds. Furthermore, the heterogeneity in OR polymorphism observed raises questions as to why, in a context in which most OR genes are highly polymorphic, a subset of these genes is not? This phenomenon may be related to the nature of their ligands and their importance in everyday life. PMID:19144169

  11. Genetic diversity of canine olfactory receptors

    Directory of Open Access Journals (Sweden)

    Hitte Christophe

    2009-01-01

    Full Text Available Abstract Background Evolution has resulted in large repertoires of olfactory receptor (OR genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations. Results We sequenced 109 OR genes considered representative of the whole OR canine repertoire, which consists of more than 800 genes, in a cohort of 48 dogs of six different breeds. SNP frequency showed the overall level of polymorphism to be high. However, the distribution of SNP was highly heterogeneous among OR genes. More than 50% of OR genes were found to harbour a large number of SNP, whereas the rest were devoid of SNP or only slightly polymorphic. Heterogeneity was also observed across breeds, with 25% of the SNP breed-specific. Linkage disequilibrium within OR genes and OR clusters suggested a gene conversion process, consistent with a mean level of polymorphism higher than that observed for introns and intergenic sequences. A large proportion (47% of SNP induced amino-acid changes and the Ka/Ks ratio calculated for all alleles with a complete ORF indicated a low selective constraint with respect to the high level of redundancy of the olfactory combinatory code and an ongoing pseudogenisation process, which affects dog breeds differently. Conclusion Our demonstration of a high overall level of polymorphism, likely to modify the ligand-binding capacity of receptors distributed differently within the six breeds tested, is the first step towards understanding why Labrador Retrievers and German Shepherd Dogs have a much greater potential for use as sniffer dogs than Pekingese dogs or Greyhounds. Furthermore, the heterogeneity in OR polymorphism observed raises questions as to why, in a context in which most OR genes are highly polymorphic, a subset of these genes is not? This phenomenon may be related to the nature of their ligands and their importance in everyday life.

  12. Evaluation of the genetic diversity of avian paramyxovirus type 4

    OpenAIRE

    Nayak, Baibaswata; Nayak, Shreeraj; Paldurai, Anandan; Kumar, Sachin; De Nardi, Roberta; Terregino , Calogero; Collins, Peter L; Samal, Siba K

    2012-01-01

    Avian paramyxoviruses (APMVs) belong to the genus Avulavirus in the family Paramyxoviridae and include at least nine serotypes, APMV-1 to -9, as well as two additional provisional serotypes. Newcastle disease virus (NDV), which comprises APMV-1, is the most extensively studied APMV because it is an important poultry pathogen. A moderate level of antigenic and genetic diversity is recognized for APMV-1 isolates, but our knowledge of the antigenic and genetic diversity of the other APMV serotyp...

  13. Genetic diversity in soybean genotypes with resistance to Heterodera glycines

    OpenAIRE

    Ana Paula Oliveira Nogueira; Rita de Cássia Teixeira Oliveira; Rosângela D’Arc de Lima Oliveira; Cosme Damião Cruz; Tuneo Sediyama; Éder Matsuo

    2011-01-01

    The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoeffi...

  14. Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

    OpenAIRE

    Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

    2013-01-01

    Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germ...

  15. Functional consequences of genetic diversity in Strongyloides ratti infections.

    OpenAIRE

    Paterson, S.; Viney, M. E.

    2003-01-01

    Parasitic nematodes show levels of genetic diversity comparable to other taxa, but the functional consequences of this are not understood. Thus, a large body of theoretical work highlights the potential consequences of parasite genetic diversity for the epidemiology of parasite infections and its possible implications for the evolution of host and parasite populations. However, few relevant empirical data are available from parasites in general and none from parasitic nematodes in particular....

  16. Genetic Diversity of Walnut Revealed by AFLP and RAPD Markers

    Directory of Open Access Journals (Sweden)

    Zheng Xu

    2012-05-01

    Full Text Available AFLP and RAPD methods were used to investigate the genetic diversity of walnuts in western Sichuan plateau and Qinba mountainous regions. 35 samples were collected from 8 different regions, and 32 RAPD primers and 28 AFLP primer combinations were identified with polymorphism bands among the entire. 324 and 2155 fragments were respectively produced by RAPD and AFLP makers, and 86.1 % of RAPD bands and 57.2% of AFLP bands showed polymorphic with the size of 180~2000 bp and 50~1800 bp, respectively. The average amplified were 10.1 fragments per primer by RAPD and 76.9 fragments per pair primer by AFLP. The more polymorphic for genetic resource in Western Sichuan Plateau was observed by both RAPD and AFLP. The high number of alleles and the high expected genetic diversity detected with RAPD and AFLP markers indicate that western China has an important genetic diversity pool and abundant genetic variance of walnuts.

  17. 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. PMID:24336928

  18. Is genetic diversity really higher in large populations?

    OpenAIRE

    Ellegren, Hans

    2009-01-01

    Analyses of mitochondrial DNA (mtDNA) have challenged the concept that genetic diversity within populations is governed by effective population size and mutation rate. A recent study in BMC Evolutionary Biology shows that variation in the rate of mutation rather than in population size is the main explanation for variations in mtDNA diversity observed among bird species.

  19. The Kuroshio current influences genetic diversity and population genetic structure of a tropical seagrass, Enhalus acoroides.

    Science.gov (United States)

    Nakajima, Yuichi; Matsuki, Yu; Lian, Chunlan; Fortes, Miguel D; Uy, Wilfredo H; Campos, Wilfredo L; Nakaoka, Masahiro; Nadaoka, Kazuo

    2014-12-01

    Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo-West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The Philippines are situated at the centre of the E. acoroides range, Yaeyama and Hainan are peripheral populations, and the Yaeyama population is at the northern limit of the species range. The powerful Kuroshio Current flows from the Philippines to Yaeyama. Genetic analyses using nine microsatellite markers indicated that reproduction of E. acoroides is mostly sexual. Clonal diversity does not decrease in northern populations, although genetic diversity does. However, the genetic diversity of the Yaeyama populations is greater than that of the Hainan populations. Significant genetic differentiation among most populations was evident; however, the Yaeyama and north-east Philippines populations were genetically similar, despite being separated by ~1100 km. An assignment test suggested that recruitment occurs from the north-east Philippines to Yaeyama. The strong current in this region is probably responsible for the extant genetic diversity and recruitment patterns. PMID:25384848

  20. 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...

  1. Analysis of Genetic Diversity in Bangladeshi Chicken using RAPD Markers

    OpenAIRE

    M.B.R. Mollah; F.B. Islam; Islam, M. S.; Ali, M. A.; Alam, M. S.(State University of New York, 12222, Albany, New York, USA)

    2009-01-01

    Understanding the genetic diversity at molecular level is a prerequisite in developing strategies for effective conservation and utilization of chicken genetic resources. We studied the genetic variation within and between Bangladeshi native (Naked Neck, Frizzle and Non-descriptive indigenous) and exotic (White Leghorn, Rhode Island Red, Commercial layer and broiler) chicken populations by Random Amplified Polymorphic DNA (RAPD). Four out of the 20 random primers exhibited sufficient variabil...

  2. Genetic Variability and Diversity in Okra (Abelmoschus esculentus L. Moench)

    OpenAIRE

    Pradip K Akotkar, D. K. And A. K. Pal

    2010-01-01

    In the present investigation an attempt has been made to evaluate the genetic variability of some yield contributingcharacters, and the genetic diversity in fifty genotypes of okra collected from the NBPGR New Delhi, India. Analysis ofvariance indicated significant difference among the genotypes for different morphological characters. High values of GCV,PCV, heritability and genetic advance (% of mean) observed for number of fruiting nodes, number of ridges per fruit, plantheight and number o...

  3. Living together apart. The hidden genetic diversity of sponge populations.

    OpenAIRE

    Blanquer, Andrea; Uriz, María Jesús

    2011-01-01

    Intraorganism genetic stability is assumed in most organisms. However, here we show for the first time intraorganism genetic heterogeneity in natural populations of marine sponges. A total of 36 different multilocus genotypes (MLGs) were detected in 13 individuals of Scopalina lophyropoda sampled at 4 distant points within each sponge. All genotypes (showing a mosaic distribution), were transmitted to the progeny, thus contributing to the high genetic diversity and low clonality r...

  4. Low genetic diversity in a marine nature reserve: re-evaluating diversity criteria in reserve design

    OpenAIRE

    Bell, J J; Okamura, B

    2005-01-01

    Little consideration has been given to the genetic composition of populations associated with marine reserves, as reserve designation is generally to protect specific species, communities or habitats. Nevertheless, it is important to conserve genetic diversity since it provides the raw material for the maintenance of species diversity over longer, evolutionary time-scales and may also confer the basis for adaptation to environmental change. Many current marine reserves are small in size and i...

  5. Genetic diversity, parasite prevalence and immunity in wild bumblebees.

    Science.gov (United States)

    Whitehorn, Penelope R; Tinsley, Matthew C; Brown, Mark J F; Darvill, Ben; Goulson, Dave

    2011-04-22

    Inbreeding and a consequent loss of genetic diversity threaten small, isolated populations. One mechanism by which genetically impoverished populations may become extinct is through decreased immunocompetence and higher susceptibility to parasites. Here, we investigate the relationship between immunity and inbreeding in bumblebees, using Hebridean island populations of Bombus muscorum. We sampled nine populations and recorded parasite prevalence and measured two aspects of immunity: the encapsulation response and levels of phenoloxidase (PO). We found that prevalence of the gut parasite Crithidia bombi was higher in populations with lower genetic diversity. Neither measure of immune activity was correlated with genetic diversity. However, levels of PO declined with age and were also negatively correlated with parasite abundance. Our results suggest that as insect populations lose heterozygosity, the impact of parasitism will increase, pushing threatened populations closer to extinction. PMID:20926436

  6. Predicting mining activity with parallel genetic algorithms

    Science.gov (United States)

    Talaie, S.; Leigh, R.; Louis, S.J.; Raines, G.L.

    2005-01-01

    We explore several different techniques in our quest to improve the overall model performance of a genetic algorithm calibrated probabilistic cellular automata. We use the Kappa statistic to measure correlation between ground truth data and data predicted by the model. Within the genetic algorithm, we introduce a new evaluation function sensitive to spatial correctness and we explore the idea of evolving different rule parameters for different subregions of the land. We reduce the time required to run a simulation from 6 hours to 10 minutes by parallelizing the code and employing a 10-node cluster. Our empirical results suggest that using the spatially sensitive evaluation function does indeed improve the performance of the model and our preliminary results also show that evolving different rule parameters for different regions tends to improve overall model performance. Copyright 2005 ACM.

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

    Directory of Open Access Journals (Sweden)

    Afrooz Alimohamadi

    2012-11-01

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

  8. Rates of inbreeding and genetic diversity in Iranian Holstein cattle.

    Science.gov (United States)

    Dadar, Mohsen; Mahyari, Saeid Ansari; Rokouei, Mohammad; Edriss, Mohammd Ali

    2014-10-01

    The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1,048,572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non-founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non-founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co-ancestry and inbreeding, which would lead to better handling of the effective population size. PMID:25041055

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

    OpenAIRE

    Kesinee Gatphayak

    2013-01-01

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

  10. 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

    Ro?. 52, ?. 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

  11. Evaluation of genetic diversity in Pampus argenteus using SSR markers.

    Science.gov (United States)

    Qin, Y; Shi, G; Sun, Y

    2013-01-01

    In order to evaluate the germplasm resources of Pampus argenteus silver pomfret, the genetic diversity and population structure of 132 silver pomfret samples collected from the three regions (the East China Sea, the Yellow Sea and the Bohai Sea) were examined using 13 polymorphic microsatellite loci. Results indicated a high level of genetic diversity. The total number of observed alleles was 68, the mean allele number was 5.46 per locus, and the mean number of effective alleles was 4.91. The polymorphism information content ranged from 0.58 to 0.88. For the 13 polymorphic microsatellite loci, the results of analysis of molecular variance indicated that 92.45% of the genetic variation was contained within populations. Unweighted pair group method with arithmetic mean cluster analysis revealed significant genealogical branches or clusters corresponding to sampling localities. We concluded that there was high genetic diversity in these silver pomfret populations, and that this diversity was related to the complex environment. These results would contribute to important knowledge of genetic diversity and population structure, which would be crucial for establishing appropriate fishery management stocks for this species. PMID:24301952

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

    Science.gov (United States)

    Tee, Kang Lan; Wong, Tuck Seng

    2013-12-01

    Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field. PMID:24012599

  13. GENETIC DIVERSITY IN ALBANIAN SHEEP BREEDS ESTIMATED BY AFLP MARKERS

    Directory of Open Access Journals (Sweden)

    Vilson Bozgo

    2010-08-01

    Full Text Available In this investigation Amplified Fragment Length Polymorphism (AFLP markers have been used to assess genetic diversity and relationship among three local Albanian sheep breeds. A total of 93 unrelated individuals were analysed by three EcoRI/TaqI primer combination that produced 92 AFLP markers. Nei’s GST index was calculated to investigate the partition of diversity within and between breeds. The mean value of this index was 0.039, indicating that only 4% of the total genetic variation is due to between breeds differences, while 96% of the diversity is accounted by differences among individuals within breeds. The mean expected heterozygosity value for the whole population was 0.259, indicating that a high level of diversity is present in Albanian sheep compared to estimates in other regions. According to what indicated by the GST index, model-based clustering did not differentiate the breeds. The results obtained by AFLP data sets indicate high diversity in Albania but small genetic distances between breeds, confirming previous results obtained with microsatellites. These results reflect Albanian sheep management practices, which have facilitated a relevant gene flow between breeds. These results are useful to design proper breeding programs suited to conserve the genetic diversity presently existing in Albanian sheep

  14. 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.

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

    Scientific Electronic Library Online (English)

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

    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 collecti [...] on (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.

  16. Ephemeral metapopulations show high genetic diversity at regional scales.

    Science.gov (United States)

    Berendonk, T U; Spitze, K; Kerfoot, W C

    2009-10-01

    One of the primary questions concerning the long-term preservation of nature and its diversity is the maintenance of genetic diversity. However, despite numerous theoretical investigations, comparative empirical information on how local extinctions influence regional genetic variation does not exist. To our knowledge, this is the first report of an empirical study comparing the genetic variation of permanent vs. ephemeral species at two scales (local variation, regional variation). This approach, utilizing a microsatellite analysis of six midge species of the genus Chaoborus generated intriguing scale-dependent results. Species that experienced repeated local extinctions had reduced genetic variation at the local level, yet the regional genetic variation was greater than in species with permanent populations. Our findings call into question the assumption that species with repeated local extinctions generally contain lower genetic diversity, especially if they experience a "nomadic" pattern of dispersal. We encourage comparative analyses of empirical genetic data at dual scales as molecular tools become more available in ecological studies. PMID:19886476

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

    International Nuclear Information System (INIS)

    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 r60%. 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)

  18. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    Directory of Open Access Journals (Sweden)

    Bisgaard Magne

    2011-02-01

    Full Text Available Abstract Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies.

  19. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Angen, Øystein

    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 comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies.

  20. Genetic diversity and the origins of cultural fragmentation

    OpenAIRE

    Ashraf, Quamrul; Galor, Oded

    2013-01-01

    Despite the importance attributed to the effects of diversity on the stability and prosperity of nations, the origins of the uneven distribution of ethnic and cultural fragmentation across countries have been underexplored. Building on the role of deeply-rooted biogeographical forces in comparative development, this research empirically demonstrates that genetic diversity, predominantly determined during the prehistoric “out of Africa” migration of humans, is an underlying cause of variou...

  1. Regional specificity of genetically diverse garlic varieties

    Science.gov (United States)

    Garlic is a profitable crop for small to medium-sized vegetable farmers. Despite the increasing market for specialty garlic, it is remarkable how little is known about the diverse types of garlic available. Farmers need to know which garlic types perform well under their growing conditions, and th...

  2. Genetic diversity analysis in Cymbopogon species using DNA markers

    Directory of Open Access Journals (Sweden)

    J. Kumar

    2009-01-01

    Full Text Available Genetic diversity of 25 accessions of Cymbopogon aromatic grasses including eight species, two hybrids and one mutant strain were analyzed using DNA markers generated by employing 20 primer pairs derived from cDNAs containing simple sequence repeat (SSR of rice genome. A total of 151 bands were produced ranging from 3 to 12 per primer pair. The polymorphic information content values varied from 0.143 to 0.916 with an average 0.715. Jaccard’s similarity coefficient ranged from 64 to 87% among the paired accessions. The level of diversity among different taxa/accessions observed during the present study was, however, low relative to the diversity level obtained due to RAPD markers in earlier studies. The pattern of genetic diversity neither matched with the known taxonomic classification, nor did it always match with the distribution of chemical constituents of the essential oils available in these accessions. Thus, present investigation though revealed poor correlation between the molecular and chemical diversity, indicating that chemical diversity in medicinal and aromatic species is not only result of genetic variability, but it also depends on a number of other factors. Thus this study may prove useful in several ways in Cymbopogon conservation and breeding programs and in the development of perfect markers though association mapping for genes involved in controlling agronomically important traits.

  3. 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. PMID:25739286

  4. Conservation of Genetic Diversity in Culture Plants

    OpenAIRE

    MAXIM A.

    2010-01-01

    The most important international document relating to the conservation of biodiversity is one adopted by theUN in Rio de Janeiro (1992) that "Convention on Biodiversity". Based on this agreement, the EU has taken a series ofmeasures to reduce genetic erosion in agriculture, which grew with the expansion of industrialized agriculture.Throughout its existence, mankind has used some 10,000 growing plant species. According to FAO statistics, today,90% of food production is ensured by some 120 gro...

  5. Genetic diversity of Kenyan native oyster mushroom (Pleurotus).

    Science.gov (United States)

    Otieno, Ojwang D; Onyango, Calvin; Onguso, Justus Mungare; Matasyoh, Lexa G; Wanjala, Bramwel W; Wamalwa, Mark; Harvey, Jagger J W

    2015-01-01

    Members of the genus Pleurotus, also commonly known as oyster mushroom, are well known for their socioeconomic and biotechnological potentials. Despite being one of the most important edible fungi, the scarce information about the genetic diversity of the species in natural populations has limited their sustainable utilization. A total of 71 isolates of Pleurotus species were collected from three natural populations: 25 isolates were obtained from Kakamega forest, 34 isolates from Arabuko Sokoke forest and 12 isolates from Mount Kenya forest. Amplified fragment length polymorphism (AFLP) was applied to thirteen isolates of locally grown Pleurotus species obtained from laboratory samples using five primer pair combinations. AFLP markers and internal transcribed spacer (ITS) sequences of the ribosomal DNA were used to estimate the genetic diversity and evaluate phylogenetic relationships, respectively, among and within populations. The five primer pair combinations generated 293 polymorphic loci across the 84 isolates. The mean genetic diversity among the populations was 0.25 with the population from Arabuko Sokoke having higher (0.27) diversity estimates compared to Mount Kenya population (0.24). Diversity between the isolates from the natural population (0.25) and commercial cultivars (0.24) did not differ significantly. However, diversity was greater within (89%; P > 0.001) populations than among populations. Homology search analysis against the GenBank database using 16 rDNA ITS sequences randomly selected from the two clades of AFLP dendrogram revealed three mushroom species: P. djamor, P. floridanus and P. sapidus; the three mushrooms form part of the diversity of Pleurotus species in Kenya. The broad diversity within the Kenyan Pleurotus species suggests the possibility of obtaining native strains suitable for commercial cultivation. PMID:25344263

  6. Assessment of genetic diversity in Cattleya intermedia Lindl. (Orchidaceae)

    Scientific Electronic Library Online (English)

    Nelson Barbosa, Machado Neto; Luiz Gonzaga Esteves, Vieira.

    2011-10-01

    Full Text Available Orchids are valuable pot plants and Cattleya intermedia is a promising species underused in breeding programs. Recently, breeding work with this species produced superior plants that are believed to be not the true species owing to the morphological differences from wild plants. The aim of this stud [...] y was to estimate the level of genetic diversity and interrelationships between wild and bred Cattleya intermedia collected at three different Brazilian states and from commercial breeders with RAPD markers. A total of 65 polymorphic bands were used to generate a genetic distance matrix. No specific groupings were revealed by the cluster analysis as bred materials were not different from wild plants. The genetic differentiation (F ST = 0.01626) was very low indicating a high gene flow in C. intermedia due to artificial crosses and a high differentiation between populations. The genetic variability available within this species is high enough to allow genetic progress in flower shape and size.

  7. Bovine Genetic Diversity Revealed By mtDNA Sequence Variation

    Science.gov (United States)

    Mitochondrial DNA single nucleotide polymorphism (SNP) data were used to determine genetic distance, nucleotide diversity, construction of haplotypes, estimation of information contents, and phylogenic relationships in bovine HapMap breeds. The Bovine International HapMap panel consists of 720 anima...

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

    Science.gov (United States)

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

  9. 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, B?etislav; Modrý, David; Lal, A. A.

    2004-01-01

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

  10. Population genetic structure and genetic diversity of soybean aphids from USA, Korea and Japan

    Science.gov (United States)

    Following its recent invasion of North America, the soybean aphid (Aphis glycines Matsumura) has become the number one insect pest of soybean (Glycine max L. Merr.) in the north central states of USA. Very little is known about the population genetic structure and genetic diversity of the soybean ap...

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

    Directory of Open Access Journals (Sweden)

    Kesinee Gatphayak

    2013-03-01

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

  12. Polyphenols in whole rice grain: genetic diversity and health benefits.

    Science.gov (United States)

    Shao, Yafang; Bao, Jinsong

    2015-08-01

    Polyphenols, such as phenolic acid, anthocyanin and proanthocyanidins, have both nutraceutical properties and functional significance for human health. Identification of polyphenolic compounds and investigation of their genetic basis among diverse rice genotypes provides the basis for the improvement of the nutraceutical properties of whole rice grain. This review focuses on current information on the identification, genetic diversity, formation and distribution patterns of the phenolic acid, anthocyanin, and proanthocyanidins in whole rice grain. The genetic analysis of polyphenol content and antioxidant capacity allows the identification of several candidate genes or quantitative trait loci (QTL) responsible for polyphenol variation, which may be useful in improvement of these phytochemicals by breeding. Future challenges such as how to mitigate the effects of climate change while improving nutraceutical properties in whole grain, and how to use new technology to develop new rice high in nutraceutical properties are also presented. PMID:25766805

  13. Assessment of Genetic Diversity in Iranian Fennels Using ISSR Markers

    Directory of Open Access Journals (Sweden)

    Kaivan Bahmani

    2012-07-01

    Full Text Available Fennel (Foeniculum vulgare Mill. is an important medicinal plant with used for various purposes in different industries. In this study 25 different ecotypes of fennel from all over Iran were collected and their genetic diversity studied by seven ISSR primers. Seven ISSR primers generated 52 amplified fragments, of which 49 were polymorphic. The highest similarity coefficient among the ecotypes was between Chahestan and Haji abad whereas the minimum similarity coefficient observed between Fozveh and Moqan. In most cases, classifications were consistent with their geographical distribution for some ecotypes (like Givi and Khalkhal in close distance and although with similarity in climate (like Damavand and Alamot with same climate. This study revealed that ISSR marker could properly separate these ecotypes based on geographical distribution and similarity in climates and showed the wide genetic diversity among Iranian fennels. In term of conservation program, it is highly recommended at least one conservation program for several accessions with near genetical distance should be conducted.

  14. Genetic diversity and molecular genealogy of local silkworm varieties

    Directory of Open Access Journals (Sweden)

    Zhouhe Du

    2013-03-01

    Full Text Available In order to explore the genetic diversity and systematic differentiation pattern among silkworm varieties, aiming to guide hybridization breeding, we sequenced a total of 72 Bmamy2 gene fragments from local silkworm varieties. The analysis of nucleotide sequence diversity and systematic differentiation indicated that there was rich genovariation in the sequencing region of Bmamy2 gene, and the base mutation rate is 5.6–8.2%, the haplotype diversity is 0.8294, and the nucleotide diversity is 0.0236±0.00122, suggesting Bmamy2 being a better marking gene with rich nucleotide sequence diversity, based on which the genetic diversity among different local silkworm varieties can be identified. The same heredity population structure is proclaimed by several analysis methods that every clade consisting of varieties from different geosystems and ecological types, while the varieties from the same geosystem and ecotype belong to different clades in the phylogeny. There is no population structure pattern that different varieties claded together according to geosystem or ecotype. It can be speculated that the silkworm origins from mixture of kinds of several voltinism mulberry silkworm, Bombyx mandarina, while the domestication events took place in several regions, from which the domesticated mulberry silkworms are all devoting to the domesticated silkworm population of today.

  15. Low genetic diversity in a marine nature reserve: re-evaluating diversity criteria in reserve design.

    Science.gov (United States)

    Bell, J J; Okamura, B

    2005-05-22

    Little consideration has been given to the genetic composition of populations associated with marine reserves, as reserve designation is generally to protect specific species, communities or habitats. Nevertheless, it is important to conserve genetic diversity since it provides the raw material for the maintenance of species diversity over longer, evolutionary time-scales and may also confer the basis for adaptation to environmental change. Many current marine reserves are small in size and isolated to some degree (e.g. sea loughs and offshore islands). While such features enable easier management, they may have important implications for the genetic structure of protected populations, the ability of populations to recover from local catastrophes and the potential for marine reserves to act as sources of propagules for surrounding areas. Here, we present a case study demonstrating genetic differentiation, isolation, inbreeding and reduced genetic diversity in populations of the dogwhelk Nucella lapillus in Lough Hyne Marine Nature Reserve (an isolated sea lough in southern Ireland), compared with populations on the local adjacent open coast and populations in England, Wales and France. Our study demonstrates that this sea lough is isolated from open coast populations, and highlights that there may be long-term genetic consequences of selecting reserves on the basis of isolation and ease of protection. PMID:16024366

  16. metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research

    Science.gov (United States)

    Lyne, Mike; Smith, Richard N; Lyne, Rachel; Aleksic, Jelena; Hu, Fengyuan; Kalderimis, Alex; Stepan, Radek; Micklem, Gos

    2013-01-01

    Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first-time users, whereas the Application Programming Interface (API) and web services provide convenient data access and tools for bioinformaticians. metabolicMine is freely available online at http://www.metabolicmine.org Database URL: http://www.metabolicmine.org PMID:23935057

  17. metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.

    Science.gov (United States)

    Lyne, Mike; Smith, Richard N; Lyne, Rachel; Aleksic, Jelena; Hu, Fengyuan; Kalderimis, Alex; Stepan, Radek; Micklem, Gos

    2013-01-01

    Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first-time users, whereas the Application Programming Interface (API) and web services provide convenient data access and tools for bioinformaticians. metabolicMine is freely available online at http://www.metabolicmine.org Database URL: http://www.metabolicmine.org. PMID:23935057

  18. Genetic diversity of noroviruses in Brazil

    Directory of Open Access Journals (Sweden)

    Julia Monassa Fioretti

    2011-12-01

    Full Text Available Norovirus (NoV infections are a major cause of acute gastroenteritis outbreaks around the world. In Brazil, the surveillance system for acute diarrhoea does not include the diagnosis of NoV, precluding the ability to assess its impact on public health. The present study assessed the circulation of NoV genotypes in different Brazilian states by partial nucleotide sequencing analysis of the genomic region coding for the major capsid viral protein. NoV genogroup II genotype 4 (GII.4 was the prevalent (78% followed by GII.6, GII.7, GII.12, GII.16 and GII.17, demonstrating the great diversity of NoV genotypes circulating in Brazil. Thus, this paper highlights the importance of a virological surveillance system to detect and characterize emerging strains of NoV and their spreading potential.

  19. Genetic diversity of noroviruses in Brazil

    Scientific Electronic Library Online (English)

    Julia Monassa, Fioretti; Mônica Simões Rocha, Ferreira; Matias, Victoria; Carmen Baur, Vieira; Maria da Penha Trindade Pinheiro, Xavier; José Paulo Gagliardi, Leite; Marize Pereira, Miagostovich.

    2011-12-01

    Full Text Available Norovirus (NoV) infections are a major cause of acute gastroenteritis outbreaks around the world. In Brazil, the surveillance system for acute diarrhoea does not include the diagnosis of NoV, precluding the ability to assess its impact on public health. The present study assessed the circulation of [...] NoV genotypes in different Brazilian states by partial nucleotide sequencing analysis of the genomic region coding for the major capsid viral protein. NoV genogroup II genotype 4 (GII.4) was the prevalent (78%) followed by GII.6, GII.7, GII.12, GII.16 and GII.17, demonstrating the great diversity of NoV genotypes circulating in Brazil. Thus, this paper highlights the importance of a virological surveillance system to detect and characterize emerging strains of NoV and their spreading potential.

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

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations.

  1. Multi-objective Genetic Algorithm for Association Rule Mining Using a Homogeneous Dedicated Cluster of Workstations

    OpenAIRE

    S. Dehuri; A. K. Jagadev; Ghosh, A.; Mall, R

    2006-01-01

    This study presents a fast and scalable multi-objective association rule mining technique using genetic algorithm from large database. The objective functions such as confidence factor, comprehensibility and interestingness can be thought of as different objectives of our association rule-mining problem and is treated as the basic input to the genetic algorithm. The outcomes of our algorithm are the set of non-dominated solutions. However, in data mining the quantity of data is growing rapidl...

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

    OpenAIRE

    LIU, YANG; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-01-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated i...

  3. Genetic diversity of Ascaris in southwestern Uganda

    DEFF Research Database (Denmark)

    Betson, Martha; Nejsum, Peter

    2012-01-01

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

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

    International Nuclear Information System (INIS)

    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 cluster 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)

  5. The genetic diversity of Sardinian myrtle (Myrtus communis L.) populations

    Scientific Electronic Library Online (English)

    Sara, Melito; Innocenza, Chessa; Patrizia, Erre; János, Podani; Maurizio, Mulas.

    2013-11-15

    Full Text Available Background: The myrtle (Myrtus communis) is a common shrub widespread in the Mediterranean Basin. Its fruit and leaves exhibit antioxidant, antibacterial and antifungal properties, and are used for their content of essential oils and for their medicinal properties, but most commonly as an ingredient [...] in locally made liquor. The uncontrolled exploitation of natural stands has reduced both the species' geographical coverage and the size of individual populations. The selection of genotypes for controlled cultivation requires a characterization of the genetic diversity present both within and between populations. Results: Genotypic variation was evaluated using ISSR profiling and genetic diversity characterized using standard population genetics approaches. Two major clusters were identified: one capturing all the candidate cultivars selected from various Sardinian localities, and the other wild individuals collected from Asinara, Corsica and Surigheddu. A moderate level of gene flow between the Sardinian and Corsican populations was identified. Discriminant analysis of principal components revealed a level of separation among the wild populations, confirming the population structure identified by the clustering methods. Conclusions: The wild accessions were well differentiated from the candidate cultivars. The level of genetic variability was high. The genetic data were compatible with the notion that myrtle has a mixed pollination system, including both out-pollination by insects and self-pollination. The candidate cultivars are suggested to represent an appropriate basis for directed breeding.

  6. Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

    Science.gov (United States)

    Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

    2014-11-01

    In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

  7. PLANT DIVERSITY OF THE ZHELTOKAMENSKIY OPEN CAST MINES

    Directory of Open Access Journals (Sweden)

    Yarova T.A.

    2012-11-01

    Full Text Available Floristic structure data of soil algae, lichens, mosses, and vascular plants are given. Rare plant species which are protected at the Ukrainian, European, and International levels were revealed. The species list of trees and bushes was conducted. The soil analysis was carried out by such parameters: pH-value, the maintenance of hygroscopic water, the maintenance of mineral substances. Vegetation biomass on the open cast mines sample areas is defined. Ecological analysis of the biotopes of registered algae species was performed. The ecological analysis of the vascular plants species biotopes was carried out.The estimation of the perspective vegetation pattern was suggested for natural restoration of the open cast mines. The plant species are selected according to the ecological and morphological characteristics for plant rehabilitation and planting of open cast mines.

  8. On the use of genetic programming for mining comprehensible rules in subgroup discovery.

    Science.gov (United States)

    Luna, José María; Romero, José Raúl; Romero, Cristóbal; Ventura, Sebastián

    2014-12-01

    This paper proposes a novel grammar-guided genetic programming algorithm for subgroup discovery. This algorithm, called comprehensible grammar-based algorithm for subgroup discovery (CGBA-SD), combines the requirements of discovering comprehensible rules with the ability to mine expressive and flexible solutions owing to the use of a context-free grammar. Each rule is represented as a derivation tree that shows a solution described using the language denoted by the grammar. The algorithm includes mechanisms to adapt the diversity of the population by self-adapting the probabilities of recombination and mutation. We compare the approach with existing evolutionary and classic subgroup discovery algorithms. CGBA-SD appears to be a very promising algorithm that discovers comprehensible subgroups and behaves better than other algorithms as measures by complexity, interest, and precision indicate. The results obtained were validated by means of a series of nonparametric tests. PMID:25415941

  9. Genome mining of ascomycetous fungi reveals their genetic potential for ergot alkaloid production.

    Science.gov (United States)

    Gerhards, Nina; Matuschek, Marco; Wallwey, Christiane; Li, Shu-Ming

    2015-06-01

    Ergot alkaloids are important as mycotoxins or as drugs. Naturally occurring ergot alkaloids as well as their semisynthetic derivatives have been used as pharmaceuticals in modern medicine for decades. We identified 196 putative ergot alkaloid biosynthetic genes belonging to at least 31 putative gene clusters in 31 fungal species by genome mining of the 360 available genome sequences of ascomycetous fungi with known proteins. Detailed analysis showed that these fungi belong to the families Aspergillaceae, Clavicipitaceae, Arthrodermataceae, Helotiaceae and Thermoascaceae. Within the identified families, only a small number of taxa are represented. Literature search revealed a large diversity of ergot alkaloid structures in different fungi of the phylum Ascomycota. However, ergot alkaloid accumulation was only observed in 15 of the sequenced species. Therefore, this study provides genetic basis for further study on ergot alkaloid production in the sequenced strains. PMID:25796201

  10. Genetic diversity in Brazilian tall coconut populations by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Francisco Elias Ribeiro

    2013-12-01

    Full Text Available The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the presentstudy was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples werecollected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles perlocus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per populationranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populationsof Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia doForte. These results reveal a high level of genetic diversity in the Brazilian populations.

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

    Science.gov (United States)

    Towner, Jonathan S; Amman, Brian R; Sealy, Tara K; Carroll, Serena A Reeder; Comer, James A; Kemp, Alan; Swanepoel, Robert; Paddock, Christopher D; Balinandi, Stephen; Khristova, Marina L; Formenty, Pierre B H; Albarino, Cesar G; Miller, David M; Reed, Zachary D; Kayiwa, John T; Mills, James N; Cannon, Deborah L; Greer, Patricia W; Byaruhanga, Emmanuel; Farnon, Eileen C; Atimnedi, Patrick; Okware, Samuel; Katongole-Mbidde, Edward; Downing, Robert; Tappero, Jordan W; Zaki, Sherif R; Ksiazek, Thomas G; Nichol, Stuart T; Rollin, Pierre E

    2009-07-01

    In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus) based on detection of Marburg virus RNA in 31/611 (5.1%) bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were collected nine months apart, demonstrating long-term virus circulation. The bat colony was estimated to be over 100,000 animals using mark and re-capture methods, predicting the presence of over 5,000 virus-infected bats. The genetically diverse virus genome sequences from bats and miners closely matched. These data indicate common Egyptian fruit bats can represent a major natural reservoir and source of Marburg virus with potential for spillover into humans. PMID:19649327

  12. Mini core germplasm collections for infusing genetic diversity in plant breeding programs

    Directory of Open Access Journals (Sweden)

    Hari D Upadhyaya*, Devvart Yadav, Naresh Dronavalli, CLL Gowda, and Sube Singh

    2010-07-01

    Full Text Available Plant genetic resources are essential components to meet future food security needs of world. Crop germplasm diversitycontributes to developing improved crop cultivars aimed at increasing crop productivity. The large size of germplasmcollections, coupled with unavailability of detailed data and information, has resulted in low use (<1% of germplasmleading to a narrow genetic base in many crops. The miniaturization of crop collections with almost full representation ofgenetic diversity in the form of mini core (~1% of the entire collection approach is an effective methodology to enrichand enhance crop improvement programs. The concept and process of developing mini core at The International CropsResearch Institute for the Semi-Arid Tropics (ICRISAT has been recognized worldwide as an “International PublicGood” (IPG. The mini core provides a means for accessing the larger collections for further exploration and also helps inproper assessment of genetic diversity and population structure and for association mapping and targeted gene mining.Use of mini core approach will lead to greater utilization of diverse germplasm for developing broad-based cultivars,especially in the context of climate change. Many national programs have shown immense interest in evaluating minicore as reflected by the supply of 114 sets of mini core of chickpea, groundnut, pigeonpea, sorghum, pearl millet, foxtailmillet and finger millet to researchers in 14 countries. Scientists have been able to identify new and diverse sources ofvariation for morpho-agronomic, quality, biotic, and abiotic stress resistance traits in various crops. The molecularcharacterization of the mini core will further enhance its use in plant breeding programs.

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

    Directory of Open Access Journals (Sweden)

    Ackermann Alejandro A

    2012-12-01

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

  14. Genetic Diversity of Echinococcus granulosus in Center of Iran

    OpenAIRE

    Pestechian, Nader; Hosseini Safa, Ahmad; Tajedini, Mohammadhasan; Rostami-Nejad, Mohammad; Mousavi, Mohammad; Yousofi, Hosseinali; Haghjooy Javanmard, Shaghayegh

    2014-01-01

    Hydatid cyst caused by Echinococcus granulosus is one of the most important parasitic diseases around the world and many countries in Asia, including Iran, are involved with this infection. This disease can cause high mortality in humans as well as economic losses in livestock. To date, several molecular methods have been used to determine the genetic diversity of E. granulosus. So far, identification of E. granulosus using real-time PCR fluorescence-based quantitative assays has not been stu...

  15. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    OpenAIRE

    Jordana Jordi; Aranguren-Méndez José; Gomez Mariano

    2001-01-01

    Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. T...

  16. Hierarchical cluster analysis of genetic diversity in Maize germplasm

    OpenAIRE

    A. Subramanian and N. Subbaraman

    2010-01-01

    An experiment was conducted to analyze the genetic diversity among 38 maize germplasm accessions of the maizegermplasm bank of Department of Millets, TNAU, Coimbatore. Observations regarding 25 morphological traits wererecorded and the data matrix was used for estimation of Euclidian distance by Un-weighted Paired Group ArithmeticAverage (UPGMA) method. Clustering was done by Sequential Agglomerative Hierarchical Non-overlapping (SAHN)clustering. The genotypes were grouped in to four clusters...

  17. Assessment of Genetic Diversity in Iranian Fennels Using ISSR Markers

    OpenAIRE

    Kaivan Bahmani; Ali Izadi-Darbandi; Ali Ashraf Jafari; Seyed Ahmad Sadat Noori; Mostafa Farajpour

    2012-01-01

    Fennel (Foeniculum vulgare Mill.) is an important medicinal plant with used for various purposes in different industries. In this study 25 different ecotypes of fennel from all over Iran were collected and their genetic diversity studied by seven ISSR primers. Seven ISSR primers generated 52 amplified fragments, of which 49 were polymorphic. The highest similarity coefficient among the ecotypes was between Chahestan and Haji abad whereas the minimum similarity coefficient observed between Foz...

  18. Isolation of Genetically Diverse Marburg Viruses from Egyptian Fruit Bats

    OpenAIRE

    Towner, Jonathan S.; Amman, Brian R.; Sealy, Tara K.; Carroll, Serena A. Reeder; Comer, James A.; Kemp, Alan; Swanepoel, Robert; Paddock, Christopher D.; Balinandi, Stephen; Khristova, Marina L.; Formenty, Pierre B. H.; Albarino, Cesar G.; Miller, David M.; Reed, Zachary D.; Kayiwa, John T.

    2009-01-01

    In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus) based on detection of Marburg virus RNA in 31/611 (5.1%) bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were collected nine months apart, demonstrating long-term virus circulation. The bat colony was estimated to be ...

  19. Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis

    OpenAIRE

    Rivarola, Maximo; Foster, Jeffrey T; Chan, Agnes P; Williams, Amber L.; Rice, Danny W; LIU, XINYUE; Melake-Berhan, Admasu; Huot Creasy, Heather; Puiu, Daniela; Rosovitz, M. J.; Khouri, Hoda M.; Beckstrom-Sternberg, Stephen M; Allan, Gerard J.; Keim, Paul; Ravel, Jacques

    2011-01-01

    Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and for...

  20. Virulence and competitive ability in genetically diverse malaria infections

    OpenAIRE

    Roode, Jacobus C.; Pansini, Riccardo; Cheesman, Sandra J.; Helinski, Michelle E. H.; Huijben, Silvie; Wargo, Andrew R.; Bell, Andrew S.; Chan, Brian H. K.; Walliker, David; Read, Andrew F.

    2005-01-01

    Explaining parasite virulence is a great challenge for evolutionary biology. Intuitively, parasites that depend on their hosts for their survival should be benign to their hosts, yet many parasites cause harm. One explanation for this is that within-host competition favors virulence, with more virulent strains having a competitive advantage in genetically diverse infections. This idea, which is well supported in theory, remains untested empirically. Here we provide evidence that within-host c...

  1. The genetic diversity of Plasmodium vivax: a review

    OpenAIRE

    Wanessa Christina de Souza-Neiras; Luciane Moreno Storti de Melo; Ricardo Luiz Dantas Machado

    2007-01-01

    The genetic diversity of Plasmodium vivax has been investigated in several malaria-endemic areas, including the Brazilian Amazon region, where this is currently the most prevalent species causing malaria in humans. This review summarizes current views on the use of molecular markers to examine P. vivax populations, with a focus on studies performed in Brazilian research laboratories. We emphasize the importance of phylogenetic studies on this parasite and discuss the perspectives created by o...

  2. Genetic diversity and recombination analysis of sweepoviruses from Brazil

    Directory of Open Access Journals (Sweden)

    Albuquerque Leonardo C

    2012-10-01

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

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

    Roullier, C.; Kambouo, R.; Paofa, J.; Mckey, D.; Lebot, V.

    2013-01-01

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

  5. Medical Association Rule Mining Using Genetic Network Programming

    Science.gov (United States)

    Shimada, Kaoru; Wang, Rouchen; Hirasawa, Kotaro; Furuzuki, Takayuki

    An efficient algorithm for building a classifier is proposed based on an important association rule mining using Genetic Network Programming (GNP). The proposed method measures the significance of the association via the chi-squared test. Users can define the conditions of important association rules for building a classifier flexibly. The definition can include not only the minimum threshold chi-squared value, but also the number of attributes in the association rules. Therefore, all the extracted important rules can be used for classification directly. GNP is one of the evolutionary optimization techniques, which uses the directed graph structure as genes. Instead of generating a large number of candidate rules, our method can obtain a sufficient number of important association rules for classification. In addition, our method suits association rule mining from dense databases such as medical datasets, where many frequently occurring items are found in each tuple. In this paper, we describe an algorithm for classification using important association rules extracted by GNP with acquisition mechanisms and present some experimental results of medical datasets.

  6. Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches.

    Science.gov (United States)

    Leroy, G; Verrier, E; Meriaux, J C; Rognon, X

    2009-06-01

    Genetic relationships between 61 dog breeds were investigated, using a sampling of 1514 animals and a panel of 21 microsatellite markers. Based on the results from distance-based and Bayesian methods, breed constituted the main genetic structure, while groups including genetically close breeds showed a very weak structure. Depending on the method used, between 85.7% and 98.3% of dogs could be assigned to their breed, with large variations according to the breed. However, breed heterozygosity influenced assignment results differently according to the method used. Within-breed and between-breed diversity variations when breeds were removed were highly negatively correlated (r = -0.963, P < 0.0001), because of the genetic structure of the breed set. PMID:19222436

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

    Science.gov (United States)

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

    2014-03-01

    Bamboo is an important member of the giant grass subfamily Bambusoideae of Poaceae. In this study, 13 bamboo accessions belonging to 5 different genera were subjected to morphological evaluation and sequence-related amplified polymorphism (SRAP) analysis. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis was used to construct a dendrogram and to estimate the genetic distances among accessions. On the basis of morphological characteristics, the 13 accessions were distinctly classified into 2 major clusters; 3 varieties, PPYX, PGNK, and PLYY were grouped as cluster A, and 10 accessions were categorized under cluster B. Similarity coefficients ranging from 0.23 to 0.96 indicated abundant genetic variation among bamboo varieties. Approximately 38 SRAP primer combinations generated 186 bands, with 150 bands (80.65%) showing polymorphisms among the 13 accessions. Based on SRAP analysis, 13 bamboo accessions were grouped into 3 major clusters. Five species comprised Cluster I (PASL, PLYY, PTSC, SCNK, and BMAK), which belongs to genus Phyllostachys. Cluster II consisted of 5 varieties, PASL, PLYY, PTSC, SCNK, and BMAK; Cluster III included 3 varieties, PGNK, PLSY, and BMRS. Comparison of the results generated by morphological and SRAP analyses showed that the classification based on SRAP markers was more concordant to the taxonomic results of Gamble than that performed using morphological characters, thus suggesting that SRAP analysis is more efficient in evaluating genetic diversity in bamboos compared to morphological analysis. The SRAP technique serves as an alternative method in assessing genetic diversity within bamboo collections. PMID:25508082

  8. Characterization and genetic diversity analysis of cotton cultivars using microsatellites

    Scientific Electronic Library Online (English)

    Cândida H.C. de Magalhães, Bertini; Ivan, Schuster; Tocio, Sediyama; Everaldo Gonçalves de, Barros; Maurílio Alves, Moreira.

    Full Text Available Genetic diversity and the relationship between varieties are of great importance for cotton breeding. Our work was designed to estimate the informativeness of the cotton (Gossypium hirsutum L.) simple sequence repeat (SSR) microsatellite locus and to estimate the genetic distance between 53 cotton c [...] ultivars as well as to select a set of SSR primers able to differentiate between the 53 cotton cultivars studied. After extracting DNA from the 53 cultivars and characterized it using 31 pairs of SSR primers we obtained a total of 66 alleles with an average of 2.13 alleles per SSR locus and values of polymorphism information content (PIC) varying from 0.18 to 0.62, the dissimilarity coefficient varying from zero to 0.41. Statistical analysis using the unweighted pair-group method using arithmetic average (UPGMA) revealed seven subgroups which were consistent with the genealogical information available for some of the cultivars. The SSR genetic profile obtained for each of the cultivars made it possible to discriminate 52 of the 53 cultivars. This study of the genetic diversity of cotton cultivars with SSR markers support the need to introduce new alleles into the gene pool of the breeding cultivars.

  9. Characterization and genetic diversity analysis of cotton cultivars using microsatellites

    Directory of Open Access Journals (Sweden)

    Cândida H.C. de Magalhães Bertini

    2006-01-01

    Full Text Available Genetic diversity and the relationship between varieties are of great importance for cotton breeding. Our work was designed to estimate the informativeness of the cotton (Gossypium hirsutum L. simple sequence repeat (SSR microsatellite locus and to estimate the genetic distance between 53 cotton cultivars as well as to select a set of SSR primers able to differentiate between the 53 cotton cultivars studied. After extracting DNA from the 53 cultivars and characterized it using 31 pairs of SSR primers we obtained a total of 66 alleles with an average of 2.13 alleles per SSR locus and values of polymorphism information content (PIC varying from 0.18 to 0.62, the dissimilarity coefficient varying from zero to 0.41. Statistical analysis using the unweighted pair-group method using arithmetic average (UPGMA revealed seven subgroups which were consistent with the genealogical information available for some of the cultivars. The SSR genetic profile obtained for each of the cultivars made it possible to discriminate 52 of the 53 cultivars. This study of the genetic diversity of cotton cultivars with SSR markers support the need to introduce new alleles into the gene pool of the breeding cultivars.

  10. Genetic and functional diversity of propagating cells in glioblastoma.

    Science.gov (United States)

    Piccirillo, Sara G M; Colman, Sue; Potter, Nicola E; van Delft, Frederik W; Lillis, Suzanne; Carnicer, Maria-Jose; Kearney, Lyndal; Watts, Colin; Greaves, Mel

    2015-01-13

    Glioblastoma (GBM) is a lethal malignancy whose clinical intransigence has been linked to extensive intraclonal genetic and phenotypic diversity and the common emergence of therapeutic resistance. This interpretation embodies the implicit assumption that cancer stem cells or tumor-propagating cells are themselves genetically and functionally diverse. To test this, we screened primary GBM tumors by SNP array to identify copy number alterations (a minimum of three) that could be visualized in single cells by multicolor fluorescence in situ hybridization. Interrogation of neurosphere-derived cells (from four patients) and cells derived from secondary transplants of these same cells in NOD-SCID mice allowed us to infer the clonal and phylogenetic architectures. Whole-exome sequencing and single-cell genetic analysis in one case revealed a more complex clonal structure. This proof-of-principle experiment revealed that subclones in each GBM had variable regenerative or stem cell activity, and highlighted genetic alterations associated with more competitive propagating activity in vivo. PMID:25533637

  11. HIV type 1 genetic diversity in newly diagnosed Cuban patients.

    Science.gov (United States)

    Machado, Liuber Y; Blanco, Madeline; Dubed, Marta; Díaz, Héctor M; Ruiz, Nancy M; Váldes, Neysi; Romay, Dania; Lobaina, Leonor I

    2012-08-01

    Knowledge of the genetic diversity of HIV-1 constitutes a fundamental premise in the epidemiological surveillance. In the present study, the HIV-1 genetic variability from 142 Cuban patients who were diagnosed with HIV-1 infection during 2009 and 2010 was determined. HIV-1 subtypes were determined by partial RT-PCR and sequencing of the HIV-1 pol gene. The phylogenetic analysis showed that 47 (33.1 %) samples were subtypes B and 95 (66.9 %) were non-B subtypes, where G, H, and C subtypes, as well as the recombinant forms CRF19_cpx, CRF18_cpx, and CRFs BG, were included. The circulation of CRF05_DF was detected for the first time in Cuba. The analyses of recombinants showed the presence of recombinant CRF18_cpx/CRF19_cpx. The study confirms the high genetic diversity of HIV-1 and the circulation of new genetic variants in the studied population, which indicates the importance of maintaining constant epidemiological surveillance in Cuba. PMID:22059433

  12. Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.)

    OpenAIRE

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N.; Aslam, M. N.; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A.; Kilian, A.; Sharpe, Andrew G.; Schondelmaier, Joerg

    2011-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified a...

  13. Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers

    Scientific Electronic Library Online (English)

    Xiao-Qiang, Wang; Soon-Wook, Kwon; Yong-Jin, Park.

    2013-09-15

    Full Text Available Background: In order to evaluate the variation among different rice types, the genetic diversity in a rice collection composed by 59 breeding lines, 23 landraces, 18 weedy rice lines, and 35 introduced lines that collected from countries worldwide was analyzed using 134 simple sequence repeat marker [...] s. Results: In total, 1264 alleles were identified (average, 9.43 per locus). Rare alleles made up a large portion (58.4%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbour-joining tree method were fairly consistent with the structure-based membership assignments for most of the accessions. A total of 105 accessions (79.5%) showed a clear relationship to each cluster, while the remaining 27 accessions (20.5%) were categorized as admixtures. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide association mapping. The mean r² value for all intrachromosomal loci pairs was 0.1286. The LD between linked markers decreased with the genetic distance between pairs of linked loci. Conclusions: These results will provide an effective aid for future allele mining, association genetics, mapping and cloning gene(s), germplasm conservation, and improvement programs.

  14. Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

    OpenAIRE

    Whitlock, Raj

    2014-01-01

    Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual sy...

  15. A Novel Method for Privacy Preserving in Association Rule Mining Based on Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Mohammad Naderi Dehkordi

    2009-08-01

    Full Text Available Extracting of knowledge form large amount of data is an important issue in data mining systems. One of most important activities in data mining is association rule mining and the new head for data mining research area is privacy of mining. Today association rule mining has been a hot research topic in Data Mining and security area. A lot of research has done in this area but most of them focused on perturbation of original database heuristically. Therefore the final accuracy of released database falls down intensely. In addition to accuracy of database the main aspect of security in this area is privacy of database that is not warranted in most heuristic approaches, perfectly. In this paper we introduce new multi-objective method for hiding sensitive association rules based on the concept of genetic algorithms. The main purpose of this method is fully supporting security of database and keeping the utility and certainty of mined rules at highest level.

  16. Genetic diversity of Qatari date palm using SSR markers.

    Science.gov (United States)

    Elmeer, K; Mattat, I

    2015-01-01

    The genetic diversity in the date palm germplasm of 59 female accessions representing 12 cultivars from different locations in Qatar was investigated using 14 loci of simple-sequence repeat (SSR) primers. A total of 94 alleles, with a mean of 6.7 alleles per locus, were scored. The number of alleles per locus varied from 3 (primer mPdCIR090) to 11 (primers mPdCIR010 and mPdCIR015). The amplified SSR band sizes ranged from 104 to 330 bp. The mean gene diversity was 0.66 and ranged from 0.39 (locus mPdCIRO93) to 0.86 (locus mPdCIR015), indicating that the Qatari date palm collection has a high degree of genetic diversity. The heterozygosity ranged from 0 (marker mPdCIR090) to 98% (marker mPdCIR010). Forty-four percent of the variability is explained at the inter-population level, while 56% of the variability is maintained within individuals. However, the loci mPdCIR044, mPdCIR057, mPdCIR090, and mPdCIR093 revealed that the total gene diversity is explained at the inter-population level. The Qatari populations Khalas, Shishi, Barhi, Hillali, Khnaizi, Gar, and Jabri showed significant differentiation compared to all other populations. The average fixation index was 0.24814, showing that about 24.81% of the genetic variation was present among populations, which correlated with analysis of molecular variance. PMID:25867305

  17. 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 diagnostic assay development can be identified.

  18. Diversity and activity of microbial communities of post mining substrates affected by Lumbricus rubellus (Oligochaeta: Lumbricidae).

    Czech Academy of Sciences Publication Activity Database

    Frouz, Jan; Krišt?fek, Václav; Elhottová, Dana; Tóth, E.M.; Borsodi, A.K.; Rusznyák, A.; Uhlí?ová, E.; Chro?áková, Alica; Baldrian, Petr; Márialigeti, K.

    2007-01-01

    Ro?. 54, Suppl. 1 (2007), s. 35. [International Congress of the Hungarian Society for Microbiology/15./. 18.07.2007-20.07.2007, Budapest] Institutional research plan: CEZ:AV0Z60660521; CEZ:AV0Z50200510 Keywords : diversity * microbial communities * post mining substrates Subject RIV: EH - Ecology, Behaviour

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

    Directory of Open Access Journals (Sweden)

    Chen Charlotte

    2012-06-01

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

  20. Genetic Diversity Among Irrigated Traditional and Modern Rice Germplasm

    Directory of Open Access Journals (Sweden)

    Khaleda Akter

    2002-01-01

    Full Text Available Forty five rice genotypes originating from Bangladesh, IRRI (Philippines, Japan and China were evaluated under irrigated ecosystem with a view to finding out genetic divergence for 10 characters including yield. The genotypes were constellated into five distinct groups with the range of three genotypes in cluster V and 16 genotypes in cluster III. The inter-cluster distances were larger than the intra-cluster distances in all cases except in cluster III, suggesting wider genetic diversity among the genotypes of different groups. The intra- cluster distance was highest in cluster III and least in cluster V. Maximum inter- cluster distance was observed between genotypes of cluster I and II followed by cluster I and III; II and IV; III and IV and the minimum was found between genotypes of cluster II and III. Plant height, grains/panicle and yield/hill were mainly responsible for genetic divergence while considering mean values. Though grains/panicle, days to flowering and grain length were positive contributors to genetic diversity based on the latent vectors. Clusters with small intra-cluster distances were considered less diverse than those with large distances. The mean yield, grains/panicle, plant height and days to flowering was lowest in cluster I and therefore, crosses involving the genotypes from this cluster with those from cluster II and III may exhibit high heterosis for earliness and grains/panicle. Crosses could also be made between clusters IV with that of II and III for evolving high yielding and early maturing varieties. Closer affinity of Bangladeshi traditional varieties was observed though some of them were in different clusters. Most of the breeding lines were included in cluster III indicating homogeneity in their pedigree.

  1. A genetic algorithm approach to recognition and data mining

    Energy Technology Data Exchange (ETDEWEB)

    Punch, W.F.; Goodman, E.D.; Min, Pei [Michigan State Univ., East Lansing, MI (United States)] [and others

    1996-12-31

    We review here our use of genetic algorithm (GA) and genetic programming (GP) techniques to perform {open_quotes}data mining,{close_quotes} the discovery of particular/important data within large datasets, by finding optimal data classifications using known examples. Our first experiments concentrated on the use of a K-nearest neighbor algorithm in combination with a GA. The GA selected weights for each feature so as to optimize knn classification based on a linear combination of features. This combined GA-knn approach was successfully applied to both generated and real-world data. We later extended this work by substituting a GP for the GA. The GP-knn could not only optimize data classification via linear combinations of features but also determine functional relationships among the features. This allowed for improved performance and new information on important relationships among features. We review the effectiveness of the overall approach on examples from biology and compare the effectiveness of the GA and GP.

  2. Relationship between genetic, chemical, and bacterial diversity in the Atlanto-Mediterranean bath sponge Spongia lamella.

    OpenAIRE

    Noyer, Charlotte; Becerro, Mikel

    2011-01-01

    Does diversity beget diversity? Diversity includes a diversity of concepts because it is linked to variability in and of life and can be applied to multiple levels. The connections between multiple levels of diversity are poorly understood. Here, we investigated the relationships between genetic, bacterial, and chemical diversity of the endangered Atlanto-Mediterranean sponge Spongia lamella. These levels of diversity are intrinsically related to sponge evolution and c...

  3. Bacterial diversity in soil from geophagic mining sites in the Qwa-Qwa region of South Africa.

    Science.gov (United States)

    de Smidt, Olga; Smit, Nellie Jacoba; Botes, Elsabe

    2015-01-01

    Geophagia is practised in many parts of the world and can be associated with medicinal treatments, ceremonial events and spiritual behaviours/practices. This is the first report on a systematic investigation and description of the bacterial diversity in soil regularly ingested by geophagic individuals using a culture-independent method. Diversity in 17 different mining sites was investigated using denaturing gradient gel electrophoresis. Genetic material from Pantoea, Stenotrophomonas, Listeria, Rhodococcus and Sphingomonads was present in most of the soil samples. Species from these genera are recognised, potential or immerging human pathogens, and are of special interest in immune-compromised individuals. Other genera able to produce a variety of bacteriocins and antimicrobial/antifungal substances inhibitory towards food borne pathogens (Dactylosporangium and Bacillus) and able to degrade a range of environmental pollutants and toxins (Duganella and Massilia) were also present. These essential insights provide the platform for adjusting culturing strategies to isolate specific bacteria, further phylogenetic studies and microbial mining prospect for bacterial species of possible economic importance. PMID:24852929

  4. Genetic diversity of disease-associated loci in Turkish population.

    Science.gov (United States)

    Karaca, Sefayet; Cesuroglu, Tomris; Karaca, Mehmet; Erge, Sema; Polimanti, Renato

    2015-04-01

    Many consortia and international projects have investigated the human genetic variation of a large number of ethno-geographic groups. However, populations with peculiar genetic features, such as the Turkish population, are still absent in publically available datasets. To explore the genetic predisposition to health-related traits of the Turkish population, we analyzed 34 genes associated with different health-related traits (for example, lipid metabolism, cardio-vascular diseases, hormone metabolism, cellular detoxification, aging and energy metabolism). We observed relevant differences between the Turkish population and populations with non-European ancestries (that is, Africa and East Asia) in some of the investigated genes (that is, AGT, APOE, CYP1B1, GNB3, IL10, IL6, LIPC and PON1). As most complex traits are highly polygenic, we developed polygenic scores associated with different health-related traits to explore the genetic diversity of the Turkish population with respect to other human groups. This approach showed significant differences between the Turkish population and populations with non-European ancestries, as well as between Turkish and Northern European individuals. This last finding is in agreement with the genetic structure of European and Middle East populations, and may also agree with epidemiological evidences about the health disparities of Turkish communities in Northern European countries. PMID:25716910

  5. Genetic diversity of breeding popcorn lines determined by SSR markers

    Scientific Electronic Library Online (English)

    Ana Paula, Ribeiro Trindade; Ronald José, Barth Pinto; Antonio Teixeira do, Amaral Júnior; Claudete Aparecida, Mangolin; Maria de Fátima Pires da, Silva Machado; Carlos Alberto, Scapim.

    2010-01-15

    Full Text Available Information about genetic dissimilarity is very important to corroborate genealogical relationships and to predict the most heterozygotic hybrid combinations. Eight popcorn S6 lines of diverse germplasm types were evaluated using simple sequence repeats (SSR) markers. Of a total of 51 evaluated poly [...] morphic primers, 15 were used for polymerase chain reaction (PCR) amplification. The genetic distance was estimated by Rogers’ modified distance. The different popcorn breeding programs in Brazil are possibly using highly similar base-populations. The genetic similarity of lines P1-3 and P8-1 was lowest, while P3-3 and P8-2 were genetically more similar. The cophenetic correlation showed that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) was reliable to discriminate the genotypes in five groups. The clusters were consistent with the estimates of genetic identity. There was a moderate coincidence degree between the groups and genealogy of lines. Higher levels of heterozygosity are expected from crosses between the group containing lines P3-3 and P7-3 with that of P1-3 and P7-4. Crosses between lines P1-3 and P8-1 are also promising.

  6. LYGUS GENETICS: INTER- AND INTRASPECIFIC MITOCHONDRIAL GENETIC DIVERSITY IN NORTH AMERICA

    Science.gov (United States)

    Mitochondrial DNA (mtDNA) was employed to investigate inter- and intraspecific genetic diversity within the Lygus genus. The main emphasis was on L. lineolaris because it is a widely dispersed species occurring in many regions of North America. Part of the mtDNA cox1 and cox2 gene regions were used ...

  7. Exploiting a wheat EST database to assess genetic diversity

    Scientific Electronic Library Online (English)

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

    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.

  8. Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1

    Directory of Open Access Journals (Sweden)

    Abrams Elaine J

    2006-03-01

    Full Text Available Abstract Background Genetic diversity of the human immunodeficiency virus type 1 (HIV-1 population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. Results We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. Conclusion Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission.

  9. Genetic diversity of polysporic isolates of Moniliophthora perniciosa (Tricholomataceae).

    Science.gov (United States)

    Ferreira, L F R; Duarte, K M R; Gomes, L H; Carvalho, R S; Leal Junior, G A; Aguiar, M M; Armas, R D; Tavares, F C A

    2012-01-01

    The causal agent of witches' broom disease, Moniliophthora perniciosa is a hemibiotrophic and endemic fungus of the Amazon basin and the most important cocoa disease in Brazil. The purpose of this study was to analyze the genetic diversity of polysporic isolates of M. perniciosa to evaluate the adaptation of the pathogen from different Brazilian regions and its association with different hosts. Polysporic isolates obtained previously in potato dextrose agar cultures of M. perniciosa from different Brazilian states and different hosts (Theobroma cacao, Solanum cernuum, S. paniculatum, S. lycocarpum, Solanum sp, and others) were analyzed by somatic compatibility grouping where the mycelium interactions were distinguished after 4-8 weeks of confrontation between the different isolates of M. perniciosa based on the precipitation line in the transition zone and by protein electrophoresis through SDS-PAGE. The diversity of polysporic isolates of M. perniciosa was grouped according to geographic proximity and respective hosts. The great genetic diversity of M. perniciosa strains from different Brazilian states and hosts favored adaptation in unusual environments and dissemination at long distances generating new biotypes. PMID:22869076

  10. The effect of chromosome geometry on genetic diversity.

    Science.gov (United States)

    Marri, Pradeep Reddy; Harris, Leigh K; Houmiel, Kathryn; Slater, Steven C; Ochman, Howard

    2008-05-01

    Although organisms with linear chromosomes must solve the problem of fully replicating their chromosome ends, this chromosome configuration has emerged repeatedly during bacterial evolution and is evident in three divergent bacterial phyla. The benefit usually ascribed to this topology is the ability to boost genetic variation through increased recombination. But because numerous processes can impact linkage disequilibrium, such an effect is difficult to assess by comparing across bacterial taxa that possess different chromosome topologies. To test directly the contribution of chromosome architecture to genetic diversity and recombination, we examined sequence variation in strains of Agrobacterium Biovar 1, which are unique among sequenced bacteria in having both a circular and a linear chromosome. Whereas the allelic diversity among strains is generated principally by mutations, intragenic recombination is higher within genes situated on the circular chromosome. In contrast, recombination between genes is, on average, higher on the linear chromosome, but it occurs at the same rate as that observed between genes mapping to the distal portion of the circular chromosome. Collectively, our findings indicate that chromosome topology does not contribute significantly to either allelic or genotypic diversity and that the evolution of linear chromosomes is not based on a facility to recombine. PMID:18493068

  11. Genetic diversity of Chrysoporthe cubensis in eastern and southern Africa

    Scientific Electronic Library Online (English)

    Grace, Nakabonge; Marieka, Gryzenhout; Brenda D., Wingfield; Michael J., Wingfield; Jolanda, Roux.

    2007-06-01

    Full Text Available Chrysoporthe cubensis is an important fungal pathogen of Eucalyptus species worldwide. The fungus is also known on many other hosts, all residing in the order Myrtales. Previous studies have suggested that Chr. cubensis might be native to South America and southeast Asia and that it has been introdu [...] ced into Africa. Recently, surveys have been conducted in eastern and southern Africa to assess the distribution of Chrysoporthe spp. in this region. Chr. cubensis was found on Eucalyptus spp. in Kenya, Malawi and Mozambique. The aim of the study reported here was to determine the genetic diversity of Chr. cubensis populations from these countries. Population diversity studies were conducted using five pairs of microsatellite markers previously developed for Chr. cubensis. Results show that there is a very low genetic diversity within the populations of Chr. cubensis from Kenya, Malawi and Mozambique, implying that the fungus was probably recently introduced in these countries. Based on phylogenetic analyses, the origin of East African Chr. cubensis is most likely Asia.

  12. PCR-Based Genetic Diversity of Rapeseed Germplasm Using RAPD Markers

    OpenAIRE

    Nisar Ahmad; Iqbal Munir; Khan, Imtiaz A.; Waqar Ali; Wisal Muhammad; Rakhshanda Habib; Raham Sher Khan; Swati, Zahoor A

    2007-01-01

    The most challenging hurdle facing Pakistan is the production of Brassica germplasm with a wider genetic base and using them properly in rapeseed genetic improvement. Genetic diversity was evaluated in 20 rapeseed lines (10 entries each of B. napus and B. campestris) using RAPD as molecular markers. Four Randomly Amplified Polymorphic DNA primers were used to estimate the genetic distances among the genotypes in all the possible combinations. The genetic diversity study revealed different lev...

  13. Polymorphic Alu insertions and genetic diversity among African populations.

    Science.gov (United States)

    Terreros, Maria C; Martinez, Laisel; Herrera, Rene J

    2005-10-01

    Thorough assessment of modern genetic diversity and interpopulation affinities within the African continent is essential for understanding the processes that have been at work during the course of worldwide human evolution. Regardless of whether autosomal, Y-chromosome, or mtDNA markers are used, allele- or haplotype-frequency data from African populations are necessary in setting the framework for the construction of global population phylogenies. In the present study we analyze genetic differentiation and population structure in a data set of nine African populations using 12 polymorphic Alu insertions (PAls). Furthermore, to place our findings within a global context, we also examined an equal number of non-African groups. Frequency data from 456 individuals presented for the first time in this work plus additional data obtained from the literature indicate an overall pattern of higher intrapopulation diversity in sub-Saharan populations than in northern Africa, a prominent differentiation between these two locations, an appreciably high degree of transcontinental admixture in Egypt, and significant discontinuity between Morocco and the Iberian peninsula. Moreover, the topologies of our phylogenetic analyses suggest that out of the studied sub-Saharan groups, the southern Bantu population of Sotho/ Tswana presents the highest level of antiquity, perhaps as a result of ancestral or acquired Khoisan genetic signals. Close affinities of eastern sub-Saharan populations with Egypt in the phylogenetic trees may indicate the existence of gene flow along the Nile River. PMID:16596946

  14. Estimation of Genetic Diversity in Genetic Stocks of Hexaploid Wheat Using Seed Storage Proteins

    Directory of Open Access Journals (Sweden)

    Tanweer Kumar

    2014-07-01

    Full Text Available Bread wheat (Triticum aestivum L. is an allohexaploid specie, consist of three genomes AABBDD having 2n = 6x = 42 chromosomes. The wheat is a staple food of human beings due to its bread making quality which is composed of seed storage proteins of wheat especially High Molecular Weight Glutenins (HMW-GS. During present research, HMW-GS were analyzed in genetic stocks of common wheat consist of Nullisomic- tetrasomic, ditelosomic and deletion lines of group 3 homoeologous chromosomes by Sodium Dodecyle Sulpahate Polyacrylamide Gel Electrophoresis (SDS-PAGE. Protocol for protein extraction and separation was optimized. The protein profiles were used to estimate genetic distances and Phylogenetic relationships among the genetic stocks were evaluated. Genetic stocks showed different banding patterns and each protein band was considered as a locus/allele. Alleles were scored as present (1 and absent (0 to generate bivariate 1-0 data matrix. A total of 45 alleles were amplified. Genetic distance among the genetic stocks ranged from 0-72%. A dendrogram was constructed using computer program Pop Gene version 3.2. Genetic stocks of wheat were clustered in 3group A, B and C comprising 4, 4 and 1 genotypes, respectively. Maximum differences were observed among Dit-3BS and NT-3B3D and hence it is recommended that these 2 genetic stocks should be crossed to obtain maximum genetic diversity in the segregating population of wheat.

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

    International Nuclear Information System (INIS)

    Full text: East Asia contains more than 50% of the world's pig population and Europe about 30% (according to FAO inventory. Both indigenous resources were domesticated from different sub-species and are assumed to be the basis of the world-wide genetic diversity in pig. Indigenous resources of Asia, however, are less defined and only rarely compared with European breeds. Taking advantage of DNA diagnostics, animals within as well as between breeds from Vietnam and Europe were analysed for numerous well defined markers in order to gain more knowledge about pig genetic biodiversity. The main objective was to investigate indigenous Vietnamese pig breeds from different local geographic regions. A set of pig breeds was chosen for this study of genetic diversity: five indigenous breeds from Vietnam (Mong Cai, Muong Khuong, Co, Meo, Tap Na), two exotic breeds kept in Vietnam (Large White, Landrace), three European commercial breeds (Pietrain, Landrace, Large White), and European Wild Boar. Samples and data from 317 animals (17 to 32 unrelated animals per breed) were collected. A panel of 27 polymorphic microsatellite loci was chosen according to FAO recommendations for diversity analyses and genetic distance studies. The loci were distributed evenly over the porcine genome with additional loci linked to immunological relevant genes (MHC, IFNG). Moreover, a few Type I loci (RYR1, FSH) were genotyped. DNA was isolated and PCR fragment lengths analysis were carried out on an ALlengths analysis were carried out on an ALF DNA sequencer (Pharmacia, Freiburg, Germany). Some of the RFLPs were analysed by agarose gel electrophoresis. Selected microsatellite alleles of equal lengths were sequenced for animals of different breeds. Within-breed diversity estimated heterozygosities and tests for Hardy-Weinberg equilibrium by taking into account sample sizes, tests per locus and breed as well as breed-locus combinations. Calculations were performed using the BIOSYS-1 software package. Breed differentiation was evaluated by the fixation indices of Wright. Genetic distances between breeds were estimated on the basis of allelic frequencies of the loci in each breed using different measures, e.g the standard Nei's distances. Distances between breeds were further analysed according to the neighbour-joining algorithm of Nei and the bootstrapping procedure of Felsenstein. In average of the marker loci, heterozygous genotypes occurred more frequently than expected, but this was, not statistically significant. Heterozygosity was higher in indigenous Vietnamese breeds than in the other breeds. Breed differentiation was shown which allowed grouping of all individuals in clusters corresponding to the breeds. Herein the Vietnamese indigenous breeds form a distinct cluster with considerable genetic distance to the European breeds. Vietnamese exotic breeds were similar to the breeds in Europe. European Wild Boar displayed closer relation with commercial breeds of European origin than with the indigenous Vietnamese breeds. The microsatellite loci which are closely linked to functional genes of immune response showed differences between breeds. This finding may indicate adaptation to local geographic conditions. Type I loci revealed considerable differences between Vietnamese and European breeds which are partly due to breeding influences. The comparative DNA sequencing showed differences between microsatellite alleles of equal lengths. About 30% of these alleles displayed length independent variants in at least one nucleotide position. Between the genetic diverse breeds, like those from Vietnam and Europe, DNA sequences between alleles differed more often. Their relevance is discussed in view of the use of microsatellite polymorphisms. (author)

  16. Articles selected by Faculty of 1000 Biology: genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ?-Proteobacteria diversity.

    OpenAIRE

    2005-01-01

    A selection of evaluations from Faculty of 1000 Biology covering genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ?-Proteobacteria diversity

  17. A Novel Association Rules Method Based on Genetic Algorithm and Fuzzy Set Strategy for Web Mining

    OpenAIRE

    Chunlai Chai; Biwei Li

    2010-01-01

    The use of fuzzy techniques has been considered to be one of the key components of data mining systems because of the affinity with human knowledge representation. A hybridization of fuzzy sets with genetic algorithms is described for Web mining in this paper. It is based on a hybrid technique that combines the strengths of rough set theory and genetic algorithm. The algorithm through the introduction of selection operators, crossover operators and mutation operators, improves the global conv...

  18. Genetics, genomics and evolution of ergot alkaloid diversity.

    Science.gov (United States)

    Young, Carolyn A; Schardl, Christopher L; Panaccione, Daniel G; Florea, Simona; Takach, Johanna E; Charlton, Nikki D; Moore, Neil; Webb, Jennifer S; Jaromczyk, Jolanta

    2015-04-01

    The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine. PMID:25875294

  19. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

    Directory of Open Access Journals (Sweden)

    Carolyn A. Young

    2015-04-01

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

  20. Genetic Diversity Analysis among Greengram genotypes using RAPD Markers

    Directory of Open Access Journals (Sweden)

    M.Pandiyan., N.Senthil, P.Sivakumar, AR.Muthiah and N.Ramamoorthi

    2010-07-01

    Full Text Available Green gram is also one of the important pulse crops. Conventional breeding methods are very much difficult to utilize in thedevelopment of new genotypes. Hence incorporation of the molecular approaches along with the conventional techniques ismost powerful method. Evaluation of the available wild accessions are more useful for selecting desirable gene sources.Genetic diversity analysis place an important role in this purpose. For this molecular analysis of selected 18 accessions ingreengram (representing all nine clusters was carried out through RAPD markers. Out of ten primers used nine werepolymorphic in which the primer OPS-11 exhibited 100 per cent polymorphism. The value of similarity indices 0.72 to 0.91indicates high genetic similarity among the selected accessions at molecular level.

  1. Paternal phylogeography and genetic diversity of East Asian goats.

    Science.gov (United States)

    Waki, A; Sasazaki, S; Kobayashi, E; Mannen, H

    2015-06-01

    This study was a first analysis of paternal genetic diversity for extensive Asian domestic goats using SRY gene sequences. Sequencing comparison of the SRY 3'-untranslated region among 210 Asian goats revealed four haplotypes (Y1A, Y1B, Y2A and Y2B) derived from four variable sites including a novel substitution detected in this study. In Asian goats, the predominant haplotype was Y1A (62%) and second most common was Y2B (30%). Interestingly, the Y2B was a unique East Asian Y chromosomal variant, which differentiates eastern and western Eurasian goats. The SRY geographic distribution in Myanmar and Cambodia indicated predominant the haplotype Y1A in plains areas and a high frequency of Y2B in mountain areas. The results suggest recent genetic infiltration of modern breeds into South-East Asian goats and an ancestral SRY Y2B haplotype in Asian native goats. PMID:25917305

  2. Genetic diversity Genetic diversity pattern in finger millet [Eleusine coracana (L. Gaertn

    Directory of Open Access Journals (Sweden)

    S. R. Shinde, S. V. Desai, and R. M. Pawar

    2013-09-01

    Full Text Available The genetic distance for 41 genotypes of finger millet collected from different geographical areas was estimated using D2 statistics. These genotypes were grouped into seven clusters. Cluster II, I, V, VI, and III comprised 17, 10, 7, 3 and 2 genotypes, respectively. The clusters IV and VII were mono-genotypic indicating wide divergence from other clusters. Most of the strains were from same origin and found to be one or more components of seven clusters indicating the presence of wide genetic variability among the material belonging to same geographical origin. The highest inter-cluster distance was observed between clusters II and VII followed by IV and VII suggesting the use of genotypes from these clusters to serve as potential parents for hybridization. The characters iron content (70.12% contributed maximum towards divergence followed by plant height (11.72% , days to physiological maturity (7.07% and days to 50% flowering (5.49%.

  3. Genetic diversity Genetic diversity pattern in finger millet [Eleusine coracana (L.) Gaertn

    OpenAIRE

    S R Shinde, S. V. Desai

    2013-01-01

    The genetic distance for 41 genotypes of finger millet collected from different geographical areas was estimated using D2 statistics. These genotypes were grouped into seven clusters. Cluster II, I, V, VI, and III comprised 17, 10, 7, 3 and 2 genotypes, respectively. The clusters IV and VII were mono-genotypic indicating wide divergence from other clusters. Most of the strains were from same origin and found to be one or more components of seven clusters indicating the presence of wide geneti...

  4. A GENERAL SURVEY ON FREQUENT PATTERN MINING USING GENETIC ALGORITHM

    OpenAIRE

    Poornamala, K.; Lawrance, R.

    2012-01-01

    In recent years, data mining is an important aspect for generating association rules among the large number of itemsets. Association rule mining is one of the techniques in data mining that that has two sub processes. First, the process called as finding frequent itemsets and second process is association rules mining. In this sub process, the rules with the use of frequent itemsets have been extracted. Researchers developed a lot of algorithms for finding frequent itemsets and association ru...

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

    Scientific Electronic Library Online (English)

    Flávio de Oliveira, Francisco; Leandro Rodrigues, Santiago; Maria Cristina, Arias.

    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 b [...] y 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.

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

    OpenAIRE

    VIVI YUSKIANTI; KEIYA ISODA

    2012-01-01

    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 s...

  7. Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin

    OpenAIRE

    Bourguiba Hedia; Audergon Jean-Marc; Krichen Lamia; Trifi-Farah Neila; Mamouni Ali; Trabelsi Samia; D’Onofrio Claudio; Asma Bayram M; Santoni Sylvain; Khadari Bouchaib

    2012-01-01

    Abstract Background Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regiona...

  8. Managing Genetic Variation to Conserve Genetic Diversity in Goats and Sheep

    Directory of Open Access Journals (Sweden)

    J. N. B. Shrestha

    2010-01-01

    Full Text Available Domestic goat and sheep populations maintained for many generations with small numbers of male and female parents, or declining in total numbers, not only endure accumulated genetic drift but also a steady rise in inbreeding, which can be directly attributed to dispersive forces of evolutionary significance that influence gene frequency. Increasing effective population size shows theoretical promise in lessening the impact on erosion of biodiversity from genetic drift. For example, doubling the effective numbers of parents which increases effective population size reduces rate of inbreeding by nearly one-half in many of the scenarios in the present study. Similarly, equalizing the number of male and female parents can decrease the variance among progeny of each parent, which in turn increases effective population size. The recurring erosion of domestic goat and sheep diversity has contributed to decreased fecundity, reduced fitness and poor adaptability, all known to influence efficiency of production. The potential loss in performance of livestock and poultry following many generations of accumulated genetic drift, which often goes unnoticed, can be predicted for specific populations from precise estimates of their mean value, additive genetic variance and heritability along with their effective number of male and female parents. For example, when the effective population size decreases from 200 to 40, the potential reduction in mean performance for economically important traits of goat and sheep populations following 20 generations of accumulated genetic drift will nearly double. In contrast, increasing effective population size from 200 to 600 will have the potential reduction in mean performance. The accumulation of favourable mutations could imply an effective population size of 100 or more, which is equal to a rise in rate of inbreeding of 0.5% or less, may be acceptable in sustaining genetic response to artificial selection in commercial breeding populations. The application of quantitative genetic principles related to inbreeding and genetic drift make it possible to safeguard against erosion of genetic diversity in endangered breeds, populations and landraces while lessening the impact from potential loss in their performance. Conservation of domestic animal diversity can be achieved by managing the erosion of genetic variation based on breeding strategies which promote the mating of sires to all dams, in either ‘random bred’ or ‘balanced pedigreed’ breeding structure for populations of endangered domestic goats and sheep. Obviously, the in-situ and ex-situ conservation of live animals, along with cryogenic preservation of their gametes, stem cells, somatic cells, blood and gonads will be complementary to conservation breeding.

  9. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers.

    Science.gov (United States)

    Aranguren-Méndez, J; Jordana, J; Gomez, M

    2001-01-01

    Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (H(E)) over all the populations varied between 0.637 and 0.684 in this study. The low G(ST) value showed that only 3.6% of the diversity was between breeds (P<0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the D(A) distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans. PMID:11559485

  10. Genetic diversity in a world germplasm collection of tall fescue

    Scientific Electronic Library Online (English)

    Romina, Cuyeu; Beatriz, Rosso; Elba, Pagano; Gabriela, Soto; Romina, Fox; Nicolás Daniel, Ayub.

    Full Text Available Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their [...] rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.

  11. Relationship and genetic diversity of mistletoe (Viscum album L. subspecies

    Directory of Open Access Journals (Sweden)

    Leon Mejnartowicz

    2011-04-01

    Full Text Available With the help of 21 putative isoenzyme loci, the genetic diversity and variations of Viscum album ssp. album L. from 42 species, subspecies, varieties and hybrids of broadleaf trees, Viscum album ssp. austriacum (Wiesb. Vollmann, from 4 populations of Scots pine (Pinus sylvestris L. and Viscum album ssp. abietis (Wiesb. Abromeit, from 8 populations of European silver fir (Abies alba Mill. were analyzed. On the dendrogram, the three investigated subspecies form three clusters, each clearly separated from the other, so we suggest a revision of the systematic nomenclature proposed to take into consideration a return to an earlier system of dividing the European mistletoe into three species: Viscum album L., Viscum abietis Beck, and Viscum laxum Boiss. et Reut. From among the 21 tested loci only one locus, SOD-A, was monomorphic. The average number of actual alleles (Na and effective alleles (Ne was 2.23 and 1.61 respectively. The observed heterozygosity (Ho varied from 0.199 in V. album ssp. abietis to 0.345 in the V.a. ssp. album populations. Average FST = 0.277 indicates that about 28% of genetic differentiation is due to an interpopulation diversity of Viscum album populations. There is a small gene flux between Viscum album populations with only one immigrant successfully entering a population per two generations (Nm = 0,653.

  12. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    Directory of Open Access Journals (Sweden)

    Jordana Jordi

    2001-07-01

    Full Text Available Abstract Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P A distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.

  13. A GENERAL SURVEY ON FREQUENT PATTERN MINING USING GENETIC ALGORITHM

    Directory of Open Access Journals (Sweden)

    K. Poornamala

    2012-10-01

    Full Text Available In recent years, data mining is an important aspect for generating association rules among the large number of itemsets. Association rule mining is one of the techniques in data mining that that has two sub processes. First, the process called as finding frequent itemsets and second process is association rules mining. In this sub process, the rules with the use of frequent itemsets have been extracted. Researchers developed a lot of algorithms for finding frequent itemsets and association rules. Recently association rule mining systems have been designed using a combination of soft computing techniques.

  14. 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].

  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-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.

  16. Genetic diversity and relationships among indigenous Mozambican cattle breeds

    Scientific Electronic Library Online (English)

    I., Bessa; I., Pinheiro; M., Matola; K., Dzama; A., Rocha; P., Alexandrino.

    2009-01-01

    Full Text Available Three indigenous Mozambican cattle breeds, namely the Angone, Landim and Bovino de Tete were characterized using six proteins, 13 autosomal microsatellite loci and one Y-specific microsatellite locus (INRA124). The Mashona breed from Zimbabwe was also studied to elucidate the origin of the Bovino de [...] Tete cattle. Expected mean heterozygosity ranged from 0.46 - 0.50 in the proteins and from 0.66 - 0.69 in the microsatellites. Population genetic variability was relatively high when compared to other African breeds. Only 4.5% of the total genetic variation could be attributed to the differences among the breeds. D A genetic distances and principal component analysis suggest that Mozambican breeds occupy an intermediate position between Indian Zebu and African taurine cattle. The genetic contribution from Indian Zebu, estimated by mR and average percentage of Zebu diagnostic alleles, was highest in the Angone breed and lowest in the Landim breed. The indicine Y-specific allele was fixed in the Angone breed (classified as Zebu), was found in 62% of the Bovino de Tete breed and was absent in the Landim breed (classified as Sanga). The hybrid nature of these breeds was also revealed by using an admixture model to infer population structure. Cluster analysis correctly assigned individuals to their rightful populations with probabilities ranging from 0.96 to 0.98, using prior population information. The results support the hypothesis of the Bovino de Tete cattle being a result of crossbreeding between Sanga and Zebu breeds. This study presents the first extensive information on the genetic diversity and relationships among Mozambican cattle breeds and with other breeds from different continents.

  17. EFFECTS OF CHEMICAL CONTAMINANTS ON GENETIC DIVERSITY IN NATURAL POPULATIONS: IMPLICATIONS FOR BIOMONITORING AND ECOTOXICOLOGY

    Science.gov (United States)

    The conservation of genetic diversity has emerged as one of the central issues in conservation biology. Although researchers in the areas of evolutionary biology, population management, and conservation biology routinely investigate genetic variability in natural populations, onl...

  18. 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.

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

    OpenAIRE

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

    2012-01-01

    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...

  20. Evaluation of the genetic diversity of avian paramyxovirus type 4.

    Science.gov (United States)

    Nayak, Baibaswata; Nayak, Shreeraj; Paldurai, Anandan; Kumar, Sachin; De Nardi, Roberta; Terregino, Calogero; Collins, Peter L; Samal, Siba K

    2013-01-01

    Avian paramyxoviruses (APMVs) belong to the genus Avulavirus in the family Paramyxoviridae and include at least nine serotypes, APMV-1 to -9, as well as two additional provisional serotypes. Newcastle disease virus (NDV), which comprises APMV-1, is the most extensively studied APMV because it is an important poultry pathogen. A moderate level of antigenic and genetic diversity is recognized for APMV-1 isolates, but our knowledge of the antigenic and genetic diversity of the other APMV serotypes is limited. APMV-4 is frequently isolated from waterfowl around the world. To date complete genome sequences of APMV-4 are available for only strains, which were isolated from ducks in Hong Kong, Korea and Belgium over a period of 37 years. We have carried out genome sequencing from the nucleocapsid (N) gene-end signal to the polymerase (L) gene-start signal of five APMV-4 strains recently isolated from Italy. Each of the eight APMV-4 strains has the same F protein cleavage site, DIQPR?F. They also share a high level of nucleotide and amino acid sequence identity: for example, the F and HN glycoproteins have greater than 97% sequence identity between the various strains. Thus, comparison of these eight strains of APMV-4 did not provide evidence of substantial diversity, in contrast to similar studies with APMV-2, -3, and -6, in which the F and HN glycoproteins exhibited up to 20-30% amino acid sequence variation within a subgroup. Reciprocal cross-HI assay using post infection chicken sera also failed to detect significant antigenic variation among the available APMV-4 strains. PMID:23178589

  1. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter].

    Science.gov (United States)

    Assefa, Kebebew; Cannarozzi, Gina; Girma, Dejene; Kamies, Rizqah; Chanyalew, Solomon; Plaza-Wüthrich, Sonia; Blösch, Regula; Rindisbacher, Abiel; Rafudeen, Suhail; Tadele, Zerihun

    2015-01-01

    Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding. PMID:25859251

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

    Directory of Open Access Journals (Sweden)

    Mol Dick

    2005-10-01

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

  3. Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data.

    Science.gov (United States)

    Leroy, G; Verrier, E; Meriaux, J C; Rognon, X

    2009-06-01

    The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37-0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier. PMID:19222437

  4. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

    OpenAIRE

    Windig Jack J; Komen Hans; Gizaw Solomon; Hanotte Olivier; Van Arendonk Johan AM

    2008-01-01

    Abstract Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits) and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. No...

  5. Consequences of geographical habitats on population structure and genetic diversity in Campanula spp.

    OpenAIRE

    Paul Arens; Valentina Scariot; Matteo Caser

    2010-01-01

    Characterization of populations by means of DNA techniques provides a tool for precise identification and a quantitative estimate of genetic diversity, crucial in evaluation of genetic fragmentation within and among populations. NBS profiling are PCR-based approaches that sample genetic variation in resistance genes (R-gene), and R gene analogs (RGA). To date, myb patterns have not been used for evaluating genetic diversity in other species. NBS primers are homologous to the conserved sequenc...

  6. Consequences of geographical habitats on population structure and genetic diversity in Campanula spp

    OpenAIRE

    CASER, Matteo; SCARIOT, VALENTINA

    2010-01-01

    Characterization of populations by means of DNA techniques provides a tool for precise identification and a quantitative estimate of genetic diversity, crucial in evaluation of genetic fragmentation within and among populations. NBS profiling are PCR-based approaches that sample genetic variation in resistance genes (R-gene), and R gene analogs (RGA). To date, myb patterns have not been used for evaluating genetic diversity in other species. NBS primers are homologous to the conserved sequ...

  7. Diversity of bacterial communities in acid mine drainage from the Shen-bu copper mine, Gansu province, China

    Scientific Electronic Library Online (English)

    Yu, Yang; Wuyang, Shi; Minxi, Wan; Yanfei, Zhang; Lihong, Zou; Jufang, Huang; Guanzhou, Qiu; Xueduan, Liu.

    2008-01-15

    Full Text Available This study presents bacterial population analyses of microbial communities inhabiting three sites of acid mine drainage (AMD) in the Shen-bu copper mine, Gansu Province, China. These sites were located next to acid-leached chalcopyrite slagheaps that had been abandoned since 1995. The pH values of t [...] hese samples with high concentrations of metals ranged from 2.0 to 3.5. Amplified ribosomal DNA restriction analysis (ARDRA) was used to characterize the bacterial population by amplifying the 16S rRNA gene of microorganisms. A total of 39 operational taxonomic units (OTUs) were obtained from the three samples and sequenced from 384 clones. Sequence data and phylogenetic analyses showed that two dominant clones (JYC-1B, JYC-1D) in sample JYC-1 represented 69.5% of the total clones affiliated with Acidithiobacillus ferrooxidans (?-Proteobacteria), and the most dominant clones of JYC-2 and JYC-3 were affiliated with Caulobacter crescentus (?-Protebacteria). At the level of bacterial divisions, differences in the relative incidence of particular phylogenetic groups among the three samples and discrepancies in physicochemical characteristics suggested that the physico-chemical characteristics had an influence on phylogenetic diversity. Furthermore, the relationships between the discrepancies of physicochemical characteristics and the diversity of the bacteria communities in the three samples suggested that the biogeochemical properties, pH and concentration of soluble metal, could be key factors in controlling the structure of the bacterial population

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

    International Nuclear Information System (INIS)

    Full text: The production status, farming systems and genetic diversity of indigenous cattle in Sri Lanka were evaluated using six geographically distinct populations in Sri Lanka, which is a small island located below the southern tip of Indian subcontinent. The indigenous cattle population of the country is considered as a non-descript type mixture of genotypes, and represent more than the half of total cattle population of 1.2 million heads. Six distinct indigenous populations (NE, NC, So, No, TK and Th) were investigated for morphological and genetic differences. The respective farming systems were also evaluated to complete the requirement in developing conservation and utilization strategies. The sampling was carried out based on the non-existence of artificial insemination facilities to assure the target populations are indigenous. The six populations were assumed genetically isolated from each other in the absence of nomadic pattern of rearing and regular cattle migration. The farming systems were analyzed using a pre-tested structured questionnaire by single visits to each location. Single visits were practiced, as there is no variation in farming system according to the period of the year. Morphometric measurements were taken during the visit and the genetic variation was assessed within and between five populations using 15 autosomal and two Y-specific microsatellite markers. The farming system analysis revealed that indigenous cattle are reared as a traditt indigenous cattle are reared as a traditional practice in all the regions of the country under limited or no input situations. Since the low productivity masks its real contribution to the rural livelihood, the level of utilization was confounded within the attributes of respective farming systems. The contribution of indigenous cattle to total tangible income ranged from 0% to 90% in different regions reflecting the high variation in the purpose of keeping indigenous cattle. Integration with crop, especially with paddy was the common feature in systems across the regions. Morphometric measurements identified the specific phenotypic characteristics resulted by geographical isolation and selective breeding. Though vary according to the regional preferences, the compact body, narrow face, small horns and humps with shades of brown and black coat colour described the indigenous cattle phenotype in general. The diversity analysis based on microsatellite genotyping indicated that indigenous cattle in Sri Lanka has a high genetic diversity with average number of alleles per locus ranging from 7.9 to 8.5. Average heterozygosity of different regions varied within a narrow range (0.72 ± 0.04 to 0.76 ± 0.03). The genetic distances (DA) between regions were low (ranged between 0.085 and 0.066) suggesting a similar mixture of genotypes across regions despite the geographical isolation. However, two genetic clusters were visible though no relationship of those clusters with the geographical distribution of different regions could be observed. Introgression of taurine cattle was evidenced in one of the cattle populations (NC) as suggested by the Y-specific microsatellite analysis (author)

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

    Directory of Open Access Journals (Sweden)

    Hoda Anila

    2012-01-01

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

  10. Soil microfungal diversity on spoil sites in Sokolov and Most lignite mining regions (Czech Republic).

    Czech Academy of Sciences Publication Activity Database

    Nováková, Alena

    Greifswald : University of Greifswald, 2006. s. 137. [Land use changes in Europe as a challenge for restoration. Ecological, economical and ethical dimensions. European Conference on Ecological Restoration /5./. 21.08.2006-25.08.2006, Greifswald] R&D Projects: GA AV ?R(CZ) 1QS600660505 Institutional research plan: CEZ:AV0Z60660521 Keywords : soil microfungal diversity * spoil sites * lignite mining regions Subject RIV: EH - Ecology, Behaviour

  11. Genetic diversity analysis of mitochondrial DNA control region in artificially propagated Chinese sucker Myxocyprinus asiaticus.

    Science.gov (United States)

    Wan, Yuan; Zhou, Chun-Hua; Ouyang, Shan; Huang, Xiao-Chen; Zhan, Yang; Zhou, Ping; Rong, Jun; Wu, Xiao-Ping

    2015-08-01

    The genetic diversity of the three major artificially propagated populations of Chinese sucker, an endangered freshwater fish species, was investigated using the sequences of mitochondrial DNA (mtDNA) control regions. Among the 89 individuals tested, 66 variable sites (7.26%) and 10 haplotypes were detected (Haplotype diversity Hd?=?0.805, Nucleotide diversity ??=?0.0287). In general, genetic diversity was lower in artificially propagated populations than in wild populations. This reduction in genetic diversity may be due to population bottlenecks, genetic drift and human selection. A stepping-stone pattern of gene flow was detected in the populations studied, showing much higher gene flow between neighbouring populations. To increase the genetic diversity, wild lineages should be introduced, and more lineages should be shared among artificially propagated populations. PMID:24409897

  12. Genetic diversity in the feline leukemia virus gag gene.

    Science.gov (United States)

    Kawamura, Maki; Watanabe, Shinya; Odahara, Yuka; Nakagawa, So; Endo, Yasuyuki; Tsujimoto, Hajime; Nishigaki, Kazuo

    2015-06-01

    Feline leukemia virus (FeLV) belongs to the Gammaretrovirus genus and is horizontally transmitted among cats. FeLV is known to undergo recombination with endogenous retroviruses already present in the host during FeLV-subgroup A infection. Such recombinant FeLVs, designated FeLV-subgroup B or FeLV-subgroup D, can be generated by transduced endogenous retroviral env sequences encoding the viral envelope. These recombinant viruses have biologically distinct properties and may mediate different disease outcomes. The generation of such recombinant viruses resulted in structural diversity of the FeLV particle and genetic diversity of the virus itself. FeLV env diversity through mutation and recombination has been studied, while gag diversity and its possible effects are less well understood. In this study, we investigated recombination events in the gag genes of FeLVs isolated from naturally infected cats and reference isolates. Recombination and phylogenetic analyses indicated that the gag genes often contain endogenous FeLV sequences and were occasionally replaced by entire endogenous FeLV gag genes. Phylogenetic reconstructions of FeLV gag sequences allowed for classification into three distinct clusters, similar to those previously established for the env gene. Analysis of the recombination junctions in FeLV gag indicated that these variants have similar recombination patterns within the same genotypes, indicating that the recombinant viruses were horizontally transmitted among cats. It remains to be investigated whether the recombinant sequences affect the molecular mechanism of FeLV transmission. These findings extend our understanding of gammaretrovirus evolutionary patterns in the field. PMID:25892717

  13. Genetic Variability and Diversity in Okra (Abelmoschus esculentus L. Moench

    Directory of Open Access Journals (Sweden)

    Pradip K. Akotkar, D.K. De and A.K. Pal

    2010-07-01

    Full Text Available In the present investigation an attempt has been made to evaluate the genetic variability of some yield contributingcharacters, and the genetic diversity in fifty genotypes of okra collected from the NBPGR New Delhi, India. Analysis ofvariance indicated significant difference among the genotypes for different morphological characters. High values of GCV,PCV, heritability and genetic advance (% of mean observed for number of fruiting nodes, number of ridges per fruit, plantheight and number of fruiting nodes indicated these characters might be controlled by additive genes. On the basis of D2analysis, the 50 genotypes could be grouped into 5 clusters. Cluster I had the highest number of genotypes (45 followed bycluster II (2. Remaining clusters were monogenotypic. Plant height had the highest contribution towards the total geneticdivergence. The highest intra-cluster distances were recorded in cluster I followed by cluster II. The maximum inter-clusterdistance was recorded between cluster IV and cluster II, followed by cluster V and cluster II. Among the 50 genotypes, IC-332454 showed the highest cluster mean for fruit yield per plant and number of fruits per plant. The genotypes which were inthe cluster V, III and II also exhibited significant performance for fruit yield per plant, number of fruits per plant and plantheight sequentially. On the basis of groupings of individual genotypes into different clusters, contribution of individualcharacter towards total genetic divergence, inter-cluster distance and cluster mean, the genotypes such as IC-9856B, IC-331157, IC-342075, IC-332453 and IC-43736 were found promising for using in the hybridization programme.

  14. Data Mining Using Neural–Genetic Approach: A Review

    OpenAIRE

    Parvez Rahi; Bhumika Gupta

    2014-01-01

    In the advance age of technology, there is an increasing availability of digital documents in various languages in various fields. Data mining is gaining popularity in field of knowledge discovery. Data mining is the knowledge discovery process by which we can analyze the large amounts of data from various data repositories and summarizing it into information useful to us. Due to its importance of extracting information/ knowledge from the large data repositories, data mining ...

  15. A Survey of Association Rule Mining Using Genetic Algorithm

    OpenAIRE

    Anubha Sharma

    2012-01-01

    Data mining is the analysis step of the "Knowledge Discovery in Databases" process, or KDD. It is the process that results in the discovery of new patterns in large data sets. It utilizes methods at the intersection of artificial intelligence, machine learning, statistics, and database systems. The overall goal of the data mining process is to extract knowledge from an existing data set and transform it into a human-understandable structure. In data mining, association rule learning is a popu...

  16. A Data Mining Approach to Discover Genetic and Environmental Factors involved in Multifactoral Diseases

    OpenAIRE

    Jourdan, L.; Dhaenens, C.; Talbi, E.G.; Gallina, S.

    2002-01-01

    In this paper, we are interested in discovering genetic factors that are involved in multifactorial diseases. Therefore, experiments have been achieved by the Biological Institute of Lille and a lot of data has been generated. To exploit this data, data mining tools are required and we propose a 2-phase optimization approach using a specific genetic algorithm. During the first step, we select significant features with a specific genetic algorithm. Then, during the second step, we cluster affe...

  17. Bioprospecting at former mining sites across Europe: microbial and functional diversity in soils.

    Science.gov (United States)

    Sprocati, Anna Rosa; Alisi, Chiara; Tasso, Flavia; Fiore, Alessia; Marconi, Paola; Langella, Francesca; Haferburg, Götz; Nicoara, Andrei; Neagoe, Aurora; Kothe, Erika

    2014-06-01

    The planetary importance of microbial function requires urgently that our knowledge and our exploitation ability is extended, therefore every occasion of bioprospecting is welcome. In this work, bioprospecting is presented from the perspective of the UMBRELLA project, whose main goal was to develop an integral approach for remediation of soil influenced by mining activity, by using microorganisms in association with plants. Accordingly, this work relies on the cultivable fraction of microbial biodiversity, native to six mining sites across Europe, different for geographical, climatic and geochemical characteristics but similar for suffering from chronic stress. The comparative analysis of the soil functional diversity, resulting from the metabolic profiling at community level (BIOLOG ECOPlates) and confirmed by the multivariate analysis, separates the six soils in two clusters, identifying soils characterised by low functional diversity and low metabolic activity. The microbial biodiversity falls into four major bacterial phyla: Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes, including a total of 47 genera and 99 species. In each soil, despite harsh conditions, metabolic capacity of nitrogen fixation and plant growth promotion were quite widespread, and most of the strains showed multiple resistances to heavy metals. At species-level, Shannon's index (alpha diversity) and Sørensen's Similarity (beta diversity) indicates the sites are indeed diverse. Multivariate analysis of soil chemical factors and biodiversity identifies for each soil well-discriminating chemical factors and species, supporting the assumption that cultured biodiversity from the six mining sites presents, at phylum level, a convergence correlated to soil factors rather than to geographical factors while, at species level, reflects a remarkable local characterisation. PMID:23775004

  18. 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.

  19. Hierarchical cluster analysis of genetic diversity in Maize germplasm

    Directory of Open Access Journals (Sweden)

    A. Subramanian and N. Subbaraman

    2010-07-01

    Full Text Available An experiment was conducted to analyze the genetic diversity among 38 maize germplasm accessions of the maizegermplasm bank of Department of Millets, TNAU, Coimbatore. Observations regarding 25 morphological traits wererecorded and the data matrix was used for estimation of Euclidian distance by Un-weighted Paired Group ArithmeticAverage (UPGMA method. Clustering was done by Sequential Agglomerative Hierarchical Non-overlapping (SAHNclustering. The genotypes were grouped in to four clusters. The grouping of the genotypes was not influenced by theirgeographical origin. Maximum dissimilarity was observed between the genotypes UMI 551 and UMI 696. Widely divergentclusters and genotypes were identified which could be further evaluated for their breeding value as parents and could beexploited in maize crop improvement.

  20. Genetic diversity of flavonoid content in leaf of hawthorn resources

    International Nuclear Information System (INIS)

    Hawthorn (Cratageus spp.) are important medicinal plants. Flavonoids are the main active ingredient in hawthorn. With the help of hawthorn leaf flavonoids efficient detection system, vitexin, rhamnosylvitexin, hyperin, rutin and quercetin of 122 hawthorn resources was precisely measured.The flavonoid contents of 10 hawthorn species were explicited. The comparation of flavonoids revealed the abundant genetic diversity of hawthorn flavones. Large variable coefficient has been observed among 5 flavonoid monomer traits. The coefficients of variation were 44.17%, 132.2%, 157.08%, 113.91% and 31.05 for Vitexin, Rhamnosylvitexin, Hyperoside, Rutin and Quercetin respectively. The sum of these 5 flavonoid monomer contents represented the total flavonoids in hawthorn. The total coefficients of variation was 44.01%. Some high-content-flavone and valuable leaf resources were found. This research could provide accurate date for further production, breeding and the effective use of medicinal resources. (author)

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

    Directory of Open Access Journals (Sweden)

    Angela R. Piergiovanni

    2010-05-01

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

  2. Genetic diversity of Gallibacterium anatis isolates from different chicken flocks

    DEFF Research Database (Denmark)

    Bojesen, A.M.; Torpdahl, Mia

    2003-01-01

    Amplified fragment length polymorphisms (AFLPs) were used to characterize the genotypic diversity of a total of 114 Gallibacterium anatis isolates originating from a reference collection representing 15 biovars from four countries and isolates obtained from tracheal and cloacal swab samples of chickens from an organic, egg-producing flock and a layer parent flock. A subset of strains was also characterized by pulsed-field gel electrophoresis and biotyping. The organic flock isolates were characterized by more than 94% genetic similarity, indicating that only a single clone was apparent in the flock. The layer parent flock isolates were grouped into two subclusters, each with similarity above 90%. One subcluster contained only tracheal isolates, while the other primarily included cloacal isolates. In conclusion, we show that AFLP analysis enables fingerprinting of G. anatis, which seems to have a clonal. population structure within natural populations. There was further evidence of clonal lineages, which may have adapted to different sites within the same animal.

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

    Science.gov (United States)

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

    2013-09-27

    Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a. PMID:23850438

  4. Genetic diversity and molecular typing of Listeria monocytogenes in China

    Directory of Open Access Journals (Sweden)

    Wang Yan

    2012-06-01

    Full Text Available Abstract Background Listeria monocytogenes can cause invasive diseases in humans and farm animals and is frequently isolated from dairy products and poultry. Listeriosis is uncommon in China but L. monocytogenes has been isolated from foods and food processing environments in China. However little is known of genetic diversity of Chinese L. monocytogenes isolates and their relationships with global isolates. Results Two hundred and twelve isolates of L. monocytogenes from food sources from 12 provinces/cities in China were analysed by serotyping, Pulsed Field Gel Electrophoresis (PFGE and Multi-locus Sequence Typing (MLST. The predominant serotypes are 1/2a, 1/2b and 1/2c accounting for 90.1% of the isolates. PFGE divided the isolates into 61 pulse types (PTs. Twenty nine PTs were represented by more than one isolates with PT GX6A16.0004 containing the most number of isolates. MLST differentiated the isolates into 36 STs, among which 15 were novel. The 3 most common STs were ST9 (29.1%, ST8 (10.7% and ST87 (9.2%, accounting for 49.0% of the isolates. Conclusions STs prevalent in other parts of the world are also prevalent in China including 7 STs (ST1-ST3, ST5, ST6, ST8, ST9 which caused maternal fetal infections or outbreaks, suggesting that these STs potentially can also cause severe human infections or outbreaks in China. Surveillance of these STs will provide important information for prevention of listeriosis. This study also enhances our understanding of genetic diversity of L. monocytogenes in China.

  5. Preliminary assessment of genetic diversity of Italian honey bees in the USA and Italy

    Science.gov (United States)

    Declining numbers of breeder queens and the concomitant loss of genetic diversity potentially could result in inbreeding and increased susceptibility to pests and disease in honey bees. Genetic diversity of commercial Italian bee colonies in the United States and Italy was assessed using microsatell...

  6. Microsatellite primers in Parietaria judaica (Urticaceae) to assess genetic diversity and structure in urban landscapes1

    OpenAIRE

    Bossu, Angèle; Bertaudière-Montès, Valérie; Dubut, Vincent; Manel, Stéphanie

    2014-01-01

    • Premise of the study: Urbanization is one of the main factors contributing to loss of genetic diversity, as the resulting landscape fragmentation and habitat loss induce species isolation. However, studies of genetic structure and diversity in urbanized landscapes are still rare. We characterized microsatellite primers for Parietaria judaica to study this environment.

  7. Assessment of genetic diversity and relationships among caladium cultivars and species using molecular markers

    Science.gov (United States)

    Caladium (Caladium hortulanum Birdsey) is an important aroid widely used in the ornamental plant industry. Concerns have been raised about possible loss of genetic diversity due to a drastic decline in the number of cultivars in the last century. This study assessed genetic diversity and relationshi...

  8. Molecular epidemiology and genetic diversity of Campylobacter jejuni in ruminants.

    Science.gov (United States)

    Grove-White, D H; Leatherbarrow, A J H; Cripps, P J; Diggle, P J; French, N P

    2011-11-01

    Multi-locus sequence typing was performed on 1003 Campylobacter jejuni isolates collected in a 2-year longitudinal study of 15 dairy farms and four sheep farms in Lancashire, UK. There was considerable farm-level variation in occurrence and prevalence of clonal complexes (CC). Clonal complexes ST61, ST21, ST403 and ST45 were most prevalent in cattle while in sheep CC ST42, ST21, ST48 and ST52 were most prevalent. CC ST45, a complex previously shown to be more common in summer months in human cases, was more prevalent in summer in our ruminant samples. Gene flow analysis demonstrated a high level of genetic heterogeneity at the within-farm level. Sequence-type diversity was greater in cattle compared to sheep, in cattle at pasture vs. housed, and in isolates from farms on the Pennines compared to the Southern Fylde. Sequence-type diversity was greatest in isolates belonging to CC ST21, ST45 and ST206. PMID:21134320

  9. Assessment of genetic diversity within sour cherry clones

    DEFF Research Database (Denmark)

    Clausen, Sabine Karin; Andersen, Sven Bode

    2013-01-01

    Harvested yields of sour cherry (Prunus cerasus) cultivar ‘Stevnsbaer’ clones grown in Denmark have been highly variable over the years, yet some propagated derived trees selected from within the two widely grown clones of ‘Stevnsbaer’ clone ‘Birgitte’ and clone ‘Viki’ have consistently produced higher yields. A number of these selections were evaluated for yield and genomic differences to investigate variation between and within the ‘Birgitte’ and ‘Viki’ clones. Variation in yield was mainly found at the clonal level. The clone ‘Viki’ was found to be the highest yielding with an average of 20 kg/tree compared to only 7.0 kg/tree from clone ‘Birgitte’. The selected trees derived from within clone ‘Birgitte’ had a significantly higher, average yield over 7 years compared to the original ‘Birgitte’, indicating that such within-clone selection may be a possible approach for selection 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 change.

  10. Genetic diversity of Leishmania infantum field populations from Brazil

    Scientific Electronic Library Online (English)

    Marcela, Segatto; Lucas Secchim, Ribeiro; Dorcas Lamounier, Costa; Carlos Henrique Nery, Costa; Márcia Rosa de, Oliveira; Sílvio Fernando Guimarães, Carvalho; Andréa Mara, Macedo; Helder Magno Silva, Valadares; Reynaldo, Dietze; Cristiana Ferreira Alves de, Brito; Elenice Moreira, Lemos.

    2012-02-01

    Full Text Available Leishmania infantum (syn. Leishmania chagasi) is the etiological agent of visceral leishmaniasis (VL) in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular metho [...] ds, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.

  11. Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.

    Science.gov (United States)

    Dubey, J P; Choudhary, S; Tilahun, G; Tiao, N; Gebreyes, W A; Zou, X; Su, C

    2013-09-01

    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 bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia. PMID:23411374

  12. Genetic diversity of pestivirus isolates in cattle from Western Austria.

    Science.gov (United States)

    Hornberg, Andrea; Fernández, Sandra Revilla; Vogl, Claus; Vilcek, Stefan; Matt, Monika; Fink, Maria; Köfer, Josef; Schöpf, Karl

    2009-03-30

    The genetic diversity of bovine viral diarrhoea virus (BVDV) isolates in infected cattle from Tyrol and Vorarlberg (Austria) was investigated. Blood samples were collected within the compulsory Austrian BVDV control programme during 2005 and 2006. The 5'-untranslated region (5'-UTR) and partially the N-terminal autoprotease (N(pro)) were amplified by one-step reverse transcriptase-polymerase chain reaction (RT-PCR) and the PCR products were subsequently sequenced. Phylogenetic analysis based on 5'-UTR and N(pro) sequences demonstrated that almost all isolates (307/310) were of the BVDV-1 genotype. They were clustered into eight different subtypes, here listed by their frequency of occurrence: BVDV-1h (143), BVDV-1f (79), BVDV-1b (41), BVDV-1d (28), BVDV-1e (6), BVDV-1a (4), BVDV-1g (3) and BVDV1-k (3). Two pestivirus isolates were typed as BVDV-2 and one isolate as BDV closely related to Gifhorn strain (BDV-3). Correlation among isolates could only be observed at the farm level, i.e., within a herd. However, no correlation between the genetic and geographical distances could be observed above the farm level. Because of the wide distribution of certain BVDV-1 subtypes and the low prevalence of herd-specific strains, a determination of tracing routes of infection was not possible. Furthermore, recombination events were not detected. PMID:19019571

  13. 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.

  14. Consumer perspectives on genetic testing, research and services for ethnoculturally diverse populations.

    Science.gov (United States)

    Weiss, J O; Allen, L; Marche-Escola, S; Savoy, M; Rosemary; Yang, S

    1998-01-01

    A panel of individuals from diverse ethnocultural backgrounds and representing a variety of genetic disorders presented their consumer perspectives on genetic programs, testing and services. Their remarks emphasized how misunderstanding and miscommunication between health care professionals and many of the populations for whom they provide services can lead to unfilled genetic service needs. Panelists recommended that health care professionals become more aware and knowledgeable about the diversity of customs, beliefs and cultures of those receiving their services. Only by building a foundation of trust and mutual respect will genetic testing, research and services become more accessible to individuals from diverse populations, their families and their communities. PMID:15178971

  15. 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.

  16. Pattern of genetic diversity among Fusarium wilt resistant castor germplasm accessions (Ricinus communis L.

    Directory of Open Access Journals (Sweden)

    K. Anjani

    2010-03-01

    Full Text Available Wilt caused by Fusarium oxysporum f.sp. ricini (Wr Gordon is one of the major yield losing diseases in castor.Cultivating wilt resistant cultivars is an effective strategy to control the disease. Utilization of diverse sources ofstable resistance is a prerequisite for durable resistance breeding. The experiment was conducted to identifygenetically diverse resistant sources in castor germplasm. Genetic diversity among 20 identified wilt resistantgermplasm was assessed using multivariate classificatory methods. Wide genetic diversity was demonstratedamong these accessions. These accessions are valuable in wilt resistance breeding programme. They wouldserve as base diverse material for wilt resistance breeding, wilt resistant genepool construction and moleculartagging of resistant genes.

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

    OpenAIRE

    Malice, Marie; Bizoux, Jean-philippe; Blas, Raul; Baudoin, Jean-pierre

    2010-01-01

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

  18. High Genetic Diversity in Geographically Remote Populations of Endemic and Widespread Coral Reef Angelfishes (genus: Centropyge)

    OpenAIRE

    Munday, Philip L.; Jones, Geoffrey P.; Hobbs, Jean-Paul A.; Lynne van Herwerden; Dean R. Jerry

    2013-01-01

    In the terrestrial environment, endemic species and isolated populations of widespread species have the highest rates of extinction partly due to their low genetic diversity. To determine if this pattern holds in the marine environment, we examined genetic diversity in endemic coral reef angelfishes and isolated populations of widespread species. Specifically, this study tested the prediction that angelfish (genus: Centropyge) populations at Christmas and Cocos Islands have low genetic divers...

  19. Genetic Structure and Diversity of the Giant Frog (Limnonectes blythii) in Northern Thailand

    OpenAIRE

    C. Suwannapoom; W. Wongkham; N. Sitasuwan; C. Phalaraksh; T. Kunpradid; M. Osathanunkul; W. Kutanan; W. Phairuang; Chomdej, S.

    2012-01-01

    The aim of this study is to analyse genetic diversity, structure and differentiation of the giant frogs (Limnonectes blythii). One hundred and sixty four individuals from 4 populations in Mae Hong Son Province, Thailand were used for the analysis of genetic polymorphism at 7 microsatellite loci. The collection showed considerable polymorphism with observed number of alleles per locus ranging for seven different loci, with an average of 3.4 alleles per locus. Mean genetic diversity of the four...

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

    OpenAIRE

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

    2013-01-01

    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 amon...

  1. Assessing the contribution of breeds to genetic diversity in conservation schemes

    Directory of Open Access Journals (Sweden)

    Groenen Martien AM

    2002-09-01

    Full Text Available Abstract The quantitative assessment of genetic diversity within and between populations is important for decision making in genetic conservation plans. In this paper we define the genetic diversity of a set of populations, S, as the maximum genetic variance that can be obtained in a random mating population that is bred from the set of populations S. First we calculated the relative contribution of populations to a core set of populations in which the overlap of genetic diversity was minimised. This implies that the mean kinship in the core set should be minimal. The above definition of diversity differs from Weitzman diversity in that it attempts to conserve the founder population (and thus minimises the loss of alleles, whereas Weitzman diversity favours the conservation of many inbred lines. The former is preferred in species where inbred lines suffer from inbreeding depression. The application of the method is illustrated by an example involving 45 Dutch poultry breeds. The calculations used were easy to implement and not computer intensive. The method gave a ranking of breeds according to their contributions to genetic diversity. Losses in genetic diversity ranged from 2.1% to 4.5% for different subsets relative to the entire set of breeds, while the loss of founder genome equivalents ranged from 22.9% to 39.3%.

  2. Genetic recolonization of mangrove: genetic diversity still increasing in the Mekong Delta 30 years after Agent Orange

    OpenAIRE

    Arnaud-haond, S.; Duarte, C. M.; Teixeira, S.; Massa, S. I.; Terrados, J.; Tri, N. H.; Hong, P. N.; Serra?o, Ester

    2009-01-01

    The widespread use of Agent Orange (a mixture of phenoxyl herbicides) over Southern Vietnam by US Forces led to the decimation of mangrove forests in the Mekong Delta. Mangrove trees Avicennia alba were sampled across the Mekong Delta; their age was assessed using models based on internode growth and samples were genotyped for 6 microsatellite loci. The evolution of genetic diversity over time elapsed since local extinction was reconstructed and compared with the genetic diversity of an unaff...

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

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos

    2014-01-01

    There is a general trend of biodiversity loss at global, regional, national and local levels. To monitor this trend, international policy processes have created a wealth of indicators over the last two decades. However, genetic diversity indicators are regrettably absent from comprehensive bio-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 diversity. Revealing benefits of genetic diversity related to ecosystem services is complex, but current trends in plantation performance offer the possibility of an indicator of benefit. Response indicators are generally much easier to define, because recognition and even quantification of, e.g., research, education, breeding, conservation, and regulation actions and programs are relatively straightforward. Only state indicators can reveal genetic patterns and processes, which are fundamental for maintaining genetic diversity. Indirect indicators of pressure, benefit, or response should therefore not be used independently of state indicators. A coherent set of indicators covering diversity-productivity-knowledge-management based on the genecological approach is proposed for application on appropriate groupsof tree species in the wild and in cultivation worldwide. These indicators realistically reflect the state, trends and potentials of the world's tree genetic resources to support sustainable growth. The state of the genetic diversity will be based on trends in population distributions and diversity patterns for selected species. The productivity of the genetic resource of trees in current use will reflect the possible potential of mobilizing the resource further. Trends in knowledge will underpin the potential capacity for development of the resource and current management of the genetic resource itself will reveal how well we are actually doing and where improvements are required.

  4. Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Gowda Cholenahalli LL

    2008-10-01

    Full Text Available Abstract Background Plant genetic resources (PGR are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA, 117 in South and South East Asia (SSEA, and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53% than kabuli (46%, while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78% of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. Conclusion The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s, and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.

  5. Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-07-06

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

  6. Gut microbiology - broad genetic diversity, yet specific metabolic niches.

    Science.gov (United States)

    John Wallace, R

    2008-05-01

    Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the 'mimosine story' in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability. PMID:22443591

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

    Scientific Electronic Library Online (English)

    Janaina Azevedo, Martuscello; Thiago Gomes dos Santos, Braz; Liana, Jank; Daniel de Noronha Figueiredo Vieira da, Cunha; Dilermando Miranda da, Fonseca.

    1975-19-01

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

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

    Directory of Open Access Journals (Sweden)

    Grünwald Niklaus J

    2011-02-01

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

  9. 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.

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

    Science.gov (United States)

    Küpper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sérgio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

    2011-01-01

    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. PMID:21637550

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

    Scientific Electronic Library Online (English)

    Juliana Morini Küpper Cardoso, Perseguini; Alisson Fernando, Chioratto; Maria Imaculada, Zucchi; Carlos Augusto, Colombo; Sérgio Augusto Moraes, Carbonell; Jorge Mauricio Costa, Mondego; Rodrigo, Gazaffi; Antonio Augusto Franco, Garcia; Tatiana de, Campos; Anete Pereira de, Souza; Luciana Benchimol, Rubiano.

    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 be [...] an, 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.

  12. Inter Simple Sequence Repeat Fingerprints for Assess Genetic Diversity of Tunisian Garlic Populations

    Directory of Open Access Journals (Sweden)

    Naouel Jabbes

    2011-11-01

    Full Text Available Garlic (Allium sativum L. that is cultivated in Tunisia is heterogeneous and unclassified with no registered local cultivars. At present, the level of genetic diversity in Tunisian garlic is almost unknown. Inter Simple Sequence Repeats (ISSR genetic markers were therefore used to assess the genetic diversity and its distribution in 31 Tunisian garlic accessions with 4 French classified clones used as control. It was the first time that ISSR markers were used to detect diversity in garlic. Seventeen ISSR primers were screened; seven primers detected 73 polymorphic bands. A high level of polymorphic loci (p was found in Tunisian populations (54%. Nei’s total genetic diversity coefficient was 0.45 and 0.34 respectively for Tunisian and French garlic. Genetic distances observed between Tunisian accessions, ranged between 38.4 and 78.1%. Factor analysis of distances’ table (AFTD did not classify accessions on the base of geographical origin or morpho-physiological characters, particularly bolting ability, but confirmed the appurtenance of analyzed accessions to sativum botanical subspecies. There was sufficient diversity detected to start a national collection of garlic germplasm which is crucial for the conservation of genetic diversity and its valorization. Keywords: Allium sativum L., ISSR markers, genetic diversity, Tunisian garlic populations.

  13. Genetic Algorithm Calibration of Probabilistic Cellular Automata for Modeling Mining Permit Activity

    Science.gov (United States)

    Louis, S.J.; Raines, G.L.

    2003-01-01

    We use a genetic algorithm to calibrate a spatially and temporally resolved cellular automata to model mining activity on public land in Idaho and western Montana. The genetic algorithm searches through a space of transition rule parameters of a two dimensional cellular automata model to find rule parameters that fit observed mining activity data. Previous work by one of the authors in calibrating the cellular automaton took weeks - the genetic algorithm takes a day and produces rules leading to about the same (or better) fit to observed data. These preliminary results indicate that genetic algorithms are a viable tool in calibrating cellular automata for this application. Experience gained during the calibration of this cellular automata suggests that mineral resource information is a critical factor in the quality of the results. With automated calibration, further refinements of how the mineral-resource information is provided to the cellular automaton will probably improve our model.

  14. Genetic diversity is positively associated with fine-scale momentary abundance of an invasive ant.

    Science.gov (United States)

    Gruber, Monica A M; Hoffmann, Benjamin D; Ritchie, Peter A; Lester, Philip J

    2012-09-01

    Many introduced species become invasive despite genetic bottlenecks that should, in theory, decrease the chances of invasion success. By contrast, population genetic bottlenecks have been hypothesized to increase the invasion success of unicolonial ants by increasing the genetic similarity between descendent populations, thus promoting co-operation. We investigated these alternate hypotheses in the unicolonial yellow crazy ant, Anoplolepis gracilipes, which has invaded Arnhem Land in Australia's Northern Territory. We used momentary abundance as a surrogate measure of invasion success, and investigated the relationship between A. gracilipes genetic diversity and its abundance, and the effect of its abundance on species diversity and community structure. We also investigated whether selected habitat characteristics contributed to differences in A. gracilipes abundance, for which we found no evidence. Our results revealed a significant positive association between A. gracilipes genetic diversity and abundance. Invaded communities were less diverse and differed in structure from uninvaded communities, and these effects were stronger as A. gracilipes abundance increased. These results contradict the hypothesis that genetic bottlenecks may promote unicoloniality. However, our A. gracilipes study population has diverged since its introduction, which may have obscured evidence of the bottleneck that would likely have occurred on arrival. The relative importance of genetic diversity to invasion success may be context dependent, and the role of genetic diversity may be more obvious in the absence of highly favorable novel ecological conditions. PMID:23139870

  15. Genetic diversity and genomic distribution of homologs encoding NBS-LRR disease resistance proteins in sunflower.

    Science.gov (United States)

    Radwan, Osman; Gandhi, Sonali; Heesacker, Adam; Whitaker, Brett; Taylor, Chris; Plocik, Alex; Kesseli, Richard; Kozik, Alexander; Michelmore, Richard W; Knapp, Steven J

    2008-08-01

    Three-fourths of the recognition-dependent disease resistance genes (R-genes) identified in plants encode nucleotide binding site (NBS) leucine-rich repeat (LRR) proteins. NBS-LRR homologs have only been isolated on a limited scale from sunflower (Helianthus annuus L.), and most of the previously identified homologs are members of two large NBS-LRR clusters harboring downy mildew R-genes. We mined the sunflower EST database and used comparative genomics approaches to develop a deeper understanding of the diversity and distribution of NBS-LRR homologs in the sunflower genome. Collectively, 630 NBS-LRR homologs were identified, 88 by mining a database of 284,241 sunflower ESTs and 542 by sequencing 1,248 genomic DNA amplicons isolated from common and wild sunflower species. DNA markers were developed from 196 unique NBS-LRR sequences and facilitated genetic mapping of 167 NBS-LRR loci. The latter were distributed throughout the sunflower genome in 44 clusters or singletons. Wild species ESTs were a particularly rich source of novel NBS-LRR homologs, many of which were tightly linked to previously mapped downy mildew, rust, and broomrape R-genes. The DNA sequence and mapping resources described here should facilitate the discovery and isolation of recognition-dependent R-genes guarding sunflower from a broad spectrum of economically important diseases. Sunflower nucleotide and amino acid sequences have been deposited in DDBJ/EMBL/GenBank under accession numbers EF 560168-EF 559378 and ABQ 58077-ABQ 57529. PMID:18553106

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

    Directory of Open Access Journals (Sweden)

    M.J. Hasan

    2014-06-01

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

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

    Scientific Electronic Library Online (English)

    Bassam, Al- Safadi; Hussam, Faouri; Rana, Elias.

    2014-12-01

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

  18. Prevalence and genetic diversity of bovine kobuvirus in China.

    Science.gov (United States)

    Chang, Jitao; Wang, Qian; Wang, Fang; Jiang, Zhigang; Liu, Yue; Yu, Li

    2014-06-01

    A total of 166 faecal specimens from diarrheic cattle were collected in China for detection of bovine kobuvirus (BKV) by reverse transcription PCR (RT-PCR) targeting the region a portion of the 3D nonstructural protein, with an amplicon size of 631 bp. The RNA corresponding to the BKV 3D region was detected in 34.9 % of faecal samples (58/166) in four major dairy-cattle-production areas in China, and sequence analysis based on the partial 3D sequences (35/58) indicated that the Chinese BKVs shared 88.9-96.2 % nucleotide sequence identity to BKV reference strains. Further phylogenetic analysis based on the complete VP1-encoding sequences (17/35) revealed that the Chinese BKVs shared 81-83.4 % nucleotide sequence identity to the U-1 strain, and these Chinese BKV strains, together with the U-1 strain, are apparently divided into four lineages, representing four genotypes of BKV, designated as A, B, C and D. Our results show that BKV infection is widely distributed, with high genetic diversity in China. PMID:24366549

  19. A Novel Association Rules Method Based on Genetic Algorithm and Fuzzy Set Strategy for Web Mining

    Directory of Open Access Journals (Sweden)

    Chunlai Chai

    2010-09-01

    Full Text Available The use of fuzzy techniques has been considered to be one of the key components of data mining systems because of the affinity with human knowledge representation. A hybridization of fuzzy sets with genetic algorithms is described for Web mining in this paper. It is based on a hybrid technique that combines the strengths of rough set theory and genetic algorithm. The algorithm through the introduction of selection operators, crossover operators and mutation operators, improves the global convergence speed, and can effectively avoid prematurity. The role of fuzzy sets in handling the different types of uncertainties/impreciseness is highlighted. Experimental results indicate that this adaptive method significantly improves the performance in Web mining.

  20. [Genetic structure and genetic diversity of Artemisia annua varieties (strains) populations based on SCoT markers].

    Science.gov (United States)

    Chen, Da-xia; Cui, Guang-lin; Zhang, Xue; Li, Long-yun

    2014-09-01

    To reveal the genetic diversity and genetic structure in Artemisia annua varieties (strains) populations, we detected the genetic polymorphism within and among eight varieties (strains) populations (192 individuals) by the approach of Start Codon Targeted Polymorphism (SCoT). The associated genetic parameters were calculated by POPGENE1.31 and the relationship was constructed based on UPGMA method. The results showed that, using 20 screened primers, a total of 145 bands were produced, of which 122 were polymorphic loci. At species level, there was a high level of genetic diversity among eight varieties (strains) populations (PPB = 84.1% ,H = 0.217 3 and H(sp) = 0.341 9). However, at the variety (strains) population level, genetic diversity was lower, the average of genetic parameters was PPB = 41.9%, H = 0.121 5, H(pop) = 0.186 8. The Nei's genetic differentiation coefficient was 0.441 0, indicate that most of the genetic variation in this species existed within the variety populations. The gene flow (N(m) = 0.633 9) was less among populations, indicating that the degree of genetic differentiation was higher. Genetic similarity coefficient were changed from 0.755 1 to 0.985 7. By clustering analysis, eight varieties (strains) were clustered into two major categories and it was also showed the same or similar genetic background varieties (strains) have a tendency to gather in the same group. Results suggest that, in variety breeding, breeders should strengthen the exchange of bred germplasm and increase mutual penetration of excellent genes, which would broaden the genetic base of A. annua. PMID:25522606

  1. Comparative genetic diversity and genetic structure of three chinese silkworm species Bombyx mori L. (Lepidoptera: Bombycidae), Antheraea pernyi Guérin-Meneville and Samia cynthia ricini donovan (Lepidoptera: Saturniidae)

    Scientific Electronic Library Online (English)

    Yan-Qun, Liu; Li, Qin; Yu-Ping, li; Huan, Wang; Run-Xi, Xia; Yong-Hong, Qi; Xi-Sheng, li; Cheng, Lu; Zhong-Huai, Xiang.

    2010-12-01

    Full Text Available The genetic diversity and genetic structure of three Chinese silkworm species Bombyx mori L., Antheraea pernyi Guérin-Meneville and Samia cynthia ricini Donovan were comparatively assessed based on RAPD markers. At the species level, A. pernyi and B. mori showed high levels of genetic diversity, whe [...] reas S. cynthia ricini showed low level of genetic diversity. However, at the strain level, A. pernyi had relatively highest genetic diversity and B. mori had lowest genetic diversity. Analysis of molecular variance (AMOVA) suggested that 60% and 72% of genetic variation resided within strains in A. pernyi and S. cynthia ricini, respectively, whereas only 16% of genetic variation occurred within strains in B. mori. In UPGMA dendrogram, individuals of A. pernyi and B. mori formed the strain-specific genetic clades, whereas those of S. cynthia ricini were distributed in a mixed way. The implications of these results for the conservation and utilization in breeding programs of three silkworm species are discussed.

  2. Comparative genetic diversity and genetic structure of three Chinese silkworm species Bombyx mori L. (Lepidoptera: Bombycidae), Antheraea pernyi Guérin-Meneville and Samia cynthia ricini Donovan (Lepidoptera: Saturniidae).

    Science.gov (United States)

    Liu, Yan-Qun; Qin, Li; Li, Yu-Ping; Wang, Huan; Xia, Run-Xi; Qi, Yong-Hong; Li, Xi-Sheng; Lu, Cheng; Xiang, Zhong-Huai

    2010-01-01

    The genetic diversity and genetic structure of three Chinese silkworm species Bombyx mori L., Antheraea pernyi Guérin-Meneville and Samia cynthia ricini Donovan were comparatively assessed based on RAPD markers. At the species level, A. pernyi and B. mori showed high levels of genetic diversity, whereas S. cynthia ricini showed low level of genetic diversity. However, at the strain level, A. pernyi had relatively highest genetic diversity and B. mori had lowest genetic diversity. Analysis of molecular variance (AMOVA) suggested that 60% and 72% of genetic variation resided within strains in A. pernyi and S. cynthia ricini, respectively, whereas only 16% of genetic variation occurred within strains in B. mori. In UPGMA dendrogram, individuals of A. pernyi and B. mori formed the strain-specific genetic clades, whereas those of S. cynthia ricini were distributed in a mixed way. The implications of these results for the conservation and utilization in breeding programs of three silkworm species are discussed. PMID:21271066

  3. Assessment of genetic diversity of Typha angustifolia in the development of cattail stands

    Directory of Open Access Journals (Sweden)

    Jae Geun Kim*

    2012-03-01

    Full Text Available Typha angustifolia has ecological characteristics of clonal growth similar to Phragmites australis. The plant spreads byclonal growth and seed dispersal. In this study, for the three stands which have different settlement age at the Baksiljiwetland in Korea, genetic diversity was estimated by random amplification of polymorphic DNA analysis to evaluate thechange in genetic diversity of T. angustifolia during stand development in the same population. Stand (ST 1 was the oldestand ST 4 was the youngest. ST 5 was in a small ditch out of the Baksilji. Although the ST 1, ST 2, and ST 3 did not differsignificantly in vegetational or physical environment, the genetic diversity estimated according to Nei’s gene diversity(h and the Shannon index (i increased in the order of ST 1 < ST 2 < ST 3 contrary to formative age. The genetic diversityof ST 4 was much higher than that of the other three stands. ST 4 has similar abiotic environmental conditions withslight T. angustifolia dominance, and seems to be in the early establishment stage. ST 5 differed from the other stands invegetational and soil environments, which can result in stressful cattail conditions. Even though the ST 5 stand was notyounger than the ST 4 stand, ST 5 showed the highest genetic diversity. Our results indicate that after early settlement ofthe T. angustifolia population, genetic diversity within the species decreased over time and that the decreasing pattern ofgenetic diversity within T. angustifolia stands is not likely to occur under stressful conditions.

  4. Genetic diversity and population structure of Plasmodium vivax isolates from Sudan, Madagascar, French Guiana and Armenia.

    Science.gov (United States)

    Menegon, Michela; Durand, Patrick; Menard, Didier; Legrand, Eric; Picot, Stéphane; Nour, Bakri; Davidyants, Vladimir; Santi, Flavia; Severini, Carlo

    2014-10-01

    Polymorphic genetic markers and especially microsatellite analysis can be used to investigate multiple aspects of the biology of Plasmodium species. In the current study, we characterized 7 polymorphic microsatellites in a total of 281 Plasmodium vivax isolates to determine the genetic diversity and population structure of P. vivax populations from Sudan, Madagascar, French Guiana, and Armenia. All four parasite populations were highly polymorphic with 3-32 alleles per locus. Mean genetic diversity values was 0.83, 0.79, 0.78 and 0.67 for Madagascar, French Guiana, Sudan, and Armenia, respectively. Significant genetic differentiation between all four populations was observed. PMID:25102032

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

    Directory of Open Access Journals (Sweden)

    Pereira Albano

    2001-05-01

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

  6. Genetic Diversity of Some Mediterranean Populations of the Cultivated Alfalfa (Medicago sativa L. Using SSR Markers

    Directory of Open Access Journals (Sweden)

    L. Touil

    2008-01-01

    Full Text Available This species study was to investigate the differentiation level among 26 populations wich 12 are locals originating from the Tunisian South and 14 introduced from Italy, Austerely, France and Morocco with two SSR markers. These highly polymorphic and co dominant markers, together with recent population genetic statistic extended to autotetraploids, offer tools to analyse genetic diversity in alfalfa. The number of alleles per locus varied between 8 and 9. The genetic similarity between these various populations is estimated by the index of Rogers and Tanimoto. Genetic diversity is analysed by two statistical procedures: Hierarchical classification and Correspondence Factorial Analysis (CFA. Four large groups were obtained.

  7. Effects of Habitat Fragmentation on Population Genetic Diversity of Endangered Plant Euonymus chloranthoides Yang

    Directory of Open Access Journals (Sweden)

    HU Shi-jun

    2013-03-01

    Full Text Available Habitat fragmentation is the main threat to the survival of many species, species response to habitat fragmentation differently; the information of genetic diversity has great significance to protect species. Euonymus chloranthoides Yang is an endangered plant endemic to Chongqing. The population of this plant in Jinyun Mountain has been fragmented seriously because of the highway construction, tour development and so on. Some populations are small and isolated. Four populations in Jinyun maintain were selected to study the effects of habitat fragmentation on population genetic diversity of E. chloranthoides. The results of ISSR experiment show that the GST is 0.406 2 which means 59.38% of the genetic diversity exists within the population, and 40.62% of the genetic diversity exists among populations, the level of population differentiation is high due to long isolation, low dispersal distance of pollen and seed. The PPB of the population with highest genetic diversity is 64.58%, The genetic diversity of Banzigou population, the smallest one, is the lowest, and the PPB of this population is 29.17%, which means small population do harm to the maintenance of genetic diversity. The gene flow (Nm is 0.730 9, which is difficult to counteract the differentiation caused by genetic drift. Cluster analysis show he nearest populations cluster first, which mean that the genetic differentiation is affected by spatial distance. In-situ conservation should be strengthened to protect the small populations, and gene flow among populations should be improved to prevent the further genetic loss of small populations.

  8. Genetic diversity and differentiation of Mongolian indigenous cattle populations

    International Nuclear Information System (INIS)

    Livestock production plays an important role in Mongolian economy. Over the last decade it has contributed to around 80-90% of the gross domestic agricultural products and to 30% of the revenues generated from exportations. Cattle is one of the five traditional and most important livestock species of Mongolia together with horse, sheep, goat and camel. Out of a total of 1.57 millions Mongolian cattle, 1.55 millions supposedly belong to three indigenous Bos taurus cattle breeds, namely Mongol, Selenge and Khalkhun Golun, all herded under extensive pastoral systems. Indigenous Mongolian cattle are generally small but look sturdy and strong. They have a well-off coat of hair, solid forward looking shoulders and short stubby snouts, and they are used for meat, milk and transport. Beef production contributes to 30% of the total meat supply in Mongolia. The Mongol breed is by the far the commonest with 1.53 million animals and it is found almost throughout the country. The Selenge breed, found in Selenge province and numbering 9000 heads, was developed in middle of the 20th century by crossing the Kazakh Whiteheaded with the local Mongol cattle. The Khalkhun Golun breed was developed from local Mongol cattle and it is distributed in Eastern and Suhbaatar provinces with about 10,000 heads. Until now, to the best of our knowledge, only a single population of Mongolian cattle has been studied with microsatellite DNA markers and no information is available on the genetic relatirmation is available on the genetic relationship between the Mongolian indigenous cattle breeds. In this study, we collected samples from two populations of the Mongol cattle (sampled at Ikhtamir soum in North Hangay province and Tsogt soum in Govi Altay province) and one population of the Khalkhun Golun cattle (sampled at Tumentsogt soum in Suhbaatar province). Samples were characterised with nine microsatellite markers MGTG4B, ILSTS005, ILSTS006, ILSTS008, ILSTS023, ILSTS028, ILSTS036, ILSTS050 and ILSTS103. To assess the genetic diversity and relationship of Mongolian cattle populations with breeds from neighboring countries and exotic breeds, data from the ILRI cattle genotyping database were included. More particularly, we used previously obtained data from Asian taurine (Hanwoo, Yanbian and Japanese Black), two European taurine (Friesian and Charolais), two African taurine (Baoule and N'Dama) and two zebu breeds (Sahiwal and Ongole). For each breed, observed (Ho) and expected (He) heterozygosities as well as the mean number of alleles (MNA) across the nine loci were calculated between pairs of populations were also estimated and a UPGMA tree was constructed. The heterozygosities (Ho and He) in Mongolian cattle populations are similar to those obtained in Northeast Asian taurine breeds but the values are higher compared to the ones obtained for the European and African taurine breeds. The Mongol cattle in North Hangay has the highest corrected MNA value (all animals or 28 animals only). The UPGMA tree, built with the Reynolds' genetic distances, shows all six Northeast Asian cattle populations clustering into one group linked to the two European taurine breed. Interestingly, the two populations of the Mongol cattle are not closely related to each other. However, bootstrap values between the Northeast Asian taurine breeds, with the exception of the bootstrap value between Yanbian and Hanwoo, are relatively low, therefore the relationship between the Northeast Asian populations should be taken with caution. Fst values between the three Mongolian cattle populations are significant (P < 0.01), with the Govi Altay population being more differentiated from the North Hangay population than from the Khalkhun Golun breed (data not shown). Our data suggest that the traditional classification of Govi Altay and North Hangay populations as one breed, the Mongol cattle, should be revisited

  9. High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis.

    Science.gov (United States)

    Song, Bao-Hua; Mitchell-Olds, Thomas

    2007-10-01

    Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to its widespread congener, Boechera stricta, which shares similar life history and mating system. Despite its rarity, B. fecunda had levels of genetic diversity similar to B. stricta for both microsatellites and nucleotide polymorphism. Populations of B. fecunda are highly differentiated, with a majority of genetic diversity existing among populations (F(ST) = 0.57). Differences in molecular diversity and allele frequencies between western and eastern population groups suggest they experienced very different evolutionary histories. PMID:17784916

  10. Present status of genetic diversity of Potamogeton praelongus populations in the Czech Republic.

    Czech Academy of Sciences Publication Activity Database

    Kitner, M.; Prausová, R.; Adamec, Lubomír

    2013-01-01

    Ro?. 53, ?. 1 (2013), s. 73-86. ISSN 0079-2047 Institutional support: RVO:67985939 Keywords : genetic diversity * micropopulation * conservation Subject RIV: EF - Botanics Impact factor: 0.388, year: 2013

  11. DEVELOPMENT OF AQUATIC MODELS FOR TESTING THE RELATIONSHIP BETWEEN GENETIC DIVERSITY AND POPULATION EXTINCTION RISK

    Science.gov (United States)

    The relationship between population adaptive potential and extinction risk in a changing environment is not well understood. Although the expectation is that genetic diversity is directly related to the capacity of populations to adapt, the statistical and predictive aspects of ...

  12. 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.

  13. Astrophysical data mining with GPU. A case study: genetic classification of globular clusters

    CERN Document Server

    Cavuoti, Stefano; Brescia, Massimo; Paolillo, Maurizio; Pescape', Antonio; Longo, Giuseppe; Ventre, Giorgio

    2013-01-01

    We present a multi-purpose genetic algorithm, designed and implemented with GPGPU / CUDA parallel computing technology. The model was derived from our CPU serial implementation, named GAME (Genetic Algorithm Model Experiment). It was successfully tested and validated on the detection of candidate Globular Clusters in deep, wide-field, single band HST images. The GPU version of GAME will be made available to the community by integrating it into the web application DAMEWARE (DAta Mining Web Application REsource (http://dame.dsf.unina.it/beta_info.html), a public data mining service specialized on massive astrophysical data. Since genetic algorithms are inherently parallel, the GPGPU computing paradigm leads to a speedup of a factor of 200x in the training phase with respect to the CPU based version.

  14. Astrophysical data mining with GPU. A case study: Genetic classification of globular clusters

    Science.gov (United States)

    Cavuoti, S.; Garofalo, M.; Brescia, M.; Paolillo, M.; Pescape', A.; Longo, G.; Ventre, G.

    2014-01-01

    We present a multi-purpose genetic algorithm, designed and implemented with GPGPU/CUDA parallel computing technology. The model was derived from our CPU serial implementation, named GAME (Genetic Algorithm Model Experiment). It was successfully tested and validated on the detection of candidate Globular Clusters in deep, wide-field, single band HST images. The GPU version of GAME will be made available to the community by integrating it into the web application DAMEWARE (DAta Mining Web Application REsource, http://dame.dsf.unina.it/beta_info.html), a public data mining service specialized on massive astrophysical data. Since genetic algorithms are inherently parallel, the GPGPU computing paradigm leads to a speedup of a factor of 200× in the training phase with respect to the CPU based version.

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

    OpenAIRE

    Hollingsworth, P. M.; Dawson, I.K.; Goodall-Copestake, W.P.; J.E. Richardson; 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 in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richne...

  16. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, caviidae) in Colombia

    OpenAIRE

    William Burgos-Paz; Mario Cerón-Muñoz; Carlos Solarte-Portilla

    2011-01-01

    The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05), genetic differe...

  17. Genetic Diversity of Dalmatian Sage (Salvia officinalis L.) as Assessed by RAPD Markers

    OpenAIRE

    Zlatko Liber; Vesna Židovec; Sandro Bogdanovi?; Ivan Radosavljevi?; Monika Pruša; Maja Filipovi?; Ines Han Dovedan; Marija Jug-Dujakovi?; Zlatko Šatovi?

    2014-01-01

    Dalmatian or common sage (Salvia officinalis L.) is an outcrossing plant species native to East Adriatic coast. Random Amplified Polymorphic DNA markers (RAPD) were used to analyze genetic diversity and structure of ten natural populations from the East-Adriatic coastal region. The highest genetic diversity was found in populations from the central and south Dalmatia, while the highest frequency down-weighted marker values were found in the northernmost populations and the southern most inlan...

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

    OpenAIRE

    Malice M.; Jp, Baudoin

    2009-01-01

    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...

  19. Genetic Diversity Within and Among Populations of Roseroot (Rhodiola rosea L.) Based on Molecular Markers

    OpenAIRE

    Pedryc, Andrzej; Bacharov, Dmitry; Szabo, Maria; Gyorgy, Zsuzsanna

    2012-01-01

    Rhodiola rosea L. is a perennial adaptogenic medicinal plant found in cool climate of the northern hemisphere. The species is very diverse both in terms of morphological characteristics and in the content of the pharmacologically active substances. The genetic diversity of four geographically distant roseroot populations was studied with ISSR and SSR markers. Using 7 ISSR primers 64 DNA fragments were generated and 85,94% of those were found to be polymorphic, indicating high genetic variabil...

  20. Assessment of genetic diversity among different indigenous Xanthomonas isolates via RAPD and ISSR

    OpenAIRE

    Fatima Sabin; Bajwa Rukhsana; Anjum Tehmina; Saleem Zafar

    2012-01-01

    The genetic diversity among seven Xanthomonas isolates representing four species was assessed using RAPD and ISSR PCR-based techniques. Both techniques revealed high degrees of polymorphisms among the studied isolates. A cluster dendrogram based on the combined data of RAPD and ISSR showed that genetic diversity exists in local isolates of Xanthomonas. In terms of percentage similarity values, the genomic variation was found to be in the range of 29.29% - 100% among the isolates. X. cam...

  1. Genetic diversity in populations of asexual and sexual bag worm moths (Lepidoptera: Psychidae)

    OpenAIRE

    Mappes Johanna; Kumpulainen Tomi; Grapputo Alessandro; Parri Silja

    2005-01-01

    Abstract Background Despite the two-fold cost of sex, most of the higher animals reproduce sexually. The advantage of sex has been suggested to be its ability, through recombination, to generate greater genetic diversity than asexuality, thus enhancing adaptation in a changing environment. We studied the genetic diversity and the population structure of three closely related species of bag worm moths: two strictly sexual (Dahlica charlottae and Siederia rupicolella) and one strictly asexual (...

  2. Comparing genetic diversity and population structure of common beans grown in Kyrgyzstan using microsatellites

    OpenAIRE

    Sergey Hegay; Mulatu Geleta; Tomas Bryngelsson; Larisa Gustavsson; Helena Persson Hovmalm; Rodomiro Ortiz

    2012-01-01

    Common bean (Phaseolus vulgaris L.) is an important export crop in Kyrgyzstan. The aim of this study was to assess the extent of genetic diversity, determine the population structure, and relate to the main gene pools grown in Kyrgyzstan. Twenty-eight common bean accessions (including five Kyrgyz cultivars, and main references from the Mesoamerica and South America) were evaluated with microsatellites. Nine polymorphic microsatellites were used to estimate genetic diversity and heterozygosity...

  3. A first assessment of the genetic diversity of Mycobacterium tuberculosis complex in Cambodia

    OpenAIRE

    Sola Christophe; Gicquel Brigitte; Refregier Guislaine; Heng Seiha; Le Moullec Stéphanie; Zhang Jian(Andrew); Guillard Bertrand

    2011-01-01

    Abstract Background Cambodia is among the 22 high-burden TB countries, and has one of the highest rates of TB in South-East Asia. This study aimed to describe the genetic diversity among clinical Mycobacterium tuberculosis complex (MTC) isolates collected in Cambodia and to relate these findings to genetic diversity data from neighboring countries. Methods We characterized by 24 VNTR loci genotyping and spoligotyping 105 Mycobacterium tuberculosis clinical isolates collected between 2007 and ...

  4. Assessment of genetic diversity of Typha angustifolia in the development of cattail stands

    OpenAIRE

    Jae Geun Kim; Heung-Tae Kim; So Jung Min

    2012-01-01

    Typha angustifolia has ecological characteristics of clonal growth similar to Phragmites australis. The plant spreads byclonal growth and seed dispersal. In this study, for the three stands which have different settlement age at the Baksiljiwetland in Korea, genetic diversity was estimated by random amplification of polymorphic DNA analysis to evaluate thechange in genetic diversity of T. angustifolia during stand development in the same population. Stand (ST) 1 was the oldestand ST 4 was the...

  5. The benefits of genetic diversity outweigh those of kin association in a territorial animal.

    OpenAIRE

    Griffiths, S. W.; Armstrong, J.D.

    2001-01-01

    The theories of kin selection and heterogeneous advantage have been central to studies of altruistic behaviour and the evolution of sex over the last 35 years. Yet they predict diametrically opposite effects of genetic diversity on population density. Close relatives gain inclusive fitness advantages by preferentially associating with and behaving altruistically towards one another. However, heterogeneous advantage, which predicts competition to be highest when genetic diversity is low, sugge...

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

    OpenAIRE

    Suh, Sangwon; Kim, Young-Sin; Cho, Chang-Yeon; Byun, Mi-Jeong; Choi, Seong-Bok; Ko, Yeoung-Gyu; Lee, Chang Woo; Jung, Kyoung-Sub; Bae, Kyoung Hun; Kim, Jae-hwan

    2014-01-01

    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/FA...

  7. Evaluation of genetic diversity in soybean (Glycine max) lines using seed protein electrophoresis

    OpenAIRE

    M. Faisal Anwar Malik; Afsari S. Qureshi; Muhammad Ashraf; Muhammad Rashid Khan; Asif Javed

    2009-01-01

    The genetic variation of seed protein was assayed by SDS-PAGE for ninety-two accessions of soybean (Glycine max). The germplasm represented five different origins/sources (Pakistan, USA, AVRDC, North Korea and Japan). To our knowledge, no studies have yet been made in Pakistan on the diversity of soybean germplasm based on protein electrophoresis. On the basis of SDS-PAGE, 26 reproducible bands were used for analysis and genetic diversity was estimated based on the number of different protein...

  8. Investigation of Genetic Diversity among Bread Wheat Cultivars (Triticum aestivum L.) Using SSR Markers

    OpenAIRE

    Reza Drikvand; Mohammad Reza Bihamta; Goodarz Najafian; Asa Ebrahimi

    2012-01-01

    The present study was conducted to understand the genetic diversity of bread wheat's that grown in Iran, and to evaluate polymorphism information content (PIC) of some wheat SSR primers. Experiment was done in the genomics Laboratory in Islamic Azad University, Khorramabad branch, Iran in 2012. Ninety-two bread wheat varieties were assayed to study the genetic diversity and polymorphism based on forty whole-genome SSR markers. Eighty alleles were identified and 2 alleles per locus were detect...

  9. SSR analysis of 38 genotypes of soybean (Glycine Max (L.) Merr.) genetic diversity in India.

    Science.gov (United States)

    Bisen, Anchal; Khare, Dhirendra; Nair, Priya; Tripathi, Niraj

    2015-01-01

    Sixteen polymorphic Simple sequence repeat (SSR) markers were used to determine the genetic diversity and varietal identification among 38 soybean (Glycine max (L.) Merr.) genotypes which are at present under seed multiplication chain in India. A total of 51 alleles with an average of 2.22 alleles per locus were detected. The polymorphic information content (PIC) among genotypes varied from 0.049 (Sat_243 and Satt337) to 0.526 (Satt431) with an average of 0.199. The pair wise genetic similarity between soybean varieties varied from 0.56 to 0.97 with an average of 0.761. These 16 SSR markers successfully distinguished 12 of the 38 soybean genotypes. These results suggest that used SSR markers are efficient for measuring genetic diversity and relatedness as well as identifying varieties of soybeans. Diverse genetic materials may be used for genetic improvements of soybean genotypes. PMID:25648255

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Effect of host-plant genetic diversity on oak canopy arthropod community structure in central Mexico

    Scientific Electronic Library Online (English)

    Efraín, Tovar-Sánchez; Leticia, Valencia-Cuevas; Patricia, Mussali-Galante; Rolando, Ramírez-Rodríguez; Elgar, Castillo-Mendoza.

    Full Text Available BACKGROUND: Recently it has been proposed that the genetic diversity of foundation species influences the structure and function of the community by creating locally stable conditions for other species and modulating ecosystem dynamics. Oak species are an ideal system to test this hypothesis because [...] many of them have a wide geographical distribution, and they are dominant elements of the forest canopy. In this study we explored the response of canopy arthropod community structure (diversity and biomass) to the level of genetic diversity of Quercus crassipes and Q. rugosa, two important canopy species. Also, we examined the effect of oak species and locality on some community structure parameters (diversity, biomass, rare species, and richness of arthropod fauna) of canopy arthropods. In total, 160 canopies were fogged in four localities at the Mexican Valley (ten trees per species per locality per season) RESULTS: Q. crassipes registered the highest number of rare species, diversity index, biomass, and richness in comparison with Q. rugosa. We found a positive and significant relationship between genetic diversity parameters and canopy arthropod diversity. However, canopy arthropod biomass registered an inverse pattern. Our results support the hypothesis that the genetic diversity of the host-plant species influences the assemblage of the canopy arthropod community CONCLUSIONS: The pattern found in our study provides a powerful tool when trying to predict the effects of the genetic diversity of the host-plant species on different community structure parameters, which permits assignment of a new conservation status to foundation species based on their genetic diversity.

  12. Efficient Spatial Data mining using Integrated Genetic Algorithm and ACO

    OpenAIRE

    K Sankar; V Venkatachalam

    2011-01-01

    Spatial data plays a key role in numerous applications such as network traffic, distributed security applications such as banking, retailing, etc., The spatial data is essential mine, useful for decision making and the knowledge discovery of interesting facts from large amounts of data. Many private institutions, organizations collect the number of congestion on the network while packets of data are sent, the flow of data and the mobility of the same. In addition other databases provide the a...

  13. Genetic diversity of Norway spruce [Picea abies (L. Karst.] in Romanian Carpathians

    Directory of Open Access Journals (Sweden)

    Raul Gheorghe Radu

    2014-07-01

    Full Text Available The genetic diversity of Romanian most important coniferous tree species, the Norway spruce, was estimated by means of allozyme markers. A total of 695 adult trees sampled from eleven populations grouped in six mountainous areas in the Romanian Carpathians were analyzed. In three metapopulations (Maramure?, Post?var and Parâng, to evaluate the influence of altitudinal gradient on genetic diversity, samples were collected from populations located at high and low altitude. At other location (ApuseniMountains we compared the narrow-crown biotype (Picea abies var. columnaris and the pyramidal crown biotype (Picea abies var. pyramidalis and explored the genetic structure of peat bog ecotype. By analyzing 7 enzyme systems and 12 enzyme coding loci, a total of 38 allelic variants have been detected. The mean value of polymorphic loci for the six sites was 86.1%, ranging between 83.3% and 91.7% and the mean expected heterozygosity was 0.115, resulting in a moderate level of genetic diversity. The highest genetic diversity (He = 0.134 was found in the narrow-crown spruce population. Apuseni metapopulation showed the highest genetic diversity (He = 0.125, being the most valuable for conservation of genetic resources. The small value of fixation index (FST = 0.009 indicates a low genetic differentiation between the six sites and AMOVA test revealed a very high level of genetic diversity within population (99%. Comparative analysis of genetic parameters showed small differences between high and low altitude populations at each site, probably due to the neutral character of the markers analyzed and the effect of gene flow between gradiental populations.

  14. Allozyme diversity and genetic structure of the leafy cactus (Pereskia guamacho [Cactaceae]).

    Science.gov (United States)

    Nassar, J M; Hamrick, J L; Fleming, T H

    2002-01-01

    We examined levels of genetic variation and genetic structure in the leafy cactus (Pereskia guamacho) in arid and semiarid zones in Venezuela. We surveyed genetic diversity within 17 populations using 19 allozyme loci. Genetic diversity was relatively high at both the species (P(s) = 89%, A(s) = 3.26, AP(s) = 3.53, H(es) = 0.24) and population (P(p) = 63%, A(p) = 1.90, AP(p) = 2.42, H(ep) = 0.20) levels. A significant deficit of heterozygote individuals was detected within populations in the Paraguana Peninsula region (F(IS) = 0.301). Relatively low levels of population differentiation were detected at macrogeographic (G(ST) = 0.112) and regional levels (G(ST) = 0.044 for peninsula region and G(ST) = 0.074 for mainland region), suggesting substantial genetic exchange among populations; however, gene flow in this species seems to be regulated by the distance among populations. Overall, estimates of genetic diversity found in P. guamacho are concordant with the pattern observed for other cacti surveyed, namely high levels of polymorphism and genetic diversity with one common allele and several rare alleles per locus. Differences in gene dispersal systems between this species and other cacti studied were not reflected in the patterns of genetic diversity observed. The concentration of the highest estimates of genetic variation in northwestern Venezuela suggests a potential reservoir of plant genetic diversity within xerophilous ecosystems in northern South America. PMID:12195035

  15. Genetic Diversity and Population Structure of North China Mountain Walnut Revealed by ISSR

    Directory of Open Access Journals (Sweden)

    Aiqing Ji

    2014-10-01

    Full Text Available North China Mountain Walnut (NCMW is one of the ancestors of extant cultivated species, and a valuable gene resource for resistance breeding of walnut in China. Inter-Simple Sequence Repeat (ISSR primers were designed to evaluate the level and pattern of genetic diversity in eight populations of NCMW. Nine ISSR primers yielded 91 amplification products with different sizes, of which 84 (92.31% were polymorphic. A high species-level genetic diversity was detected with Nei’s (H = 0.2592 and Shannon’s diversity (I = 0.4003. In contrast, the population-level genetic diversity was relatively lower (PPB = 43.27%, H = 0.1347, I = 0.1862. Coefficient of populations differentiation (GST was 0.5066, indicating that inter-population and intra-population variation contributed 50.66% and 49.34% respectively to the total genetic variability. This relative level of variation was further supported by AMOVA analysis. Limited gene flow (Nm = 0.5133., habitat fragmentation and geographical isolation might be responsible for the population structure of NCMW. UPGMA cluster analysis classified the eight populations into three groups which showed no significant relationship between the genetic similarity coefficient and geographic origin but showed remarkable association with morpho-physiological characters, particularly nut traits. The results of the study provide species-level and population-level genetic profiles for further exploitation and conservation of genetic diversity of NCMW.

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

    International Nuclear Information System (INIS)

    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)

  17. Genetic Diversity and Differentiation of Juniperus thurifera in Spain and Morocco as Determined by SSR

    Science.gov (United States)

    Teixeira, Helena; Rodríguez-Echeverría, Susana; Nabais, Cristina

    2014-01-01

    Juniperus thurifera L. is an important tree endemic to the western Mediterranean basin that it is able to grow in semi-arid climates. It nowadays exhibits a disjunct distribution pattern, occurring in North Africa, Spain, France and the Italian Alps. The Strait of Gibraltar has acted as an efficient barrier against gene flow between African and European populations, which are considered different subspecies by some authors. We aimed at describing the intraspecific genetic diversity of J. thurifera in populations from the Iberian Peninsula and Morocco and the phylogeographical relationships among these populations. The ploidy level of J. thurifera was examined and eleven nuclear microsatellites (nSSRs) developed for J. thurifera were assessed for genotyping this species. Six nSSRs were polymorphic and subsequently used to assess the genetic diversity and structure of the studied populations. Genotyping of the tetraploid J. thurifera using nuclear microsatellites supports the separation of Moroccan and Spanish populations into two genetically differentiated groups that correspond to the proposed subspecies africana and thurifera. High values of within population genetic diversity were found, that accounted for 90% of the total genetic variance, while population structure was weak. The estimators of genetic diversity were higher in populations of Spain than in populations of Morocco pointing for a possible loss of genetic diversity during the spread of this species to Africa from Europe. PMID:24533164

  18. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

    Directory of Open Access Journals (Sweden)

    Windig Jack J

    2008-07-01

    Full Text Available Abstract Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. Non-genetic aspects included threats (e.g. low population size, low preferences by farmers and current merits (economic, ecological and cultural merits. Threat analysis identified eight of the 14 breeds as threatened. Analysis of current merits showed that sub-alpine and arid-lowland breeds contribute most to farmer livelihoods in comparison to other breeds. The highest contribution to the genetic diversity conserved was from the Simien breed. Simien showed high between-breed (low between-breed kinship = 0.04 as well as high within-breed diversity (low within-breed kinship = 0.09 and high HE = 0.73 and allelic richness = 6.83. We combined the results on threat status, current breed merits and contributions to genetic diversity to produce a ranking of the 14 breeds for conservation purposes. Our results balance the trade-offs between conserving breeds as insurance against future uncertainties and current sustainable utilization. The ranking of breeds provides a basis for conservation strategies for Ethiopian sheep and contributes to a regional or global conservation plan.

  19. 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.

  20. Efficient Spatial Data mining using Integrated Genetic Algorithm and ACO

    Directory of Open Access Journals (Sweden)

    K Sankar

    2011-05-01

    Full Text Available Spatial data plays a key role in numerous applications such as network traffic, distributed security applications such as banking, retailing, etc., The spatial data is essential mine, useful for decision making and the knowledge discovery of interesting facts from large amounts of data. Many private institutions, organizations collect the number of congestion on the network while packets of data are sent, the flow of data and the mobility of the same. In addition other databases provide the additional information about the client who has sent the data, the server who has to receive the data, total number of clients on the network, etc. These data contain a mine of useful information for the network traffic risk analysis. Initially study was conducted to identify and predict the number of nodes in the system; the nodes can either be a client or a server. It used a decision tree that studies from the traffic risk in a network. However, this method is only based on tabular data and does not exploit geo routing location. Using the data, combined to trend data relating to the network, the traffic flow, demand, load, etc., this work aims at deducing relevant risk models to help in network traffic safety task. The existing work provided a pragmatic approach to multi-layer geo-data mining. The process behind was to prepare input data by joining each layer table using a given spatial criterion, then applying a standard method to build a decision tree. The existing work did not consider multi-relational data mining domain. The quality of a decision tree depends, on the quality of the initial data which are incomplete, incorrect or non relevant data inevitably leads to erroneous results. The proposed model develops an ant colony algorithm integrated with GA for the discovery of spatial trend patterns found in a network traffic risk analysis database. The proposed ant colony based spatial data mining algorithm applies the emergent intelligent behavior of ant colonies. The experimental results on a network traffic (trend layer spatial database show that our method has higher efficiency in performance of the discovery process compared to other existing approaches using non-intelligent decision tree heuristics.

  1. Genetic diversity in populations of Xanthomonas campestris pv. camestris in cruciferous weeds in central coastal California

    Science.gov (United States)

    Xanthomonas campestris pv. campestris infects a large number of cruciferous plants, including weeds. California has one of the largest and most diverse populations of wild cruciferous plants in the world. Although considerable information is available on the genetic diversity of X. campestris pv. ca...

  2. Genetic diversity and population structure of Fusicladium effusum on pecan in the U.S.A.

    Science.gov (United States)

    Fusicladium effusum causes pecan scab, which is the most destructive disease of pecan in the U.S.A. The disease is known to be spread through asexually produced conidia in rain splash and wind. The fungus has demonstrated pathogenic diversity, yet there is no information on its genetic diversity or ...

  3. STUDIES ON GENETIC DIVERSITY AMONG ALTERNARIA BLIGHT TOLERANT INDIAN MUSTARD GENOTYPES USING SSR MARKERS

    OpenAIRE

    VISALAKSHI CHANDRA; USHA PANT; RAM BHAJAN; Singh, A K

    2014-01-01

    Brassica species represents one of the most important oilseed crops in India, nevertheless their diversity is still to be studied. an understainding of genetic diversity is essential for proper utilization of genotypes in the target oriented research programmes. 37 diverse Indian mustard genotypes including recombinant line, indigenous lines, exotic lines with alternaria blight tolerant (PAB 9511) and susceptible check (Varuna) were utilized. Ten A and C genomes specific SSR markers were used...

  4. Evaluation of Genetic Diversity of Iranian Pomegranate Cultivars Using Fruit Morphological Characteristics and AFLP Markers

    OpenAIRE

    Mehdi KHAYAT; Hossein NEMATI; Farsi, Mohammad; Zahra NEMATI; Amin MIRSHAMSI KAKHKI; Ali TEHRANIFAR

    2012-01-01

    The present research evaluated the diversity of a number of Iranian pomegranate cultivars using fruit morphological characteristics and AFLP markers. Thirty-one pomegranate cultivars were collected from Yazd Pomegranate Collection in Iran to study their diversity. Seven AFLP primer combinations were used to amplify a total of 112 polymorphic fragments (47.26%). By use of AFLPs, a low genetic diversity level was detected among cultivars. The relationship between fruit characteristics was analy...

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

    OpenAIRE

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

    2013-01-01

    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 fi...

  6. Restriction of Francisella novicida Genetic Diversity during Infection of the Vector Midgut

    OpenAIRE

    Reif, Kathryn E.; Palmer, Guy H.; Crowder, David W.; Ueti, Massaro W.; Noh, Susan M.

    2014-01-01

    The genetic diversity of pathogens, and interactions between genotypes, can strongly influence pathogen phenotypes such as transmissibility and virulence. For vector-borne pathogens, both mammalian hosts and arthropod vectors may limit pathogen genotypic diversity (number of unique genotypes circulating in an area) by preventing infection or transmission of particular genotypes. Mammalian hosts often act as “ecological filters” for pathogen diversity, where novel variants are frequently e...

  7. Social Organization of Crop Genetic Diversity. The G × E × S Interaction Model

    OpenAIRE

    Geo Coppens d’Eeckenbrugge; Christian Leclerc

    2011-01-01

    A better knowledge of factors organizing crop genetic diversity in situ increases the efficiency of diversity analyses and conservation strategies, and requires collaboration between social and biological disciplines. Four areas of anthropology may contribute to our understanding of the impact of social factors on crop diversity: ethnobotany, cultural, cognitive and social anthropology. So far, most collaborative studies have been based on ethnobotanical methods, focusing on farmers’ indivi...

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

    OpenAIRE

    Sherwin, William B

    2010-01-01

    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 inf...

  9. Algal diversity in flowing waters at an acidic mine drainage "barrens" in central Pennsylvania, USA.

    Science.gov (United States)

    Prasanna, Radha; Ratha, Sachitra Kumar; Rojas, Claudia; Bruns, Mary Ann

    2011-11-01

    Microscopic investigations were undertaken to decipher the diversity in the lotic algal communities from acidic waters (pH 2.4-3.2) flowing overland in sheets and channels at an acid mine drainage (AMD) barrens near Kylertown, PA, USA. Microscopic observations, supplemented with taxonomic keys, aided in identification of the dominant algae, and measurement of carbon from adjacent soils was undertaken. The unicellular protist Euglena sp. was most abundant in slower flowing waters (i.e., pool near point of emergence and surficial flow sheets), while Ulothrix sp. was most abundant in faster flowing water from the central stream channel. A diverse range of unicellular microalgae such as Chlorella, Cylindrocystis, Botryococcus, and Navicula and several filamentous forms identified as Microspora, Cladophora, and Binuclearia were also recorded. The observed high algal diversity may be related to the long duration of AMD flow at this site which has led to the development of adapted algal communities. The comparatively higher carbon content in soil materials adjacent to slower flowing water sampling locations provides evidence for the important role of algae as primary producers in this extreme environment. PMID:22038419

  10. Isolation, sequencing, and genetic diversity of microsatellite loci from Begonia x tuberhybrida Voss. germplasm.

    Czech Academy of Sciences Publication Activity Database

    Wiesner, Ivo; Wiesnerová, Dana; Demelová, B.; T?asáková, J.

    Praha : ?SBMB, 2008 - (?erný, R.). s. 91 [Biochemický sjezd /21./. 14.09.2008-17.09.2008, ?eské Bud?jovice] R&D Projects: GA AV ?R 1QS500510566 Keywords : genetic diversity * microsatellite * Begonia x tuberhybrida Subject RIV: EB - Genetics ; Molecular Biology

  11. Genetic diversity of Ovis aries populations near domestication centers and in the new world

    Science.gov (United States)

    Domestic sheep in Kazakhstan may provide an interesting source of genetic variability due to their proximately to the center of domestication and the Silk Route. Additionally, those breeds have never been compared to new world sheep populations. This report compares genetic diversity among five Kaza...

  12. Genetic diversity of grayling (Thymallus thymallus L.) populations in the Czech Republic inferred from microsatellite markers.

    Czech Academy of Sciences Publication Activity Database

    Papoušek, Ivo; Hala?ka, Karel; Kohout, Jan; Šlechta, Vlastimil; Vetešník, Lukáš; Mendel, Jan

    Klaipeda : Klaipedos Universitetas, 2009. s. 80. ISBN 978-9955-18-452-2. [European Congress of Ichthyology /13./. 06.09.2009-12.09.2009, Klaipeda] R&D Projects: GA AV ?R 1QS500450513 Institutional research plan: CEZ:AV0Z60930519 Keywords : genetic diversity * grayling * microsatellites Subject RIV: EB - Genetics ; Molecular Biology

  13. Genetic diversity of four protected indigenous chicken breeds in China using microsatellite markers

    Scientific Electronic Library Online (English)

    Lin, Wei; Bin, Chen; Xiao-ying, Li; Sheng-gui, Liu; Jing-jing, Wang.

    Full Text Available The genetic diversity of four protected indigenous chicken breeds was evaluated with 25 microsatellite markers. Polymorphism information content (PIC), heterozygosity with the estimator of genetic differentiation F ST and Nei's genetic distance were evaluated. The results showed that these four prot [...] ected local chicken populations showed high levels of diversity. The proportion of inter-population subdivision among the four protected local chicken populations was 16.0%. The average heterozygosity was 0.514, 0.581, 0.567 and 0.589 in Dongan, Xuefeng black-bone, Xianghuang and Taoyuan chickens, respectively, while the average PIC estimates were 0.455, 0.581, 0.557 and 0.576. A phylogenetic tree was constructed using genetic distance and the neighbour-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 breeds estimated by microsatellite analysis may be useful as an initial guide for the effective conservation of chicken genetic diversity and developing conservation strategies.

  14. Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

    Science.gov (United States)

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

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. PMID:22253801

  15. Effect of mining landscape history on local species diversity: a case study of the Yimin open-pit coal mine in Inner Mongolia

    Directory of Open Access Journals (Sweden)

    Sarula Kang

    2014-03-01

    Full Text Available The exploration and utilization of mineral resources accelerates local economic and social development and simultaneously exacerbates the effects of climate and landscape changes, resulting in landscape fragmentation. Landscape change is widely considered as a major threat to species loss at a regional and global scale. However, how species diversity responds to landscape changes on a temporal scale has usually been ignored. In this study, we explored relationships between landscape and biodiversity (species level and functional group level during different years (1975, 1990, 2000 and 2010 at the Yimin open-pit coal mine, a mine that has been exploited for more than 30 years and that has produced obvious fragmentation effects on the landscape in Hulunbuir City. The ongoing patterns of transformation of the landscape were measured using the landscape dominance index, the habitat integral index of connectivity (IIC, and the habitat probability of connectivity (PC at seven different spatial scales. The main results were as follows: The present species diversity is significantly correlated with the landscape pattern indices of previous and earlier mining at a medium-sized spatial scale (4–8 km buffers. Different plant functional groups responded in various ways to changing landscape patterns. The species richness of perennial rhizome grasses was significantly correlated with the present small-scale landscape pattern (1–3 km, and the species richness of perennial forbs was significantly correlated with the previous and earlier mining large-scale landscape patterns (4–10 km. Perennial bunchgrasses were not significantly correlated with landscape patterns. We concluded that the time lag expressed by changes in plant species diversity occurred in response to changing patterns of construction and configurations of habitats in the landscape. The regional species pool determined the local species diversity. The connected habitat patches within a 4–8 km buffer region represented the principal species pool. The propagation strategies and dispersal traits of various functional groups were important mechanisms maintaining species diversity in a fragmented area.

  16. Study of Genetic Diversity and Relationships of Diploid and Tetraploid Annual Medics Using Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    S. A. Mohammadi

    2006-10-01

    Full Text Available Annual medics are used for hey production, soil protection, biological fixation of N2 and green manure. In the present study, the inter and intra specific genetic diversity and relatedness of 4 diploid and two tetraploid (M. rugosa and M. scutellata annual medics were evaluated using microsatellite markers. PCR analysis was performed on genomic DNA from individual plant and PCR products were detected using standard polyacrylamide sequencing gel. Totally twenty five polymorphic alleles were observed in the studied species. Average intra-specific genetic diversity ranged from zero (0.0 in both M. rugosa and M. scutellata to 0.114 in M. minima species, and the level of genetic diversity was similar in both M. orbicularis and M. truncatula species. Analysis of molecular variance (AMOVA was used to partition the overall genetic diversity into within and among species, and between diploids and tetraploids. The results revealed significant (P<0.05 inter and intra-specific genetic variation. Pairwise comparisons based on Fst indicated significant differences among all of the species. Clustering analysis using UPGMA algorithm based on coancestary coefficient revealed a clear genetic relationship among species. The hypothesis on a common origin of two tetraploid species was supported by UPGMA clustering and phylogenetic analysis. The high level of Genetic diversity in spiny pod species respect to spineless pod species suggested the high importance of species with spiny pods in annual medics evolution. The findings support the usefulness of microsatellite markers for assessing inter and intra specific genetic diversity, differentiation and genetic relationships.

  17. Population genetic diversity in Chinese pomegranate (Punica granatum L.) cultivars revealed by fluorescent-AFLP markers.

    Science.gov (United States)

    Yuan, Zhaohe; Yin, Yanlei; Qu, Jianlu; Zhu, Liqin; Li, Yun

    2007-12-01

    Eighty-five pomegranate (Punica granatum L.) cultivars from six geographical populations located at Shandong, Anhui, Shaanxi, Henan, Yunnan, and Xinjiang Provinces were studied for its population genetic diversity by means of fluorescent-AFLP markers. The results indicated that 135-185 polymorphic loci were amplified by eight pairs of primers at species level. An average of 158.25 polymorphic loci was amplified for each primer combination. The polymorphism percentage ranged from 62.5% to 86.11%, and the average polymorphism percentage was 73.26%. This indicated that there was plentiful genetic diversity in pomegranate cultivars. The genetic diversity at the species level was higher than that at the population level. The order of the genetic diversity was Henan population > Xinjiang population > Shaanxi population > Anhui population > Shandong population > Yunnan population. Variance analysis showed that there was significant difference between populations in genetic diversity. The genetic differentiation coefficient between populations (G(ST)) was 0.2018, which indicated that gene differentiation was mainly within the population, and between populations, it accounted for 20.18% of the total variation. Gene flow (Nm) between the populations measured was 1.9027 based on the genetic differentiation coefficient between populations, indicating that there was mild gene flow between populations. The UPGMA cluster analysis showed that most accessions from the same population were clustered together, but there was partly gene exchange. All genetic parameters indicated that there was plentiful genetic diversity in pomegranate cultivars in China, of which Henan population was significantly higher than the other populations, and it had wide application foreground in pomegranate breeding in China. PMID:18155618

  18. Diversidad y estructura genética de Pinus johannis / Genetic diversity and genetic structure in Pinus johannis

    Scientific Electronic Library Online (English)

    Verónica, García-Gómez; Carlos, Ramírez-Herrera; Celestino, Flores-López; Javier, López-Upton.

    2014-12-01

    Full Text Available Pinus johannis M.-F. Robert-Passini es un pino piñonero endémico de México que crece en poblaciones pequeñas. El objetivo del presente estudio fue estimar el nivel de la diversidad genética y el grado de diferenciación entre poblaciones en la distribución natural de P. johannis. Se recolectaron estr [...] óbilos maduros de 130 árboles de cuatro poblaciones. El genotipo de cada árbol se determinó en una muestra de seis megagametofitos y se analizaron nueve sistemas enzimáticos con 16 loci. En las cuatro poblaciones el número de alelos varió de 31 a 35. El número promedio de alelos por locus fue 2.1 y el porcentaje promedio de loci polimórficos 88. La heterocigosidad promedio fue 0.231, y la heterocigosidad promedio esperada fue 0.245. Un déficit de individuos heterocigóticos (F IS = 0.116 y F IT = 0.176) se encontró en las cuatro poblaciones juntas y en cada una de ellas. La diferenciación genética entre poblaciones fue moderada (F ST = 0.062).La diversidad genética en P. johannis fue alta con un nivel moderado de diferenciación entre poblaciones. Abstract in english Pinus johannis M.-F. Robert-Passini is an endemic pinion nut pine of Mexico that grows in small populations. The objective of this study was to estimate the level of genetic diversity and degree of differentiation among populations in the natural distribution of P. johannis. Mature strobili were col [...] lected from 130 tree of four populations. The genotype of each tree was determined in a sample of six megagametophytes, and nine enzyme systems with 16 loci were analyzed. In the four populations the number of alleles varied from 31 to 35. The average number of alleles per locus was 2.1, and the average percentage of polymorphic loci was 88 %. Average heterozygosity was 0.231, and expected average heterozygosity was 0.245. A deficit of heterozygous individuals (F IS = 0.116 and F IT = 0.176) was found in the four populations together and in each of them. The genetic differentiation among populations was moderate (F ST = 0.062).Genetic diversity of P. johannis was high with a moderate level of differentiation among populations.

  19. Genetic diversity and structure of Astrocaryum jauari (Mart.) palm in two Amazon river basins

    OpenAIRE

    Liliane D. Santos Oliveira; Santiago L. Ferreyra Ramos; Maria T. Gomes Lopes; Gabriel Dequigiovanni; Elizabeth Ann Veasey; Jeferson L. Vasconcelos de Macêdo; Jacqueline S. Batista; Kyara M. Formiga; Ricardo Lopes

    2014-01-01

    Astrocaryum jauari is a non-domesticated palm that is exploited by poachers. Our objective was to investigate the organization of the genetic diversity and structure of three A. jauari populations. The study was carried out in the state of Amazonas, between the municipalities of Coari and Manaus. Nine microsatellite loci were used for the genetic analyses. High genetic variation was found, with a mean number of alleles per locus varying from 3.9 to 4.4. The average observed hetero...

  20. Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

    OpenAIRE

    Deulvot Chrystel; Charrel Hélène; Marty Amandine; Jacquin Françoise; Donnadieu Cécile; Lejeune-Hénaut Isabelle; Burstin Judith; Aubert Grégoire

    2010-01-01

    Abstract Background Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction. In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in d...

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

    OpenAIRE

    Rabinowicz Pablo D; Chan Agnes P; Allan Gerard J; Foster Jeffrey T; Ravel Jacques; Jackson Paul J; Keim Paul

    2010-01-01

    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 surv...

  2. Genetic structure and diversity of the endangered bath sponge Spongia lamella.

    OpenAIRE

    Pe?rez-portela, R.; Noyer, Charlotte; Becerro, Mikel

    2014-01-01

    1.Natural populations of Mediterranean commercial sponges have declined substantially over recent decades. The present study explored the distribution of genetic diversity of the endangered bath sponge Spongia lamella along the western Mediterranean and the Portuguese coast. Seven microsatellite markers were used to genotype 231 individuals scattered over nine populations. Basic genetic descriptors and population genetic analyses based on FST test, analyses of the molecular variance (AM...

  3. Genetic Diversity among Flue-cured Tobacco Cultivars Based on RAPD and AFLP Markers

    Directory of Open Access Journals (Sweden)

    Han Yao Zhang

    2008-12-01

    Full Text Available The aim of this work was to study the genetic diversity among flue-cured tobacco cultivars. RAPD and AFLP analyses were used to assess the genetic similarity among selected accessions of flue-cured tobacco. Seventy eight RAPD and 154 AFLP polymorphic bands were obtained and used to assess the genetic diversity among 28 tobacco accessions. The cultivar relationships were estimated through the cluster analysis (UPGMA based on RAPD data and AFLP data. The accessions were grouped into three major clusters and these shared common ancestry clustered together.

  4. Genetic Diversity, Population Structure and Linkage Disequilibrium in Elite Chinese Winter Wheat Investigated with SSR Markers

    OpenAIRE

    Chen, Xiaojie; Min, Donghong; Yasir, Tauqeer Ahmad; Hu, Yin-Gang

    2012-01-01

    To ascertain genetic diversity, population structure and linkage disequilibrium (LD) among a representative collection of Chinese winter wheat cultivars and lines, 90 winter wheat accessions were analyzed with 269 SSR markers distributed throughout the wheat genome. A total of 1,358 alleles were detected, with 2 to 10 alleles per locus and a mean genetic richness of 5.05. The average genetic diversity index was 0.60, with values ranging from 0.05 to 0.86. Of the three genomes of wheat, ANOVA ...

  5. Distribution of genetic diversity in wild European populations of prickly lettuce (Lactuca serriola): implications for plant genetic resources management

    OpenAIRE

    Wiel, C. C. M.; Sretenovic Rajicic, T.; Treuren, R.; Dehmer, K. J.; Linden, C. G.; Hintum, T. J. L.

    2010-01-01

    Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The aut...

  6. Assessment of Genetic Diversity in Seed Plants Based on a Uniform ? Criterion

    Directory of Open Access Journals (Sweden)

    Bin Ai

    2014-12-01

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

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

    DEFF Research Database (Denmark)

    Desta, Zeratsion Abera; Orabi, Jihad

    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 major groups. This is the first report of the genetic diversity and structure of Eritrean bread wheat. © 2013 NIAB.

  8. Comparative population genomics in animals uncovers the determinants of genetic diversity.

    Science.gov (United States)

    Romiguier, J; Gayral, P; Ballenghien, M; Bernard, A; Cahais, V; Chenuil, A; Chiari, Y; Dernat, R; Duret, L; Faivre, N; Loire, E; Lourenco, J M; Nabholz, B; Roux, C; Tsagkogeorga, G; Weber, A A-T; Weinert, L A; Belkhir, K; Bierne, N; Glémin, S; Galtier, N

    2014-11-13

    Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies. PMID:25141177

  9. Hitchhiker’s guide to genetic diversity in socially structured populations

    Directory of Open Access Journals (Sweden)

    L. S. PREMO

    2012-02-01

    Full Text Available When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking. A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration. Under conditions in which genetic and cultural variants are transmitted symmetrically, neutral genes may also hitchhike to higher frequencies on the coattails of adaptive cultural traits through a process called cultural hitchhiking. Cultural hitchhiking has been proposed to explain why some species of matrilineal whales display relatively low levels of mitochondrial DNA diversity, and it may be applicable to humans as well. This paper provides a critical review of recent models of both types of hitch­­hi­king in socially structured populations. The models’ assumptions and predictions are compared and discussed in the hope that studies of reduced genetic diversity in humans might improve our understanding of reduced genetic diversity in other species, and vice versa [Current Zoology 58 (1: 287-297, 2012].

  10. Genetic diversity and fitness in black-footed ferrets before and during a bottleneck.

    Science.gov (United States)

    Wisely, S M; Buskirk, S W; Fleming, M A; McDonald, D B; Ostrander, E A

    2002-01-01

    The black-footed ferret (Mustela nigripes) is an endangered North American carnivore that underwent a well-documented population bottleneck in the mid-1980s. To better understand the effects of a bottleneck on a free-ranging carnivore population, we used 24 microsatellite loci to compare genetic diversity before versus during the bottleneck, and compare the last wild population to two historical populations. We also compared genetic diversity in black-footed ferrets to that of two sibling species, the steppe polecat (Mustela eversmanni) and the European polecat (Mustela putorius). Black-footed ferrets during the bottleneck had less genetic diversity than steppe polecats. The three black-footed ferret populations were well differentiated (F(ST) = 0.57 +/- 0.15; mean +/- SE). We attributed the decrease in genetic diversity in black-footed ferrets to localized extinction of these genetically distinct subpopulations and to the bottleneck in the surviving subpopulation. Although genetic diversity decreased, female fecundity and juvenile survival were not affected by the population bottleneck. PMID:12407208

  11. Stress-related hormones and genetic diversity in sea otters (Enhydra lutris)

    Science.gov (United States)

    Larson, S.; Monson, D.; Ballachey, B.; Jameson, R.; Wasser, S.K.

    2009-01-01

    Sea otters (Enhydra lutris) once ranged throughout the coastal regions of the north Pacific, but were extirpated throughout their range during the fur trade of the 18th and 19th centuries, leaving only small, widely scattered, remnant populations. All extant sea otter populations are believed to have experienced a population bottleneck and thus have lost genetic variation. Populations that undergo severe population reduction and associated inbreeding may suffer from a general reduction in fitness termed inbreeding depression. Inbreeding depression may result in decreased testosterone levels in males, and reduced ability to respond to stressful stimuli associated with an increase in the stress-related adrenal glucocorticoid hormones, cortisol and corticosterone. We investigated correlations of testosterone, cortisol, and corticosterone with genetic diversity in sea otters from five populations. We found a significant negative correlation between genetic diversity and both mean population-level (r2 = 0.27, P < 0.001) and individual-level (r2 = 0.54, P < 0.001) corticosterone values, as well as a negative correlation between genetic diversity and cortisol at the individual level (r2 = 0.17, P = 0.04). No relationship was found between genetic diversity and testosterone (P = 0.57). The strength of the correlations, especially with corticosterone, suggests potential negative consequences for overall population health, particularly for populations with the lowest genetic diversity. ?? 2009 by the Society for Marine Mammalogy.

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

    DEFF Research Database (Denmark)

    Pham, Lan Doan; Do, Duy Ngoc

    2013-01-01

    Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese indigenous cattle populations, using microsatellite markers. A total of 410 individuals from six indigenous cattle populations and an exotic breed was characterized using 27 microsatellite markers A total of 362 alleles was detected and the number of alleles per locus ranged from 8 (INRA005 and ILSTS005) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean FIS=0.05) and genetic differentiation (mean FST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic diversity.

  13. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.

    Science.gov (United States)

    Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F

    2015-01-01

    The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. PMID:25919952

  14. Genetic diversity of domestic pigs as revealed by microsatellites: a mini review

    Directory of Open Access Journals (Sweden)

    C. Moran

    2011-02-01

    Full Text Available Of the several hundred breeds of pigs in the world, many are in danger of extinction and others are threatened by inefficient use or loss due to cross breeding. Special efforts are required to conserve these genetic resources for food security and rural development but it is not possible to conserve all breeds. Microsatellites, which are short tandem nucleotide repeats found scattered throughout the genome of eukaryotes, have been used to evaluate genetic diversity present within livestock populations to assist in rationalising breed conservation programmes and ensure the greatest possible conservation of diversity. This review provides insights into the use of microsatellite markers to reveal origin, genetic structure and diversity within and across various domestic pig breeds around the world. However, in future, microsatellites may be replaced by panels of single nucleotide polymorphism (SNP markers for genome-wide population genetic analysis. Meanwhile, microsatellites are still widely employed and for some species may never be replaced by SNP.

  15. Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

    Science.gov (United States)

    Hitt, Nathaniel P.; Chambers, Douglas B.

    2014-01-01

    Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish (Lepomis cyanellus) and Creek Chub (Semotilus atromaculatus) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

  16. Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and other drivers along an acid mine drainage.

    Science.gov (United States)

    Volant, Aurélie; Bruneel, Odile; Desoeuvre, Angélique; Héry, Marina; Casiot, Corinne; Bru, Noëlle; Delpoux, Sophie; Fahy, Anne; Javerliat, Fabien; Bouchez, Olivier; Duran, Robert; Bertin, Philippe N; Elbaz-Poulichet, Françoise; Lauga, Béatrice

    2014-10-01

    Deciphering the biotic and abiotic factors that control microbial community structure over time and along an environmental gradient is a pivotal question in microbial ecology. Carnoulès mine (France), which is characterized by acid waters and very high concentrations of arsenic, iron, and sulfate, provides an excellent opportunity to study these factors along the pollution gradient of Reigous Creek. To this end, biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. Patterns of spatial and temporal variations in bacterial community composition linked to changes in the physicochemical conditions suggested that species-sorting processes were at work in the acid mine drainage. Arsenic, temperature, and sulfate appeared to be the most important factors that drove the composition of bacterial communities along this continuum. Time series investigation along the pollution gradient also highlighted habitat specialization for some major members of the community (Acidithiobacillus and Thiomonas), dispersal for Acidithiobacillus, and evidence of extinction/re-thriving processes for Gallionella. Finally, pyrosequencing revealed a broader phylogenetic range of taxa than previous clone library-based diversity. Overall, our findings suggest that in addition to environmental filtering processes, additional forces (dispersal, birth/death events) could operate in AMD community. PMID:25070063

  17. Genetic diversity and structure in the Sado captive population of the Japanese crested ibis.

    Science.gov (United States)

    Urano, Kensuke; Tsubono, Kanako; Taniguchi, Yukio; Matsuda, Hirokazu; Yamada, Takahisa; Sugiyama, Toshie; Homma, Kosuke; Kaneko, Yoshinori; Yamagishi, Satoshi; Iwaisaki, Hiroaki

    2013-06-01

    The Japanese crested ibis Nipponia nippon is a critically threatened bird. We assessed genetic diversity and structure in the Sado captive population of the Japanese crested ibis based on 24 and 50 microsatellite markers developed respectively for the same and related species. Of a total of 74 loci, 19 showed polymorphisms in the five founder birds of the population, and therefore were useful for the analysis of genetic diversity and structure. Genetic diversity measures, A, ne, He, Hoand PIC, obtained by genotyping of the 138 descendants were similar to those of other species with population bottlenecks, and thus considerably low. The low level of genetic diversity resulting from such bottlenecks was consistent with the results of lower genetic diversity measures for the Sado captive relative to the Chinese population that is the source population for the Sado group as determined using previously reported data and heterozygosity excess by Hardy-Weinberg equilibrium tests. Further, individual clustering based on the allele-sharing distance and Bayesian model-based clustering revealed that the founder genomes were equally at population in total, and with various admixture patterns at individual levels inherited by the descendants. The clustering results, together with the result of inheritance of all alleles of the microsatellites from the founders to descendants, suggest that planned mating in captive-breeding programs for the population has succeeded in maintaining genetic diversity and minimizing kinship. In addition, the Bayesian model-based clustering assumed two different components of genomes in the Sado captive Japanese crested ibis, supporting a considerably low level of genetic diversity. PMID:23721466

  18. Greater Genetic Diversity in Spatially Restricted Coral Reef Fishes Suggests Secondary Contact among Differentiated Lineages

    Directory of Open Access Journals (Sweden)

    M. Julian Caley

    2011-09-01

    Full Text Available The maintenance of genetic diversity is a central goal of conservation. It is the raw material for evolutionary change and if lost, can accelerate extinction of species. According to theory, total genetic diversity should be less in species with restricted ranges and in populations on the margins of distributional ranges, making such species or populations more vulnerable to environmental perturbations. Using mtDNA and nuclear Inter Simple Sequence Repeat (ISSR data we investigated how the genetic diversity and structure of three con-generic species pairs of coral reef fishes (Pomacentridae was related to species’ range size and position of populations within these ranges. Estimates of genetic structure did not differ significantly among species, but mtDNA and nucDNA genetic diversities were up to 10 times greater in spatially restricted species compared to their widespread congeners. In two of the three species pairs, the distribution of genetic variation indicated secondary contact among differentiated lineages in the spatially restricted species. In contrast, the widespread species displayed a typical signature of population expansion suggesting recent genetic bottlenecks, possibly associated with the (re colonization of the Great Barrier Reef. These results indicate that historical processes, involving hybridization and founder effects, possibly associated with Pleistocene sea level fluctuations, have differentially influenced the widespread and spatially restricted coral reef damselfish species studied here.

  19. Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin

    Directory of Open Access Journals (Sweden)

    Bourguiba Hedia

    2012-04-01

    Full Text Available Abstract Background Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L., which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. Results According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secondary centre of diversification. Conclusions A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the ‘Irano-Caucasian’ gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.

  20. 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.

  1. GENETIC DIVERSITY OF TOXOPLASMA GONDII ISOLATES FROM CHICKENS FROM BRAZIL

    Science.gov (United States)

    Until recently, Toxoplasma gondii was considered clonal with very little genetic variability. Recent studies indicate that T. gondii isolates from Brazil are genetically and biologically different from T. gondii isolates from USA and Europe. In the present study, we retyped 151 free range chicken is...

  2. Literature mining of genetic variants for curation: quantifying the importance of supplementary material.

    Science.gov (United States)

    Jimeno Yepes, Antonio; Verspoor, Karin

    2014-01-01

    A major focus of modern biological research is the understanding of how genomic variation relates to disease. Although there are significant ongoing efforts to capture this understanding in curated resources, much of the information remains locked in unstructured sources, in particular, the scientific literature. Thus, there have been several text mining systems developed to target extraction of mutations and other genetic variation from the literature. We have performed the first study of the use of text mining for the recovery of genetic variants curated directly from the literature. We consider two curated databases, COSMIC (Catalogue Of Somatic Mutations In Cancer) and InSiGHT (International Society for Gastro-intestinal Hereditary Tumours), that contain explicit links to the source literature for each included mutation. Our analysis shows that the recall of the mutations catalogued in the databases using a text mining tool is very low, despite the well-established good performance of the tool and even when the full text of the associated article is available for processing. We demonstrate that this discrepancy can be explained by considering the supplementary material linked to the published articles, not previously considered by text mining tools. Although it is anecdotally known that supplementary material contains 'all of the information', and some researchers have speculated about the role of supplementary material (Schenck et al. Extraction of genetic mutations associated with cancer from public literature. J Health Med Inform 2012;S2:2.), our analysis substantiates the significant extent to which this material is critical. Our results highlight the need for literature mining tools to consider not only the narrative content of a publication but also the full set of material related to a publication. PMID:24520105

  3. Genetic diversity of indigenous Rhizobium leguminosarum bv. viciae isolates nodulating two different host plants during soil restoration with alfalfa

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, X.X.; Kosier, B.; Priefer, U.B. [Rheinisch-Westfaelische TH Aachen, Aachen (Germany)

    2001-09-01

    A total of 360 Rhizobium leguminosarum bv. viciae strains was isolated from three brown-coal mining restoration fields of different age and plant cover (without and in the first and second year of alfalfa, Medicago sativa, cultivation) using two host species (Vicia hirsuta and Pisum sativum) as capture plants. The strains were genetically typed by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-generated 16S-23S ribosomal DNA intergenic spacer regions (IGS-RFLP) and characterized by plasmid profiles and RFLP analysis of amplified nodABC genes. The R. leguminosarum bv. viciae population was dominated by the same group of strains (irrespective of the trap plant used). According to type richness, the genetic diversity of indigenous R. leguminosarum in the second year of restoration was lower than in the first year and it resembled that of the fallow field, except for plasmid types, in which it was higher than that of the fallow field. Some of the less frequent nodABC genotypes were associated with distinct chromosomal IGS genotypes and symbiotic plasmids (pSyms) of different sizes, indicating that horizontal transfer and rearrangements of pSym can occur in natural environments. However, the dominant pSym and chromosomal genotypes were strictly correlated suggesting a genetically stable persistence of the prevailing R. leguminosarum bv, viciae genotypes in the absence of its host plant.

  4. Genetic Diversity through the Looking Glass: Effect of Enrichment Bias

    OpenAIRE

    Dunbar, J; White, S; Forney, L.

    1997-01-01

    The effect of enrichment bias on the diversity of 2,4-dichlorophenoxyacetate (2,4-D)-degrading (2,4-D(sup+)) bacteria recovered from soil was evaluated by comparing the diversity of isolates obtained by direct plating to the diversity of isolates obtained from 85 liquid batch cultures. By the two methods, a total of 159 isolates were purified from 1 g of soil and divided into populations based on repeated extragenic palindromic sequence PCR (rep-PCR) genomic fingerprints. Approximately 42% of...

  5. Measurement of quantitative species diversity on reclaimed coal mine lands: A brief overview of the Wyoming regulatory proposal

    International Nuclear Information System (INIS)

    The Wyoming Land Quality Division (LQD) Coal Rules and Regulations require mine operators to specify quantitative procedures for evaluating postmining species diversity and composition. Currently, permit commitments range from deferring to commit to a quantitative procedure until some future date to applying various similarity/diversity indices for comparison of reclaimed lands to native vegetation communities. Therefore, the LQD began trying to develop a standardized procedure to evaluate species diversity and composition, while providing operator flexibility. Review of several technical publications on the use of similarity and diversity indices, and other measurement techniques indicate that a consensus has not been reached on which procedure is most appropriate for use on reclaimed mine lands. In addition, implementation of many of the recommended procedures are not practical with regards to staff and data limitations. As a result, the LQD has developed an interim procedure, based on site-specific baseline data, to evaluate postmining species diversity and composition success with respect to bond release requests. This paper reviews many of the recommended procedures, outlines some of the pros and cons, and provides a specific example of how the proposed interim procedure was applied to an actual coal mine permit. Implementation of this or a similar procedure would allow for site-specific standardization of permits and regulatory requirements, thus reducing reviewulatory requirements, thus reducing review time and reducing some of the subjectivity surrounding a component of the Wyoming bond release requirements

  6. Genetically Diverse Group A Streptococci from Children in Far-Western Nepal Share High Genetic Relatedness with Isolates from Other Countries

    OpenAIRE

    Sakota, Varja; Fry, Alicia M.; Lietman, Thomas M.; Facklam, Richard R.; Li, Zhongya; Beall, Bernard

    2006-01-01

    The genetic diversity of group A streptococci (GAS) throughout much of the world has not been adequately explored. To assess genetic variation among GAS in western Nepal, 120 noninvasive GAS, collected from eight different villages, were genetically characterized using emm typing, sof sequencing, and multilocus sequence typing (MLST). A high level of genetic diversity was observed among these isolates, with 51 genotypes based upon 51 multilocus sequence types (STs), 45 emm sequence types, and...

  7. Estimation of Genetic Diversity of Four Chrysanthemum Mini Cultivars Using RAPD

    Directory of Open Access Journals (Sweden)

    J. Chatterjee

    2005-01-01

    Full Text Available The objective of the present study was to estimate the genetic relationship among the different Chrysanthemum cultivars with relation to their morphological and biochemical characteristics and geographical distribution. DNA fingerprinting using RAPD is very easy and inexpensive way to study the genetic diversity. Genetic distance between four mini Chrysanthemum cultivars was studied through RAPD analysis. Total of 40 primers have been screened from which four have been trailed for all the four genotypes. Similarity among the cultivars was very high showing low genetic diversity, which is quite expected. One of these primers can differentiate cultivars from each other. So RAPD can be used successfully to estimate the genetic distance and also for the species identification.

  8. Approximate Bayesian computation reveals the factors that influence genetic diversity and population structure of foxsnakes.

    Science.gov (United States)

    Row, J R; Brooks, R J; MacKinnon, C A; Lawson, A; Crother, B I; White, M; Lougheed, S C

    2011-11-01

    Contemporary geographical range and patterns of genetic diversity within species reflect complex interactions between multiple factors acting across spatial and temporal scales, and it is notoriously difficult to disentangle causation. Here, we quantify patterns of genetic diversity and genetic population structure using mitochondrial DNA sequences (101 individuals, cytochrome b) and microsatellites (816 individuals, 12 loci) and use Approximate Bayesian computation methods to test competing models of the demographic history of eastern and western foxsnakes. Our analyses indicate that post-glacial colonization and past population declines, probably caused by the infilling of deciduous forest and cooler temperatures since the mid-Holocene, largely underpin large-scale genetic patterns for foxsnakes. At finer geographical scales, our results point to more recent anthropogenic habitat loss as having accentuated genetic population structure by causing further declines and fragmentation. PMID:21848978

  9. Genetic diversity and relationships among Italian Merino derived breeds assessed by microsatellites

    Directory of Open Access Journals (Sweden)

    Francesca Maria Sarti

    2010-01-01

    Full Text Available The conservation of genetic variability is one of the main objectives in the field of genetics applied to domestic livestock. Among molecular markers, microsatellites are particularly appreciated and widely utilized for the study of animal genome. In this study a genetic characterization of three Italian Merino derived sheep breeds was carried out by 30 microsatellites markers; the genetic relationships between these breeds and the Spanish ancestors were also investigated. All the microsatellites examined resulted polymorphic and a total of 375 alleles were detected. FIS values of the three Italian Merinos demonstrate a low level of inbreeding. The results show a good genetic variability of all the studied breeds; at the same time, the genetic identity of each breed is confirmed. These molecular data can be utilized to improve the present selection schemes and the plans to preserve genetic diversity.

  10. Estimation of breed contributions to present and future genetic diversity of 44 North Eurasian cattle breeds using core set diversity measures

    OpenAIRE

    Popov Ruslan; Kiselyova Tatyana; Ivanova Zoya; Ammosov Innokentyi; Vilkki Johanna; Kalm Ernst; Li Meng; Tapio Ilma; Kantanen Juha; Bennewitz Jörn; Meuwissen Theo HE

    2006-01-01

    Abstract Extinction of breeds threatens genetic diversity of livestock species. The need to conserve genetic diversity is widely accepted but involves in general two questions: (i) is the expected loss of diversity in a set of breeds within a defined future time horizon large enough to establish a conservation plan, and if so (ii) which breeds should be prioritised for such a conservation plan? The present study uses a marker assisted methodology to address these questions. The methodology co...

  11. Genetic diversity, population structure, conservation and utilization of Theobroma cacao L., genetic resources in the Dominican Republic

    Science.gov (United States)

    Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic, which ranks 11th in the world and number one in organic cacao exports. In an effort to identify propagation mistakes, and estimate genetic diversity and population structure in cacao germplasm accessions a...

  12. Genome-wide genetic diversity of rove beetle populations along a metal pollution gradient.

    Science.gov (United States)

    Giska, Iwona; Babik, Wies?aw; van Gestel, Cornelis A M; van Straalen, Nico M; Laskowski, Ryszard

    2015-09-01

    To what extent chemical contamination affects genetic diversity of wild populations remains an open question in ecotoxicology. Here we used a genome-wide approach (615 nuclear RADseq loci containing 3017 SNPs) and a mtDNA fragment (ATP6) to analyze the effect of long-term exposure to elevated concentrations of metals (Cd, Pb, Zn) on genetic diversity in rove beetle (Staphylinus erythropterus) populations living along a pollution gradient in Poland. In total, 96 individuals collected from six sites at increasing distance from the source of pollution were analyzed. We found weak differentiation between populations suggesting extensive gene flow. The highest genetic diversity was observed in a population inhabiting the polluted site with the highest metal availability. This may suggest increased mutation rates, possibly in relation to elevated oxidative stress levels. The polluted site could also act as an ecological sink receiving numerous migrants from neighboring populations. Despite higher genetic diversity at the most polluted site, there was no correlation between the genetic diversity and metal pollution or other soil properties. We did not find a clear genomic signature of local adaptation to metal pollution. Like in some other cases of metal tolerance in soil invertebrates, high mobility may counteract possible effects of local selective forces associated with soil pollution. PMID:25988435

  13. Genetic diversity of Persea bombycina from goalpara district of Assam, India

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    Azizur Rahman

    2012-02-01

    Full Text Available Assam of the northeastern region of India is unique in terms of its rich biodiversity and multiple ethnicity of its people. The impact of the resultant socio-religio-cultural diversity is also reflected in the diverse traditional ways of silkworm farming. We report the genetic diversity of Persea bombycinaSom” from different locations of Goalpara district of Assam, India, where random amplified polymorphic DNA (RAPD marker was used in this study. RAPD analyses of ten genotypes of “Som” from Goalpara district of Assam, India with B19 RAPD primer generated 86 bands, showing an average of 8.6 bands per sample and 30.2% (26 bands of these were polymorphic. The number of bands per accession ranged from 5 to 10 with a mean of 8.6 and the size range of the amplified bands was 250 - 6000 bp. In a UPGMA phenetic dendrogram based on Jaccard’s coefficient, the P. bombycina accessions showed a high level of genetic variation, as indicated by genetic similarity and revealed 10 “Som” genotypes in to three major clusters. This study may be useful in identifying diverse genetic stocks of P. bombycina, which may then be conserved on a priority basis. The RAPD primer used in this study was able to distinguish all the 10 genotypes of “Som” plants, which can be used to assess genetic diversity.

  14. Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses

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    Blaney Kate M

    2008-12-01

    Full Text Available Abstract Background Febrile respiratory illness (FRI has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV and enteroviruses (HEV which are frequent causes of FRI. Resequencing Pathogen Microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking. Results Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV, which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen Microarray RPM-Flu v.30/31 (Tessarae RPM-Flu. The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level. Conclusion This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.

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

    International Nuclear Information System (INIS)

    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)

  16. Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

    OpenAIRE

    Grzebelus, Dariusz; Iorizzo, Massimo; Senalik, Douglas; Ellison, Shelby; Cavagnaro, Pablo; Macko-podgorni, Alicja; Heller-uszynska, Kasia; Kilian, Andrzej; Nothnagel, Thomas; Allender, Charlotte; Simon, Philipp W.; Baranski, Rafal

    2013-01-01

    Carrot is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to develop a saturated genetic linkage map of carrot. We analyzed a set of 900 DArT markers in a collection of plant materials comprising 94 cultivated and 65 wild carrot accessions. The accessions were attribu...

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

    Directory of Open Access Journals (Sweden)

    Lutz Richard A

    2011-04-01

    Full Text Available Abstract 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 Galápagos 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 (recolonization events.

  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. Description and analysis of genetic diversity among squash accessions

    Scientific Electronic Library Online (English)

    Athanasios L., Tsivelikas; Olga, Koutita; Anastasia, Anastasiadou; George N., Skaracis; Ekaterini, Traka-Mavrona; Metaxia, Koutsika-Sotiriou.

    2009-04-01

    Full Text Available A abobrinha de inverno compõe um cultivo agrícola com valor econômico determinado exercendo, no entanto, um papel importante em zonas caracterizadas por um cultivo menos intensivo. Na Grécia, o cultivo da abobrinha se baseia, principalmente, em variedades locais conservadas a muitos anos por agricul [...] tores locais. Uma parte do cultivo nuclear da abobrinha, que é conservada pelo Banco Grego de Genes, foi melhorada utilizando-se dados morfológicos e moleculares, especialmente dezesseis cultivos de abobrinha classificados incompletamente, que foram diferenciados apenas com base em características morfológicas, em relação a uma avaliação à resistência contra o Fusarium Oxysporum, em dois isolamentos. Foi realizada uma análise molecular utilizando DNA Polimórficos Casual Amplificados índices (RAPDs), revelando um alto nível de polimorfismo. Para estudar a diversidade genética entre a coleção de abobrinhas, um procedimento de agrupamento foi realizado usando-se o algoritmo U.P.G.M.A. Dois dendrogramas independentes, um morfofisiológico e outro para dados moleculares, foram coletados, classificando as coleções em dois e três grupos básicos, respectivamente. Apesar do número diferente dos grupos, foram introduzidas muitas semelhanças entre os dois dendrogramas e um terceiro dendrograma foi produzido como resultado da combinação dos dois primeiros, baseado na distância de Gower e no algoritmo de agrupamento U.P.G.M.A. Para determinar o número ótimo dos grupos, a aproximação "upper tail" foi aplicada. O grupo mais aceitável das coleções foi conseguido usando-se índices RAPD, assim como a combinação dos dois grupos de dados diferentes, classificando as coleções em três grupos consideravelmente diferentes. Os grupos que correspondem às três espécies cultivadas diferentemente, que correspondem às três espécies cultivadas diferentemente por C.máxima Duch., C.moschata Duch. e C. pepo L. além disso, os mesmos resultados foram conseguidos usando-se a "Principal Component Analysis". Abstract in english In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium [...] oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

  20. High genetic diversity and small genetic variation among populations of Magnolia wufengensis (Magnoliaceae), revealed by ISSR and SRAP marker

    Scientific Electronic Library Online (English)

    Liyuan, Chen; Faju, Chen; Suichao, He; Luyi, Ma.

    2014-11-01

    Full Text Available Background Genetic diversity and genetic variation of 10 populations and subpopulations of Magnolia wufengensis, a new and endangered endemic species, were examined by inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) molecular markers. Compared with other endang [...] ered endemic Magnolia taxa, M. wufengensis holds a relatively high level of genetic variation. Result Total genetic diversity was found to be 87.7% for ISSR and 88.0% for SRAP markers. For polymorphic loci (P), the effective mean number of alleles (Ae) was 1.414 for ISSR markers and 1.458 for SRAP markers, while the mean expected heterozygosity (H) was 0.256 using ISSR and 0.291 for SRAP markers. Within-population variation was estimated for P as 74.9% using ISSR and 74.6% with SRAP markers; the number of alleles Ae was 1.379 with ISSR and 1.397 for SRAP and H 0.235 with ISSR and 0.247 for SRAP markers. Conclusion The analysis of molecular variation of both ISSR and SRAP marker systems indicated that most genetic variation is within populations, with values of 90.64% and 82.92% respectively. Mantel tests indicated a moderate association between the two marker systems and a low correlation between genetic and geographic distances. High levels of genetic diversity and low levels of population divergence suggest that genetic drift is not currently of great concern for this species. Severe habitat loss and fragmentation, predominantly ascribed to anthropogenic pressures, caused in-situ developing restriction of this species. Action for conserving this rare species for its long-term survival should be taken immediately.

  1. Genetic diversity of Mycosphaerella fijiensis in Brazil analyzed using an ERIC-PCR marker.

    Science.gov (United States)

    Silva, G F; Paixão, R D V; Queiroz, C B; Santana, M F; Souza, A; Sousa, N R; Hanada, R E; Gasparotto, L

    2014-01-01

    The Enterobacterial repetitive intergenic consensus (ERIC) marker was used to analyze the genetic variability of Mycosphaerella fijiensis, the causative agent of Black Sigatoka disease in banana plants. A total of 123 isolates were used, which were divided into populations based on their original hosts and collection sites in Brazil. A total of 9 loci were amplified, 77.8% of which were found to be polymorphic. The genetic diversity found in the population was 0.20. Analysis of molecular variance (AMOVA) demonstrated that the highest level of genetic variation is within populations. Cluster analysis revealed three main groups in Brazil, with no correlation between geographic and genetic distance. PMID:25299083

  2. Landscape prerequisites for the survival of a modelled metapopulation and its neutral genetic diversity are affected by climate change

    OpenAIRE

    Cobben, M.M.P.; Verboom, J.; Opdam, P.F.M.; Hoekstra, R.F.; Jochem, R.; Smulders, M. J. M.

    2012-01-01

    In response to climate change a species may move, adapt, or go extinct. For the adaptability of a population its genetic diversity is essential, but climate change-induced range shifts can cause a loss of genetic diversity. We investigated how landscape structure affects the level and distribution of genetic diversity in metapopulations subject to climate change-induced range shifts. For this we used the spatially explicit, individual-based model METAPHOR which simulates metapopulation demogr...

  3. Assessment of Genetic Diversity and Distance of Lipoprotein Lipase Between Red Jungle Fowl and Domestic Chicken Breeds

    OpenAIRE

    Musa, Hassan H.; Cheng, Jin H.; Bao, Wen B.; Wu, Sheng L.; Qi Xu; Chen, Guo H.

    2007-01-01

    Polymerase chain reaction single strand conformation polymorphism (PCR-SSCP) was used to analyze lipoprotein lipase gene polymorphism in Red Jungle Fowl (Gallus gallus spadiceus), Rugao, Anka, Wenchang and Slikies chicken populations. The results shows high lipoprotein lipase gene diversity, effective number of allele and Shannon information index in Silikes population. The average total genetic diversity (HT), genetic diversity within population (HS) and coefficient of genetic differentiatio...

  4. Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

    OpenAIRE

    Furlan, Elise; Stoklosa, J; Griffiths, J.; Gust, N; ELLIS, R; Huggins, R M; Weeks, A.R

    2012-01-01

    Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, ...

  5. Positive correlation between genetic diversity and fitness in a large, well-connected metapopulation

    Directory of Open Access Journals (Sweden)

    Baguette Michel

    2008-11-01

    Full Text Available Abstract Background Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range. Results We demonstrate that: (1 lower genetic diversity was coupled to a sharp decrease in adult lifetime expectancy, a key component of individual fitness; (2 genetic diversity was positively correlated to the number of dispersing individuals (indicative of landscape functional connectivity and adult population size; (3 parameters inferred from capture-recapture procedures (population size and dispersal events between patches correlated much better with genetic diversity than estimates usually used as surrogates for population size (patch area and descriptors of habitat quality and dispersal (structural connectivity index. Conclusion Our results suggest that dispersal is a very important factor maintaining genetic diversity. Even at a very local spatial scale in a metapopulation consisting of large high-density populations interconnected by considerable dispersal rates, genetic diversity can be decreased and directly affect the fitness of individuals. From a biodiversity conservation perspective, this study clearly shows the benefits of both in-depth demographic and genetic analyses. Accordingly, to ensure the long-term survival of populations, conservation actions should not be blindly based on patch area and structural isolation. This result may be especially pertinent for species at their range margins, particularly in this era of rapid environmental change.

  6. Genetic diversity in populations of asexual and sexual bag worm moths (Lepidoptera: Psychidae

    Directory of Open Access Journals (Sweden)

    Mappes Johanna

    2005-06-01

    Full Text Available Abstract Background Despite the two-fold cost of sex, most of the higher animals reproduce sexually. The advantage of sex has been suggested to be its ability, through recombination, to generate greater genetic diversity than asexuality, thus enhancing adaptation in a changing environment. We studied the genetic diversity and the population structure of three closely related species of bag worm moths: two strictly sexual (Dahlica charlottae and Siederia rupicolella and one strictly asexual (D. fennicella. These species compete for the same resources and share the same parasitoids. Results Allelic richness was comparable between the sexual species but it was higher than in the asexual species. All species showed high heterozygote deficiency and a large variation was observed among FIS values across loci and populations. Large genetic differentiation was observed between populations confirming the poor dispersal ability of these species. The asexual species showed lower genotype diversity than the sexual species. Nevertheless, genotype diversity was high in all asexual populations. Conclusion The three different species show a similar population structure characterised by high genetic differentiation among populations and low dispersal. Most of the populations showed high heterozygote deficiency likely due to the presence of null alleles at most of the loci and/or to the Wahlund effect. Although the parthenogenetic D. fennicella shows reduced genetic diversity compared to the sexual species, it still shows surprisingly high genotype diversity. While we can not totally rule out the presence of cryptic sex, would explain this high genotype diversity, we never observed sex in the parthenogenetic D. fennicella, nor was there any other evidence of this. Alternatively, a non-clonal parthenogenetic reproduction, such as automictic thelytoky, could explain the high genotypic diversity observed in D. fennicella.

  7. Genetic Diversity of Dalmatian Sage (Salvia officinalis L. as Assessed by RAPD Markers

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    Zlatko Liber

    2014-09-01

    Full Text Available Dalmatian or common sage (Salvia officinalis L. is an outcrossing plant species native to East Adriatic coast. Random Amplified Polymorphic DNA markers (RAPD were used to analyze genetic diversity and structure of ten natural populations from the East-Adriatic coastal region. The highest genetic diversity was found in populations from the central and south Dalmatia, while the highest frequency down-weighted marker values were found in the northernmost populations and the southern most inland population. Although analysis of molecular variance (AMOVA revealed that most of the genetic diversity was attributable to differences among individuals within populations, highly significant ?ST values suggested the existence of genetic differentiation among populations. By assuming Hardy-Weinberg equilibrium within populations, the calculated FST value among population was moderate. Bayesian model-based clustering method revealed that at K = 2 all individuals belonging to two northern populations were assigned to a separate cluster from the individuals belonging to the rest of the population. At K = 3, the newly formed cluster grouped the majority of individuals belonging to populations from central Dalmatia. The high correlation between matrices of genetic and geographical distances showed that isolation by distance may play a considerable role in overall structuring of the genetic diversity.

  8. Patterns of genetic diversity in southern and southeastern Araucaria angustifolia (Bert. O. Kuntze relict populations

    Directory of Open Access Journals (Sweden)

    Maria Isabel Ferreira de Souza

    2009-01-01

    Full Text Available Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil of Araucaria angustifolia in comparison with populations in the main area of the species continuous natural distribution (southern Brazil, was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27, despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16, thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10%-15%. From Bayesian analysis, it is suggested that the nine populations tested form five "genetic clusters" (K = 5. Five of these populations, located in the northernmost limit of distribution of the species, represent three "genetic clusters". These results are in agreement with the pattern of geographic distribution of the studied populations.

  9. 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. PMID:25178197

  10. Patterns of genetic diversity in southern and southeastern Araucaria angustifolia (Bert.) O. Kuntze relict populations

    Scientific Electronic Library Online (English)

    Maria Isabel Ferreira de, Souza; Fabiano, Salgueiro; Mariana, Carnavale-Bottino; Durvalina Benedita, Félix; Marcio, Alves-Ferreira; Juliana Vitoria Messias, Bittencourt; Rogério, Margis.

    Full Text Available Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil) of Araucaria angustifolia in comparison with populations in the main [...] area of the species continuous natural distribution (southern Brazil), was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27), despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16), thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10%-15%). From Bayesian analysis, it is suggested that the nine populations tested form five "genetic clusters" (K = 5). Five of these populations, located in the northernmost limit of distribution of the species, represent three "genetic clusters". These results are in agreement with the pattern of geographic distribution of the studied populations.

  11. 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 ?PT 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.

  12. Large-scale longitudinal gradients of genetic diversity: a meta-analysis across six phyla in the Mediterranean basin

    OpenAIRE

    Conord, Cyrille; Gurevitch, Jessica; Fady, Bruno

    2012-01-01

    Biodiversity is the diversity of life at all scales, from genes to ecosystems. Predicting its patterns of variation across the globe is a fundamental issue in ecology and evolution. Diversity within species, that is, genetic diversity, is of prime importance for understanding past and present evolutionary patterns, and highlighting areas where conservation might be a priority. Using published data on the genetic diversity of species whose populations occur in the Mediterranean basin, we calcu...

  13. Status and diversity of arbuscular mycorrhizal fungi and its role in natural regeneration on limestone mined spoils

    Directory of Open Access Journals (Sweden)

    ANUJ KUMAR SINGH

    2011-04-01

    Full Text Available Singh AK, Jamaluddin (2011 Status and diversity of arbuscular mycorrhizal fungi and its role in natural regeneration on limestone mined spoils. Biodiversitas 12: 107-111. Limestone mined spoils are devoid of adequate population of beneficial microbial flora. Arbuscular mycorrhizal fungi (AMF are very important constituent of plant- soil-microbe system. In mined spoils the population of AMF is greatly reduced and hence the spoils become very inhospitable for establishment of vegetation. In the present investigation, status of AMF population and its effect on natural regeneration process is studied. It is well known fact that the arbuscular mycorrhizal fungi play very important role in establishment of vegetation in degraded lands. Plantation of seedlings inoculated with arbuscular mycorrhizal fungi provide favorable soil conditions for naturally growing vegetation in the mined overburden spoils. Physico-chemical properties of soil are converted suitable for planted species and thus it allows other species to grow and also provide shade to protect the herbaceous vegetation. Introduction of plant species attracts immigration of other species and if they established, may result into a very distinctive floral cover on disturbed lands. Thus, invasion of native plant species along with planted species may play a significant role in increasing the plant diversity on mined

  14. 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.

  15. Genetic Diversity and Population Structure of Siberian apricot (Prunus sibirica L. in China

    Directory of Open Access Journals (Sweden)

    Ming Li

    2013-12-01

    Full Text Available The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow, and largely attributable to the cross-pollination and self-incompatibility reproductive system. A STRUCTURE (model-based program analysis revealed that the 21 populations can be divided into two main groups, mainly based on geographic differences and genetic exchanges. The entire wild Siberia apricot population in China could be divided into two subgroups, including 107 accessions in subgroup (SG 1 and 147 accessions in SG 2. A Mantel test revealed a significant positive correlation between genetic and geographic distance matrices, and there was a very significant positive correlation among three marker datasets. Overall, we recommend a combination of conservation measures, with ex situ and in situ conservation that includes the construction of a core germplasm repository and the implement of in situ conservation for populations HR, MY, and ZY.

  16. Genetic Structure and Diversity of the Giant Frog (Limnonectes blythii in Northern Thailand

    Directory of Open Access Journals (Sweden)

    C. Suwannapoom

    2012-08-01

    Full Text Available The aim of this study is to analyse genetic diversity, structure and differentiation of the giant frogs (Limnonectes blythii. One hundred and sixty four individuals from 4 populations in Mae Hong Son Province, Thailand were used for the analysis of genetic polymorphism at 7 microsatellite loci. The collection showed considerable polymorphism with observed number of alleles per locus ranging for seven different loci, with an average of 3.4 alleles per locus. Mean genetic diversity of the four populations with moderate level, but in populations with lower genetic diversity. Furthermore, the NJ tree approach clustering conWrmed the results of PAM is more differentiated than the others. The signiWcant levels of genetic structure among the sites were found in which could be resulting from isolation by distance rather than a position relative to habitat. The results of this study indicate that genetic structure could be useful for evaluation of neutral genetic variation particularly as the basis for inferring population and species capacity for species conservation and management decisions.

  17. Genetic Diversity in Introduced Golden Mussel Populations Corresponds to Vector Activity

    Science.gov (United States)

    Ghabooli, Sara; Zhan, Aibin; Sardiña, Paula; Paolucci, Esteban; Sylvester, Francisco; Perepelizin, Pablo V.; Briski, Elizabeta; Cristescu, Melania E.; MacIsaac, Hugh J.

    2013-01-01

    We explored possible links between vector activity and genetic diversity in introduced populations of Limnoperna fortunei by characterizing the genetic structure in native and introduced ranges in Asia and South America. We surveyed 24 populations: ten in Asia and 14 in South America using the mitochondrial cytochrome c oxidase subunit I (COI) gene, as well as eight polymorphic microsatellite markers. We performed population genetics and phylogenetic analyses to investigate population genetic structure across native and introduced regions. Introduced populations in Asia exhibit higher genetic diversity (HE?=?0.667–0.746) than those in South America (HE?=?0.519–0.575), suggesting higher introduction effort for the former populations. We observed pronounced geographical structuring in introduced regions, as indicated by both mitochondrial and nuclear markers based on multiple genetic analyses including pairwise ?ST, FST, Bayesian clustering method, and three-dimensional factorial correspondence analyses. Pairwise FST values within both Asia (FST?=?0.017–0.126, P?=?0.000–0.009) and South America (FST?=?0.004–0.107, P?=?0.000–0.721) were lower than those between continents (FST?=?0.180–0.319, P?=?0.000). Fine-scale genetic structuring was also apparent among introduced populations in both Asia and South America, suggesting either multiple introductions of distinct propagules or strong post-introduction selection and demographic stochasticity. Higher genetic diversity in Asia as compared to South America is likely due to more frequent propagule transfers associated with higher shipping activities between source and donor regions within Asia. This study suggests that the intensity of human-mediated introduction vectors influences patterns of genetic diversity in non-indigenous species. PMID:23533614

  18. Prevalence, antimicrobial susceptibility, and genetic diversity of Pseudomonas aeruginosa as intestinal colonizer in the community.

    Science.gov (United States)

    Valenza, Giuseppe; Tuschak, Christian; Nickel, Silke; Krupa, Elzbieta; Lehner-Reindl, Verena; Höller, Christiane

    2015-09-01

    In this study we determined the prevalence of intestinal carriage, the antimicrobial susceptibility rates, and the genetic diversity of Pseudomonas aeruginosa in the community. From July 2010 to December 2011, a total of 2110 nonreplicate fecal samples from individuals living in Bavaria were collected. Samples were screened for P. aeruginosa by a selective medium and antimicrobial susceptibility was determined by disc diffusion technique. Genetic diversity was assessed by multilocus sequence typing (MLST). Intestinal colonization was detected in 31 of 2110 (1.47%) individuals. None of the isolates showed resistance to aztreonam, imipenem, meropenem, ciprofloxacin, amikacin or colistin. Twenty-five isolates could be assigned to 20 different sequence types (STs), whereas the remaining 6 could not be assigned. Interestingly, four isolates belonged to ST253. These data show that intestinal colonization by P. aeruginosa occurs in the community with high genetic diversity and low rates of antimicrobial resistance. PMID:25832457

  19. Consequences of harvesting for genetic diversity in American ginseng (Panax quinquefolius L.): A simulation study

    Science.gov (United States)

    Cruse-Sanders, J. M.; Hamrick, J.L.; Ahumada, J.A.

    2005-01-01

    American ginseng, Panax quinquefolius L., is one of the most heavily traded medicinal plants in North America. The effect of harvest on genetic diversity in ginseng was measured with a single generation culling simulation program. Culling scenarios included random harvest at varying levels, legal limit random harvest and legal limit mature plant harvest. The legal limit was determined by the proportion of legally harvestable plants per population (% mature plants per population). Random harvest at varying levels resulted in significant loss of genetic diversity, especially allelic richness. Relative to initial levels, average within-population genetic diversity (H e) was significantly lower when plants were culled randomly at the legal limit (Mann-Whitney U = 430, p ginseng populations. ?? Springer 2005.

  20. Self-Adaptation Mechanism to Control the Diversity of the Population in Genetic Algorithm

    CERN Document Server

    Jassadapakorn, Chaiwat; 10.5121/ijcsit.2011.3409

    2011-01-01

    One of the problems in applying Genetic Algorithm is that there is some situation where the evolutionary process converges too fast to a solution which causes it to be trapped in local optima. To overcome this problem, a proper diversity in the candidate solutions must be determined. Most existing diversity-maintenance mechanisms require a problem specific knowledge to setup parameters properly. This work proposes a method to control diversity of the population without explicit parameter setting. A self-adaptation mechanism is proposed based on the competition of preference characteristic in mating. It can adapt the population toward proper diversity for the problems. The experiments are carried out to measure the effectiveness of the proposed method based on nine well-known test problems. The performance of the adaptive method is comparable to traditional Genetic Algorithm with the best parameter setting.

  1. Evaluation of Genetic Diversity of Iranian Pomegranate Cultivars Using Fruit Morphological Characteristics and AFLP Markers

    Directory of Open Access Journals (Sweden)

    Mehdi KHAYAT

    2012-05-01

    Full Text Available The present research evaluated the diversity of a number of Iranian pomegranate cultivars using fruit morphological characteristics and AFLP markers. Thirty-one pomegranate cultivars were collected from Yazd Pomegranate Collection in Iran to study their diversity. Seven AFLP primer combinations were used to amplify a total of 112 polymorphic fragments (47.26%. By use of AFLPs, a low genetic diversity level was detected among cultivars. The relationship between fruit characteristics was analyzed using the principal component analysis (PCA. The cluster analysis based on both fruit characteristics and AFLP data indicated that cultivars were not grouped according to their geographic origins. Moreover, the correlation between the diversity matrix based on fruit characteristics and Dice’s genetic similarity coefficient was insignificant (r=0.06. The results obtained from this study can improve the conservation and management of pomegranate germplasm resources and could be helpful in optimizing breeding programs.

  2. Bringing genetic diversity to the forefront of conservation policy and management

    DEFF Research Database (Denmark)

    Hoban, S.M.; Hauffe, H.C.

    2013-01-01

    In this essay we explore questions on how to increase the visibility and utility of genetic information for biodiversity managers and policy makers. This is discussed in the light of Aichi CBD Target 13, which for the first time impels signatories to minimise genetic erosion and safeguard genetic diversity. Drawing on qualitative results from a questionnaire sent to European conservation professionals by the ConGRESS Framework 7 Support Action (http://www.congressgenetics.eu), we summarise our preliminary findings on the attitudes and experiences of European conservation professionals in using genetics. We then discuss the implications of these findings for academics involved in conservation genetics and suggest that a much closer partnership between academic conservation geneticists and conservation practitioners is necessary if the full potential of genetic tools in conservation is to be realised. © 2013 Springer Science+Business Media Dordrecht.

  3. Genetic diversity assessment in sorghum accessions using qualitative morphological and amplified fragment length polymorphism markers

    Scientific Electronic Library Online (English)

    Abe Shegro, Gerrano; Maryke Tine, Labuschagne; Angeline, van Biljon; Nemera Geleta, Shargie.

    2014-10-01

    Full Text Available Qualitative morphological and amplified fragment length polymorphism (AFLP) markers were compared for assessment of genetic diversity. Nine qualitative morphological traits were recorded to compare genetic relationships among 17 sorghum accessions with information derived from six AFLP primer combin [...] ations analysis. The mean morphological genetic similarity was lower in comparison to similarity computed using AFLP markers. Genetic similarity measured by AFLP markers was similar within the Ethiopian and South African material, as well as between South African and Ethiopian material. Morphological similarity was much higher in the Ethiopian material than in the South African material, indicating that the genotypes were related. The two techniques described genetic variability in different ways. Dendrogram generated from the morphological data matrix separated accession 216737 as being genetically distinct from the rest of the accessions. Accessions M101 and 97MW6127 were the most dissimilar accessions based on AFLP data.

  4. Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies.

    Science.gov (United States)

    Nyman, Tommi; Valtonen, Mia; Aspi, Jouni; Ruokonen, Minna; Kunnasranta, Mervi; Palo, Jukka U

    2014-09-01

    Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea 'mainland' and two the 'aquatic islands' composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control-region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post-colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea. PMID:25535558

  5. A simple method for estimating genetic diversity in large populations from finite sample sizes

    Directory of Open Access Journals (Sweden)

    Rajora Om P

    2009-12-01

    Full Text Available Abstract Background Sample size is one of the critical factors affecting the accuracy of the estimation of population genetic diversity parameters. Small sample sizes often lead to significant errors in determining the allelic richness, which is one of the most important and commonly used estimators of genetic diversity in populations. Correct estimation of allelic richness in natural populations is challenging since they often do not conform to model assumptions. Here, we introduce a simple and robust approach to estimate the genetic diversity in large natural populations based on the empirical data for finite sample sizes. Results We developed a non-linear regression model to infer genetic diversity estimates in large natural populations from finite sample sizes. The allelic richness values predicted by our model were in good agreement with those observed in the simulated data sets and the true allelic richness observed in the source populations. The model has been validated using simulated population genetic data sets with different evolutionary scenarios implied in the simulated populations, as well as large microsatellite and allozyme experimental data sets for four conifer species with contrasting patterns of inherent genetic diversity and mating systems. Our model was a better predictor for allelic richness in natural populations than the widely-used Ewens sampling formula, coalescent approach, and rarefaction algorithm. Conclusions Our regression model was capable of accurately estimating allelic richness in natural populations regardless of the species and marker system. This regression modeling approach is free from assumptions and can be widely used for population genetic and conservation applications.

  6. Enhancing Genetic Diversity Through Induced Mutagenesis in Vegetatively Propagated Plants

    International Nuclear Information System (INIS)

    Conventionally, crop improvement strategies rely not only on the availability of heritable genetic variations within utilizable genetic backgrounds, but also on the transferability of the traits they control through hybridizations between the parental stocks. Procedures for producing hybrids of sexually reproducing plants are routine, while for vegetatively propagated plants, hybridizations are usually impractical. Therefore, the improvement of crops that lack botanical seeds necessitates alternative strategies for generating and utilizing genetic variations. Induced mutagenesis generates allelic variants of genes that modulate the expression of traits. Some of the major drawbacks to the widespread use of induced mutations for vegetatively propagated plants include the difficulties of heterozygosity of the genetic backgrounds, the incidence of chimeras and the confounding effects of linkage drags in putative mutants. In general, the inherent inefficiencies of time and space economies associated with induced mutagenesis are further exacerbated in vegetatively propagated crops mostly on account of the need for continual propagation. We highlight the mitigating roles on these drawbacks of judicious integration of validated biotechnologies and other high throughput forward genetics assays in induced mutagenesis pipelines. Using cassava and banana as models, we demonstrate the use of cell and tissue biology to achieve homozygosity, minimize or eliminate chimeras, and signi minimize or eliminate chimeras, and significantly shorten the duration of the generation of mutants. Additionally, use of these biotechnologies to attain significantly reduced propagation footprints while evaluating putative mutants without compromising population size is also presented. We also posit that molecular biology approaches, especially reverse genetics and transcriptome assays, contribute significantly to enhancing the efficiency levels of the induced mutagenesis processes. The implications for crop improvement and functional genomics via the concerted application of biotechnologies in the generation, identification, and tagging of mutation events in the genomes of vegetatively propagated crops are also discussed. (author)

  7. Assessment of genetic diversity by DNA profiling and its significance in silkworm, Bombyx mori.

    Science.gov (United States)

    Nagaraju, J G; Singh, L

    1997-08-01

    Silkworm genetic resources that are being maintained in different countries are yet to be adequately tapped to develop elite varieties that are suited to different agro-eco-climatic conditions of countries like India. This is mostly due to unavailability of efficient protocols that could uncover usable genetic variability in silkworms. Molecular markers are known to provide unambiguous estimates of genetic variability of populations since they are independent of confounding effects of environment. The DNA fingerprinting assays, based on random amplified polymorphic DNA (RAPD) and banded krait minor satellite DNA (Bkm) 2(8) multilocus probes, which successfully characterise the diverse silkworm genotypes at their DNA level, are described. The use of these two DNA fingerprinting assays in estimation of within- and between-population genetic diversity is discussed. PMID:9378144

  8. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, caviidae) in Colombia

    Scientific Electronic Library Online (English)

    William, Burgos-Paz; Mario, Cerón-Muñoz; Carlos, Solarte-Portilla.

    Full Text Available The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allel [...] ic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p

  9. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers

    OpenAIRE

    Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh

    2013-01-01

    A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 lan...

  10. Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

    OpenAIRE

    Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed

    2014-01-01

    Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal ...

  11. Genetic Diversity among Flue-cured Tobacco Cultivars Based on RAPD and AFLP Markers

    Scientific Electronic Library Online (English)

    Han Yao, Zhang; Xiao Zhen, Liu; Chuan Sheng, He; Yu Ming, Yang.

    1097-11-01

    Full Text Available The aim of this work was to study the genetic diversity among flue-cured tobacco cultivars. RAPD and AFLP analyses were used to assess the genetic similarity among selected accessions of flue-cured tobacco. Seventy eight RAPD and 154 AFLP polymorphic bands were obtained and used to assess the geneti [...] c diversity among 28 tobacco accessions. The cultivar relationships were estimated through the cluster analysis (UPGMA) based on RAPD data and AFLP data. The accessions were grouped into three major clusters and these shared common ancestry clustered together.

  12. Assessment of genetic diversity among different indigenous Xanthomonas isolates via RAPD and ISSR

    Directory of Open Access Journals (Sweden)

    Fatima Sabin

    2012-01-01

    Full Text Available The genetic diversity among seven Xanthomonas isolates representing four species was assessed using RAPD and ISSR PCR-based techniques. Both techniques revealed high degrees of polymorphisms among the studied isolates. A cluster dendrogram based on the combined data of RAPD and ISSR showed that genetic diversity exists in local isolates of Xanthomonas. In terms of percentage similarity values, the genomic variation was found to be in the range of 29.29% - 100% among the isolates. X. campestris (Mangifera indica remained unclustered in cluster dendrogram and revealed a unique genomic profile compared to other isolates used in this study.

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

    OpenAIRE

    Tang, G. Q.; Xue, J.; Lian, M. J.; Yang, R. F.; Liu, T. F.; Zeng, Z. Y.; Jiang, A. A.; Jiang, Y. Z.; Zhu, L.; Bai, L.; Wang, Z.; Li, X. W.

    2013-01-01

    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 i...

  14. AFLP analysis of the genetic diversity of Meloidogyne chitwoodi and M. fallax, major agricultural pests.

    Science.gov (United States)

    Fargette, Mireille; Lollier, Virginie; Phillips, Mark; Blok, Vivian; Frutos, Roger

    2005-05-01

    M. chitwoodi and M. fallax populations are clustered and separated from the other species studied. The genetic diversity observed for M. incognita, M. arenaria, M. javanica, M. hapla, and M. mayaguensis correlates well with the previously validated species. Two main groups can be identified within the M. chitwoodi/M. fallax cluster, the first group comprises only M. chitwoodi populations whereas the second group is made of M. chitwoodi and M. fallax populations. Moreover, M. chitwoodi displays a higher genetic diversity than M. fallax and is characterised by the presence of several clusters. PMID:15948634

  15. Genetic diversity and population structure of leafy kale and Brassica rupestris Raf. in south Italy

    DEFF Research Database (Denmark)

    Maggioni, Lorenzo; von Bothmer, Roland

    2014-01-01

    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.

  16. Rapid anti-pathogen response in ant societies relies on high genetic diversity

    DEFF Research Database (Denmark)

    Ugelvig, Line V; Kronauer, Daniel Jan Christoph

    2010-01-01

    Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by genetic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic behaviours (grooming and hygienic behaviour) of workers from genetically homogeneous and diverse colonies after exposure of their brood to the entomopathogenic fungus Metarhizium anisopliae. While workers from diverse colonies performed intensive allogrooming and quickly removed larvae covered with live fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest that reduced genetic diversity compromises the ability of Cardiocondyla colonies to quickly detect or react to the presence of pathogenic fungal spores before an infection is established, thereby affecting the dynamics of social immunity in the colony.

  17. Genetic Diversity and Population Genetic Structure Analysis of Echinococcus granulosus sensu stricto Complex Based on Mitochondrial DNA Signature

    Science.gov (United States)

    Sharma, Monika; Fomda, Bashir Ahmad; Mazta, Saligram; Sehgal, Rakesh; Bagicha Singh, Balbir; Malla, Nancy

    2013-01-01

    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. PMID:24349394

  18. Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation.

    Science.gov (United States)

    Wanjala, Bramwel W; Obonyo, Meshack; Wachira, Francis N; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A; Proud, Janice; Hanson, Jean

    2013-01-01

    Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation. PMID:23671788

  19. Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers.

    Science.gov (United States)

    Verma, Sushma; Singh, Shweta; Sharma, Suresh; Tewari, S K; Roy, R K; Goel, A K; Rana, T S

    2015-04-01

    Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes. PMID:25964716

  20. Assessment of genetic diversity and relationships among Osmanthus fragrans cultivars using AFLP markers

    Scientific Electronic Library Online (English)

    Wang Jun, Yuan; Yuan Ji, Han; Mei Fang, Dong; Fu De, Shang.

    2011-01-15

    Full Text Available This study was conducted to reveal genetic diversity among 100 Osmanthus fragrans cultivars using amplified fragment length polymorphism (AFLP) markers. Eight AFLP primer combinations produced a total of 443 polymorphic fragments with an average of 64 per primer combination. The percentage of polymo [...] rphic bands (86.81%), the resolving power (Rp) (32.71) and the PIC values (0.331) showed the efficiency of used primer combinations. The revealed AFLP makers were effective in distinguishing all the cultivars considered. Cluster analysis were performed to assess patterns of diversity among cultivars and showed the abundant genetic diversity. The overall distribution pattern of molecular variation suggested that 93.33% of the total genetic variance was within the identified groups and 6.67% of the genetic variation was among the identified groups. Our results showed that AFLP markers are useful for Osmanthus fragrans germplasm discrimination as well as for investigation of genetic diversity and variation. The information will facilitate germplasm identi?cation, conservation and new cultivar development.

  1. Population structure and genetic diversity of maize inbreds derived from tropical hybrids.

    Science.gov (United States)

    Lanes, E C M; Viana, J M S; Paes, G P; Paula, M F B; Maia, C; Caixeta, E T; Miranda, G V

    2014-01-01

    The objectives of this study were to identify the population structure and to assess the genetic diversity of maize inbreds. We genotyped 81 microsatellite loci of 90 maize inbreds that were derived from tropical hybrids and populations. The population structure analysis was based on a Bayesian approach. Each subpopulation was characterized for the effective number of alleles, gene diversity, and number of private alleles. We also performed an analysis of molecular variance and computed a measure of population differentiation (FST). The genetic distances were computed from the similarity index of Lynch and the dissimilarity measures proposed by Smouse and Peakall. The cluster analyses were based on the unweighted pair-group method using arithmetic averages and Tocher method. The clustering efficiency was assessed by the error rate of the discriminant analysis. We also performed a principal coordinates analysis. The population structure analysis revealed three tropical heterotic pools, which have been used by worldwide and Brazilian maize seed companies. The degree of genetic differentiation and of intra- and inter-population genetic diversity for these tropical heterotic pools are comparable to that observed for temperate and subtropical heterotic pools. The higher allelic frequency variation within each tropical heterotic pool and the high genetic diversity between the inbreds were evidence of heterotic groups within the main tropical heterotic pools. PMID:25222235

  2. Population genetic structure and genetic diversity of soybean aphid collections from the USA, South Korea, and Japan.

    Science.gov (United States)

    Jun, Tae-Hwan; Michel, Andrew P; Wenger, Jacob A; Kang, Sung-Taeg; Mian, M A Rouf

    2013-06-01

    Following its recent invasion of North America, the soybean aphid (Aphis glycines Matsumura) has become the number one insect pest of soybean (Glycine max L. Merr.) in the north central states of the USA. A few studies have been conducted on the population genetic structure and genetic diversity of the soybean aphid and the source of its invasion in North America. Molecular markers, such as simple sequence repeats (SSRs) are very useful in the evaluation of population structure and genetic diversity. We used 18 SSR markers to assess the genetic diversity of soybean aphid collections from the USA, South Korea, and Japan. The aphids were collected from two sites in the USA (Indiana and South Dakota), two sites in South Korea (Yeonggwang district and Cheonan city), and one site in Japan (Utsunomiya). The SSR markers were highly effective in differentiating among aphid collections from different countries. The level of differentiation within each population and among populations from the same country was limited, even in the case of the USA where the two collection sites were more than 1200 km apart. PMID:23957674

  3. Study on Seed Morphology and Genetic Diversity of Jatropha curcas L. from Different Provenances

    Directory of Open Access Journals (Sweden)

    Junjiao Guan

    2013-02-01

    Full Text Available Jatropha curcas L., a multipurpose shrub has acquired signi?cant economic importance for its seed oil which can be converted to biodiesel, is emerging as an alternative to petro-diesel. The present study aims at characterization of the seed morphology and genetic diversity of Jatropha curcas L. from eight different provenances for providing support for the breeding and allocation of seed. Five traits were investigated, including hundred seed weight, seed length, width, lateral diameter, seed length and width ratio. The genetic diversity of eight populations from different provenances was estimated using DALP method (5 primers. The results showed that seed morphology had significant variation among locations. Five DALP primers generated highly reproducible and stable DNA fragments. 219 of 244 loci were polymorphic, i.e., PPB was 89.75%. And POPGENE analysis indicated the total Nei’s gene diversity (H was 0.2878, the total Shannon's Information index (I was 0.4331, and the coefficient of Gene differentiation (Gst was 0.8200 among populations, namely 82.00% genetic variation occurring among populations and 20.00% remaining within population. It was suggested that a high level of genetic variation should be occur among the different populations of J. curcas. The high genetic differentiation among the populations could be caused by not only the limited gene flow (Nm = 0.1097 but also the genetic drift. The result indicates that the seed morphology among populations showed some certain differentiation. The eight populations had high level of genetic diversity and show apparent genetic differentiation. So that provenance selection has great potentiality.

  4. Castanea spp. biodiversity conservation: collection and characterization of the genetic diversity of an endangered species

    OpenAIRE

    Bounous, Giancarlo; Cerutti, Alessandro Kim; Torello Marinoni, Daniela; Mellano, Maria Gabriella; Donno, Dario; Beccaro, Gabriele Loris; Boccacci, Paolo; Canterino, Sara

    2012-01-01

    Centuries of co-evolution between Castanea spp. biodiversity and human populations has resulted in the spread of rich and varied chestnut genetic diversity throughout most of the world, especially in mountainous and forested regions. Its plasticity and adaptability to different pedoclimates and the wide genetic variability of the species determined the spread of many different ecotypes and varieties in the wild. Throughout the centuries, man has used, selected and preserved these different...

  5. Low worldwide genetic diversity in the killer whale (Orcinus orca): implications for demographic history.

    OpenAIRE

    Hoelzel, A R; Natoli, A.; Dahlheim, M.; Olavarria, C.; Baird, R W; Black, N

    2002-01-01

    A low level of genetic variation in mammalian populations where the census population size is relatively large has been attributed to various factors, such as a naturally small effective population size, historical bottlenecks and social behaviour. The killer whale (Orcinus orca) is an abundant, highly social species with reduced genetic variation. We find no consistent geographical pattern of global diversity and no mtDNA variation within some regional populations. The regional lack of varia...

  6. Genetic diversity and symbiotic compatibility among rhizobial strains and Desmodium incanum and Lotus spp. plants

    OpenAIRE

    Granada, Camille E.; Strochein, Marcos; Vargas, Luciano K.; Bruxel, Manuela; de Sá, Enilson Luiz Saccol; Passaglia, Luciane M.P.

    2014-01-01

    This work aimed to evaluate the symbiotic compatibility and nodulation efficiency of rhizobia isolated from Desmodium incanum, Lotus corniculatus, L. subbiflorus, L. uliginosus and L. glaber plants by cross-inoculation. Twelve reference strains and 21 native isolates of rhizobia were genetically analyzed by the BOX-PCR technique, which showed a high genetic diversity among the rhizobia studied. The isolates were also characterized based on their production of indolic compounds and siderophore...

  7. Genetic Diversity and Population Structure of Miscanthus sinensis Germplasm in China

    Science.gov (United States)

    He, Junrong; Yang, Junpin; Pan, Lei; Sun, Dongfa; Peng, Junhua

    2013-01-01

    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. PMID:24116066

  8. Molecular strategies for genetic diversity analysis and development of markers linked to resistance traits in apple

    OpenAIRE

    Liang, Wei

    2013-01-01

    The goal of many plant scientists’ research is to explain natural phenotypic variation in term of simple changes in DNA sequence. DNA-based molecular markers are extensively used for the construction of genome-wide molecular maps and to perform genetic analysis for simple and complex traits. The PhD thesis was divided into two main research lines according to the different approaches adopted. The first research line is to analyze the genetic diversity in an Italian apple germplasm collectio...

  9. Dybowski's sika deer (Cervus nippon hortulorum): genetic diversity of native Primorian and introduced Czech populations.

    Czech Academy of Sciences Publication Activity Database

    Krojerová-Prokešová, Jarmila; Baran?eková, Miroslava; Vallo, Peter; Voloshina, I. V.; Koubek, Petr

    Moscow : IUGB, 2009, s. 1-5. ISBN 978-5-7035-2118-2. [IUGB Congress /29./. Moscow (RU), 17.08.2009-22.08.2009] R&D Projects: GA ?R GA524/09/1569; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60930519 Keywords : Dybowski's sika deer * genetic diversity Subject RIV: EB - Genetics ; Molecular Biology http://www.iugb-moscow2009.ru/cd/docs/ps/Krojerova_poster_1_report_eng.pdf

  10. Estimation of Genetic Diversity in Capsicum Germplasm Using Randomly Amplified Polymorphic DNA

    OpenAIRE

    Imtiaz Ahmed Khan

    2010-01-01

    Present study was undertaken to estimate genetics diversity in local and exotic genotypes ofCapsicum (chili) using Randomly Amplified polymorphic DNA (RAPD) primers. Four RAPD primes wereused to amplify genomic DNA from twenty five Capsicum genotypes. DNA fragments of various sizes rangingfrom 100bp to >1000bp were amplified in various Capsicum genotypes. On an average 3 alleles per genotypewere amplified during present study. Estimates of Genetic distances (GD) ranged from 0 to 100%. Twentyf...

  11. Comparison of AFLP and SSR for Genetic Diversity Analysis of Brassica napus Hybrids

    OpenAIRE

    Li Li(State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China); Chokchai Wanapu; Xianqun Huang; Tuan Huang; Qiyi Li; Yi Peng; Guimin Huang

    2011-01-01

    The AFLP and SSR markers were used to estimate the genetic diversity of 25 Brassica napus hybrids attending Guizhou regional test. The fingerprints obtained with both the AFLP and SSR markers revealed high levels of heterozygosity. Nine AFLP primer combinations produced 16 loci, while 11 SSR primer pairs generated 22 loci. The mean of expected heterozygosity, Shannon’s information index, and genetic differentiation obtained by SSR were higher than those by AFLP, indicating that the SSR method...

  12. SSR DNA marker aided genetic diversity assessment of selected willow clones

    OpenAIRE

    Singh N.B.; Joshi S.; Choudhary P.; Sharma J.P.

    2013-01-01

    Around 100 clones of tree willows were subjected for nursery screening twice on morphometric traits. Genetic diversity was assessed in twenty-five genetically superior willow clones hailing from six countries using 16 SSR primers. Fourteen primers amplified the DNA but only ten showed polymorphism. Total 34 bands were scored, out of that 27 were found to be polymorphic and 7 were monomorphic. Three primers showed 100% polymorphism whereas 79.4% polymorphism...

  13. Genetic diversity analysis in cuban traditional rice germplasm using micro satellite markers

    International Nuclear Information System (INIS)

    At the present study, the potential of micro satellite markers to assess the extent of genetic variability in Cuban traditional rice varieties was proved. The work was aimed at identifying alternative genetic diversity pools in this material in comparison to the most important commercial cultivars used in Cuban rice breeding program. For this, 52 traditional accessions, eleven cultivars representing the most planted Cuban material during the last decades and two parent cultivars were studied

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

    Science.gov (United States)

    Zhao, Hua; Wang, Bo; He, Junrong; Yang, Junpin; Pan, Lei; Sun, Dongfa; Peng, Junhua

    2013-01-01

    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. PMID:24116066

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

    Science.gov (United States)

    Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

    2014-01-01

    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 subpopulations. PMID:24963708

  16. Genetic Diversity among Barley Populations from West China Based on RAMP and RAPD Markers

    OpenAIRE

    Pu, Z. E.; Hou, Y. C.; Xu, X. X.; Yan, Z. H.; Wei, Y. M.; Lan, X. J.; Zheng, Y. L.

    2009-01-01

    Using RAMP and RAPD for detecting the genetic diversity of 46 barley accessions, collected from west China. Seventeen primer combinations produced 104 discernible RAMP fragments of which 96 (91%) were polymorphic. The number of fragments per primer combination varied from 2 to 11, with the mean of 6.18. The mean of Polymorphism Information Content (PIC) for the RAMPs was 0.752. On the basis of 96 polymorphic fragments, each genotype had a unique banding profile and the Genetic Similarit...

  17. Genetic diversity of Gallibacterium isolates from California turkeys

    OpenAIRE

    Bojesen, Anders Miki; Shivaprasad, H. L.

    2007-01-01

    Abstract The aim of the present study was to investigate the genetic diversity of Gallibacterium isolates recovered from lesions in turkeys. Gallibacterium has been isolated from various bird species including turkeys, yet no larger investigations have been made to characterise Gallibacterium isolates from turkeys genetically. In the present investigation we genotyped 53 Gallibacterium isolates from turkeys, whereof 50 originated from 29 different flocks in California and the remai...

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

    Directory of Open Access Journals (Sweden)

    NikoBeerenwinkel

    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.

  19. Genetic diversity assessment of wild Malus sieversii populations in Kazakhstan

    Science.gov (United States)

    Malus sieversii is one of the major progenitor species of the dessert apple, Malus x domestica. Wild M. sieversii trees are found in the mountainous regions of Kazakhstan and other central Asian countries. The Plant Genetic Resources Unit (PGRU) in Geneva, NY maintains large field and seed collectio...

  20. Demography, genetic diversity, and population relationships among Argentinean Mapuche Indians

    Scientific Electronic Library Online (English)

    Alicia S., Goicoechea; Francisco R., Carnese; Alicia L., Caratini; Sergio, Avena; Maria, Salaberry; Francisco M., Salzano.

    2000-09-01

    Full Text Available Dados relativos a fertilidade, mortalidade e migração de quatro comunidades de índios Mapuche localizadas em uma área linear na direção nordeste-sudoeste com 215 km de extensão na Província de Rio Negro, Argentina, foram associados com a informação genética fornecida por nove sistemas de grupos sang [...] üíneos e os haplogrupos do DNA mitocondrial. Ambos os tipos de informação apontam claramente para uma dicotomia, as quatro populações sendo divididas em grupos de duas. O principal fator responsável por esta separação é provavelmente graus diferentes de mistura com não-índios. A variabilidade genética total foi muito similar em todos os grupos, aquela entre populações sendo de apenas 10% deste valor. Foi confirmada a baixa prevalência do antígeno Diego(a) entre os Mapuche. O fato de que heterogeneidade genética significativa e conjuntos populacionais diversos foram observados em uma região territorial tão pequena demonstra a sensibilidade dos enfoques demográfico e genético no esclarecimento da história humana. Abstract in english Fertility, mortality and migration data from four Mapuche Indian communities located along a 215-km NE-SW linear area in the Province of Río Negro, Argentina, were collated with genetic information furnished by nine blood group systems and by mtDNA haplogroups. The demographic and genetic data indic [...] ated a clear dichotomy, which split the four populations into two groups of two. Differing degrees of non-Indian exchanges was probably the main determining factor for this separation. Total genetic variability was very similar in all groups, and the interpopulational variability accounted for only 10% of the total variability. A low prevalence of the Diego(a) antigen among the Mapuche was confirmed. The fact that significant genetic heterogeneity and population clusters were found in such a small territorial region attests to the sensitivity of demographic and genetic approaches in unraveling human history.

  1. Temporal analysis of mtDNA variation reveals decreased genetic diversity in least terns

    Science.gov (United States)

    Draheim, Hope M.; Baird, Patricia; Haig, Susan M.

    2012-01-01

    The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. We used historical museum specimens (pre-1960) and contemporary (2001–2005) samples to examine range-wide phylogeographic patterns and investigate potential loss in the species' genetic variation. We obtained sequences (522 bp) of the mitochondrial gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species' range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. However, we detected potential reductions in genetic diversity in contemporary samples from California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Our results offer unique insights into changes in the Least Tern's genetic diversity over the past century and highlight the importance and utility of museum specimens in studies of conservation genetics.

  2. Genetic diversity in Fusarium solani f. sp. pisi based on SSR markers

    Directory of Open Access Journals (Sweden)

    Ni Xiang

    2012-11-01

    Full Text Available Pea root rot, caused by Fusarium solani f. sp. pisi (Fsp, is one of the most important diseases on pea (Pisum sativum. Assessing the genetic diversity of the pathogen isolates from different geographical regions is crucially important for understanding of the genetic background of this pathogen and intelligently deploying host resistance. We screened SSRs in complete genome sequence of Nectria haematococca MPVI, and 107 SSR loci were selected for designing markers, from which 24 polymorphic primer pairs were developed. The 24 primer pairs were used to assess genetic diversity of 96 Fsp isolates from different geographical regions. Among 24 SSR markers, a total of 132 alleles were detected among the 96 Fsp isolates, the number ofalleles for each of the loci ranged from 3 to 15 with an average of 5.5. The genetic diversity was estimated to range from 0.4855 to 0.8264 with the average value of 0.738. Using these markers, 93 genotypes were detected. When the genetic similarity coefficient was 0.8, 96 Fsp isolates were clustered into 10 groups by phylogeneticanalysis. There was no correlation between SSR profile and either geographic origin or pathogenicity. Analysis of AMOVA revealed that variation mainly presented within Fsp populations (86.14%, and genetic differentiation of Fsp was significantly affected by geographical conditions and ecological environment.

  3. Assessment of genetic diversity in Chinese eared pheasant using fluorescent-AFLP markers

    DEFF Research Database (Denmark)

    Li, Xiujuan; Zhu, Yaohong

    2010-01-01

    The eared pheasant consists of four species: white eared pheasant (Crossoptilon crossoptilon), Tibetan eared pheasant (Crossoptilon harmani), blue eared pheasant (Crossoptilon auritum), and brown eared pheasant (Crossoptilon mantchuricum). These species are found only in China, and are also on the list of the world’s threatened species. In this paper, 74 individuals from the four eared pheasant species were assessed for population genetic diversity by means of fluorescent-AFLP markers. A total of 429 AFLP peaks were amplified by 11 pairs of fluorescent EcoRI/TaqI primer combinations. Out of all markers, 329 AFLPs were polymorphic. Each primer combination produced in reactions from 19 to 72 fragments and the polymorphic peaks percentage ranged from 53.33% to 86.11% with an average of 74.36% polymorphic bands. Genetic distance between species and genetic diversity within species were evaluated using Jaccard’s similarity coefficients (SC) and the corresponding dendrogram. It was found that there was a moderate genetic distance between the four species (SC = 0.674–0.832). Brown eared pheasant was genetically closely related to blue eared pheasant (SC = 0.832), while white eared pheasant was more closely related to Tibetan eared pheasant (SC = 0.812). Genetic diversity was lower in brown eared pheasant (SC = 0.913) and Tibetan eared pheasant (SC = 0.903) than in white eared pheasant (SC = 0.832) and blue eared pheasant (SC = 0.853).

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

    International Nuclear Information System (INIS)

    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 ithe urgent necessity of widen it

  5. 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.

  6. Consequences of geographical habitats on population structure and genetic diversity in Campanula spp.

    Directory of Open Access Journals (Sweden)

    Paul Arens

    2010-01-01

    Full Text Available Characterization of populations by means of DNA techniques provides a tool for precise identification and a quantitative estimate of genetic diversity, crucial in evaluation of genetic fragmentation within and among populations. NBS profiling are PCR-based approaches that sample genetic variation in resistance genes (R-gene, and R gene analogs (RGA. To date, myb patterns have not been used for evaluating genetic diversity in other species. NBS primers are homologous to the conserved sequences in the Nucleotide-Binding-Site of the NBS-LRR class of R-genes. A total of 12 populations from five Campanula species (C. barbata L., C. latifolia L., C. rapunculoides L., C. spicata L. and C. trachelium L., autochthonous of the West Italian Alps, were genotyped via nucleotide-binding site (NBS and myb gene profiling. The selected markers produced a total of 361 bands, showing high levels of polymorphism. Genetic diversity among and within species and population structure was evaluated by different statistical analyses performed using TREECON software, Mantel Nonparametric Test, NTSYS package, AMOVA and STRUCTURE. The correlation between genetic variability and geographical location suggests that the five Campanula species have been subjected to long-term evolutionary processes consistent with the natural fragmentation of continuous mountains areas.

  7. Genetic Diversity of mtDNA D-loop Polymorphisms in Laotian Native Fowl Populations

    OpenAIRE

    KAWABE, K.; Worawut, R.; Taura, S.; Shimogiri, T.; Nishida, T.; Okamoto, S.

    2014-01-01

    Here, we studied the genetic diversity of native fowls in Laos by analyzing a mitochondrial DNA (mtDNA) sequence polymorphism. A 546-bp fragment of the mtDNA D-loop region was sequenced in 129 chickens from the areas of Vientiane, Luang Prabang and Pakse. In total, 29 haplotypes were identified and formed five clades. Haplotype diversity and nucleotide diversity of the native fowls in Laos were 0.85536±0.0172 and 0.010158±0.005555, respectively. Although the Laotian native fowls were distribu...

  8. ASSESSMENT OF GENETIC DIVERSITY IN CROATIAN WINTER WHEAT VARIETIES USING SSR AND AFLP MARKERS

    Directory of Open Access Journals (Sweden)

    Sonja Petrovi?

    2012-12-01

    Full Text Available Sustaining and developing of genetic diversity in winter wheat germplasm is one of the main prerequisite for success in future winter wheat breeding programs. Selection of diverse parents is essential for creation of superior new varieties. Danger of genetic erosion specially exists in smaller breeding programs and selection for limited production area with similar growing conditions. Croatian winter wheat breeding has a long tradition but it is relatively small compared to countries with bigger growing areas. Use of molecular markers in evaluating genetic diversity of winter wheat varieties is limited in Croatian breeding programs. Therefore, aim of this study was to evaluate genetic diversity of Croatian winter wheat varieties using SSR and AFLP markers as a powerful tool for assessing genetic diversity. Forty winter wheat varieties, from three Croatian breeding centres and foreign centres were included in the study. A set of 26 microsatellite primers were used, covering three wheat genomes and 42 chromosomes by 0.66 average genetic distance. The largest calculated distance was between the varieties Zlatna Dolina and Lela (dij=0.98, while most similar varieties were Super Žitarka and Barbara with the distance value of dij=0.21. Four AFLP marker combinations generated 108 polymorphic bands with average of 34 specific bands per primer combination. On the average 27 polymorphic bands were generated with average PIC value of 0.34. Specific polymorphic bands were discriminant for the three varieties Žitarka, Super Žitarka and Barbara, which, therefore, can be used for their identification. Grouping of varieties was in accordance with their origin (breeding centre and pedigree data.

  9. Genetic diversity analysis of highly incomplete SNP genotype data with imputations: an empirical assessment.

    Science.gov (United States)

    Fu, Yong-Bi

    2014-05-01

    Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data. PMID:24626289

  10. Population Structure and Genetic Diversity of a Medicinal Plant Species Retama raetam in Southern Tunisia

    Directory of Open Access Journals (Sweden)

    Faouzia Yahyaoui

    2014-01-01

    Full Text Available Retama raetam is a stem-assimilating, C3, evergreen, medicinal plant species, desert legume common to arid ecosystems around the Mediterranean basin. This study addresses the genetic diversity and relationship among and within three populations collected from different habitats in southern Tunisia by Random Amplified Polymorphic DNA (RAPD. Estimates of the percentage of polymorphic bands, Shannon’s diversity information index and Nei’s gene diversity index were determined. Results showed that population from the Island Djerba has the lowest Nei’s gene diversity; this also was for Shannon diversity index. An analysis of molecular variance indicated that the majority of variation existed within populations (68% and that there was significant differentiation among populations (?PT = 0.316, pR. raetam in southern Tunisia and will be useful for conservation managers to work out an effective strategy to protect this important species.

  11. Association between host's genetic diversity and parasite burden in damselflies.

    Science.gov (United States)

    Kaunisto, K M; Viitaniemi, H M; Leder, E H; Suhonen, J

    2013-08-01

    Recent research indicates that low genetic variation in individuals can increase susceptibility to parasite infection, yet evidence from natural invertebrate populations remains scarce. Here, we studied the relationship between genetic heterozygosity, measured as AFLP-based inbreeding coefficient fAFLP , and gregarine parasite burden from eleven damselfly, Calopteryx splendens, populations. We found that in the studied populations, 5-92% of males were parasitized by endoparasitic gregarines (Apicomplexa: Actinocephalidae). Number of parasites ranged from none to 47 parasites per male, and parasites were highly aggregated in a few hosts. Mean individual fAFLP did not differ between populations. Moreover, we found a positive association between individual's inbreeding coefficient and parasite burden. In other words, the more homozygous the individual, the more parasites it harbours. Thus, parasites are likely to pose strong selection pressure against inbreeding and homozygosity. Our results support the heterozygosity-fitness correlation hypothesis, which suggests the importance of heterozygosity for an individual's pathogen resistance. PMID:23865399

  12. Genetic diversity of soybean accessions using seed storage proteins

    International Nuclear Information System (INIS)

    Soybean, Glycine max (L) Merrill, is the most important grain legume in the world that has a fairly wide range of adaptations to different climatic conditions. The present study was conducted to assess genetic variations on 139 Soybean genotypes collected from different countries including Australia, Brazil, India, Japan, Pakistan, Tiwan, USA, Yugoslavia and China. A total of 17 bands have been identified for 139 Soybean genotypes which include 9 monomorphic bands and 8 polymorphic bands. Total number of bands was found highest for India (215) while these were lowest for Yugoslavia (33). Cluster analysis, clustered these accessions into 10 clusters without having any indication of grouping on the basis of their relationships to their regions. Pairwise comparisons based on Nei and Li similarities for inter-population genetic distances of soybean accessions ranged from 0.14 to 1.12. Genetic distances for soybean germplasm from different countries were found highest for Brazil (0.97+-0.03) while it was lowest for Taiwan (0.91+-0.02). Clustering for Soybean groups was clustered into three clusters including Korea, Taiwan in the first group while Yugoslavia and Japan were clustered in the second group. The third cluster was comprised of Soybean genotypes from China, Pakistan, USA, India Brazil and Australia. Total seed storage protein variation was partitioned by AMOVA on the basis of their origins into within-population and among-population components which revealed 10.00% of the total variation resided among countries and 90.0% within countries. Genetic patterns obtained from this study can help soybean breeders to make better plan for selecting germplasm from wide sources for a specific purposes. (author)

  13. Genetic diversity analysis of groundnut genotypes using SSR markers

    OpenAIRE

    D. Shoba, N. Manivannan and P.Vindhiyavarman

    2010-01-01

    Groundnut (Arachis hypogaea L.), an important oilseed crop is a rich source of oil and protein. Molecular marker technologies are the effectivetools and they are used for the assessment of genetic variability because they are not influenced by the environment. Among the molecularmarkers, Simple Sequence Repeat (SSR) has proved to be the most powerful tool for variety identification in groundnut and has much potential ingenetic and breeding studies. Among the 17 SSR primer pairs used for asses...

  14. Inhibition of BET Bromodomain Targets Genetically Diverse Glioblastoma

    OpenAIRE

    Cheng, Z; Gong, Y.; Y. Ma; Lu, K; Lu, X; Pierce, LA; Thompson, RC; Muller, S; Knapp, S; Wang, J.

    2013-01-01

    PURPOSE: Glioblastoma is refractory to conventional therapies. The bromodomain and extraterminal domain (BET) proteins are epigenetic readers that selectively bind to acetylated lysine residues on histone tails. These proteins recently emerged as important therapeutic targets in NUT midline carcinoma and several types of hematopoietic cancers. In this study, the therapeutic potential of a novel BET bromodomain inhibitor, JQ1, was assessed in a panel of genetically heterogeneous glioblastoma s...

  15. Exploring Genetic Susceptibility to Cancer in Diverse Populations

    OpenAIRE

    Haiman, Christopher A.; Stram, Daniel O.

    2010-01-01

    Incidence rates for many cancers differ markedly by race/ethnicity and furthering our understanding of the genetic and environmental causes of such disparities is a scientific and public health need. Genome-wide association studies (GWAS) are widely acknowledged to provide important information about the etiology of common cancers. To date, these studies have been primarily conducted in European-derived populations. There are important reasons for extending the reach of GWAS studies to other ...

  16. Phenotypic Switching and Genetic Diversity of Cryptococcus neoformans

    OpenAIRE

    Sukroongreung, Samaniya; Lim, Shirlene; Tantimavanich, Srisurang; Eampokalap, Boonchaoy; Carter, Dee; Nilakul, Churairatana; Kulkeratiyut, Suriyaphongse; Tansuphaswadikul, Somsit

    2001-01-01

    Niger seed agar was used as a primary plating medium for the isolation of Cryptococcus neoformans from cerebrospinal fluid specimens from AIDS patients with untreated primary cryptococcosis. The medium was used as the primary means to detect variations in the colony morphology of the yeast. To search for phenotypic and genetic variations, nine patients individually harboring two or three types of colony morphology were studied. Intraindividual isolates from nine patients had minor variations ...

  17. The Effect of Chromosome Geometry on Genetic Diversity

    OpenAIRE

    Marri, Pradeep Reddy; Harris, Leigh K.; Houmiel, Kathryn; Slater, Steven C.; Ochman, Howard

    2008-01-01

    Although organisms with linear chromosomes must solve the problem of fully replicating their chromosome ends, this chromosome configuration has emerged repeatedly during bacterial evolution and is evident in three divergent bacterial phyla. The benefit usually ascribed to this topology is the ability to boost genetic variation through increased recombination. But because numerous processes can impact linkage disequilibrium, such an effect is difficult to assess by comparing across bacterial t...

  18. Genetic diversity and chemical polymorphism of some Thymus species.

    Science.gov (United States)

    Rustaiee, Ali Reza; Yavari, Alireza; Nazeri, Vahideh; Shokrpour, Majid; Sefidkon, Fatemeh; Rasouli, Musa

    2013-06-01

    To ascertain whether there are chemical and genetic relationships among some Thymus species and also to determine correlation between these two sets of data, the essential-oil composition and genetic variability of six populations of Thymus including: T. daenensis ?ELAK. (two populations), T. fallax FISCH. & C.A.MEY., T. fedtschenkoi RONNIGER, T. migricus KLOKOV & DES.-SHOST., and T. vulgaris L. were analyzed by GC and GC/MS, and also by randomly amplified polymorphic DNA (RAPD). Thus, 27 individuals were analyzed using 16 RAPD primers, which generated 264 polymorphic scorable bands and volatiles isolated by distillation extraction were subjected to GC and GC/MS analyses. The yields of oils ranged from 2.1 to 3.8% (v/w), and 34 components were identified, amounting to a total percentage of 97.8-99.9%. RAPD Markers allowed a perfect distinction between the different species based on their distinctive genetic background. However, they did not show identical clustering with the volatile-oil profiles. PMID:23776024

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

    Directory of Open Access Journals (Sweden)

    Almeida Leonardo D

    2007-12-01

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

  20. Genetic diversity in Monoporeia affinis at polluted and reference sites of the Baltic Bothnian Bay.

    Science.gov (United States)

    Guban, Peter; Wennerström, Lovisa; Elfwing, Tina; Sundelin, Brita; Laikre, Linda

    2015-04-15

    The amphipod Monoporeia affinis plays an important role in the Baltic Sea ecosystem as prey and as detritivore. The species is monitored for contaminant effects, but almost nothing is known about its genetics in this region. A pilot screening for genetic variation at the mitochondrial COI gene was performed in 113 individuals collected at six sites in the northern Baltic. Three coastal sites were polluted by pulp mill effluents, PAHs, and trace metals, and two coastal reference sites were without obvious connection to pollution sources. An off-coastal reference site was also included. Contaminated sites showed lower levels of genetic diversity than the coastal reference ones although the difference was not statistically significant. Divergence patterns measured as ?ST showed no significant differentiation within reference and polluted groups, but there was significant genetic divergence between them. The off-coastal sample differed significantly from all coastal sites and also showed lower genetic variation. PMID:25701944

  1. Infections by Babesia caballi and Theileria equi in Jordanian equids: epidemiology and genetic diversity.

    Czech Academy of Sciences Publication Activity Database

    Qablan, M. A.; Oborník, Miroslav; Petrželková, Klára Judita; Sloboda, M.; Shudiefat, M. F.; Ho?ín, P.; Lukeš, Julius; Modrý, David

    2013-01-01

    Ro?. 140, ?. 9 (2013), s. 1096-1103. ISSN 0031-1820 R&D Projects: GA ?R GA523/09/1972 Institutional research plan: CEZ:AV0Z60220518 Institutional support: RVO:68081766 ; RVO:60077344 Keywords : Jordan * equine * Theileria equi * Babesia caballi * genetic diversity Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.350, year: 2013

  2. Genetic Diversity of Spanish Melons (Cucumis melo L.) of the Madrid Provenance

    Science.gov (United States)

    The genetic diversity of five Group Inodorus landraces having a historic presence in the town of Villaconejos, Spain (near Madrid) and four reference accessions (one accession Group Flexuosus) (Lopez-Sese et al, 2002), was assessed using the allelic variation at 19 SSR loci. Seventy-two polymorphic...

  3. Genetic diversity of mango cultivars estimated using Start Codon Targeted (SCoT) markers

    Science.gov (United States)

    Diversity and genetic relationships among 23 mango germplasm accessions, collected from different locations in Guangxi province in China, were analyzed by using a novel and simple gene targeted DNA marker: Start Codon Targeted (SCoT) markers. This technique uses a single, 18-mer primer PCR amplifica...

  4. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    Science.gov (United States)

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations. PMID:23450090

  5. High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region

    OpenAIRE

    Douaihy, Bouchra; Vendramin, Giovanni G.; Boratyn?ski, Adam; Machon, Nathalie; Bou Dagher-kharrat, Magda

    2011-01-01

    Juniperus excelsa constitutes a precious woody species of high ecological value able to grow up to Mountain treeline around the Mediterranean. Nuclear microsatellites were used to shed light on genetic diversity and differentiation of different Mediterranean populations. This information is essential in planning conservation strategies and reforestation programs.

  6. Low genetic diversity among pathogenic strains of Erwinia psidii from Brazil

    OpenAIRE

    Ana C. O. Teixeira; Marques, Abi S. A.; Ferreira, Marisa A. S. V.

    2009-01-01

    Erwinia psidii causes bacterial disease of guava in Brazil. Phenotypic and molecular characterization through rep-PCR fingerprinting of 42 strains from different geographical regions showed that E. psidii populations in Brazil have a low level of genetic diversity and suggest that contaminated plant material is the main source for pathogen dissemination in the country.

  7. Lack of Genetic Diversity in Newly Sequenced Porcine Circovirus Type 1 Strains Isolated 20 Years Apart

    OpenAIRE

    Tomba?cz, Kata; Patterson, Robert; Grierson, Sylvia S.; Werling, Dirk

    2014-01-01

    The complete genome sequences of a porcine circovirus type 1 (PCV1) strain isolated in 1990 and one isolated in 2011 were obtained and compared to the sequences of other available PCV1 isolates. Phylogenetic analyses revealed very low genetic diversity among these viruses, indicating an advanced state in the evolution of PCV1.

  8. Genetic diversity of lake whitefish in lakes Michigan and Huron: sampling, standardization, and research priorities

    Science.gov (United States)

    Stott, Wendylee; VanDeHey, Justin A.; Sloss, Brian L.

    2010-01-01

    We combined data from two laboratories to increase the spatial extent of a genetic data set for lake whitefish Coregonus clupeaformis from lakes Huron and Michigan and saw that genetic diversity was greatest between lakes, but that there was also structuring within lakes. Low diversity among stocks may be a reflection of relatively recent colonization of the Great Lakes, but other factors such as recent population fluctuation and localized stresses such as lamprey predation or heavy exploitation may also have a homogenizing effect. Our data suggested that there is asymmetrical movement of lake whitefish between Lake Huron and Lake Michigan; more genotypes associated with Lake Michigan were observed in Lake Huron. Adding additional collections to the calibrated set will allow further examination of diversity in other Great Lakes, answer questions regarding movement among lakes, and estimate contributions of stocks to commercial yields. As the picture of genetic diversity and population structure of lake whitefish in the Great Lakes region emerges, we need to develop methods to combine data types to help identify important areas for biodiversity and thus conservation. Adding genetic data to existing models will increase the precision of predictions of the impacts of new stresses and changes in existing pressures on an ecologically and commercially important species.

  9. Genetic Diversity Assessment of Rarely Cultivated Traditional Indica Rice (Oryza sativa L.) Varieties

    OpenAIRE

    Rekha, T; Kottackal Poulose Martin; Sreekumar, V. B.; Joseph Madassery

    2011-01-01

    Random amplified polymorphic DNA fingerprinting was performed to assess the genetic diversity among rarely cultivated traditional indica rice (Oryza sativa L.) varieties collected from a tribal hamlet of Kerala State, India. A total of 664 DNA bands amplified by 15 primers exhibited 72.9% polymorphism (an average of 32.3 polymorphic bands per primer). The varieties Jeerakasala and...

  10. Genetic diversity and population structure of cacao landraces in Northern and Central coastal Ecuador

    Science.gov (United States)

    Knowledge about genetic diversity among the landraces is essential for developing on-farm conservation strategy in modern agroecosystems. The “arriba” cacao is a group of landraces that are still used today for cacaoa production in the coastal plains and valleys of Ecuador. The strongly rising deman...

  11. Minimal genetic diversity in the facultatively outcrossing perennial pepperweed (Lepidium latifolium) invasion

    Science.gov (United States)

    Perennial pepperweed (Lepidium latifolium L.) is a Eurasian plant species that is invasive in North America. The invasion often forms large, dense monocultural stands. We investigated the genetic diversity along transects in dense populations in the western USA using Amplified Fragment Length Polymo...

  12. Genetic Diversity of Isoniazid-Resistant Mycobacterium tuberculosis Isolates Collected in Poland and Assessed by Spoligotyping?

    OpenAIRE

    Augustynowicz-Kope?, Ewa; Jagielski, Tomasz; Zwolska, Zofia

    2008-01-01

    The genetic compositions of 71 isoniazid-resistant Mycobacterium tuberculosis strains from Poland were determined by spoligotyping. Nearly 80% of the isolates belonged to either the T or the Haarlem family. The genotypic diversity was largely due to variation within those families. The scarcity of imported genotypes suggested that the M. tuberculosis population studied has an endemic nature.

  13. Genetic Diversity of Spiroplasma citri strains from Different Regions, Hosts, and Isolation Dates

    Science.gov (United States)

    Spiroplasma citri, a phloem-limited, leafhopper-transmitted pathogen, causes citrus stubborn disease (CSD). Losses due to CSD in California orchards has grown over the past decade. To investigate the possibility of introduction or emergence of a new spiroplasma strain, a study of genetic diversity ...

  14. 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

    2009-03-01

    Full Text Available Abstract After the recent publication of our article (Leroy, Genetics Selection Evolution 2009 41:5, we found several errors in the published Table Three, concerning the computation of contribution to within-breed diversity (CW. We apologize to the readers for these errors, which are corrected in the present erratum.

  15. Diversity of the breadfruit complex (Artocarpus, Moraceae): Genetic characterization of critical germplasm

    Science.gov (United States)

    Breadfruit (Artocarpus altilis, Moraceae) is a traditional staple starch crop in Oceania and has been introduced throughout the tropics. This study uses microsatellite markers to characterize the genetic diversity of breadfruit and its wild relatives housed in the USDA National Plant Germplasm Syste...

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

    OpenAIRE

    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 outcrossi...

  17. Understanding Genetic Diversity and Population Structure of a Poa pratensis Worldwide Collection through Morphological, Nuclear and Chloroplast Diversity Analysis

    Science.gov (United States)

    Russi, Luigi; Marconi, Gianpiero; Sharbel, Timothy F.; Veronesi, Fabio; Albertini, Emidio

    2015-01-01

    Poa pratensis L. is a forage and turf grass species well adapted to a wide range of mesic to moist habitats. Due to its genome complexity little is known regarding evolution, genome composition and intraspecific phylogenetic relationships of this species. In the present study we investigated the morphological and genetic diversity of 33 P. pratensis accessions from 23 different countries using both nuclear and chloroplast molecular markers as well as flow cytometry of somatic tissues. This with the aim of shedding light on the genetic diversity and phylogenetic relationships of the collection that includes both cultivated and wild materials. Morphological characterization showed that the most relevant traits able to distinguish cultivated from wild forms were spring growth habit and leaf colour. The genome size analysis revealed high variability both within and between accessions in both wild and cultivated materials. The sequence analysis of the trnL-F chloroplast region revealed a low polymorphism level that could be the result of the complex mode of reproduction of this species. In addition, a strong reduction of chloroplast SSR variability was detected in cultivated materials, where only two alleles were conserved out of the four present in wild accessions. Contrarily, at nuclear level, high variability exist in the collection where the analysis of 11 SSR loci allowed the detection of a total of 91 different alleles. A Bayesian analysis performed on nuclear SSR data revealed that studied materials belong to two main clusters. While wild materials are equally represented in both clusters, the domesticated forms are mostly belonging to cluster P2 which is characterized by lower genetic diversity compared to the cluster P1. In the Neighbour Joining tree no clear distinction was found between accessions with the exception of those from China and Mongolia that were clearly separated from all the others. PMID:25893249

  18. Mine simulation

    Energy Technology Data Exchange (ETDEWEB)

    Panagiotou, G.N.; Sturgul, J.R. [eds.] [National Technical University of Athens, Athens (Greece)

    1997-12-31

    The technical sessions covered: simulation - open pit mining operations; simulation - underground mining operations; general topics; expert systems - genetic algorithms; neural networks; mine safety - training; modelling, planning and production scheduling; rock mechanics; and mine equipment. The book contains abstracts of the papers. The full papers are included on the enclosed CD-ROM.

  19. Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae

    Directory of Open Access Journals (Sweden)

    Shao Ai-Juan

    2010-04-01

    Full Text Available Abstract Background Cultivation of medicinal plants is not only a means for meeting current and future demands for large volume production of plant-based drug and herbal remedies, but also a means of relieving harvest pressure on wild populations. Scutellaria baicalensis Georgi (Huang-qin or Chinese skullcap is a very important medicinal plant in China. Over the past several decades, wild resource of this species has suffered rapid declines and large-scale cultivation was initiated to meet the increasing demand for its root. However, the genetic impacts of recent cultivation on S. baicalensis have never been evaluated. In this study, the genetic diversity and genetic structure of 28 wild and 22 cultivated populations were estimated using three polymorphic chloroplast fragments. The objectives of this study are to provide baseline data for preserving genetic resource of S. baicalensis and to evaluate the genetic impacts of recent cultivation on medicinal plants, which may be instructive to future cultivation projects of traditional Chinese medicinal plants. Results Thirty-two haplotypes of S. baicalensis (HapA-Y and Hap1-7 were identified when three chloroplast spacers were combined. These haplotypes constituted a shallow gene tree without obvious clusters for cultivated populations, suggesting multiple origins of cultivated S. baicalensis. Cultivated populations (hT = 0.832 maintained comparable genetic variation with wild populations (hT = 0.888, indicating a slight genetic bottleneck due to multiple origins of cultivation. However, a substantial amount of rare alleles (10 out of 25 haplotypes within wild populations lost during the course of S. baicalensis cultivation. The genetic differentiation for cultivated group (GST = 0.220 was significantly lower than that of wild group (GST = 0.701. Isolation by distance analysis showed that the effect of geographical isolation on genetic structure was significant in wild populations (r = 0.4346, P r = 0.0599, P = 0.2710. These genetic distribution patterns suggest that a transient cultivation history and the extensive seed change among different geographical areas during the course of S. baicalensis cultivation. Conclusions Although cultivated S. baicalensis maintains comparable genetic diversity relative to wild populations, recent cultivation has still imposed profound impacts on genetic diversity patterns of the cultivated S. baicalensis populations, i.e., the loss of rare alleles and homogenization of cultivated populations. This study suggests that conservation-by-cultivation is an effective means for protecting genetic resources of S. baicalensis, however, the wild resources still need to be protected in situ and the evolutionary consequences of extensive seed exchange mediated by human being should be monitored carefully.

  20. PCR-Based Genetic Diversity of Rapeseed Germplasm Using RAPD Markers

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    Nisar Ahmad

    2007-01-01

    Full Text Available The most challenging hurdle facing Pakistan is the production of Brassica germplasm with a wider genetic base and using them properly in rapeseed genetic improvement. Genetic diversity was evaluated in 20 rapeseed lines (10 entries each of B. napus and B. campestris using RAPD as molecular markers. Four Randomly Amplified Polymorphic DNA primers were used to estimate the genetic distances among the genotypes in all the possible combinations. The genetic diversity study revealed different levels of polymorphism for RAPD primers GLA07, GLB07, GLD18 and GLE07 that resulted in amplification of 3.2, 1.5, 3.0 and 3.5 scorable bands (loci per genotype of Brassica napus and 2.5, 1.3, 2.6 and 3.7 scorable bands (loci per genotype of B. campestris. Among Brassica napus genotypes, maximum genetic distance (79% was observed between Torch+Maluka, Torch+Baro and Torch+Global, while, maximum genetic distance (91% was observed between T-16 and P1-367601 genotypes of Brassica campestris. Individual genetic distance observed among the B. napus and B. campestris lines ranged from 21.50 to 59.41% and 53.75 to 60.09%, respectively. The dissimilarity coefficient matrix of these lines based on the data of four RAPD markers using UPGMA (Unweighted Pair Group of Arithmetic Means method was also used to construct a dendrogram. The dendrogram analysis indicated that lines Torch and 366822 of B. napus, while 2163 and P1-392029 of B. campestris were genetically apart from other lines. These results provide valuable information for fingerprinting that can be used in a synergistic way to create wider genetic base and augment the breeding program of Brassica in Pakistan.

  1. Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country

    Directory of Open Access Journals (Sweden)

    Sitthi-amorn Chitr

    2009-07-01

    Full Text Available Abstract Background The population structure of the causative agents of human malaria, Plasmodium sp., including the most serious agent Plasmodium falciparum, depends on the local epidemiological and demographic situations, such as the incidence of infected people, the vector transmission intensity and migration of inhabitants (i.e. exchange between sites. Analysing the structure of P. falciparum populations at a large scale, such as continents, or with markers that are subject to non-neutral selection, can lead to a masking and misunderstanding of the effective process of transmission. Thus, knowledge of the genetic structure and organization of P. falciparum populations in a particular area with neutral genetic markers is needed to understand which epidemiological factors should be targeted for disease control. Limited reports are available on the population genetic diversity and structure of P. falciparum in Thailand, and this is of particular concern at the Thai-Myanmar and Thai-Cambodian borders, where there is a reported high resistance to anti-malarial drugs, for example mefloquine, with little understanding of its potential gene flow. Methods The diversity and genetic differentiation of P. falciparum populations were analysed using 12 polymorphic apparently neutral microsatellite loci distributed on eight of the 14 different chromosomes. Samples were collected from seven provinces in the western, eastern and southern parts of Thailand. Results A strong difference in the nuclear genetic structure was observed between most of the assayed populations. The genetic diversity was comparable to the intermediate level observed in low P. falciparum transmission areas (average HS = 0.65 ± 0.17, where the lowest is observed in South America and the highest in Africa. However, uniquely the Yala province, had only a single multilocus genotype present in all samples, leading to a strong geographic differentiation when compared to the other Thai populations during this study. Comparison of the genetic structure of P. falciparum populations in Thailand with those in the French Guyana, Congo and Cameroon revealed a significant genetic differentiation between all of them, except the two African countries, whilst the genetic variability of P. falciparum amongst countries showed overlapping distributions. Conclusion Plasmodium falciparum shows genetically structured populations across local areas of Thailand. Although Thailand is considered to be a low transmission area, a relatively high level of genetic diversity and no linkage disequilibrium was found in five of the studied areas, the exception being the Yala province (Southern peninsular Thailand, where a clonal population structure was revealed and in Kanchanaburi province (Western Thailand. This finding is particularly relevant in the context of malaria control, because it could help in understanding the special dynamics of parasite populations in areas with different histories of, and exposure to, drug regimens.

  2. Assessment of sorghum genetic resources for genetic diversity and drought tolerance using molecular markers and agro-morphological traits

    International Nuclear Information System (INIS)

    Forty sorghum genotype were investigated for genetic diversity and drought tolerance. Diversity parameters were estimated using 16 simple sequence repeats markers. For assessment of drought tolerance, the genotype were field evaluated under normal and drought stress condition for two seasons in three environments, in Sudan. In total, 98 SSRs alleles were detected with an average of 6.1 alleles per locus. The estimated polymorphic information contents ranged from 0.33 to 0.86. The genetic similarity ranged from 0.00 to 0.88 with a low mean of 0.32. The dendrogram, generated from the UPGMA cluster analysis, showed two main clusters differentiated into nine sub-clusters with close relationship to morphological characters and pedigree information. Mantel statistics revealed a good fit of the cophenetic values to the original data set (r= 0.88). The overall mean genetic diversity was 0.67. Significant differences were detected among genotypes under both normal and drought stressed conditions for all measured traits. Based on the relative yield, the most drought-tolerant genotypes were Arfa Gadamak, Wad Ahmed, El-Najada, Korcola, ICSR 92003 And Sham Sham. Drought five days delay in flowering, and the earliest genotypes were PI 569695, PI 570446, PI 569953, Dwarf White Milo and PI 56995. (Author)

  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 analysis of sugarcane parents in Chinese breeding programmes using gSSR markers.

    Science.gov (United States)

    You, Qian; Xu, Liping; Zheng, Yifeng; Que, Youxiong

    2013-01-01

    Sugarcane is the most important sugar and bioenergy crop in the world. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 115 sugarcane genotypes used for parental crossing were genotyped based on five genomic simple sequence repeat marker (gSSR) loci and 88 polymorphic alleles of loci (100%) as detected by capillary electrophoresis. The values of genetic diversity parameters across the populations indicate that the genetic variation intrapopulation (90.5%) was much larger than that of interpopulation (9.5%). Cluster analysis revealed that there were three groups termed as groups I, II, and III within the 115 genotypes. The genotypes released by each breeding programme showed closer genetic relationships, except the YC series released by Hainan sugarcane breeding station. Using principle component analysis (PCA), the first and second principal components accounted for a cumulative 76% of the total variances, in which 43% were for common parents and 33% were for new parents, respectively. The knowledge obtained in this study should be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the demand of sugarcane cultivation for sugar and bioenergy use. PMID:23990759

  5. Genetic diversity in selected stud and commercial herds of the Afrikaner cattle breed

    Scientific Electronic Library Online (English)

    L, Pienaar; J.P, Grobler; F.W.C, Neser; M.M, Scholtz; H, Swart; K, Ehlers; M, Marx.

    Full Text Available The Afrikaner is one of three indigenous cattle breeds found in South Africa. Afrikaner cattle were originally extensively used for crossbreeding purposes and breed development. The objective of this study was to determine the genetic diversity of selected stud and commercial herds from the whole So [...] uth African Afrikaner population, as well as to determine the genetic structure among these herds. Assignment methods (based on STRUCTURE software) revealed a real structure consisting of four genetic populations (K = 4). Estimates of genetic diversity did not support the hypothesis of significant loss of genetic diversity in any individual Afrikaner herd. Heterozygosity estimates ranged from 0.456 - 0.737 within individual populations, with an overall heterozygosity estimate of 0.568 for the Afrikaner breed. The average number of alleles per locus was regarded as being 2.67 - 7.78, with an average of 5.18 alleles per locus. It could be concluded that a moderate to high degree of variation is still present within the Afrikaner cattle breed, despite the recent decline in numbers of this indigenous breed.

  6. Diversity and genetic structure in natural populations of Geonoma schottiana Mart (Arecaceae: implications for conservation

    Directory of Open Access Journals (Sweden)

    Dulcinéia de Carvalho

    2011-06-01

    Full Text Available Geonoma schottiana is an underbrush palm which is found in high densities in tropical forests. This species is known for having an asynchronous fruit producing pattern, over all seasons of the year, thus being an important food source for frugivores. This work aims to determine the diversity and spatial genetic structure of two natural populations, referred to as MC I and MC II, of which 60 individuals were sampled, in Poço Bonito Biological Reserve, Lavras, Minas Gerais state. Results of 10 polymorphic isozyme loci indicated a high genetic diversity for the species (?e = 0.428 and ?o = 0.570, with an mean number of alleles per locus of 2.0. Estimates of Cockerham’s coancestry coefficients indicated an absence of intrapopulation (f = -0.343 and interpopulation inbreeding (F = -0.161, suggesting that on average populations are not endogamous. A high genetic divergence was found between populations (teta = 13.5%, in comparison to most tropical species (<5%. Consequently, the estimated historical gene flow was low (Nm = 0.40. The analysis of spatial distribution of G. schottiana genotypes in MCI revealed a random distribution of genotypes. The high genetic diversity indices found suggest that the populations in question favor in situ genetic conservation, consequently favoring the conservation of riparian environments.

  7. Investigation of Genetic Diversity among Bread Wheat Cultivars (Triticum aestivum L. Using SSR Markers

    Directory of Open Access Journals (Sweden)

    Reza Drikvand

    2012-12-01

    Full Text Available The present study was conducted to understand the genetic diversity of bread wheat's that grown in Iran, and to evaluate polymorphism information content (PIC of some wheat SSR primers. Experiment was done in the genomics Laboratory in Islamic Azad University, Khorramabad branch, Iran in 2012. Ninety-two bread wheat varieties were assayed to study the genetic diversity and polymorphism based on forty whole-genome SSR markers. Eighty alleles were identified and 2 alleles per locus were detected. The majority of SSR markers showed a high level of polymorphism. PIC values ranged from 0.12 (XBARC 148 to 0.80 (XBARC 54, with an average of 0.59 per primer, which indicates that markers were highly informative. According to similarity matrix, genetic similarity value ranged from 0.17 to 0.88. The lowest and highest genetic similarity were observed between ‘Mihan’ and ‘Star’ (No 31 and 57, ‘Azadi’ and ‘Mahdavi’ (No 4 and 6, respectively. Cluster analysis using the UPGMA method based on Jaccard coefficients was performed. Based on cluster analysis, 92 wheat cultivars were grouped in six clusters. Results indicated that Iranian grown wheat cultivars had high genetic diversity which could be exploited in wheat breeding programs.

  8. Genetic diversity and geographic distribution of hantaviruses in Russia.

    Science.gov (United States)

    Garanina, S B; Platonov, A E; Zhuravlev, V I; Murashkina, A N; Yakimenko, V V; Korneev, A G; Shipulin, G A

    2009-08-01

    Haemorrhagic fever with renal syndrome (HFRS) is the most prevalent zoonotic disease in Russia. It is caused by several hantavirus species hosted by small rodents. We describe spatial and temporal patterns of HFRS incidence in the Russian Federation, and the geographic distribution of prevalent hantavirus species: Puumala (PUUV) and Dobrava (DOBV). Partial sequencing of nucleocapsid and glycoprotein genes of 117 PUUV strains and 78 DOBV strains revealed several distinct genetic subgroups. The RNA of Volga PUUV subgroup was detected in patients with HFRS and bank voles Myodes glareolus in the Volga Federal District, where the highest HFRS incidence rate has been registered yearly. The RNA of Siberian PUUV subgroup was found in M. glareolus in the trans-Ural Tyumen and Omsk Provinces, where human HFRS cases have been rare. During an HFRS outbreak in 2007 in the Central Federal District, when more than 1000 patients were affected, specific subgroups of DOBV were discovered in patients and rodents, mainly in the striped field mouse Apodemus agrarius. DOBV strains might have 8–9% of nucleotide difference although they were collected at places separated by 30–100 km. The RNA of a unique DOBV subgroup was discovered in the southern semi-desert Astrakhan Province, mainly in A. agrarius and tamarisk jird Meriones tamariscinus. No human HFRS cases were diagnosed in this province. Russian PUUV and DOBV strains have no close homologues among European strains. Our DOBV strains might be genetically grouped together with Central European DOBV strains isolated from A. agrarius, but not from Apodemus flavicollis. The Volga PUUV subgroup is to some extent similar to Baltic PUUV strain, and Finnish PUUV strains resemble the strains from the Siberian PUUV subgroup. Thus, PCRbased monitoring and typing provided the opportunity to delineate and expand the area of hantaviruses in Russia and to identify their new genetic variants. PMID:19486318

  9. Genetic Diversity of Old Chicken Breeds Kept in Poland

    Directory of Open Access Journals (Sweden)

    Martino Cassandro

    2013-09-01

    Full Text Available The aim of this study was to compare the genetic variation of five local chicken breeds reared in Poland. Twenty-seven microsatellite markers were investigated in 138 birds belonging to five breeds: Miniature Cochin (MCO, Gold Italian (GI, Green Legged Partridge (GLP, Silver Italian (SI and White Leghorn (WL. One hundred eighty five alleles were detected in the overall population, with a mean number of 6.85 ± 3.32 alleles per locus. For the local breeds, the observed and expected heterozygosity ranged from a minimum of 0.287 to a maximum of 0.458 and from 0.397 to 0.499 for the GI and SI breeds, respectively. The overall population heterozygote deficiency was 0.430, the average Wright’s inbreeding coefficient (FIS was 0.061 and the heterozygote deficiency due to breed subdivision was 0.393. Wright’s fixation index was slightly positive for all breeds excluding MCO (FIS = -0.476 and the estimated molecular inbreeding (fij within breed ranged from 0.296 (GLP and SI to 0.361 (WL evidencing limited coancestry. Mean allelic richness, obtained with rarefaction method based on sixteen observations, was 2.12 being the WL the less variable (1.79. Tomiuk and Loeschcke’s DTL genetic distance values were used to draw a neighbornet network which separated the cluster made of MCO and GLP from the cluster of GI, WL and SI. The results arising from our microsatellites analysis represent a starting point for the valorization of these local Polish chicken breeds for monitoring and preserving their genetic variability.

  10. Evaluation of genetic diversity of an algerian durum wheat (Triticum durum Desf. collection

    Directory of Open Access Journals (Sweden)

    Boudour Leila

    2011-09-01

    Full Text Available Durum wheat (Triticum durum Desf. has been extensively cultivated in Algeria for many centuries. During this long period, the species encountered a large diversification implied by the great diversity of climates that led to great genetic diversity of the species. The purpose of this study is to improve the management of phytogenetic resources that can serve as potential breeders for the amelioration of wheat. The study aims at evaluating the diversity of 1019 accessions of durum wheat from different regions of Algeria and which are stored at the Constantine ITGC. The analysis of the results concerning phenological and morphophysiological characters revealed an important intra and intervarietal genetic variability. Subsequently it appeared that the 1019 accessions belong to 19 botanic varieties that differ mainly by the cob, silk and grain colours. Among the characters involved in this study, some appeared to have a direct connection with the adaptation to water stress and thus allowed us identifying the most resistant varieties.

  11. Genetic diversity predicts outcomes in head and neck cancer

    Science.gov (United States)

    A new measure of the heterogeneity – the variety of genetic mutations – of cells within a tumor appears to predict treatment outcomes of patients with the most common type of head and neck cancer. In the May 20 issue of the journal Cancer, investigators at Massachusetts General Hospital (a component of the Dana-Farber Cancer Institute) and Massachusetts Eye and Ear Infirmary describe how their measure was a better predictor of survival than most traditional risk factors in a small group of patients with squamous cell carcinoma of the head and neck.

  12. Comparison study of genetic diversity between rice varieties from northeast China and Japan

    International Nuclear Information System (INIS)

    The genetic diversity of 18 rice varieties from northeast China and 13 rice varieties from Japan were investigated by 20 phenotypic traits and SSR assay with 40 pairs of primers. The results showed that 82 phenotypic variation and 108 alleles were detected. With an average of 2.54 alleles on every locus the phenotypic variation and alleles in northeast China were 72 and 103, respectively, and 63 and 94 were respectively with an average of 2.32 alleles on every locus in Japanese varieties. Genetic variation among different varieties varied greatly and among different groups varied slightly. Genetic diversity of varieties in northeast China was much higher than those in Japan, and 94.7% of the alleles from Japanese varieties were included in the varieties from northeast China. The available specific alleles were already very limited in the varieties from Japan and can not meet the rice breeding requirements for northeastern China. (authors)

  13. Genetic diversity and virulence of Colletotrichum lupini isolates collected in Chile

    Scientific Electronic Library Online (English)

    Ricardo, Riegel; Débora, Véliz; Ingrid, von Baer; Yerko, Quitral; Manuel, Muñoz.

    2010-06-01

    Full Text Available All nineteen Colletotrichum isolates causing anthracnose in lupin plants growing in southern Chile belong to Colletotrichum lupini, confirming an absence of interspecific variation in the causal agent of anthracnose. Nevertheless, intraspecific genetic diversity was detected with random amplified po [...] lymorphic DNA (RAPD) markers. Based on a multiloci analysis, 14 molecular phenotypes were described among the local C. lupini isolates. The largest genetic distance between two isolates was 0.57. The analyzed isolates showed clear differences in virulence on susceptible cultivar 'Kiev Mutant' with disease severity ranging from 15 to 75% of seedlings. The high degree of DNA polymorphism, the large number of different molecular phenotypes, and the variation in virulence suggest the existence of different strains. Study of strain virulence and diversity may aid in the development of more efficient genetic improvement programs for anthracnose tolerance.

  14. Genetic diversity and virulence of Colletotrichum lupini isolates collected in Chile

    Directory of Open Access Journals (Sweden)

    Ricardo Riegel

    2010-06-01

    Full Text Available All nineteen Colletotrichum isolates causing anthracnose in lupin plants growing in southern Chile belong to Colletotrichum lupini, confirming an absence of interspecific variation in the causal agent of anthracnose. Nevertheless, intraspecific genetic diversity was detected with random amplified polymorphic DNA (RAPD markers. Based on a multiloci analysis, 14 molecular phenotypes were described among the local C. lupini isolates. The largest genetic distance between two isolates was 0.57. The analyzed isolates showed clear differences in virulence on susceptible cultivar 'Kiev Mutant' with disease severity ranging from 15 to 75% of seedlings. The high degree of DNA polymorphism, the large number of different molecular phenotypes, and the variation in virulence suggest the existence of different strains. Study of strain virulence and diversity may aid in the development of more efficient genetic improvement programs for anthracnose tolerance.

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

    Scientific Electronic Library Online (English)

    Ana Veruska Cruz da, Silva; Karla Cristina Santos, Freire; Ana da Silva, Lédo; Allívia Rouse Carregosa, Rabbani.

    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.

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

    International Nuclear Information System (INIS)

    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)

  17. Genetic diversity among Juglans regia L. genotypes assessed by morphological traits and microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    Mahmoodi, R.; Rahmani, F.; Rezaee, R.

    2013-06-01

    In this study, genetic diversity was assayed among 16 accessions and five cultivars of Persian walnut (Juglans regia L.) using morphological traits and nine simple sequence repeat (SSR) markers. Samples were collected from Agriculture Research Center of Urmia city (North West Iran). Study on important morphological traits revealed genetic similarity of -0.6 to 0.99 based on CORR coefficient. The microsatellite marker system produced 34 alleles in range of 160-290 bp. The minimum (2) and maximum (7) number of alleles were obtained from WGA71 and WGA202 genetic loci, respectively. The mean number of alleles per locus was 4.25. Jaccards similarity coefficient ranged from 0.13 to 0.76. The results of this paper indicate high diversity among these genotypes which could be used for breeding management. (Author) 28 refs.

  18. GENETIC DIVERSITY OF WINTER BREAD WHEAT (TRITICUM AESTIVUM L. SSP. VULGARE

    Directory of Open Access Journals (Sweden)

    Sonja Petrovi?

    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.

  19. Model-based conservation planning of the genetic diversity of Phellodendron amurense Rupr due to climate change

    OpenAIRE

    Wan, Jizhong; Wang, Chunjing; YU, Jinghua; Nie, Siming; Han, Shijie; Zu, Yuangang; Chen, Changmei; Yuan, Shusheng; Wang, Qinggui

    2014-01-01

    Climate change affects both habitat suitability and the genetic diversity of wild plants. Therefore, predicting and establishing the most effective and coherent conservation areas is essential for the conservation of genetic diversity in response to climate change. This is because genetic variance is a product not only of habitat suitability in conservation areas but also of efficient protection and management. Phellodendron amurense Rupr. is a tree species (family Rutaceae) that is endangere...

  20. Genetic Diversity and Distribution Patterns of Host Insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau

    OpenAIRE

    Quan, Qing-mei; Chen, Ling-ling; Wang, Xi; Li, Shan; Yang, Xiao-ling; Zhu, Yun-guo; Wang, Mu; Cheng, Zhou

    2014-01-01

    The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable medicinal fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotid...

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

    Science.gov (United States)

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

    2013-03-01

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

  2. CUDA-accelerated genetic feedforward-ANN training for data mining

    International Nuclear Information System (INIS)

    We present an implementation of genetic algorithm (GA) training of feedforward artificial neural networks (ANNs) targeting commodity graphics cards (GPUs). By carefully mapping the problem onto the unique GPU architecture, we achieve order-of-magnitude speedup over a conventional CPU implementation. Furthermore, we show that the speedup is consistent across a wide range of data set sizes, making this implementation ideal for large data sets. This performance boost enables the genetic algorithm to search a larger subset of the solution space, which results in more accurate pattern classification. Finally, we demonstrate this method in the context of the 2009 UC San Diego Data Mining Contest, achieving a world-class lift on a data set of 94682 e-commerce transactions.

  3. CUDA-accelerated genetic feedforward-ANN training for data mining

    Energy Technology Data Exchange (ETDEWEB)

    Patulea, Catalin; Peace, Robert; Green, James, E-mail: cpatulea@sce.carleton.ca, E-mail: rpeace@sce.carleton.ca, E-mail: jrgreen@sce.carleton.ca [School of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 (Canada)

    2010-11-01

    We present an implementation of genetic algorithm (GA) training of feedforward artificial neural networks (ANNs) targeting commodity graphics cards (GPUs). By carefully mapping the problem onto the unique GPU architecture, we achieve order-of-magnitude speedup over a conventional CPU implementation. Furthermore, we show that the speedup is consistent across a wide range of data set sizes, making this implementation ideal for large data sets. This performance boost enables the genetic algorithm to search a larger subset of the solution space, which results in more accurate pattern classification. Finally, we demonstrate this method in the context of the 2009 UC San Diego Data Mining Contest, achieving a world-class lift on a data set of 94682 e-commerce transactions.

  4. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, caviidae in Colombia

    Directory of Open Access Journals (Sweden)

    William Burgos-Paz

    2011-01-01

    Full Text Available The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05, genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations.

  5. 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. 

  6. Genetic diversity in three invasive clonal aquatic species in New Zealand

    Directory of Open Access Journals (Sweden)

    Sorrell Brian K

    2010-06-01

    Full Text Available Abstract Background Elodea canadensis, Egeria densa and Lagarosiphon major are dioecious clonal species which are invasive in New Zealand and other regions. Unlike many other invasive species, the genetic variation in New Zealand is very limited. Clonal reproduction is often considered an evolutionary dead end, even though a certain amount of genetic divergence may arise due to somatic mutations. The successful growth and establishment of invasive clonal species may be explained not by adaptability but by pre-existing ecological traits that prove advantageous in the new environment. We studied the genetic diversity and population structure in the North Island of New Zealand using AFLPs and related the findings to the number of introductions and the evolution that has occurred in the introduced area. Results Low levels of genetic diversity were found in all three species and appeared to be due to highly homogeneous founding gene pools. Elodea canadensis was introduced in 1868, and its populations showed more genetic structure than those of the more recently introduced of E. densa (1946 and L. major (1950. Elodea canadensis and L. major, however, had similar phylogeographic patterns, in spite of the difference in time since introduction. Conclusions The presence of a certain level of geographically correlated genetic structure in the absence of sexual reproduction, and in spite of random human dispersal of vegetative propagules, can be reasonably attributed to post-dispersal somatic mutations. Direct evidence of such evolutionary events is, however, still insufficient.

  7. Fluorescent amplified fragment length polymorphism (fAFLP) analyses and genetic diversity in Litopenaeus vannamei (Penaeidae)

    Scientific Electronic Library Online (English)

    Michelle Mantovani, Gonçalves; Manoel Victor Franco, Lemos; Pedro Manoel, Galetti Junior; Patrícia Domingues de, Freitas; Manuel Antonio Andrade, Furtado Neto.

    Full Text Available The Pacific white shrimp, Litopenaeus vannamei (Penaeidae), represents about 95% of all Brazilian shrimp production. The Brazilian L. vannamei foundation broodstock was made up of specimens collected from different American Pacific sites, but little information was collected on the genetic structure [...] of the broodstock. We used the fluorescence amplified fragment length polymorphism (fAFLP) method to study the genetic diversity of L. vannamei broodstock lines 03CMF1 and 03CBF1 originally produced by breeder-shrimps imported mainly from Panama and Ecuador, although wild individuals from other localities may also have been used in producing these two lines. Our results showed a total of 93 polymorphic bands ranging from 50 to 500 bp, the mean Nei's genetic diversity calculated for the total sample was 13.4% and identity and genetic distance analyses indicated high genetic homogeneity within and between both the broodstock lineages studied which suggests that they had similar genetic structure. These results may represent an important tool for the appropriate management of L. vannamei broodstocks.

  8. Genetic Diversity in Alpine and Foothill Populations of Campanula rotundifolia (Campanulaceae).

    Science.gov (United States)

    Bingham; Ranker

    2000-05-01

    Climatic constraints on insects in alpine environments have important consequences for the biology of their plant mutualists; in particular, reduced insect diversity and activity in alpine plant populations can result in pollinator-limited seed set and, potentially, in low genetic diversity. However, highly effective pollination by bumblebees in alpine populations can compensate for low visitation rates. In this study we hypothesized that, because of highly effective pollination by bumblebees, alpine populations of Campanula rotundifolia would not experience more frequent cycles of pollinator limitation than low-elevation populations and would therefore exhibit comparable levels of genetic variability and inbreeding to those found in foothill populations. Enzyme electrophoresis was used to assess genetic variability at nine putative loci in alpine and foothill populations of C. rotundifolia in Colorado. Genetic variability in C. rotundifolia was found to be comparable to that reported for other long-lived herbaceous perennials. Measures of genetic variability and fixation indices did not differ between high- and low-elevation populations and were consistent with Hardy-Weinberg expectations. Nonsignificant F(ST) values indicated no genetic differentiation among all populations. PMID:10817976

  9. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, Caviidae) in Colombia.

    Science.gov (United States)

    Burgos-Paz, William; Cerón-Muñoz, Mario; Solarte-Portilla, Carlos

    2011-10-01

    The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05), genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations. PMID:22215979

  10. Host genetic diversity enables Ebola hemorrhagic fever pathogenesis and resistance.

    Science.gov (United States)

    Rasmussen, Angela L; Okumura, Atsushi; Ferris, Martin T; Green, Richard; Feldmann, Friederike; Kelly, Sara M; Scott, Dana P; Safronetz, David; Haddock, Elaine; LaCasse, Rachel; Thomas, Matthew J; Sova, Pavel; Carter, Victoria S; Weiss, Jeffrey M; Miller, Darla R; Shaw, Ginger D; Korth, Marcus J; Heise, Mark T; Baric, Ralph S; de Villena, Fernando Pardo-Manuel; Feldmann, Heinz; Katze, Michael G

    2014-11-21

    Existing mouse models of lethal Ebola virus infection do not reproduce hallmark symptoms of Ebola hemorrhagic fever, neither delayed blood coagulation and disseminated intravascular coagulation nor death from shock, thus restricting pathogenesis studies to nonhuman primates. Here we show that mice from the Collaborative Cross panel of recombinant inbred mice exhibit distinct disease phenotypes after mouse-adapted Ebola virus infection. Phenotypes range from complete resistance to lethal disease to severe hemorrhagic fever characterized by prolonged coagulation times and 100% mortality. Inflammatory signaling was associated with vascular permeability and endothelial activation, and resistance to lethal infection arose by induction of lymphocyte differentiation and cellular adhesion, probably mediated by the susceptibility allele Tek. These data indicate that genetic background determines susceptibility to Ebola hemorrhagic fever. PMID:25359852

  11. Annotation and genetic diversity of the chicken collagenous lectins.

    Science.gov (United States)

    Hamzi?, Edin; Pinard-van der Laan, Marie-Hélène; Bed'Hom, Bertrand; Juul-Madsen, Helle Risdahl

    2015-06-01

    Collectins and ficolins are multimeric proteins present in various tissues and are actively involved in innate immune responses. In chickens, six different collagenous lectins have been characterized so far: mannose-binding lectin (MBL), surfactant protein A (SP-A), collectin 10 (COLEC10), collectin 11 (COLEC11), collectin 12 (COLEC12), lung lectin (LL) and one ficolin (FCN). However, the structural and functional features of the chicken collectins and ficolin are still not fully understood. Therefore, the aims of this study were: (i) to make an overview of the genetic structure and function of chicken collectins and the ficolin, (ii) to investigate the variation in the chicken collectins and the ficolin gene in different chicken populations, and (iii) to assess the presence of MBL gene variants in different chicken populations. We performed comparative genomic analysis using publically available data. The obtained results showed that collectins and ficolins have conserved protein sequences and gene structure across all vertebrate groups and this is especially notable for COLEC10, COLEC11 and COLEC12. For the purpose of studying the genetic variation, 179 animals from 14 populations were genotyped using 31 SNPs covering five genomic regions. The obtained results revealed low level of heterozygosity in the collagenous lectins except for the COLEC12 gene and the LL-SPA-MBL region compared to heterozygosity at neutral microsatellite markers. In addition, the MBL gene variants were assessed in different chicken populations based on the polymorphisms in the promoter region. We observed 10 previously identified MBL variants with A2/A8 and A4 as the most frequent alleles. PMID:25721364

  12. Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds

    DEFF Research Database (Denmark)

    Hall, S J G; Lenstra, J A

    2012-01-01

    Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n?=?54) were found, but many correlations were non-significant (n?=?100) or significantly negative (n?=?11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds.

  13. Patterns of genetic diversity of local pig populations in the State of Pernambuco, Brazil

    Directory of Open Access Journals (Sweden)

    Elizabete Cristina da Silva

    2011-08-01

    Full Text Available This study estimated the genetic diversity and structure of 12 genetic groups (GG of locally adapted and specialized pigs in the state of Pernambuco using 22 microsatellite markers. Nine locally adapted breeds (Baé, Caruncho, Canastra, Canastrão, Mamelado, Moura, Nilo, Piau and UDB (Undefined Breed and 3 specialized breeds (Duroc, Landrace and Large White, totaling 190 animals, were analyzed. The Analysis of Molecular Variance (AMOVA showed that 3.2% of the total variation was due to differences between genetic groups, and 3.6% to differences between local and commercial pigs. One hundred and ninety eight alleles were identified and apart from the Large White breed, all GG presented Hardy-Weinberg Equilibrium deviations for some loci. The total and effective allele means were lower for Duroc (3.65 and 3.01 and higher for UDB (8.89 and 4.53 and Canastra (8.61 and 4.58. Using Nei's standard genetic distance and the UPGMA method, it was possible to observe that the Landrace breed was grouped with the local genetic groups Canastra, Moura, Canastrão, Baé and Caruncho. Due to the complex admixture pattern, the genetic variability of the 12 genetic groups can be analyzed by distributing the individuals into two populations as demonstrated by a Bayesian analysis, corroborating the results from AMOVA, which revealed a low level of genetic differentiation between the inferred populations.

  14. Patterns of genetic diversity of local pig populations in the State of Pernambuco, Brazil

    Scientific Electronic Library Online (English)

    Elizabete Cristina da, Silva; Wilson Moreira, Dutra Junior; Patrícia, Ianella; Manoel Adrião, Gomes Filho; Cláudio José Parro de, Oliveira; Débora Nathália de Moura, Ferreira; Alexandre Rodrigues, Caetano; Samuel Rezende, Paiva.

    1691-16-01

    Full Text Available This study estimated the genetic diversity and structure of 12 genetic groups (GG) of locally adapted and specialized pigs in the state of Pernambuco using 22 microsatellite markers. Nine locally adapted breeds (Baé, Caruncho, Canastra, Canastrão, Mamelado, Moura, Nilo, Piau and UDB (Undefined Breed [...] )) and 3 specialized breeds (Duroc, Landrace and Large White), totaling 190 animals, were analyzed. The Analysis of Molecular Variance (AMOVA) showed that 3.2% of the total variation was due to differences between genetic groups, and 3.6% to differences between local and commercial pigs. One hundred and ninety eight alleles were identified and apart from the Large White breed, all GG presented Hardy-Weinberg Equilibrium deviations for some loci. The total and effective allele means were lower for Duroc (3.65 and 3.01) and higher for UDB (8.89 and 4.53) and Canastra (8.61 and 4.58). Using Nei's standard genetic distance and the UPGMA method, it was possible to observe that the Landrace breed was grouped with the local genetic groups Canastra, Moura, Canastrão, Baé and Caruncho. Due to the complex admixture pattern, the genetic variability of the 12 genetic groups can be analyzed by distributing the individuals into two populations as demonstrated by a Bayesian analysis, corroborating the results from AMOVA, which revealed a low level of genetic differentiation between the inferred populations.

  15. Genetic diversity of locally adapted sheep from Pantanal region of Mato Grosso do Sul.

    Science.gov (United States)

    Crispim, B A; Grisolia, A B; Seno, L O; Egito, A A; Vargas Junior, F M; Souza, M R

    2013-01-01

    Sheep of the Pantaneiro breed and seven other breeds, raised in the State of Mato Grosso do Sul, Brazil, were genotyped using eight microsatellite loci. The aim of the present study was to determine the genetic variability, phylogenetic relationship, and patterns of gene introgression and miscegenation among the animals surveyed, to obtain information about the genetic structure of locally adapted sheep in Mato Grosso do Sul. A total of 195 animals were used for genetic analysis. The Pantaneiro breed had the largest average number of alleles/locus (9.25), and higher allelic richness (6.95), while the Dorper population had the lowest values for these parameters (4.88 and 3.86, respectively). Analysis of genetic distance values and genetic structure between populations made it possible to characterize these animals with regard to distinct genetic groups. Average expected heterozygosity ranged from 0.72 (Pantaneiro) to 0.55 (Dorper), while average observed heterozygosity ranged from 0.63 (White Dorper) to 0.54 (Dorper). On the basis of the statistical parameters evaluated, it was possible to demonstrate that when compared to other populations, the Pantaneiro breed represented a reservoir of genetic diversity with rare and useful alleles for genetic improvement, emphasizing the importance of preserving the breed. PMID:24301918

  16. Genetic diversity of carotenoid-rich bananas evaluated by Diversity Arrays Technology (DArT

    Directory of Open Access Journals (Sweden)

    Edson P. Amorim

    2009-01-01

    Full Text Available The aim of this work was to evaluate the carotenoid content and genetic variability of banana accessions from the Musa germplasm collection held at Embrapa Cassava and Tropical Fruits, Brazil. Forty-two samples were analyzed, including 21 diploids, 19 triploids and two tetraploids. The carotenoid content was analyzed spectrophotometrically and genetic variability was estimated using 653 DArT markers. The average carotenoid content was 4.73 µg.g-1, and ranged from 1.06 µg.g-1 for the triploid Nanica (Cavendish group to 19.24 µg.g-1 for the triploid Saney. The diploids Modok Gier and NBA-14 and the triploid Saney had a carotenoid content that was, respectively, 7-fold, 6-fold and 9-fold greater than that of cultivars from the Cavendish group (2.19 µg.g-1. The mean similarity among the 42 accessions was 0.63 (range: 0.24 to 1.00. DArT analysis revealed extensive genetic variability in accessions from the Embrapa Musa germplasm bank.

  17. Genetic diversity of carotenoid-rich bananas evaluated by Diversity Arrays Technology (DArT)

    Scientific Electronic Library Online (English)

    Edson P., Amorim; Alberto D., Vilarinhos; Kelly O., Cohen; Vanusia B.O., Amorim; Janay A. dos, Santos-Serejo; Sebastião Oliveira e, Silva; Kátia N., Pestana; Vânia J. dos, Santos; Norma S., Paes; Damares C., Monte; Ronaldo V. dos, Reis.

    Full Text Available The aim of this work was to evaluate the carotenoid content and genetic variability of banana accessions from the Musa germplasm collection held at Embrapa Cassava and Tropical Fruits, Brazil. Forty-two samples were analyzed, including 21 diploids, 19 triploids and two tetraploids. The carotenoid co [...] ntent was analyzed spectrophotometrically and genetic variability was estimated using 653 DArT markers. The average carotenoid content was 4.73 µg.g-1, and ranged from 1.06 µg.g-1 for the triploid Nanica (Cavendish group) to 19.24 µg.g-1 for the triploid Saney. The diploids Modok Gier and NBA-14 and the triploid Saney had a carotenoid content that was, respectively, 7-fold, 6-fold and 9-fold greater than that of cultivars from the Cavendish group (2.19 µg.g-1). The mean similarity among the 42 accessions was 0.63 (range: 0.24 to 1.00). DArT analysis revealed extensive genetic variability in accessions from the Embrapa Musa germplasm bank.

  18. Allele-mining and natural diversity in wheat powdery mildew resistance genes

    International Nuclear Information System (INIS)

    Using map-based cloning, we have isolated the Pm3b powdery mildew resistance gene from hexaploid bread wheat (Triticum aestivum L.). Based on haplotype studies, we have developed molecular tools to isolate all the 10 known Pm3 genes conferring resistance. We found that the Pm3 genes form a true allelic series and that they are highly conserved at the molecular level. The molecular work on Pm3 resistance genes has lead to very diagnostic tools for these genes which support the cloning of new functional alleles from this locus by allele-mining. We have used these tools to screen for new Pm3 alleles in the gene pools of (i) wild and domesticated tetraploid accessions and (ii) hexaploid wheat landraces. The Pm3 locus is conserved in tetraploid wheat, allowing a comparative evolutionary study of the same resistance locus in a domesticated species and one of its wild ancestors. We have identified 61 Pm3 allelic sequences from wild and domesticated tetraploid wheat subspecies. These alleles showed low sequence diversity, differing by few polymorphic sequence blocks that were further reshuffled between alleles by gene conversion and recombination. A new functional gene was identified in a wild wheat accession from Syria. This gene, Pm3k, conferred intermediate resistance to powdery mildew and consists of a mosaic of gene segments derived from non-functional alleles. From the hexaploid wheat gene pool, a set of 1320 landraces, mostly from Asia, was screened for powdery mildew rom Asia, was screened for powdery mildew resistance and the presence of a Pm3 haplotype. Most of these lines were found to contain a susceptible Pm3 allele which is closely related to the functional Pm3 resistance genes. We have also identified resistant lines with new types of Pm3 allelic sequences, resulting from point mutations, gene conversion and illegitimate recombination events. These new alleles are currently tested for resistance activity in a transient expression assay. (author)

  19. Genetic diversity of grasspea and its relative species revealed by SSR markers.

    Science.gov (United States)

    Wang, Fang; Yang, Tao; Burlyaeva, Marina; Li, Ling; Jiang, Junye; Fang, Li; Redden, Robert; Zong, Xuxiao

    2015-01-01

    The study of genetic diversity between Lathyrus sativus L. and its relative species may yield fundamental insights into evolutionary history and provide options to meet the challenge of climate changes. 30 SSR loci were employed to assess the genetic diversity and population structure of 283 individuals from wild and domesticated populations from Africa, Europe, Asia and ICARDA. The allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information content (PIC) was 0.5340 and 0.4817, respectively. A model based population structure analysis divided the germplasm resources into three subgroups: the relative species, the grasspea from Asia, and the grasspea from Europe and Africa. The UPGMA dendrogram and PCA cluster also demonstrated that Asian group was convincingly separated from the other group. The AMOVA result showed that the cultivated species was quite distinct from its relative species, however a low level of differentiation was revealed among their geographic origins. In all, these results provided a molecular basis for understanding genetic diversity of L. sativus and its relatives. PMID:25793712

  20. 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.

  1. Genetic Diversity Within and Among Populations of Roseroot (Rhodiola rosea L. Based on Molecular Markers

    Directory of Open Access Journals (Sweden)

    Andrzej PEDRYC

    2012-11-01

    Full Text Available Rhodiola rosea L. is a perennial adaptogenic medicinal plant found in cool climate of the northern hemisphere. The species is very diverse both in terms of morphological characteristics and in the content of the pharmacologically active substances. The genetic diversity of four geographically distant roseroot populations was studied with ISSR and SSR markers. Using 7 ISSR primers 64 DNA fragments were generated and 85,94% of those were found to be polymorphic, indicating high genetic variability at the species level (gene diversity = 0.33, Shannon index = 0.48. Lower level of diversity was detected at the population level (Shannon-index ranged from 0.2173 to 0.2696. Only four out of the eight SSR markers used were informative during this study. The primer pairs for these four SSR markers produced 25 fragments with an average of 6.25 putative alleles per locus. Observed heterozygosity ranged from 0.4 to 1.0, whereas expected heterozygosity ranged from 0.47 to 0.84. Cluster analysis based on both markers revealed the same groups, individuals clustered according to their geographic origin. The Southern-Uralian population was the most genetically isolated. ITS analysis was used for the determination whether these Southern-Uralian individuals belong to the same species.

  2. Genetic diversity and relationships among Dutch elm disease tolerant Ulmus pumila L. accessions from China.

    Science.gov (United States)

    Zalapa, Juan E; Brunet, Johanne; Guries, Raymond P

    2008-07-01

    Elm breeding programs worldwide have relied heavily on Asian elm germplasm, particularly Ulmus pumila, for the breeding of Dutch elm disease tolerant cultivars. However, the extent and patterning of genetic variation in Asian elm species is unknown. Therefore, the objective of this research was to determine the extent of genetic diversity among 53 U. pumila accessions collected throughout the People's Republic of China. Using 23 microsatellite loci recently developed in the genus Ulmus, a total of 94 alleles were identified in 15 polymorphic and 4 monomorphic loci. The average number of alleles per locus was 4.9, with a range of 1-11 alleles. Gene diversity estimates per locus ranged from 0.08 to 0.87, and the non-exclusion probability for the 15 polymorphic loci combined was 0.7 x 10(-9). Nineteen region-specific alleles were identified, and regional gene diversity estimates were moderately high (0.48-0.57). The genetic relationships among accessions and regions were estimated by UPGMA and principal coordinate analysis. Both techniques discriminated all accessions and regions. Two microsatellite markers (UR175 + UR123 or Ulm-3) were sufficient to discriminate up to 99.7% of the accessions studied. This research provides useful information for DNA-based fingerprinting, breeding, ecological studies, and diversity assessment of elm germplasm. PMID:18545273

  3. Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

    Scientific Electronic Library Online (English)

    Zahida Hassan, Pervaiz; M. Ashiq, Rabbani; Ishtiaq, Khaliq; Stephen R, Pearce; Salman A, Malik.

    2010-05-15

    Full Text Available Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice (Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Paki [...] stan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection.

  4. The statistics of genetic diversity in rapidly adapting populations.

    Science.gov (United States)

    Desai, Michael

    2013-03-01

    Evolutionary adaptation is driven by the accumulation of beneficial mutations, but the sequence-level dynamics of this process are poorly understood. The traditional view is that adaptation is dominated by rare beneficial ``driver'' mutations that occur sporadically and then rapidly increase in frequency until they fix (a ``selective sweep''). Yet in microbial populations, multiple beneficial mutations are often present simultaneously. Selection cannot act on each mutation independently, but only on linked combinations. This means that the fate of any mutation depends on a complex interplay between its own fitness effect, the genomic background in which it arises, and the rest of the sequence variation in the population. The balance between these factors determines which mutations fix, the patterns of sequence diversity within populations, and the degree to which evolution in replicate populations will follow parallel (or divergent) trajectories at the sequence level. Earlier work has uncovered signatures of these effects, but the dynamics of genomic sequence evolution in adapting microbial populations have not yet been directly observed. In this talk, I will describe how full-genome whole-population sequencing can be used to provide a detailed view of these dynamics at high temporal resolution over 1000 generations in 40 adapting Saccharomyces cerevisiaepopulations. This data shows how patterns of sequence evolution are driven by a balance between chance interference and hitchhiking effects, which increase stochastic variation in evolutionary outcomes, and the deterministic action of selection on individual mutations, which favors parallel solutions in replicate populations.

  5. Quantifying genetic diversity under a broad spectrum of deleterious mutations

    Science.gov (United States)

    Good, Benjamin; Desai, Michael

    2013-03-01

    Recent studies have shown that selection against deleterious mutations may play a major role in shaping observed patterns of sequence variation in natural populations. However, our understanding of these patterns remains limited, since selection creates correlations along the genome that are difficult to disentangle from each other. Previous theoretical work has focused on the qualitative effects of selection on sequence diversity, using simplified models in which all selected mutations have the same fitness cost. Yet is known that deleterious mutations follow a wide distribution in most organisms, so it is necessary to extend our theoretical predictions to this more general case before we can make quantitative connections with existing data. The evolutionary dynamics of this regime are complicated: extant mutant lineages represent large, correlated fluctuations away from the background expectation, which hinders efforts to apply existing methods based on deterministic or ``mean-field'' approximations. Here, we will describe recent progress towards this goal, which is based on a ``coarse-graining'' of the underlying distribution of fitnesses in the population.

  6. Genetic diversity of Mycoplasma hyopneumoniae isolates of abattoir pigs.

    Science.gov (United States)

    Charlebois, Audrey; Marois-Créhan, Corinne; Hélie, Pierre; Gagnon, Carl A; Gottschalk, Marcelo; Archambault, Marie

    2014-01-31

    Mycoplasma hyopneumoniae, the causative agent of porcine enzootic pneumonia, is present in swine herds worldwide. However, there is little information on strains infecting herds in Canada. A total of 160 swine lungs with lesions suggestive of enzootic pneumonia originating from 48 different farms were recovered from two slaughterhouses and submitted for gross pathology. The pneumonic lesion scores ranged from 2% to 84%. Eighty nine percent of the lungs (143/160) were positive for M. hyopneumoniae by real-time PCR whereas 10% (16/160) and 8.8% (14/160) were positive by PCR for M. hyorhinis and M. flocculare, respectively. By culture, only 6% of the samples were positive for M. hyopneumoniae (10/160). Among the selected M. hyopneumoniae-positive lungs (n=25), 9 lungs were co-infected with M. hyorhinis, 9 lungs with PCV2, 2 lungs with PRRSV, 12 lungs with S. suis and 10 lungs with P. multocida. MLVA and PCR-RFLP clustering of M. hyopneumoniae revealed that analyzed strains were distributed among three and five clusters respectively, regardless of severity of lesions, indicating that no cluster is associated with virulence. However, strains missing a specific MLVA locus showed significantly less severe lesions and lower numbers of bacteria. MLVA and PCR-RFLP analyses also showed a high diversity among field isolates of M. hyopneumoniae with a greater homogeneity within the same herd. Almost half of the field isolates presented less than 55% homology with selected vaccine and reference strains. PMID:24345410

  7. Fengshui forests conserve genetic diversity: a case study of Phoebe bournei (Hemsl.) Yang in southern China.

    Science.gov (United States)

    Ge, Y J; Liu, Y J; Shen, A H; Lin, X C

    2015-01-01

    Fengshui forests (sacred groves) are important in traditional Chinese culture and home to many endangered species. These forests may provide protection for some endangered plant species outside the nature reserves, but little is known about their role in genetic conservation. Using inter-simple sequence repeat (ISSR) markers, we compared the genetic diversity of 6 populations of Phoebe bournei (Hemsl.) Yang, a commercially important woody species, which is under second-class national protection and endemic to China. Samples were collected from the nature reserves and Fengshui forests in southern China. Herein, we show that Fengshui forest populations are capable of maintaining some level of genetic diversity. For nature reserve populations, the average NA and NE were 1.58 and 1.39, respectively; and for Fengshui forests, they were 1.39 and 1.12, respectively. For nature reserve populations, Nei's gene diversity (H) and Shannon's index (I) were 0.32 and 0.11, respectively; and for Fengshui forests, they were 0.22 and 0.07, respectively. We discuss the reasons for the genetic differences between populations of the Fengshui forests and nature reserves and propose conservation strategies for the Fengshui forest. PMID:25867344

  8. High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region

    Science.gov (United States)

    Douaihy, Bouchra; Vendramin, Giovanni G.; Boraty?ski, Adam; Machon, Nathalie; Bou Dagher-Kharrat, Magda

    2011-01-01

    Background and aims Juniperus excelsa is an important woody species in the high mountain ecosystems of the eastern Mediterranean Basin where it constitutes the only coniferous species found at the tree line. The genetic diversity within and among J. excelsa populations of the eastern Mediterranean Basin is studied in the light of their historical fragmentation. Methodology Nuclear microsatellites originally developed for Juniperus communis and J. przewalskii were tested on 320 individuals from 12 different populations originating from Lebanon, Turkey, Cyprus, Greece and the Ukraine. Principal results Among the 31 nuclear microsatellite primers tested, only three produced specific amplification products, with orthology confirmed by sequence analysis. They were then used for genetic diversity studies. The mean number of alleles and the expected heterozygosity means were Na=8.78 and He=0.76, respectively. The fixation index showed a significant deviation from Hardy–Weinberg equilibrium and an excess of homozygotes (FIS=0.27–0.56). A moderate level of genetic differentiation was observed among the populations (FST=0.075, P2000 m) in Lebanon. These populations were differentiated from the other populations that are grouped into three sub-clusters. Conclusions High levels of genetic diversity were observed at species and population levels. The high level of differentiation in the high-mountain Lebanese populations reflects a long period of isolation or possibly a different origin. The admixture observed in other populations from Lebanon suggests a more recent separation from the Turkish–southeastern European populations. PMID:22476474

  9. 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.

  10. Evaluation of Genetic Diversity in Aegilops geniculata Roth Accessions using Morphological and RAPD Markers

    Directory of Open Access Journals (Sweden)

    A. Mahjoub

    2009-01-01

    Full Text Available Thirteen Aegilops geniculata Roth (geniculate goat grass accessions from collection of the North and Central Tunisian (Cap-Bon, Mogodses, Kroumiry and the Dorsal areas were used to assess its genetic diversity by morphological and Random Amplified Polymorphic DNA (RAPD data and to evaluate relationship between morphological and RAPD markers. Nineteen morphological traits were analyzed on all accessions using Principal Analysis Component (PCA and clusters were constrained based on median joining distances. Nineteen arbitrary universal primers were used for the amplification of random DNA sequences and generated 212 bands ranging from 0.5 to 3 kb with 71.27% polymorphism across the 13 accessions. Both RAPD and morphological data classified accessions in two main groups. Both methods were used to compare how morphological traits and RAPD molecular markers described accessions relationship and showed a high degree of variation among analyzed accessions, indicating an important source of genetic diversity that can be used in future breeding programs. Morphological PCA traits and cluster indicated climatic stage. In fact, they grouped Ae. geniculata accessions according to genetic criteria such as earliness and high kernel yield. Comparison of morphological and molecular data using the Mantel test indicated a non significant correlation (r = -0.268. Nevertheless, RAPD and selected morphological characters appear as useful and complementary techniques for evaluation of genetic diversity in Ae. geniculata.

  11. Investigation of genetic diversity in black gram [vigna mungo (l.) hepper

    International Nuclear Information System (INIS)

    In the present investigation 34 Pakistani Black gram cultivars were evaluated through morphological traits, SDS-PAGE analysis and random amplified polymorphic markers (RAPD) which revealed considerable amount of genetic diversity in this species. Among the morphological traits, dry pod weight (71.79%), number of branches per plant (51.16%) and biological yield (50.12%) showed highest level of coefficient of variation. Percent frequency distribution also showed highest level of genetic diversity. Positive significant correlation was observed between numbers of pods per plant and dry pod length (p=0.01); grain yield and number of seeds per plant (p=0.02), and 100 seeds weight and biological yield (p=0.04). A total of 20 cultivars were identified and characterized on the basis of maximum and minimum value for 10 quantitative traits. The combinations of 20 cultivars are having practical application for breeding program as well as for direct selection of super cultivar. Among the biochemical and molecular makers, RAPD marker showed high level genetic similarity difference (0.00-4.00) as compared to SDS-PAGE (0.00- 2.45). RAPD analysis is considered the best option for determining Black gram genetic diversity pattern and Gene Bank management. (author)

  12. Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey.

    Science.gov (United States)

    Pérez-Espona, S; Pérez-Barbería, F J; Goodall-Copestake, W P; Jiggins, C D; Gordon, I J; Pemberton, J M

    2009-02-01

    The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area. PMID:19002206

  13. A Study of Genetic Diversity in Sardari Wheat Ecotypes Using AFLP Markers and Agronomic Traits

    Directory of Open Access Journals (Sweden)

    A Siosemardeh

    2009-04-01

    Full Text Available Studying genetic diversity is important because a decrease in genetic variability might result in a reduction of the plasticity of the crops to respond to changes in climate, pathogen populations, or agricultural practices. In this study, 72 Sardari wheat (Triticum aestivum L. ecotypes were analyzed by AFLP markers and 17 phenotypic characters. Three pairs of EcoRI/MseI primer combinations produced 1582 polymorphic bands (with mean percentage of polymorphic 73.92%. Cluster analysis using Jaccard coefficient and the entire AFLP data divided all ecotypes into eight major groups. Mean, coefficient of variation, phenotypic, genotypic and environment variance were calculated in each quantitative character. Cluster analysis using Euclidian distance through the quantitative characters divided all ecotypes into six major groups. Comparison of genetic distances obtained from AFLP and agronomic data showed low correlation between the two diversity measurements (0.02. The results showed a high degree of genetic diversity between the Sardari ecotypes, suggesting that Sardari is not a single cultivar, but it is the mass of ecotypes and could be introduced in the gene bank.

  14. Genetic Diversity and Pathogenicity of Cylindrocarpon destructans Isolates Obtained from Korean Panax ginseng.

    Science.gov (United States)

    Song, Jeong Young; Seo, Mun Won; Kim, Sun Ick; Nam, Myeong Hyeon; Lim, Hyoun Sub; Kim, Hong Gi

    2014-06-01

    We analyzed the genetic diversity of Cylindrocarpon destructans isolates obtained from Korean ginseng (i.e., Panax ginseng) roots by performing virulence tests and nuclear ribosomal gene internal transcribed spacer (ITS) and mitochondrial small subunit (mt SSU) rDNA sequence analysis. The phylogenetic relationship analysis performed using ITS DNA sequences and isolates from other hosts helped confirm that all the Korean C. destructans isolates belonged to Nectria/Neonectria radicicola complex. The results of in vivo and ex vivo virulence tests showed that the C. destructans isolates could be divided into two groups according to their distinctive difference in virulence and the genetic diversity. The highly virulent Korean isolates in pathogenicity group II (PG II), together with foreign isolates from P. ginseng and P. quinquefolius, formed a single group. The weakly virulent isolates in pathogenicity group I, together with the foreign isolates from other host plants, formed another group and exhibited a greater genetic diversity than the isolates of PG II, as confirmed by the mt SSU rDNA sequence analysis. In addition, as the weakly virulent Korean isolates were genetically very similar to the foreign isolates from other hosts, they were likely to originate from hosts other than the ginseng plants. PMID:25071387

  15. Genetic diversity of Y-short tandem repeats in Chinese native cattle breeds.

    Science.gov (United States)

    Xin, Y P; Zan, L S; Liu, Y F; Tian, W Q; Wang, H B; Cheng, G; Li, A N; Yang, W C

    2014-01-01

    The aim of this study is to use Y-chromosome gene polymorphism method to investigate regional differences in genetic variation and population evolution history of the Chinese native cattle breeds. Six Y-chromosome short tandem repeat (Y-STR) loci (UMN0929, UMN0108, UMN0920, INRA124, UMN2404, and UMN0103) were analyzed using 1016 healthy and heterogenetic males and 90 females of 9 native cattle breeds (Qinchuan, Jinnan, Zaosheng, Luxi, Nanyang, Jiaxian, Dabieshan, Yanbian, and Menggu) in China. Allele frequency and gene diversity were calculated for the various populations. The results indicated that Y-STRs in the 6 loci have polymorphisms and genetic diversity in Chinese cattle populations. The genetic diversity analysis revealed that the Chinese cattle populations have a close genetic relationship. The analysis of INRA124, UMN2404, and UMN0103 loci revealed the original history of Chinese cattle because of which cattle belonging to Bos taurus or Bos indicus could be determined. Interestingly, a declining zebu introgression was displayed from South to North and from East to West in the Chinese geographical distribution, which implied that cattle population from various regions of China had been subjected to somewhat different evolutionary history. This conclusion supported other evidences such as earlier archaeological, historical research, and blood protein polymorphism analysis. PMID:25501167

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

    Science.gov (United States)

    Dillon, Shannon; McEvoy, Rachel; Baldwin, Darren S; Rees, Gavin N; Parsons, Yvonne; Southerton, Simon

    2014-01-01

    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. PMID:25093589

  17. Preliminary Studies on Genetic Diversity of Selected Polish Local Chicken Varieties

    Directory of Open Access Journals (Sweden)

    Piotr ANTOS

    2013-03-01

    Full Text Available The study was aimed at evaluation of the applicability of selected microsatellite markers in examining genetic diversity in five Polish local chicken varieties (two groups of native crested chickens, crestless native chickens from Subcarpathian region and two groups of native miniature chickens and reveal their genetic relationships to five purebreds (Leghorn, Rhode Island Red, Sussex, Greenleg Partridge, Minorca. About 22.8% (overall FST = 0.228 of the genetic variation was explained by differences between breeds and varieties. The DA genetic distances between five Polish native varieties and five purebreds varied between 0.154 and 0.440. The results obtained in this study indicate the great value of the collection and suggest the need for formal protection of these local Polish chicken varieties.

  18. Microsatellite analysis of genetic diversity in wild and farmed Emus (Dromaius novaehollandiae).

    Science.gov (United States)

    Hammond, E L; Lymbery, A J; Martin, G B; Groth, D; Wetherall, J D

    2002-01-01

    The emu (Dromaius novaehollandiae) occupies most regions of the Australian continent and in recent times has been farmed for meat, oil, and leather. Very little is known about the genetic structure of natural or farmed populations of these birds. We report a preliminary study of genetic variation in emus undertaken by typing birds from five farms and two natural populations at five polymorphic microsatellite loci. Genetic diversity was high for all populations and there was little evidence of inbreeding, with most populations conforming to Hardy-Weinberg equilibrium for most loci. Significant heterozygote deficiencies at one locus in a number of populations were detected and may indicate the presence of null alleles. Comparisons of allele frequencies showed little evidence of genetic differentiation either among farmed populations or between farmed and natural populations. PMID:12547928

  19. Genetic diversity in the parthenogenetic reproducing tardigrade Echiniscus testudo (Heterotardigrada: Echiniscoidea)

    DEFF Research Database (Denmark)

    JØrgensen, Aslak; Faurby, SØren

    2013-01-01

    Little is known about the genetic structure of microscopic animals from mosses and lichens. A few studies have investigated the geographic variation in tardigrades from mosses, but so far no study has investigated the intra-population or local clonal lineage variation. Echiniscus testudo (Echiniscoidea: Echiniscidae) belongs to a large cosmopolitan genus of terrestrial tardigrades comprising more than 150 species. It is a common tardigrade in mosses in the temperate part of the Northern hemisphere, and is highly tolerant of desiccation and freezing. In a previous study, we reported a maximum of 1.28% sequence variation (uncorrected p-distance) in cytochrome c oxidase subunit I (COI) haplotypes between clonal lineages covering a large geographical area. However, in this previous study we used pooled specimens to constitute a sample, and the genetic diversity from single specimens within a locality therefore remains unknown. Accordingly, the present study investigates the COI sequence variation and haplotype diversity between single specimens of E. testudo collected at three Danish localities, separated by 80 m and 186 km. A total of 10 COI haplotypes were found in the present study (Et2, Et3, Et9, Et12-Et18); only three of these were previously reported (Et2, Et3 and Et9). The uncorrected COI sequence diversity ranged between 0-2.07%, with haplotype Et18 having the highest genetic difference. The second most variable haplotypes (Et14, Et15, and Et17) all showed a maximum diversity of 1.19% compared to the other haplotypes. No general pattern of haplotype distribution was evident. Our data suggest that E. testudo has dispersed across the Baltic sea as haplotypes Et3, Et13 and Et14 are present at all three localities. The most likely dispersal mode is passive wind dispersal in the cryptobiotic tun stage. The current study emphasises that numerous sequences from single specimens are needed to describe the genetic diversity within single moss cushions.

  20. Genetic diversity in the parthenogenetic reproducing tardigrade Echiniscus testudo (Heterotardigrada: Echiniscoidea

    Directory of Open Access Journals (Sweden)

    Reinhardt Møbjerg Kristensen

    2013-07-01

    Full Text Available Little is known about the genetic structure of microscopic animals from mosses and lichens. A few studies have investigated the geographic variation in tardigrades from mosses, but so far no study has investigated the intra-population or local clonal lineage variation. Echiniscus testudo (Echiniscoidea: Echiniscidae belongs to a large cosmopolitan genus of terrestrial tardigrades comprising more than 150 species. It is a common tardigrade in mosses in the temperate part of the Northern hemisphere, and is highly tolerant of desiccation and freezing. In a previous study, we reported a maximum of 1.28% sequence variation (uncorrected p-distance in cytochrome c oxidase subunit I (COI haplotypes between clonal lineages covering a large geographical area. However, in this previous study we used pooled specimens to constitute a sample, and the genetic diversity from single specimens within a locality therefore remains unknown. Accordingly, the present study investigates the COI sequence variation and haplotype diversity between single specimens of E. testudo collected at three Danish localities, separated by 80 m and 186 km. A total of 10 COI haplotypes were found in the present study (Et2, Et3, Et9, Et12-Et18; only three of these were previously reported (Et2, Et3 and Et9. The uncorrected COI sequence diversity ranged between 0-2.07%, with haplotype Et18 having the highest genetic difference. The second most variable haplotypes (Et14, Et15, and Et17 all showed a maximum diversity of 1.19% compared to the other haplotypes. No general pattern of haplotype distribution was evident. Our data suggest that E. testudo has dispersed across the Baltic sea as haplotypes Et3, Et13 and Et14 are present at all three localities. The most likely dispersal mode is passive wind dispersal in the cryptobiotic tun stage. The current study emphasises that numerous sequences from single specimens are needed to describe the genetic diversity within single moss cushions.