WorldWideScience

Sample records for genetic diversity mining

  1. Copper tolerance and genetic diversity of Porcellionides sexfasciatus (ISOPODA) in a highly contaminated mine habitat.

    Science.gov (United States)

    Costa, Dalila; Bouchon, Didier; van Straalen, Nico M; Sousa, José Paulo; Ribeiro, Rui

    2013-04-01

    Organisms inhabiting metal-contaminated areas may develop metal tolerance, with either phenotypic adjustments or genetic changes (adaptation) or with both. In the present study, three populations of the terrestrial isopod Porcellionides sexfasciatus, collected at an abandoned mine area, were compared to assess the effects of metal contamination on tolerance to lethal and sublethal levels of copper, through comparison of survival, avoidance, and feeding. The effects of metal contamination on genetic diversity were considered using random amplified polymorphic DNA (RAPD) markers. No evidence of increased metal tolerance of the population inhabiting the contaminated site was found. There was no correlation between metal exposure and within-population genetic variance, but the three populations were clearly separated from each other. In conclusion, the populations of P. sexfasciatus in the mine landscape live rather isolated from each other and show no differential tolerance to Cu or indications of genetic erosion. Their phenotypic plasticity provides a means to survive despite exposure to extremely high metal concentrations in the soil. PMID:23322508

  2. 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.

  3. 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

  4. 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).

  5. Imposing genetic diversity.

    Science.gov (United States)

    Sparrow, Robert

    2015-01-01

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

  6. 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...

  7. Genetic diversity in experimental metapopulations

    OpenAIRE

    Bakker, Johanna,

    2008-01-01

    The biological diversity. of our planet is rapidly declining. Because of habitat deterioration and fragmentation, many species have been reduced to small, more. or less isolated populations. with. an increased extinction risk. Such small populations suffering from temporary extinctions, but connected through (limited) migration constitute a metapopulation. The genetic diversity in a metapopulation is mostly decided by "genetic drift" removing genetic variation from small populations, and by "...

  8. XML Mining Using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Amitava Nag

    2011-06-01

    Full Text Available 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 Algorithm (GA we can improve the scenario. The major advantage of using GA in the discovery of frequent item sets 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 item sets from XML database using genetic algorithm.

  9. Genetic Diversity and Human Equality.

    Science.gov (United States)

    Dobzhansky, Theodosius

    The idea of equality often, if not frequently, bogs down in confusion and apparent contradictions; equality is confused with identity, and diversity with inequality. It would seem that the easiest way to discredit the idea of equality is to show that people are innately, genetically, and, therefore, irremediably diverse and unlike. The snare is,…

  10. Genetic diversity in Entamoeba histolytica

    Indian Academy of Sciences (India)

    C Graham Clark; Mehreen Zaki; Ibne Karim Md Ali

    2002-11-01

    Genetic diversity within Entamoeba histolytica led to the re-description of the species 10 years ago. However, more recent investigation has revealed significant diversity within the re-defined species. Both protein-coding and non-coding sequences show variability, but the common feature in all cases is the presence of short tandem repeats of varying length and sequence. The ability to identify strains of E. histolytica may lead to insights into the population structure and epidemiology of the organism.

  11. The genetic diversity of Plasmodium vivax populations.

    OpenAIRE

    Cui, L.; Escalante, AA; Imwong, M; Snounou, G.

    2003-01-01

    Little is known of the genetic diversity and population structure of Plasmodium vivax, a debilitating and highly prevalent malaria parasite of humans. This article reviews the known polymorphic genetic markers, summarizes current data on the population structure of this parasite and discusses future prospects for using knowledge of the genetic diversity to improve control measures.

  12. Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes

    Science.gov (United States)

    Li, Xiaofang; Zhu, Yong-Guan; Shaban, Babak; Bruxner, Timothy J. C.; Bond, Philip L.; Huang, Longbin

    2015-01-01

    Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses. PMID:26286020

  13. Genetic diversity in a crop metapopulation

    OpenAIRE

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

    2010-01-01

    The need to protect crop genetic resources has sparked a growing interest in the genetic diversity maintained in traditional farming systems worldwide. Although traditional seed management has been proposed as an important determinant of genetic diversity and structure in crops, no models exist that can adequately describe the genetic effects of seed management. We present a metapopulation model that accounts for several features unique to managed crop populations. Using traditional maize agr...

  14. Genetic Diversity and Societally Important Disparities.

    Science.gov (United States)

    Rosenberg, Noah A; Kang, Jonathan T L

    2015-09-01

    The magnitude of genetic diversity within human populations varies in a way that reflects the sequence of migrations by which people spread throughout the world. Beyond its use in human evolutionary genetics, worldwide variation in genetic diversity sometimes can interact with social processes to produce differences among populations in their relationship to modern societal problems. We review the consequences of genetic diversity differences in the settings of familial identification in forensic genetic testing, match probabilities in bone marrow transplantation, and representation in genome-wide association studies of disease. In each of these three cases, the contribution of genetic diversity to social differences follows from population-genetic principles. For a fourth setting that is not similarly grounded, we reanalyze with expanded genetic data a report that genetic diversity differences influence global patterns of human economic development, finding no support for the claim. The four examples describe a limit to the importance of genetic diversity for explaining societal differences while illustrating a distinction that certain biologically based scenarios do require consideration of genetic diversity for solving problems to which populations have been differentially predisposed by the unique history of human migrations. PMID:26354973

  15. Genetic Diversity and Societally Important Disparities

    Science.gov (United States)

    Rosenberg, Noah A.; Kang, Jonathan T. L.

    2015-01-01

    The magnitude of genetic diversity within human populations varies in a way that reflects the sequence of migrations by which people spread throughout the world. Beyond its use in human evolutionary genetics, worldwide variation in genetic diversity sometimes can interact with social processes to produce differences among populations in their relationship to modern societal problems. We review the consequences of genetic diversity differences in the settings of familial identification in forensic genetic testing, match probabilities in bone marrow transplantation, and representation in genome-wide association studies of disease. In each of these three cases, the contribution of genetic diversity to social differences follows from population-genetic principles. For a fourth setting that is not similarly grounded, we reanalyze with expanded genetic data a report that genetic diversity differences influence global patterns of human economic development, finding no support for the claim. The four examples describe a limit to the importance of genetic diversity for explaining societal differences while illustrating a distinction that certain biologically based scenarios do require consideration of genetic diversity for solving problems to which populations have been differentially predisposed by the unique history of human migrations. PMID:26354973

  16. Genetic diversity and structure of livestock breeds

    OpenAIRE

    Wilkinson, Samantha

    2012-01-01

    This thesis addresses the genetic characterisation of livestock breeds, a key aspect of the long-term future breed preservation and, thus, of primary interest for animal breeders and management in the industry. First, the genetic diversity and structure of breeds were investigated. The application of individual-based population genetic approaches at characterising genetic structure was assessed using the British pig breeds. All approaches, except for Principle Component Anal...

  17. 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.

  18. Genetic diversity in farm animals - a review

    OpenAIRE

    Groeneveld, L. F.; Lenstra, J A; Eding, H.; TORO, M.A.; Scherf, B.; PILLING, D; Negrini, R.; Finlay, E.K; Jianlin, H.; Groeneveld, E; S. Weigend; Globaldiv, Consortium

    2010-01-01

    Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattl...

  19. European pig genetic diversity: a minireview.

    Science.gov (United States)

    Ollivier, L

    2009-07-01

    An evaluation of the European pig diversity has been carried on by several countries, with the support of the European Union over the period of 1994 to 2000. This article presents an overview of the results of this investigation, focussing on two genetic marker techniques, namely microsatellites (MS) and amplification of fragment length polymorphism (AFLP). Nearly 200 loci were characterised on about 50 individuals from each of 59 to 71 breeds, according to the marker considered. The analysis of diversity, based on genetic distances, led to similar conclusions for the two marker types (MS and AFLP), in spite of a markedly lower total diversity of AFLP compared to MS. The analysis of the MS loci showed that the allelic diversity pattern among breeds was quasi-independent from the diversity pattern based on allele frequencies. Genetic distances showed no particular clustering of local with international breeds, confirming the genetic uniqueness of the European local breeds compared to mainstream international breeds. The taxonomy of the local breeds revealed a cluster of the Iberian type breeds, in contrast with a wider dispersal of the breeds from other countries. Phylogeny often disagreed with documented breeds' history, showing the complex migration/admixture patterns which underlie the breeds' relationships. Methodologies developed in this investigation as well as the database and the DNA depository created should provide support for further innovative research in the field of domestic animal diversity management. PMID:22444811

  20. 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...

  1. 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.

  2. Genetic diversity of eleven European pig breeds

    OpenAIRE

    Foulley Jean-Louis; Geldermann Hermann; Beeckmann Petra; Jørgensen Claus B; Nissen Peter H; Andersson Leif; Giuffra Elisabetta; Groenen Martien AM; Milan Denis; Legault Christian; Iannuccelli Nathalie; Laval Guillaume; Chevalet Claude; Ollivier Louis

    2000-01-01

    Abstract A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed signific...

  3. Genetic diversity of 11 European pig breeds

    OpenAIRE

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

    2000-01-01

    A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly red...

  4. Genetic diversity of eleven European pig breeds

    OpenAIRE

    Laval, Guillaume; Iannuccelli, Nathalie; Legault, Christian; Milan, Denis; Groenen, Martien; Giuffra, Elisabetta; Andersson, Leif; Nissen, Peter; Jørgensen, Claus; Beeckmann, Petra; Geldermann, Hermann; Foulley, Jean-Louis; Chevalet, Claude; Ollivier, Louis

    2000-01-01

    A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly red...

  5. Genetic erosion of diversity in cereals

    OpenAIRE

    Petrovi? Sofija; Dimitrijevi? Miodrag

    2012-01-01

    Cereals play an important role in human nutrition. Consequently, one of the main goals in breeding is to obtain varieties with high genetic potential for yield. Modern agricultural production includes the expansion of intensive varieties over large areas that lead to narrow selection criteria in breeding programs. The consequence is a drastic reduction in the number of species and genotypes (genetic erosion), or harming biological diversity of local populat...

  6. Genetic Diversity of Neisseria gonorrhoeae Housekeeping Genes

    OpenAIRE

    Viscidi, Raphael P.; Demma, James C.

    2003-01-01

    Molecular typing of Neisseria gonorrhoeae strains is an important tool for epidemiological studies of gonococcal infection and transmission. The recently developed multilocus sequence typing (MLST) method is based on the genetic variation among housekeeping genes. As a preliminary investigation for the development of such a method, we characterized the genetic diversity at 18 gonococcal housekeeping gene loci. Approximately 17,500 nucleotides, spanning 18 loci, were sequenced from 24 isolates...

  7. Diversity of potato genetic resources

    OpenAIRE

    Machida-Hirano, Ryoko

    2015-01-01

    A considerable number of highly diverse species exist in genus Solanum. Because they can adapt to a broad range of habitats, potato wild relatives are promising sources of desirable agricultural traits. Potato taxonomy is quite complex because of introgression, interspecific hybridization, auto- and allopolyploidy, sexual compatibility among many species, a mixture of sexual and asexual reproduction, possible recent species divergence, phenotypic plasticity, and the consequent high morphologi...

  8. Crop genetic diversity benefits farmland biodiversity in cultivated fields

    OpenAIRE

    Chateil, Carole; Goldringer, Isabelle; Tarallo, Léa; Kerbiriou, Christian; Le Viol, Isabelle; Ponge, Jean-François; Salmon, Sandrine; Gachet, Sophie; Porcher, Emmanuelle

    2013-01-01

    This study tested whether increasing crop genetic diversity benefited farmland biodiversity in bread wheat (Triticum aestivum) fields, using an experimental approach in which arthropod and wild plant diversity were compared in a genetically homogeneous wheat variety vs. a variety mixture. The diversity of wild plant species was not affected by crop genetic diversity. However, we showed for the first time a positive impact of crop genetic diversity on below (collembola) and aboveground arthrop...

  9. Genetic diversity of eleven European pig breeds

    Directory of Open Access Journals (Sweden)

    Foulley Jean-Louis

    2000-03-01

    Full Text Available Abstract A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly reduced heterozygosity. Breed differentiation was significant as shown by the high among-breed fixation index (overall FST = 0.27, and confirmed by the clustering based on the genetic distances between individuals, which grouped essentially all individuals in 11 clusters corresponding to the 11 breeds. The genetic distances between breeds were first used to construct phylogenetic trees. The trees indicated that a genetic drift model might explain the divergence of the two German breeds, but no reliable phylogeny could be inferred among the remaining breeds. The same distances were also used to measure the global diversity of the set of breeds considered, and to evaluate the marginal loss of diversity attached to each breed. In that respect, the French Basque breed appeared to be the most "unique" in the set considered. This study, which remains to be extended to a larger set of European breeds, indicates that using genetic distances between breeds of farm animals in a classical taxonomic approach may not give clear resolution, but points to their usefulness in a prospective evaluation of diversity.

  10. Genetic Diversity of Tunisian Barley Accessions Based on Microsatellite Markers

    OpenAIRE

    F. Guasmi; L. Touil; K. Feres; W. Elfelah; T. Triki; Ferchichi, A.

    2008-01-01

    Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a three of mapped SSRs to examine the genetic diversity of Tunisian barley accessions and to establish phylogenetic ...

  11. 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.

  12. Fitness Uniform Selection to Preserve Genetic Diversity

    OpenAIRE

    Hutter, Marcus

    2001-01-01

    In evolutionary algorithms, the fitness of a population increases with time by mutating and recombining individuals and by a biased selection of more fit individuals. The right selection pressure is critical in ensuring sufficient optimization progress on the one hand and in preserving genetic diversity to be able to escape from local optima on the other. We propose a new selection scheme, which is uniform in the fitness values. It generates selection pressure towards sparse...

  13. 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.

  14. 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.

  15. Genetic diversity between human metapneumovirus subgroups

    International Nuclear Information System (INIS)

    Complete consensus nucleotide sequences were determined for human metapneumovirus (HMPV) isolates CAN97-83 and CAN98-75, representing the two proposed genotypes or genetic subgroups of HMPV. The overall level of genome nucleotide sequence identity and aggregate proteome amino acid sequence identity between the two HMPV subgroups were 80 and 90%, respectively, similar to the respective values of 81 and 88% between the two antigenic subgroups of human respiratory syncytial virus (HRSV). The diversity between HMPV subgroups was greatest for the SH and G proteins (59 and 37% identity, respectively), which were even more divergent than their HRSV counterparts (72 and 55% cross-subgroup identity, respectively). It is reasonable to anticipate that the two genetic subgroups of HMPV represent antigenic subgroups approximately comparable to those of HRSV

  16. 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...

  17. Determination of Mitochondrial Genetic Diversity in Mammals

    OpenAIRE

    Nabholz, Benoit; Mauffrey, Jean-François; Bazin, Eric; Galtier, Nicolas; Glemin, Sylvain

    2008-01-01

    Mitochondrial DNA (mtDNA) is one of the most popular population genetic markers. Its relevance as an indicator of population size and history has recently been questioned by several large-scale studies in animals reporting evidence for recurrent adaptive evolution, at least in invertebrates. Here we focus on mammals, a more restricted taxonomic group for which the issue of mtDNA near neutrality is crucial. By analyzing the distribution of mtDNA diversity across species and relating it to allo...

  18. Genetic erosion of diversity in cereals

    Directory of Open Access Journals (Sweden)

    Petrovi? Sofija

    2012-01-01

    Full Text Available Cereals play an important role in human nutrition. Consequently, one of the main goals in breeding is to obtain varieties with high genetic potential for yield. Modern agricultural production includes the expansion of intensive varieties over large areas that lead to narrow selection criteria in breeding programs. The consequence is a drastic reduction in the number of species and genotypes (genetic erosion, or harming biological diversity of local populations, and spontaneous relatives (biodiversity in cereals. Based on detailed inventories of the territory of Montenegro and to some extent in Eastern Serbia, a endangerment of gene pool in cereals could be denoted. The reason for this is a transition to another type of agricultural production, changing land purposes, the presence of nursing homes, and use of intensive varieties. Old varieties and local populations represent the original genetic variability that could be used in breeding programs and organic production. It is therefore essential to take measures to preserve the genetic resources of cereals.

  19. 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...

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

    Science.gov (United States)

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

    2012-01-01

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

  1. 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...

  2. Immigrants' Genes: Genetic Diversity and Economic Development in the US

    OpenAIRE

    Ager, Philipp; Brückner, Markus

    2013-01-01

    We examine the effect of genetic diversity on economic development in the United States. Our estimation strategy exploits that immigrants from different countries of origin differed in their genetic diversity and that these immigrants settled in different regions. Based on a sample of over 2250 counties, we find that increases in genetic diversity of US counties that arose due to immigration during the 19th century had a significant positive effect on US counties' economic development. We als...

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

    Science.gov (United States)

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species diversity and genetic diversity interact to influence community structure may be critically important for predicting the consequences of biodiversity loss. PMID:23858643

  4. 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.

  5. 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.

  6. 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.

  7. A REVIEW ON GENETIC DIVERSITY OF WILD PLANTS BY USING DIFFERENT GENETIC MARKERS

    OpenAIRE

    Muhammad Younas Khan Barozai, Sazia Saeed

    2012-01-01

    Biodiversity is the variation of life at all levels of biological organization. One of the important components of biological diversity is the genetic diversity. Genetic diversity refers to the variation of genes or entire genome within and between populations of organisms. Keeping in view the significance of genetic diversity in wild plants, some research articles based on important wild plant genera and species of angiosperms including few rare, threatened, endemic, medicinal and e...

  8. 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.

  9. 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 from a well-studied country is an illustration of the limited knowledge of the microbial diversity. Finally, Article I separates a group of closely related fungi that could not be determined by morphology by using a phylogenetic analysis combining three marker genes. Using multiple markers makes it possible 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.

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

    OpenAIRE

    Ajmone Marsan, Paolo; Colli, Licia; Han, Jian Lin; Achilli, A.; Lancioni, H.; Joost, Stéphane; Crepaldi, Paola; Pilla, Fabio; Stella, Alessandra; Taberlet, Pierre; Boettcher, Paul; Negrini, Riccardo; Lenstra, J A

    2014-01-01

    The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers for each of the main livestock species, FAO has promoted the meta-analysis of local datasets, to achieve a global view of molecular genetic diversity. Analysis within the EU Globaldiv project of two ...

  11. Surviving with low genetic diversity: the case of albatrosses

    OpenAIRE

    Milot, Emmanuel; Weimerskirch, Henri; Duchesne, Pierre; Bernatchez, Louis

    2007-01-01

    Low genetic diversity is predicted to negatively impact species viability and has been a central concern for conservation. In contrast, the possibility that some species may thrive in spite of a relatively poor diversity has received little attention. The wandering and Amsterdam albatrosses (Diomedea exulans and Diomedea amsterdamensis) are long-lived seabirds standing at an extreme along the gradient of life strategies, having traits that may favour inbreeding and low genetic diversity. Dive...

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

    OpenAIRE

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

    2012-01-01

    Abstract Background Understanding the population structure of Plasmodium species through genetic diversity studies can assist in the design of more effective malaria control strategies, particularly in vaccine development. Central America is an area where malaria is a public health problem, but little is known about the genetic diversity of the parasite’s circulating species. This study aimed to investigate the allelic frequency and molecular diversity of five surface antigens in field isolat...

  13. Genetic diversity of human RNase 8

    Directory of Open Access Journals (Sweden)

    Chan Calvin C

    2012-01-01

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

  14. 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.

  15. Beauveria bassiana: Quercetinase production and genetic diversity

    Science.gov (United States)

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

    2011-01-01

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

  16. 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.

  17. 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.

  18. Flooding stress: acclimations and genetic diversity.

    Science.gov (United States)

    Bailey-Serres, J; Voesenek, L A C J

    2008-01-01

    Flooding is an environmental stress for many natural and man-made ecosystems worldwide. Genetic diversity in the plant response to flooding includes alterations in architecture, metabolism, and elongation growth associated with a low O(2) escape strategy and an antithetical quiescence scheme that allows endurance of prolonged submergence. Flooding is frequently accompanied with a reduction of cellular O(2) content that is particularly severe when photosynthesis is limited or absent. This necessitates the production of ATP and regeneration of NAD(+) through anaerobic respiration. The examination of gene regulation and function in model systems provides insight into low-O(2)-sensing mechanisms and metabolic adjustments associated with controlled use of carbohydrate and ATP. At the developmental level, plants can escape the low-O(2) stress caused by flooding through multifaceted alterations in cellular and organ structure that promote access to and diffusion of O(2). These processes are driven by phytohormones, including ethylene, gibberellin, and abscisic acid. This exploration of natural variation in strategies that improve O(2) and carbohydrate status during flooding provides valuable resources for the improvement of crop endurance of an environmental adversity that is enhanced by global warming. PMID:18444902

  19. Genetic diversity patterns in five protist species occurring in lakes.

    Science.gov (United States)

    Logares, Ramiro; Boltovskoy, Andrés; Bensch, Staffan; Laybourn-Parry, Johanna; Rengefors, Karin

    2009-05-01

    Little is known about the extent of the genetic diversity and its structuring patterns in protist species living in lakes. Here, we have investigated the genetic diversity patterns within five dinoflagellate species (Peridinium aciculiferum, Peridinium cinctum, Peridiniopsis borgei, Polarella glacialis, Scrippsiella aff. hangoei) that are present in lakes and sometimes, in marine habitats located in polar and temperate regions. A total of 68 clonal strains were investigated using Amplified Fragment Length Polymorphism (AFLP), a sensitive genetic fingerprinting technique. All used strains within each species had identical ITS nuclear ribosomal DNA sequences, a characteristic that indicates that they likely belong to the same species. We found a wide variability in the genetic diversity among species (between 20% and 90% of polymorphic loci; Nei's gene diversity between 0.08 and 0.37). In some cases, our analyses suggested the presence of different genetically homogeneous subgroups (genetic populations) within the same water body. Thus, it appears that different genetic populations can coexist within the same lake despite the likely occurrence of recombination that tends to homogenize the gene pool. Overall, our results indicated that a large number of dinoflagellate genotypes are present in lake populations, instead of a few dominating ones. In addition, our study shows that protists with identical ITS sequences can harbor considerable amounts of genetic diversity. PMID:19162540

  20. 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.

  1. Exploiting a wheat EST database to assess genetic diversity

    OpenAIRE

    Ozge Karakas; Filiz Gurel; Ahu Altinkut Uncuoglu

    2010-01-01

    Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived ...

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

    DEFF Research Database (Denmark)

    Hughes, William Owen Hamar; Boomsma, Jacobus Jan

    2006-01-01

    Polyandry is often difficult to explain because benefits of the behaviour have proved elusive. In social insects, polyandry increases the genetic diversity of workers within a colony and this has been suggested to improve the resistance of the colony to disease. Here we examine the possible impact of host genetic diversity on parasite evolution by carrying out serial passages of a virulent fungal pathogen through leaf-cutting ant workers of known genotypes. Parasite virulence increased over the ...

  3. Genetic diversity of Ascaris in southwestern Uganda

    DEFF Research Database (Denmark)

    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

    2012-01-01

    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...

  4. 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

  5. Nested core collections maximizing genetic diversity in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    McKhann, Heather I; Camilleri, Christine; Bérard, Aurélie; Bataillon, Thomas; David, Jacques L; Reboud, Xavier; Le Corre, Valérie; Caloustian, Christophe; Gut, Ivo G; Brunel, Dominique

    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...

  6. 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

  7. 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.

    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...

  8. Intelligence Service Of Web Mining With Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Kolli Prabhakara Rao

    2013-10-01

    Full Text Available The Main objective of this paper is to eliminate user uninterested rules and find the optimal patterns or association rules. Association rules are important basis of describing Web user’s behavior characteristic. Traditional algorithms of Web association rule mining, based on statistics, usually pays attention to the analysis on existing data, they can’t offer effective means and optimizing measure and cannot find out the latent and possible rules. In this paper we are proposing an efficient web association rule mining approach with Apriori algorithm and genetic algorithm features like cross over and mutation for generation of the optimal patterns.

  9. 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...

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    Afrooz Alimohamadi

    2012-12-01

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

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

    International Nuclear Information System (INIS)

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

  13. 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.

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

    Science.gov (United States)

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

    2014-01-01

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied. PMID:25551388

  15. Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

    Science.gov (United States)

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

    2014-01-01

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied. PMID:25551388

  16. 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.

  17. 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

  18. Genetic Diversity in the Interference Selection Limit

    OpenAIRE

    Good, Benjamin H.; Walczak, Aleksandra M; Neher, Richard A.; Desai, Michael M.

    2014-01-01

    Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics fails to account for interference between linked mutations, which grows increasingly severe as the density of selected polymorphisms increases. Here, we describe a simple limit that emerges when interference is common, in which the fitness effects of individ...

  19. An Analysis of Diversity in Genetic Programming

    OpenAIRE

    Gustafson, Steven Matt

    2004-01-01

    Genetic programming is a metaheuristic search method that uses a population of variable-length computer programs and a search strategy based on biological evolution. The idea of automatic programming has long been a goal of artificial intelligence, and genetic programming presents an intuitive method for automatically evolving programs. However, this method is not without some potential drawbacks. Search using procedural representations can be complex and inefficient. In addition, variable si...

  20. Great ape genetic diversity and population history

    DEFF Research Database (Denmark)

    Prado-Martinez, Javier; Sudmant, Peter H.; Kidd, Jeffrey M.; Li, Heng; Kelley, Joanna L.; Lorente-Galdos, Belen; Veeramah, Krishna R.; Woerner, August E; O'Connor, Timothy D; Santpere, Gabriel; Cagan, Alexander; Theunert, Christoph; Casals, Ferran; Laayouni, Hafid; Munch, Kasper; Hobolth, Asger; Halager, Anders Egerup; Malig, Maika; Hernandez-Rodriguez, Jessica; Hernando-Herraez, Irene; Prüfer, Kay; Pybus, Marc; Johnstone, Laurel; Lachmann, Michael; Alkan, Can; Twigg, Dorina; Petit, Natalia; Baker, Carl; Hormozdiari, Fereydoun; Fernandez-Callejo, Marcos; Dabad, Marc; Wilson, Michael L; Stevison, Laurie; Camprubí, Cristina; Carvalho, Tiago; Ruiz-Herrera, Aurora; Vives, Laura; Mele, Marta; Abello, Teresa; Kondova, Ivanela; Bontrop, Ronald E; Pusey, Anne; Lankester, Felix; Kiyang, John A; Bergl, Richard A; Lonsdorf, Elizabeth; Myers, Simon; Ventura, Mario; Gagneux, Pascal; Comas, David; Siegismund, Hans Redlef; Blanc, Julie; Agueda-Calpena, Lidia; Gut, Marta; Fulton, Lucinda; Tishkoff, Sarah A; Mullikin, James C; Wilson, Richard K.; Gut, Ivo G; Gonder, Mary Katherine; Ryder, Oliver A; Hahn, Beatrice H; Navarro, Arcadi; Akey, Joshua M; Bertranpetit, Jaume; Reich, David; Mailund, Thomas; Schierup, Mikkel Heide; Hvilsom, Christina; Andrés, Aida M; Wall, Jeffrey D; Bustamante, Carlos D; Hammer, Michael F; Eichler, Evan E; Marques-Bonet, Tomas

    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...

  1. High Performance Data mining by Genetic Neural Network

    Directory of Open Access Journals (Sweden)

    Dadmehr Rahbari

    2013-10-01

    Full Text Available Data mining in computer science is the process of discovering interesting and useful patterns and relationships in large volumes of data. Most methods for mining problems is based on artificial intelligence algorithms. Neural network optimization based on three basic parameters topology, weights and the learning rate is a powerful method. We introduce optimal method for solving this problem. In this paper genetic algorithm with mutation and crossover operators change the network structure and optimized that. Dataset used for our work is stroke disease with twenty features that optimized number of that achieved by new hybrid algorithm. Result of this work is very well incomparison with other similar method. Low present of error show that our method is our new approach to efficient, high-performance data mining problems is introduced.

  2. 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.

  3. 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.

  4. Mining protein networks for synthetic genetic interactions

    Directory of Open Access Journals (Sweden)

    Zhao Shan

    2008-10-01

    Full Text Available Abstract Background The local connectivity and global position of a protein in a protein interaction network are known to correlate with some of its functional properties, including its essentiality or dispensability. It is therefore of interest to extend this observation and examine whether network properties of two proteins considered simultaneously can determine their joint dispensability, i.e., their propensity for synthetic sick/lethal interaction. Accordingly, we examine the predictive power of protein interaction networks for synthetic genetic interaction in Saccharomyces cerevisiae, an organism in which high confidence protein interaction networks are available and synthetic sick/lethal gene pairs have been extensively identified. Results We design a support vector machine system that uses graph-theoretic properties of two proteins in a protein interaction network as input features for prediction of synthetic sick/lethal interactions. The system is trained on interacting and non-interacting gene pairs culled from large scale genetic screens as well as literature-curated data. We find that the method is capable of predicting synthetic genetic interactions with sensitivity and specificity both exceeding 85%. We further find that the prediction performance is reasonably robust with respect to errors in the protein interaction network and with respect to changes in the features of test datasets. Using the prediction system, we carried out novel predictions of synthetic sick/lethal gene pairs at a genome-wide scale. These pairs appear to have functional properties that are similar to those that characterize the known synthetic lethal gene pairs. Conclusion Our analysis shows that protein interaction networks can be used to predict synthetic lethal interactions with accuracies on par with or exceeding that of other computational methods that use a variety of input features, including functional annotations. This indicates that protein interaction networks could plausibly be rich sources of information about epistatic effects among genes.

  5. Diversity-Oriented Synthesis as a Tool for Chemical Genetics

    Directory of Open Access Journals (Sweden)

    Elena Lenci

    2014-10-01

    Full Text Available Chemical genetics is an approach for identifying small molecules with the ability to induce a biological phenotype or to interact with a particular gene product, and it is an emerging tool for lead generation in drug discovery. Accordingly, there is a need for efficient and versatile synthetic processes capable of generating complex and diverse molecular libraries, and Diversity-Oriented Synthesis (DOS of small molecules is the concept of choice to give access to new chemotypes with high chemical diversity. In this review, the combination of chemical genetics and diversity-oriented synthesis to identify new chemotypes as hit compounds in chemical biology and drug discovery is reported, giving an overview of basic concepts and selected case studies.

  6. 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 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)

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

    Indian Academy of Sciences (India)

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

    2006-08-01

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

  8. Genetic diversity measures of the Croatian Spotted goat

    Directory of Open Access Journals (Sweden)

    Pavi? Vesna

    2011-01-01

    Full Text Available In the present study, microsatellite data of 20 loci were generated and utilized to evaluate genetic variability of the Croatian Spotted goat. Genetic variability was high, with means for expected gene diversity of 0.771, observed heterozygosity of 0.759, and 8.1 for the total number of alleles per locus. There are no indications for deviations from random breeding within the population. Level of inbreeding was only 2% and non-significant. The population was found to deviate significantly under infinitive allele model (IAM and two phase model (TPM, while stepwise mutation model (SMM and qualitative mode-shift test of allele frequencies indicate the absence of genetic bottleneck in the recent past in the population of the Croatian Spotted goat. High level of genetic diversity, as it is presented in this study, may be seen as an initial guide for conservation decisions in the future.

  9. 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.

  10. The genetic diversity of Plasmodium vivax: a review

    Scientific Electronic Library Online (English)

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

    2007-06-01

    Full Text Available 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. vi [...] vax 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 our increasing understanding of genetic diversity and population structure of this parasite for the development of new control strategies, including vaccines, and more effective drugs for the treatment of P. vivax malaria.

  11. The genetic diversity of Plasmodium vivax: a review

    Directory of Open Access Journals (Sweden)

    Wanessa Christina de Souza-Neiras

    2007-06-01

    Full Text Available 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 our increasing understanding of genetic diversity and population structure of this parasite for the development of new control strategies, including vaccines, and more effective drugs for the treatment of P. vivax malaria.

  12. The population genetics of mimetic diversity in Heliconius butterflies

    OpenAIRE

    Kronforst, Marcus R.; Gilbert, Lawrence E.

    2007-01-01

    Theory predicts strong stabilizing selection on warning patterns within species and convergent evolution among species in Müllerian mimicry systems yet Heliconius butterflies exhibit extreme wing pattern diversity. One potential explanation for the evolution of this diversity is that genetic drift occasionally allows novel warning patterns to reach the frequency threshold at which they gain protection. This idea is controversial, however, because Heliconius butterflies are unlikely to experie...

  13. Diversity-Oriented Synthesis as a Tool for Chemical Genetics

    OpenAIRE

    Elena Lenci; Antonio Guarna; Andrea Trabocchi

    2014-01-01

    Chemical genetics is an approach for identifying small molecules with the ability to induce a biological phenotype or to interact with a particular gene product, and it is an emerging tool for lead generation in drug discovery. Accordingly, there is a need for efficient and versatile synthetic processes capable of generating complex and diverse molecular libraries, and Diversity-Oriented Synthesis (DOS) of small molecules is the concept of choice to give access to new chemotypes with high che...

  14. 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

  15. Eestimation of genetic diversity in walnut

    International Nuclear Information System (INIS)

    Juglans regia L. belonging to the family Juglandaceae inhabits the northern parts of Pakistan. Biochemical analysis of the plant is not well documented in the country. Present research was the first documented attempt to study total seed storage proteins in 20 genotypes of Juglans regia collected from Swat, Dir and Chitral areas. A protocol was optimized for extraction and separation of seed storage protein from unprocessed seeds. Comparatively simple banding pattern (as compared to legumes and cereals) was observed in Juglans regia L. A total of 114 protein loci were detected in 20 genotypes giving an average of approximately 7 alleles per genotype. Genetic distances estimated during present study range from 0 to 60. Medium values of Genetic Distances (GDmax= 60%) was estimated among three comparisons. Twenty genotypes were grouped in three clusters based on dendrogram analysis. Genotypes collected from Chitral valley were predominantly grouped in one cluster. (author)

  16. 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...

  17. Assessment of genetic diversity in the sorghum reference set using EST-SSR markers.

    Science.gov (United States)

    Ramu, P; Billot, C; Rami, J-F; Senthilvel, S; Upadhyaya, H D; Ananda Reddy, L; Hash, C T

    2013-08-01

    Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping. PMID:23708149

  18. Genetic diversity among ancient Nordic populations.

    Science.gov (United States)

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

    2010-01-01

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

  19. 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.

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

    OpenAIRE

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

    2013-01-01

    Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid w...

  1. 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

  2. Genetic diversity and population structure of begomoviruses infecting sweet potato

    Science.gov (United States)

    Begomoviruses infecting sweet potatoes (Ipomoea batatas) exhibit high genetic diversity, and approximately eight species including Sweet potato leaf curl virus (SPLCV) have been described from different regions around the world. In this study, the complete genomic sequences of 17 geographically dist...

  3. Assessment of Genetic Diversity in Tea Genotypes Through RAPD Primers

    Directory of Open Access Journals (Sweden)

    Habib Ahmad

    2007-01-01

    Full Text Available This study communicates the result of 24 promising tea genotypes evaluated through 11 Randomly Amplified Polymorphic DNA primers. High level of genetic diversity was observed on DNA level among the genotypes. The results of cluster analysis based on RAPDs revealed that four major groups could be recognized in tea grown in Mansehra District.

  4. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    Directory of Open Access Journals (Sweden)

    GULNAR SHIKHSEYIDOVA

    2015-06-01

    Full Text Available To determine the genetic diversity of durum wheat, 41 accessions from Morocco, Ethiopia, Turkey, Lebanon, Kazakhstan, China, and Mongolia were analyzed through Inter-Simple Sequence Repeats (ISSR molecular markers. Out of the used twenty primers, 15 primers that included a considerable polymorphism were selected for the analyses. Among the genotypes under study, 163 fragments (73.7% were polymorph. Several indexes were used to determine the most appropriate primers. While UBC812, UBC864, UBC840, and UBC808 primers were among those markers which produced the highest number of bands and polymorphic bands, they also dedicated the highest rate of polymorphic index content (PIC. These primers also possessed the highest amounts of effective multiplex ratio (EMR and marker index (MI. Therefore, these primers can be recommended for genetic evaluation of the durum wheat. The results of cluster analysis and principle component analysis indicated that the observed genetic diversity in wheat materials under study is geographically structured. The results also indicated that the genetic diversity index based on ISSR markers was higher for Turkey, Lebanon, Morocco, and Ethiopia accessions than for other countries. The high level of polymorphism in this collections durum wheat would agree with the suggestion that Fertile Crescent and parts of Africa are first possible diversity center of this crop.

  5. Determination of genetic diversity among some almond accessions

    Directory of Open Access Journals (Sweden)

    Pinar Hasan

    2015-01-01

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

  6. 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.

  7. GENETIC RESOURCES AND DIVERSITY IN DAIRY BUFFALOES OF PAKISTAN

    Directory of Open Access Journals (Sweden)

    M. SAJJAD KHAN, NAZIR AHMAD1 AND MUQARRAB ALI KHAN2

    2007-10-01

    Full Text Available Buffalo is the main dairy animal in Pakistan. There are five known buffalo breeds in the country namely: Nili, Ravi, Nili-Ravi, Kundhi and Azi Kheli (or Azakhale. Population trend is available for Nili-Ravi and Kundhi breeds and is positive. Azi-Kheli breed was included in 2006 livestock census for the first time. General production system is low-input extensive system but high input intensive system prevails around most cities in the form of buffalo colonies for supplying fresh milk. Buffaloes are seasonal breeders. Vast diversity exits both at phenotypic and genetic level. Economic traits have a wide variation and genetic control is moderate for production traits but very low for reproduction traits. Inbreeding is inimical to genetic diversity and has been reported to deteriorate productivity. Efforts to improve productivity of the species are needed alongwith sustainable utilization of existing resources.

  8. Genetic Diversity of Arginine Catabolic Mobile Element in Staphylococcus epidermidis

    Science.gov (United States)

    Miragaia, Maria; de Lencastre, Herminia; Perdreau-Remington, Francoise; Chambers, Henry F.; Higashi, Julie; Sullam, Paul M.; Lin, Jessica; Wong, Kester I.; King, Katherine A.; Otto, Michael; Sensabaugh, George F.; Diep, Binh An

    2009-01-01

    Background The methicillin-resistant Staphylococcus aureus clone USA300 contains a novel mobile genetic element, arginine catabolic mobile element (ACME), that contributes to its enhanced capacity to grow and survive within the host. Although ACME appears to have been transferred into USA300 from S. epidermidis, the genetic diversity of ACME in the latter species remains poorly characterized. Methodology/Principal Findings To assess the prevalence and genetic diversity of ACME, 127 geographically diverse S. epidermidis isolates representing 86 different multilocus sequence types (STs) were characterized. ACME was found in 51% (65/127) of S. epidermidis isolates. The vast majority (57/65) of ACME-containing isolates belonged to the predominant S. epidermidis clonal complex CC2. ACME was often found in association with different allotypes of staphylococcal chromosome cassette mec (SCCmec) which also encodes the recombinase function that facilities mobilization ACME from the S. epidermidis chromosome. Restriction fragment length polymorphism, PCR scanning and DNA sequencing allowed for identification of 39 distinct ACME genetic variants that differ from one another in gene content, thereby revealing a hitherto uncharacterized genetic diversity within ACME. All but one ACME variants were represented by a single S. epidermidis isolate; the singular variant, termed ACME-I.02, was found in 27 isolates, all of which belonged to the CC2 lineage. An evolutionary model constructed based on the eBURST algorithm revealed that ACME-I.02 was acquired at least on 15 different occasions by strains belonging to the CC2 lineage. Conclusions/Significance ACME-I.02 in diverse S. epidermidis isolates were nearly identical in sequence to the prototypical ACME found in USA300 MRSA clone, providing further evidence for the interspecies transfer of ACME from S. epidermidis into USA300. PMID:19893740

  9. Mitochondrial DNA perspective of Serbian genetic diversity.

    Science.gov (United States)

    Davidovic, Slobodan; Malyarchuk, Boris; Aleksic, Jelena M; Derenko, Miroslava; Topalovic, Vladanka; Litvinov, Andrey; Stevanovic, Milena; Kovacevic-Grujicic, Natasa

    2015-03-01

    Although south-Slavic populations have been studied to date from various aspects, the population of Serbia, occupying the central part of the Balkan Peninsula, is still genetically understudied at least at the level of mitochondrial DNA (mtDNA) variation. We analyzed polymorphisms of the first and the second mtDNA hypervariable segments (HVS-I and HVS-II) and informative coding-region markers in 139 Serbians to shed more light on their mtDNA variability, and used available data on other Slavic and neighboring non-Slavic populations to assess their interrelations in a broader European context. The contemporary Serbian mtDNA profile is consistent with the general European maternal landscape having a substantial proportion of shared haplotypes with eastern, central, and southern European populations. Serbian population was characterized as an important link between easternmost and westernmost south-Slavic populations due to the observed lack of genetic differentiation with all other south-Slavic populations and its geographical positioning within the Balkan Peninsula. An increased heterogeneity of south Slavs, most likely mirroring turbulent demographic events within the Balkan Peninsula over time (i.e., frequent admixture and differential introgression of various gene pools), and a marked geographical stratification of Slavs to south-, east-, and west-Slavic groups, were also found. A phylogeographic analyses of 20 completely sequenced Serbian mitochondrial genomes revealed not only the presence of mtDNA lineages predominantly found within the Slavic gene pool (U4a2a*, U4a2a1, U4a2c, U4a2g, HV10), supporting a common Slavic origin, but also lineages that may have originated within the southern Europe (H5*, H5e1, H5a1v) and the Balkan Peninsula in particular (H6a2b and L2a1k). PMID:25418795

  10. 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.

  11. The diversity of culturable airborne fungi in an active South African gold mine

    Scientific Electronic Library Online (English)

    C.H., Pohl; W., Kriel; P., Venter; E., Van Heerden; J., Albertyn.

    2007-08-01

    Full Text Available Several studies have been conducted on the presence and diversity of airborne fungal spores in residential and occupational areas. This is the first investigation on this topic in the mining environment. The impact of fungi-especially as opportunistic pathogens-on their health and productivity needs [...] to be assessed, considering the compromised health of a large number of HIV-infected miners in South Africa. Accordingly, the aim of this study was to determine the abundance of fungal spores as well as the diversity of culturable airborne fungi in an active gold mine. The results indicate that three of the sampled sites in the mine contain abundant numbers of culturable airborne fungi. The first site was next to an auxiliary extraction fan, which could act as an accumulator for airborne fungal spores from the rest of the mine. The two other sites had high human activity, disturbances from which may contribute to an elevated fungal load in the air. The presence of timber supports at one site may serve as a growth substrate for several fungal genera. The diversity of filamentous fungal genera increased from outside the mine to deeper into the mine, whereas the diversity of yeast genera followed an opposite trend, with no yeasts detected deep in the mine. Although most of the isolates identified are not pathogens, they could still have a negative impact (either as opportunistic pathogens or allergens) on workers, especially immunocompromised persons if exposed to them for prolonged periods.

  12. 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.

  13. Optimization of Association Rule Mining through Genetic Algorithm

    OpenAIRE

    RUPALI HALDULAKAR,; Prof. JITENDRA AGRAWAL

    2011-01-01

    Strong rule generation is an important area of data mining. In this paper we design a novel method for generation of strong rule. In which a general Apriori algorithm is used to generate the rules after that we use the optimization techniques. Genetic algorithm is one of the best ways to optimize the rules .In this direction for the optimization of the rule set we design a new fitness function that uses the concept ofsupervised learning then the GA will be able to generate the stronger rule set.

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

    Science.gov (United States)

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

    2015-01-01

    Background Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Methods Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. Results We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST’ = 0.075, ? = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia. Conclusion Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman. PMID:26469349

  15. Genetic Diversity in Brassica Species Using SDS-PAGE Analysis

    Directory of Open Access Journals (Sweden)

    Rahman Md. Mukhlesur

    2004-01-01

    Full Text Available Eighty five different cultivars of Brassica rapa, B.juncea, B.napus, B. carinata, B. oleracea and hexaploid Brassica, collected from Bangladesh, Japan, China and Denmark, were analyzed for seed and leaf protein variations by SDS-PAGE to identify the polymorphic genetic markers for evaluation of genetic resources. Ten polymorphic markers were identified from seed protein and no identifiable polymorphic band was found from leaf protein. However, polymorphic markers clearly distinguished these Brassica species. Brassica rapa var. `yellow sarson` of Bangladesh origin showed uniquely identifiable four polymorphic bands for seed protein in contrast to the other B.rapa of brown-seeded type. The Bangladeshi and Japanese cultivars of B. rapa differed among protein quantity. Analytical results of SDS-PAGE for seed protein showed that hexaploid Brassica has the highest indices, such as % of polymorphic band, the degree of phenotypic diversity (Ho, diversity value for genetic marker (HEP and the sum of the effective number of alleles (SENA. The genetic diversity values of hexaploid Brassica were followed by amphidiploid (B. napus, B. juncea, B. carinata and diploid (B. oleracea, B. rapa species, respectively.

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

    Science.gov (United States)

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

    2015-01-01

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy's zebra E. grevyi and the mountain zebra E. zebra. The Grevy's zebra and the mountain zebra are endangered, and hybridization between the Grevy's zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy's zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy's and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy's zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy's zebra. PMID:26294133

  17. 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.

  18. 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...

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

    Science.gov (United States)

    Tarpy, David R; Vanengelsdorp, Dennis; Pettis, Jeffrey S

    2013-08-01

    Honey bee (Apis mellifera) queens mate with unusually high numbers of males (average of approximately 12 drones), although there is much variation among queens. One main consequence of such extreme polyandry is an increased diversity of worker genotypes within a colony, which has been shown empirically to confer significant adaptive advantages that result in higher colony productivity and survival. Moreover, honey bees are the primary insect pollinators used in modern commercial production agriculture, and their populations have been in decline worldwide. Here, we compare the mating frequencies of queens, and therefore, intracolony genetic diversity, in three commercial beekeeping operations to determine how they correlate with various measures of colony health and productivity, particularly the likelihood of queen supersedure and colony survival in functional, intensively managed beehives. We found the average effective paternity frequency (m e ) of this population of honey bee queens to be 13.6?±?6.76, which was not significantly different between colonies that superseded their queen and those that did not. However, colonies that were less genetically diverse (headed by queens with m e ???7.0) were 2.86 times more likely to die by the end of the study when compared to colonies that were more genetically diverse (headed by queens with m e ?>?7.0). The stark contrast in colony survival based on increased genetic diversity suggests that there are important tangible benefits of increased queen mating number in managed honey bees, although the exact mechanism(s) that govern these benefits have not been fully elucidated. PMID:23728203

  20. 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 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)

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

    OpenAIRE

    Ming Li; Zhong Zhao; Xingjun Miao; Jingjing Zhou

    2013-01-01

    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 f...

  2. 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.

  3. Genetic diversity and genetic structure of the rare and endangered species, Primula ranunculoides

    Directory of Open Access Journals (Sweden)

    Deyun Wang

    2013-09-01

    Full Text Available The rare and endangered species Primula ranunculoides is endemic to China and is of reasonably high potential horticultural value. The genetic diversity and structure of the species was examined by surveying variation at nine microsatellite loci across 222 individuals sampled from seven natural populations. The results indicated that there was relatively low genetic diversity present within populations (He = 0.330, Ho = 0.286 and high genetic differentiation among populations. Levels of population genetic diversity and effective population size were both correlated with plant density, rather than population census size or population area. Gene flow between populations was low (Nm = 0.730 and an AMOVA analysis showed that 48.08% of the total genetic diversity was attributable to among populations and the rest (51.92% to variation within populations. Bayesian assignment and principal coordinate analyses supported clustering of the seven populations into four groups, which were correlated with topographical features. This suggested that Lianghu Plain (Dongtinghu Plain and Jianghan Plain and the farming area of Xiushui and Wuning counties were major barriers to gene flow, causing high divergence between different mountain populations. Based on the genetic structure of P. ranunculoides, four management units for conservation purposes are proposed, i.e. the Jiulingshan, Mufushan, Qizimeishan and Yinlu units.

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

    Directory of Open Access Journals (Sweden)

    Ermis Yanes Paz

    2012-01-01

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

  5. 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.

  6. Genetic diversity and maternal origin of Bangladeshi chicken.

    Science.gov (United States)

    Bhuiyan, M S A; Chen, Shanyuan; Faruque, S; Bhuiyan, A K F H; Beja-Pereira, Albano

    2013-06-01

    Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (?ST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of indigenous chicken of Bangladesh. These results suggest that Bangladeshi indigenous chickens still have abundant genetic diversity and have originated from multiple maternal lineages, and further conservation efforts are warranted to maintain the diversity. PMID:23640100

  7. A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL ANALYSIS OF GENETIC DIVERSITY

    Science.gov (United States)

    In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data that indicate whether the observed patterns are the result of historical or contemporary processes. In general, genetic measures focus...

  8. 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...

  9. DETECTION OF GENETIC DIVERSITY OF TRITICALE BY MICROSATELLITE MARKERS

    OpenAIRE

    Andrej Trebichalský; Želmíra Balážová; Zdenka Gálová; Milan Ch?apek; Marián Tomka

    2013-01-01

    The aim of our work was to detect genetic variability in the set of 59 winter and spring triticale (x Triticosecale Witt.) varieties using 5 wheat SSR markers. Totally, 35 alleles with an average number of 7 alleles per locus were detected. The highest number of alleles showed out Xbarc 004 (9). Based on the number and frequencies of alleles, the diversity index (DI), the probability of identity (PI) and the polymorphic information content (PIC) of SSR markers were calculated. The polymorphic...

  10. Description and analysis of genetic diversity among squash accessions

    OpenAIRE

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

    2009-01-01

    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 acces...

  11. Genetic diversity of Plasmodium vivax isolates from Azerbaijan

    OpenAIRE

    Majori Giancarlo; Aliyev Namig; Gasimov Elkhan; Mammadov Suleyman; Noyer Jean; Cligny Alexandra; Menegon Michela; Leclerc Marie; Severini Carlo

    2004-01-01

    Abstract Background Plasmodium vivax, although causing a less serious disease than Plasmodium falciparum, is the most widespread of the four human malarial species. Further to the recent recrudescence of P. vivax cases in the Newly Independent States (NIS) of central Asia, a survey on the genetic diversity and dissemination in Azerbaijan was undertaken. Azerbaijan is at the crossroads of Asia and, as such, could see a rise in the number of cases, although an effective malaria control programm...

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

    OpenAIRE

    Leon Mejnartowicz

    2006-01-01

    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...

  13. 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...

  14. Insights into Penicillium roqueforti Morphological and Genetic Diversity

    OpenAIRE

    Gillot, Guillaume; Jany, Jean-Luc; Coton, Monika; Le Floch, Gaétan; Debaets, Stella; Ropars, Jeanne; López-Villavicencio, Manuela; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana; Coton, Emmanuel

    2015-01-01

    Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing me...

  15. Genetic Diversity of the Cameroon Indigenous Chicken Ecotypes

    OpenAIRE

    T.C. Keambou; B.A. Hako; Ommeh, S; C. Bembide; E.P. Ngono; Y. Manjeli; F. Wamonje; Nzuki; B. Wanjala; Wamalwa, M.; Cho, C Y; R.A. Skilton; Djikeng, A

    2014-01-01

    Cameroon has a wide range of agro-ecological zones, having indigenous chicken populations which are thought to be adapted and diversified. Genetic diversity of the Cameroon chicken populations from agro-ecological zones I, II, III and IV was assessed using 25 microsatellite markers. A total of 314 chickens were genotyped, revealing 226 distinct alleles and 24 private alleles (10.62%). The mean polymorphic information content was 0.57. The average observed, ...

  16. 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...

  17. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

    2011-01-01

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

  18. DETECTION OF GENETIC DIVERSITY OF TRITICALE BY MICROSATELLITE MARKERS

    Directory of Open Access Journals (Sweden)

    Andrej Trebichalský

    2013-02-01

    Full Text Available The aim of our work was to detect genetic variability in the set of 59 winter and spring triticale (x Triticosecale Witt. varieties using 5 wheat SSR markers. Totally, 35 alleles with an average number of 7 alleles per locus were detected. The highest number of alleles showed out Xbarc 004 (9. Based on the number and frequencies of alleles, the diversity index (DI, the probability of identity (PI and the polymorphic information content (PIC of SSR markers were calculated. The polymorphic information content (PIC ranged from 0.264 to 0.920 with an average of 0.654, which is generally considered sufficient for this purpose. For the assessment of genetic diversity the dendrogram, based on the hierarchical cluster analysis using UPGMA algorithm was prepared. Fifty nine triticale cultivars were grouped into three major clusters. The cultivar Terelland 22 (USA separated as unique one, second subcluster contained 3 cultivars and third one 55 cultivars. It was not possible to differentiate 15 genotypes between each other. For better differentiation it is necessary to use more polymorphic microsatellite markers. Results showed the utility of microsatellite markers for estimation of genetic diversity of triticale genotypes leading to genotype identification.

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

    International Nuclear Information System (INIS)

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

  20. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction.

    Science.gov (United States)

    Nayak, Spurthi N; Song, Jian; Villa, Andrea; Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C; Kuhn, David N; Glaz, Barry; Gilbert, Robert A; Comstock, Jack C; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

  1. Genetic Diversity in Natural Populations of New World Leishmania

    Scientific Electronic Library Online (English)

    Elisa, Cupolillo; Hooman, Momen; Gabriel, Grimaldi Jr.

    1998-09-01

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

  2. Genetic Diversity in Natural Populations of New World Leishmania

    Directory of Open Access Journals (Sweden)

    Elisa Cupolillo

    1998-09-01

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

  3. Genetic and Functional Diversity of Propagating Cells in Glioblastoma

    Directory of Open Access Journals (Sweden)

    Sara G.M. Piccirillo

    2015-01-01

    Full Text Available 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.

  4. 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

  5. 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...

  6. 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.

  7. Genetic diversity and networks of exchange: a combined approach to assess intra-breed diversity

    Directory of Open Access Journals (Sweden)

    Dumasy Jean-François

    2012-05-01

    Full Text Available Abstract Background Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow due to exchanges between herds. To quantify this relation, molecular data and analyses of the exchanges were combined for three endangered Belgian breeds. Methods For each breed, between 91 and 225 sheep were genotyped with 19 microsatellites. Genetic differentiations between breeds and among herds within a breed were evaluated and the genetic structure of the breeds was described using Bayesian clustering (Structure. Exchanges of animals between 20, 46 and 95 herds according to breed were identified via semi-directed interviews and were analyzed using the concepts of the network theory to calculate average degrees and shortest path lengths between herds. Correlation between the Reynolds’ genetic distances and the shortest path lengths between each pair of herds was assessed by a Mantel test approach. Results Genetic differentiation between breeds was high (0.16. Overall Fst values among herds were high in each breed (0.17, 0.11 and 0.10. Use of the Bayesian approach made it possible to identify genetic groups of herds within a breed. Significant correlations between the shortest path lengths and the Reynolds’ genetic distances were found in each breed (0.87, 0.33 and 0.41, which demonstrate the influence of exchanges between herds on the genetic diversity. Correlation differences between breeds could be explained by differences in the average degree of the animal exchange networks, which is a measure of the number of exchanges per herd. The two breeds with the highest average degree showed the lowest correlation. Information from the exchange networks was used to assign individuals to the genetic groups when molecular information was incomplete or missing to identify donors for a cryobank. Conclusions A fine-scale picture of the population genetic structure at the herd level was obtained for the three breeds. Network analysis made it possible to highlight the influence of exchanges on genetic structure and to complete or replace molecular information in establishing a conservation program.

  8. 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.

  9. 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

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

    Indian Academy of Sciences (India)

    A. K. Gupta; M. Chauhan; S. N. Tandon; Sonia

    2005-12-01

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (± s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, $F_{\\text{IS}}$ (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode–shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

  11. 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.

  12. 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...

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

    OpenAIRE

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

    2014-01-01

    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 ...

  14. Microsatellite analysis of the genetic diversity in the Black Slavonian pig

    OpenAIRE

    Bradi? Martina; Uremovi? Marija; Uremovi? Z.; Mio? B.; Konja?i? M.; Lukovi? Z.; Safner T.

    2007-01-01

    This research is focused on the genetic diversity and population structure of the Black Slavonian pig, with the aim of assessing the situation regarding the endangerment of genetic diversity, and defining the further role of this breed in the preseration of its genetic diversity. Genetic population parameters were assessed in 42 animals at 8 microsatellite loci. On three of the observed loci there was a deviation from the Hardy-Weinberg (HW) equilibrium with P<0.01, one locus showe...

  15. 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.

  16. 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.

  17. Genetic basis of transcriptome diversity in Drosophila melanogaster.

    Science.gov (United States)

    Huang, Wen; Carbone, Mary Anna; Magwire, Michael M; Peiffer, Jason A; Lyman, Richard F; Stone, Eric A; Anholt, Robert R H; Mackay, Trudy F C

    2015-11-01

    Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive but is essential for predicting adaptive evolution, for selecting agriculturally important animals and crops, and for personalized medicine. Gene expression may provide a link between variation in DNA sequence and organismal phenotypes, and its abundance can be measured efficiently and accurately. Here we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). We found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. We found that NTRs often were negatively correlated with the expression of protein-coding genes, which we exploited to annotate NTRs functionally. We identified regulatory variants for the mean and variance of gene expression, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression were concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation. PMID:26483487

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

    Directory of Open Access Journals (Sweden)

    Juan Miguel Cordero-Solórzano

    2015-06-01

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

  19. 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.

  20. Exploiting a wheat EST database to assess genetic diversity

    Directory of Open Access Journals (Sweden)

    Ozge Karakas

    2010-01-01

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

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

    International Nuclear Information System (INIS)

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

  2. Genetic diversity of Ranunculus acris L. (Ranunculaceae) populations in relation to species diversity and habitat type in grassland communities.

    Science.gov (United States)

    Odat, Nidal; Jetschke, Gottfried; Hellwig, Frank H

    2004-05-01

    Correlates between genetic diversity at intra- and interpopulation levels and the species diversity in plant communities are rarely investigated. Such correlates may give insights into the effect of local selective forces across different communities on the genetic diversity of local plant populations. This study has employed amplified fragment length polymorphism to assess the genetic diversity within and between 10 populations of Ranunculus acris in relation to the species diversity (richness and evenness) of grassland communities of two different habitat types, 'seminatural' and 'agriculturally improved', located in central Germany. Within-population genetic diversity estimated by Nei's unbiased gene diversity (HE) was high (0.258-0.334), and was not correlated with species richness (Pearson's r = -0.17; P = 0.64) or species evenness (Pearson's r = 0.15; P = 0.68) of the plant communities. However, the genetic differentiation between R. acris populations was significantly correlated with the difference in species evenness (Mantel's r = 0.62, P = 0.02), but not with difference in species richness of plant communities (r = -0.17, P = 0.22). Moreover, we also found that populations of R. acris from the 'seminatural' habitat were genetically different (amova, P < 0.05) from those in 'agriculturally improved' habitats, suggesting that gene flow between these habitat types is limited. The results reported in this study may indicate that habitat characteristics influence the genetic diversity of plant species. PMID:15078460

  3. 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...

  4. Molecular assessment of genetic diversity in mung bean germplasm

    Indian Academy of Sciences (India)

    G. Roopa Lavanya; Jyoti Srivastava; Shirish A. Ranade

    2008-04-01

    RAPD profiles were used to identify the extent of diversity among 54 accessions of mung bean that included both improved and local land races. Out of the 40 primers screened, seven primers generated 174 amplification products with an average of 24.85 bands per primer. The RAPD profiles were analysed for Jaccard’s similarity coefficients that was found to be in the range from 0 to 0.48, indicating the presence of wide range of genetic diversity at molecular level. Cluster analysis was carried out based on distances (1-similarity coefficient) using neighbour-joining method in Free Tree package. The dendrogram resolved all the accessions into two major clusters, I (with 11 accessions) and II (with 43 accessions). However, the cluster was further divided into four subclusters (II A with six, II B with nine, II C with 15 and II D with 13 accessions). The distribution of the accessions in different clusters and subclusters appeares to be related to their performance in field conditions for 10 morphological traits that were scored. This study indicated that the RAPD profiles provide an easy and simple technique for preliminary genetic diversity assessment of mung bean accessions that may reflect morphological trait differences among them.

  5. 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.

  6. 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.

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

    OpenAIRE

    Nisar Ahmad; Iqbal Munir; Imtiaz A. khan; 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...

  8. DEVELOPMENT AND ASSESSMENT OF EST-SSR MARKER FOR THE GENETIC DIVERSITY AMONG TOBACCOS (Nicotiana tabacum L.).

    Science.gov (United States)

    Cai, C; Yang, Y; Cheng, L; Tong, C; Feng, J

    2015-06-01

    Because of the advantages of EST-SSR markers, it has been employed as powerful markers for genetic diversity analysis, comparative mapping and phylogenetic studies. In this study, a total of 429,869 tobacco (Nicotiana tabacum L.) ESTs were downloaded from the public databases, which offers an opportunity to identify SSRs in ESTs by data mining, and 38,165 SSRs were identified from 379,967 uni-ESTs with the frequency of one SSR per 5.52 kb. Mono- and tri-nucleotide repeat motifs were the dominant repeat types, accounting for 40.53 and 34.51% of all SSRs, respectively. After eliminating mononucleotide-containing sequences, 86 pairs of primers were designed to amplify in four tobacco accessions. Only 15 primers (17.44%) showed polymorphism, and then they were further used to assess genetic diversity of 20 tobacco accessions. Unweighted pair-group method with arithmetic average dendrograms (UPGMA) and principal coordinates analysis plots (PCA) revealed genetic differentiation between N. rustica and N. tabacum, and between oriental tobacco and other accessions of N. tabacum. The present study reported the development of EST-SSR markers in tobacco by exploiting EST databases, and confirmed the effective way to develop markers. These EST-SSRs can serve in studies on cultivar identification, genetic diversity analysis, and genetics in tobacco. PMID:26310032

  9. 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 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)

  10. Simple sequence repeat-based analysis of the genetic diversity and population genetic structure of populations of Siniperca chuatsi.

    Science.gov (United States)

    Sun, C F; Ye, X; Tian, Y Y; Dong, J J

    2015-01-01

    In order to provide genetic information for the selective breeding of Siniperca chuatsi, 14 microsatellite DNA loci were used to evaluate the genetic diversity and structure of four farmed populations and one wild population in China. The four cultivated populations were Foshan (FS), Jiangmen (JM), Nanjing (NJ), and Hongze Lake (HZL), and the wild population was collected from the Hubei HuangGang section of the Yangtze River (HG). All five populations exhibited high genetic diversity (HE values of between 0.608 and 0.633); the highest was found in the wild population (HE = 0.633). Genetic differentiation within the populations was relatively low (FST < 0.15); 5.44% of the genetic variation was between the populations and 94.56% was within the populations. The greatest genetic distance was between JM and HG (0.1894), which had the lowest genetic identity (0.8725). NJ and HG had the shortest genetic distance (0.0365) and the highest genetic identity (0.9641). A phylogenetic analysis revealed that FS, JM, and HZL were clustered into one group, while NJ and HG were in another group, suggesting that the wild and NJ populations were closely related. Our results demonstrate that although the farmed populations have maintained a relatively high genetic diversity, they exhibit lower genetic diversity and higher genetic differentiation than the wild population. These results provide evidence that wild resources should be used for breeding, in order to maintain genetic diversity and ensure sustainable S. chuatsi farming. PMID:26345868

  11. 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%.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Insights into Penicillium roqueforti Morphological and Genetic Diversity.

    Science.gov (United States)

    Gillot, Guillaume; Jany, Jean-Luc; Coton, Monika; Le Floch, Gaétan; Debaets, Stella; Ropars, Jeanne; López-Villavicencio, Manuela; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana; Coton, Emmanuel

    2015-01-01

    Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection. PMID:26091176

  17. 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.

  18. 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.

  19. 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.

  20. Genetic diversity and variability in two Italian autochthonous donkey genetic types assessed by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Donato Matassino

    2014-01-01

    Full Text Available Since 13rd century, Italian domestic autochthonous donkey population has been characterised by Mediterranean grey mousy cruciate ancestral phenotype, currently typical of Amiata donkey (AD genetic type. This phenotype persisted up to the 16th century when a marked introduction of Hispanic and French big sized and dark bay or darkish coloured sires occurred. In the context of a safeguard programme of Latial Equide resources, the aim of this research was to evaluate the genetic diversity and similarity between the AD breed and an autochthonous donkey population native from Lazio, the Viterbese donkey (VD, using molecular markers. A total of 135 animals (50 AD and 85 VD were genetically characterised by using 16 short tandem repeat markers. A high genetic differentiation between populations (FST=0.158; P<0.01 and a low betweenbreeds genetic similarity (0.233±0.085 were observed. Correspondence analysis, the result of STRUCTURE software analysis and analysis of molecular variance would seem to indicate genetically different entities as well. It would be desirable to increase the number of comparison with other breeds to better understand the origin of VD. Moreover, results obtained in this study suggest that the loss of genetic variation observed in VD could mainly derive from unnoticed sub-population structuring (Wahlund effect, rather than to other factors such as inbreeding, null alleles or selection influence.

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

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.; Van Ba, N.; Minh, L. T. A.; Hoan, T. X.; Cuong, V. C.; Kadarmideen, Haja

    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 ge...

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

    OpenAIRE

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

    2009-01-01

    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 anthropogen...

  3. Genetic Diversity of Sitobion avenae (Homoptera: Aphididae) Populations from Different Geographic Regions in China

    OpenAIRE

    Xin, Juan-Juan; Shang, Qing-Li; Desneux, Nicolas; Gao, Xi-Wu

    2014-01-01

    Sitobion avenae is a major agricultural pest of wheat in China. Using microsatellite markers, we studied the potential gene flow, genetic diversity, genetic differentiation, and genetic structure of seven S. avenae populations from different regions of China (Beijing, Hebei, Henan, Hubei, Jiangsu, Shandong, and Shanxi provinces). The populations from Henan, Shandong, and Jiangsu showed high levels of genic and genotypic diversity. By contrast, the genic diversity in the Beijing and Hebei popu...

  4. Peak and Persistent Excess of Genetic Diversity Following an Abrupt Migration Increase

    OpenAIRE

    Alcala, Nicolas; Streit, Daniela; Goudet, Jérôme; Vuilleumier, Séverine

    2013-01-01

    Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species’ lifetim...

  5. 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

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

    Science.gov (United States)

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

    2015-01-01

    Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population or an environmental change. PMID:26207812

  7. Role of telomere dysfunction in genetic intratumor diversity.

    Science.gov (United States)

    Genescà, Anna; Pampalona, Judit; Frías, Cristina; Domínguez, Daniel; Tusell, Laura

    2011-01-01

    Most solid tumors are unable to maintain the stability of their genomes at the chromosome level. Indeed, cancer cells display highly rearranged karyotypes containing translocations, amplifications, deletions, and gains and losses of whole chromosomes, which reshuffle steadily. This chromosomal instability most likely occurs early in the development of cancer, and may represent an important step in promoting the multiple genetic changes required for the initiation and/or progression of the disease. Different mechanisms may underlie chromosome instability in cancer cells, but a prominent role for telomeres, the tip of linear chromosomes, has been determined. Telomeres are ribonucleoprotein structures that prevent natural chromosome ends being recognized as DNA double-strand breaks, by adopting a loop structure. Loss of telomere function appears from either alteration on telomere-binding proteins or from the progressive telomere shortening that normally occurs under physiological conditions in the majority of cells in tissues. Importantly, unmasked telomeres may either trigger the senescent phenotype that has been linked to the aging process or may initiate the chromosome instability needed for cancer development, depending on the integrity of the DNA damage checkpoint responses. Telomere dysfunction contributes to chromosome instability through end-to-end chromosome fusions entering breakage-fusion-bridge (BFB) cycles. Resolution of chromatin bridge intermediates is likely to contribute greatly to the generation of segmental chromosome amplification events, unbalanced chromosome rearrangements, and whole chromosome aneuploidy. Noteworthy is the fact that telomere length heterogeneity among individuals may directly influence the scrambling of the genome at tumor initiation. However, reiterated BFB cycles would randomly reorganize the cell karyotype, thus increasing the genetic diversity that characterizes tumor cells. Even though a direct link is still lacking, multiple evidence lead one to believe that telomere dysfunction directly contributes to cancer development in humans. The expansion of highly unstable cells due to telomere dysfunction enhances the genetic diversity needed to fuel specific mutations that may promote cell immortalization and the acquisition of a tumor phenotype. PMID:21925300

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

    DEFF Research Database (Denmark)

    Nash, David Richard; Lomborg, Andreas Eg

    2008-01-01

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

  9. 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...

  10. 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 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)

  11. Genetic diversity of Plasmodium vivax isolates from Azerbaijan

    Directory of Open Access Journals (Sweden)

    Majori Giancarlo

    2004-11-01

    Full Text Available Abstract Background Plasmodium vivax, although causing a less serious disease than Plasmodium falciparum, is the most widespread of the four human malarial species. Further to the recent recrudescence of P. vivax cases in the Newly Independent States (NIS of central Asia, a survey on the genetic diversity and dissemination in Azerbaijan was undertaken. Azerbaijan is at the crossroads of Asia and, as such, could see a rise in the number of cases, although an effective malaria control programme has been established in the country. Methods Thirty-six P. vivax isolates from Central Azerbaijan were characterized by analysing the genetic polymorphism of the circumsporozoite protein (CSP and the merozoite surface protein 1 (MSP-1 genes, using PCR amplifications and amplicons sequencing. Results Analysis of CSP sequences showed that all the processed isolates belong to the VK 210 type, with variations in the alternation of alanine residue (A or aspartic acid residue (D in the repeat motif GDRA(A/DGQPA along the sequence. As far as MSP-1 genotyping is concerned, it was found that the majority of isolates analysed belong to Belem and Sal I types. Five recombinant isolates were also identified. Combined analysis with the two genetic markers allowed the identification of 19 plasmodial sub-types. Conclusion The results obtained in the present study indicate that there are several P. vivax clones circulating in Azerbaijan and, consequently, a careful malaria surveillance could be of paramount importance to identify, at early stage, the occurrence of possible P. vivax malaria outbreaks.

  12. Genetic diversity of Plasmodium vivax isolates from Azerbaijan

    Science.gov (United States)

    Leclerc, Marie Claude; Menegon, Michela; Cligny, Alexandra; Noyer, Jean Louis; Mammadov, Suleyman; Aliyev, Namig; Gasimov, Elkhan; Majori, Giancarlo; Severini, Carlo

    2004-01-01

    Background Plasmodium vivax, although causing a less serious disease than Plasmodium falciparum, is the most widespread of the four human malarial species. Further to the recent recrudescence of P. vivax cases in the Newly Independent States (NIS) of central Asia, a survey on the genetic diversity and dissemination in Azerbaijan was undertaken. Azerbaijan is at the crossroads of Asia and, as such, could see a rise in the number of cases, although an effective malaria control programme has been established in the country. Methods Thirty-six P. vivax isolates from Central Azerbaijan were characterized by analysing the genetic polymorphism of the circumsporozoite protein (CSP) and the merozoite surface protein 1 (MSP-1) genes, using PCR amplifications and amplicons sequencing. Results Analysis of CSP sequences showed that all the processed isolates belong to the VK 210 type, with variations in the alternation of alanine residue (A) or aspartic acid residue (D) in the repeat motif GDRA(A/D)GQPA along the sequence. As far as MSP-1 genotyping is concerned, it was found that the majority of isolates analysed belong to Belem and Sal I types. Five recombinant isolates were also identified. Combined analysis with the two genetic markers allowed the identification of 19 plasmodial sub-types. Conclusion The results obtained in the present study indicate that there are several P. vivax clones circulating in Azerbaijan and, consequently, a careful malaria surveillance could be of paramount importance to identify, at early stage, the occurrence of possible P. vivax malaria outbreaks. PMID:15535878

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

    OpenAIRE

    van der Meer, Sascha; Jacquemyn, Hans

    2015-01-01

    Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on th...

  14. 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...

  15. 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...

  16. [Genetic diversity of microsatellite loci in captive Amur tigers].

    Science.gov (United States)

    Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

    2004-09-01

    The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten microsatellie loci had high or medium polymorphism in these Amur tigers and had high genetic diversity. At the same time, we only found even bases variability which showed the even bases repeat sequence (CA/GT) maybe the basic unit for length variability of microsatellite in all loci. In this study, the samples were made up of 75 hair specimens, 23 blood specimens and 15 tissue specimens, we obtained the genome DNA from hairs using the non-invasive DNA technology and demonstrated that DNA derived from hair samples is as good as that obtained from blood samples for the analysis of microsatellite polymorphism. These results imply that microsatellite DNA markers and non-invasive DNA technology can help study the genetic diversity of Amur tiger. This method could be used in the captive management of other endangered species. PMID:15640074

  17. A nonlinear relationship between genetic diversity and productivity in a polyphagous seed beetle.

    Science.gov (United States)

    Burls, K J; Shapiro, J; Forister, M L; Hoelzer, G A

    2014-05-01

    There has been a renewed interest in the effects of genetic diversity on population-level and community-level processes. Many of these studies have found non-additive, positive effects of diversity, but these studies have rarely examined ecological mechanisms by which diverse populations increase productivity. We used the seed beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae) to study genetic diversity in insect host preference and fecundity and its effects on total productivity and resource use. We created genetically distinct lineages that varied in host preference and fecundity and then assembled groups consisting of one, three, five, or all ten lineages. We found that lineages with intermediate diversity had the highest productivity, though resource use did not change in diverse groups. In addition, lineages showed substantial plasticity in host preference when preference was assayed either individually or in groups, and productivity was much lower in groups than predicted by individual assays. These results highlight the interplay of genetic diversity, resource variation, and phenotypic plasticity in determining the ecological consequences of genetic diversity. In addition, when plasticity modifies a population's response to population density, this may create a complex interaction between genetic diversity and density, influencing selective pressures on the population and potentially maintaining genetic diversity across generations. PMID:24535057

  18. Estimating genetic diversity across the neutral genome with the use of dense marker maps

    Directory of Open Access Journals (Sweden)

    Bijma Piter

    2010-05-01

    Full Text Available Abstract Background With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity. Methods A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one, an additional population was produced with a lower marker density i.e. 166 SNP markers. For each marker interval based on adjacent markers, the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity. Results The simulated population had an average minor allele frequency of 0.28 and an LD (r2 of 0.26, comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated, and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density, both for specific regions (r = 0.19-0.20 and large regions (r = 0.61-0.64 over the genome. For the population with a lower marker density, the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity. Conclusions Genetic diversities of ungenotyped regions of the genome (i.e. between markers estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity.

  19. Improved Genetic Algorithm Based on Simulated Annealing and Quantum Computing Strategy for Mining Association Rules

    Directory of Open Access Journals (Sweden)

    Dongsheng Liu

    2010-11-01

    Full Text Available Association rules mining is an important content in data mining. It can discover the relations of different attributes by analyzing and disposing data which is in database. This paper proposes a novel data mining algorithm to enhance the capability of exploring valuable information from databases with continuous values. The algorithm combines with quantum-inspired genetic algorithm and simulated annealing to find interesting association rules. The final best sets of membership functions in all the populations are then gathered together to be used for mining association rules. The experiment result demonstrates that the proposed approach could generate more association rules than other algorithms.

  20. Genetic diversity assessment of summer squash landraces using molecular markers.

    Science.gov (United States)

    Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E

    2013-07-01

    Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash. PMID:23666102

  1. 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.

  2. 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)

  3. Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

    OpenAIRE

    Cousins, Matthew M.; DONNELL, Deborah; Eshleman, Susan H

    2013-01-01

    We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutati...

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

    Directory of Open Access Journals (Sweden)

    Ming-Cheng Luo

    2013-03-01

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

  5. 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

  6. Genetic diversity of Ehrlichia ruminantium strains in Cameroon

    Directory of Open Access Journals (Sweden)

    Seraphine N. Esemu

    2014-02-01

    Full Text Available In order to investigate the extent of genetic diversity among Ehrlichia ruminantium strains in Cameroon, a partial fragment (800 bp of the E. ruminantium map1 gene was amplified by nested polymerase chain reaction in 121 of 156 E. ruminantium pCS20-positive DNA samples extracted from ticks and cattle collected from two ranches. Deoxyribonucleic acid sequencing of the map1 gene products indicated the presence of at least 21 genotypes at the nucleotide level and 16 genotypes at the amino acid level circulating within the study sites. Some of the genotypes were identical to Antigua (U50830, Blaaukrans (AF368000 or UmBanein (U50835, whilst the others were new genotypes. Twenty-four representative sequences were deposited in GenBank and given accession numbers JX477663 – JX477674 (for sequences of tick origin and JX486788 – JX486799 (for sequences of cattle origin. Knowledge of E. ruminantium strain diversity could be important in understanding the epidemiology of heartwater

  7. 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.

  8. 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.

  9. Genetic diversity analysis of groundnut genotypes using SSR markers

    Directory of Open Access Journals (Sweden)

    D. Shoba, N. Manivannan and P.Vindhiyavarman

    2010-12-01

    Full Text Available 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 assessing the genetic diversity, 6 primer pairs (24.0 per cent werepolymorphic. The genotype TMV 2 was susceptible to rust and late leaf spot diseases and it was separately clustered in the dendrogram andamong the eleven foliar disease resistant genotypes, the genotypes viz., COG 0423, COG 0436 and COG 0432 were distantly clustered fromTMV 2. Hence, by using the genotypes viz., TMV 2, COG 0423, COG 0436 and COG 0432, three combinations viz., TMV 2 x COG 0423, TMV2 x COG 0436 and TMV 2 x C0G 0432 could be made for further studies.

  10. 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...

  11. Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

    OpenAIRE

    Jun LIU; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng; Huang, Li-nan

    2014-01-01

    Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing app...

  12. 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 ...

  13. 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...

  14. 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...

  15. 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.

  16. Genetic diversity in Algerian maize (Zea mays L) landraces using SSR markers

    OpenAIRE

    Aci, Miyassa M.; Revilla Temiño, Pedro; Morsli, Abdelkader; Djemel, Abderrahmane; Belalia, Nawal; Kadri, Yasser; Khelifi-Saloui, Majda; Ordás López, Bernardo; Khelifi, Lakhdar

    2013-01-01

    In the Sahara, maize (Zea mays L) has been adapted to extreme environmental conditions during the last five centuries; therefore, this germplasm has a potential value as source of tolerance to stress. No previous report of the genetic diversity of Saharan maize has been published so far. The objective of this study was to determine the genetic diversity of a collection of Saharan maize. Fifteen accessions representing the geographic diversity of Algeria were characterized with 18 SSR. Most lo...

  17. 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; Jerry, Dean R.

    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...

  18. Genetic diversity in Brassica species and Eruca sativa for yield associated parameters

    OpenAIRE

    Kanwal Mahwish; Farhatullah; Rabbani Ashiq M.; Iqbal Sidra; Fayyaz Laila; Afzal M.

    2014-01-01

    Brassica species are vulnerable to narrow genetic base due to the ignorance of their wild relatives which possess many superior characters. This study was aimed to explore the genetic diversity in five Brassica species from U triangle as well as in their wild relative Eruca sativa. For the complete insight of genetic diversity, four accessions, each from five species of genus Brassica along with one species of Eruca collected from different geographical loc...

  19. Genetic Diversity Assessment of Sorghum Landraces in Zimbabwe Using Microsatellites and Indigenous Local Names

    OpenAIRE

    Chakauya, E.; P. Tongoona; E.A. Matibiri; Grum, M.

    2006-01-01

    Landraces of sorghum are grown throughout Zimbabwe and frequently given names describing important traits they possess or their origin. Little is known about the genetic diversity of this germplasm, the consistency of the relationship between names and genetic identity and thereby the usefulness of names in developing strategies for germplasm conservation and use. This study analysed the genetic diversity of 52 uncharacterised genotypes from two districts of Zimbabwe, Nyanga North and Tsholot...

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

    OpenAIRE

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

    2008-01-01

    Recent work has demonstrated considerable benefits of intracolonial genetic diversity for the productivity of honeybee colonies: single-patriline colonies have depressed foraging rates, smaller food stores and slower weight gain relative to multiple-patriline colonies. We explored whether differences in the use of foraging-related communication behaviour (waggle dances and shaking signals) underlie differences in foraging effort of genetically diverse and genetically uniform colonies. We crea...

  1. 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...

  2. Genetic diversity within and between European pig breeds using microsatellite markers

    OpenAIRE

    SanCristobal, M.; Chevalet, C.; Haley, C. S.; Joosten, R.; Rattink, A P; Harlizius, B.; Groenen, M.A.M.

    2006-01-01

    An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chine...

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

    OpenAIRE

    Colombo Carlos; Second Gérard; Valle Tereza Losada; Charrier André

    1998-01-01

    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 cons...

  4. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron

    OpenAIRE

    Wu, Fu Qin; Shen, Shi Kang; Zhang, Xin Jun; Wang, Yue Hua; Sun, Wei Bang

    2015-01-01

    This is the first study of the genetic diversity and structure of the big tree rhododendron, Rhododendron protistum var. giganteum, which is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. We detected moderate to high genetic diversity at the species level, but low genetic differentiation between the two extant populations. These results suggest that some rare and endangered species are able to maintain high...

  5. Characterization of Genetic Diversity in the Nematode Pristionchus pacificus from Population-Scale Resequencing Data

    OpenAIRE

    Rödelsperger, Christian; Neher, Richard A.; Weller, Andreas M.; Eberhardt, Gabi; Witte, Hanh; Mayer, Werner E; Dieterich, Christoph; Sommer, Ralf J

    2014-01-01

    The hermaphroditic nematode Pristionchus pacificus is an established model system for comparative studies with Caenorhabditis elegans in developmental biology, ecology, and population genetics. In this study, we present whole-genome sequencing data of 104 P. pacificus strains and the draft assembly of the obligate outcrossing sister species P. exspectatus. We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. P. pacificu...

  6. 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%.

  7. Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers.

    Science.gov (United States)

    Deu, M; Sagnard, F; Chantereau, J; Calatayud, C; Hérault, D; Mariac, C; Pham, J-L; Vigouroux, Y; Kapran, I; Traore, P S; Mamadou, A; Gerard, B; Ndjeunga, J; Bezançon, G

    2008-05-01

    Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa. PMID:18273600

  8. 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.; Serrão, 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...

  9. Genetic Diversity, Morphological Uniformity and Polyketide Production in Dinoflagellates (Amphidinium, Dinoflagellata)

    OpenAIRE

    Murray, Shauna A.; Garby, Tamsyn; Hoppenrath, Mona; Brett A. Neilan

    2012-01-01

    Dinoflagellates are an intriguing group of eukaryotes, showing many unusual morphological and genetic features. Some groups of dinoflagellates are morphologically highly uniform, despite indications of genetic diversity. The species Amphidinium carterae is abundant and cosmopolitan in marine environments, grows easily in culture, and has therefore been used as a ‘model’ dinoflagellate in research into dinoflagellate genetics, polyketide production and photosynthesis. We have investigated the ...

  10. 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.

  11. 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.

    2012-09-01

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

  12. Genetic diversity 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.

  13. 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

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

    Directory of Open Access Journals (Sweden)

    Janaina Azevedo Martuscello

    2012-09-01

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

  15. 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 groups of 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.

  16. High level of genetic diversity among spelt germplasm revealed by microsatellite markers.

    Science.gov (United States)

    Bertin, P; Grégoire, D; Massart, S; de Froidmont, D

    2004-12-01

    The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 - proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 +/- 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs. PMID:15644962

  17. Mining Classification Rules by Using Genetic Algorithms with Non-random Initial Population and Uniform Operator

    OpenAIRE

    GÜNDO?AN, Korkut Koray; Alata?, Bilal; Karci, Ali

    2004-01-01

    Classification is a supervised learning method that induces a classification model from a database and is one of the most commonly applied data mining task. The frequently employed techniques are decision tree or neural network-based classification algorithms. This work presents an efficient genetic algorithm (GA) for classification rule mining technique that discovers comprehensible IF-THEN rules using a generalized uniform population method and a uniform operator inspired from the ...

  18. 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.

  19. 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.

  20. 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.

  1. HIV Populations Are Large and Accumulate High Genetic Diversity in a Nonlinear Fashion

    OpenAIRE

    Maldarelli, Frank; Kearney, Mary; PALMER, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A; Davey, Richard T.; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A; REHM, Catherine; Greer, Sarah E; Lucey, Daniel L.; Danley, Kristen

    2013-01-01

    HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence a...

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    M.J. Hasan

    2014-06-01

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

  4. Assessment of genetic diversity in germplasm of linseed

    International Nuclear Information System (INIS)

    Abstract:- A set of 55 linseed accessions including a check variety (Chandni) were evaluated under rainfed conditions during three crop seasons i.e. 2008-09, 2009-10 and 2010-11. Data were recorded for days to flower initiation, flower completion, maturity, reproductive period, plant height, branches per plant, bolls per plant, plot biomass, harvest index and seed yield. Wide ranges between the mean values with high CV values were exhibited by plant height, bolls per plant, biomass and seed yield accompanied with maximum values of variances and standard deviation, revealed the existence of greater genetic diversity in the accessions for these traits. Dendrogram based on Euclidean distance coefficient using 10 quantitative traits, grouped all the linseed accessions into 13 clusters. Cluster II was the biggest and had 33 accessions followed by Cluster I having 11 accessions. For the development of high yielding varieties, best performing accessions of Clusters I and II could be used in hybridization programme by crossing with accessions of Clusters VII, VIII, IX and X followed by selection in segregating populations. (author)

  5. Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger.

    Science.gov (United States)

    Deu, Monique; Sagnard, F; Chantereau, J; Calatayud, C; Vigouroux, Y; Pham, J L; Mariac, C; Kapran, I; Mamadou, A; Gérard, B; Ndjeunga, J; Bezançon, G

    2010-05-01

    The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger's agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976-2003). Global genetic differentiation between the two collections was very low (F (st) = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F (st), and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers' management has globally preserved sorghum genetic diversity in Niger. PMID:20062963

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    S. Dehuri

    2006-01-01

    Full Text Available 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 rapidly both in size and dimensions. Furthermore, the multi-objective genetic algorithm (MOGA tends to be slow in comparison with most classical rule mining methods. Hence, to overcome these difficulties we propose a fast and scalability technique using the inherent parallel processing nature of genetic algorithm and a homogeneous dedicated network of workstations (NOWs. Our algorithm exploit both data and control parallelism by distributing the data being mined and the population of individuals across all available processors. The experimental result shows that the algorithm has been found suitable for large database with an encouraging speed up.

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

    DEFF Research Database (Denmark)

    Topping, Christopher John; Østergaard, Siri; Pertoldi, Cino; Bach, Lars Arve

    2003-01-01

    Altering environmental conditions affects the genetic composition of populations via demographic and selective responses by creating of variety of population substructuring types. Classical genetic approaches can predict the genetic composition of populations under long-term or structurally stable conditions, but exclude factors such as animal behaviour, environmental structure, and breeding biology, all of which influence genetic diversity. Most populations are unique in some of these character...

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

    Science.gov (United States)

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

    2013-11-01

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

  10. Genetic diversity of Heterobasidion spp. in Scots pine, Norway spruce and European silver fir stands

    OpenAIRE

    Piotr ?akomy; Zbigniew Broda; Antoni Werner

    2007-01-01

    Investigations of genetic diversity of Heterobasidion spp. in Scots pine, Norway spruce and European silver fir stands indicated that almost all of identified genets occurring in those stands were small and occupied only a single stump. In some cases two, three or even four genets could effectively exist in an individual stump. Genetic similarity of H. annosum s.s. genets varied from 0% to 62%, H. parviporum from 0% to 38% and H. abietinum from 0% to 55%. The oldest and biggest genet was foun...

  11. 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

  12. 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.

  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. Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers

    Scientific Electronic Library Online (English)

    Thaura, Ghneim Herrera; Duina, Posso Duque; Iris, Pérez Almeida; Gelis, Torrealba Núñez; Alejandro J, Pieters; César P, Martinez; Joe M, Tohme.

    2008-12-01

    Full Text Available In Venezuela, pedigree analyses indicate that the rice varieties currently under cultivation are closely related. Effective breeding programs, based on knowledge of the genetic diversity of cultivars, are needed to broaden the genetic bases of rice germplasm in the country. In this study, we used a [...] set of 48 simple-sequence-repeat (SSR) markers to assess the genetic diversity of 11 Venezuelan rice cultivars, released by the National Rice Breeding Program between 1978 and 2007. A total of 203 alleles were detected, the number of alleles (NA) per marker ranged from 2 to 9, with an average of 4.23. The average genic diversity (H) over all SSR loci for the 18 genotypes was 0.524, ranging from 0.105 to 0.815. Positive correlations were found between H at each locus, NA, the allele size range and the maximum number of repeats. Venezuelan cultivars showed lower H (mean = 0.37) and NA (total = 124, mean = 2.58) than the whole sample. UPGMA-cluster-analysis based on genetic distance coefficients clearly separated all the genotypes, and showed that the Venezuelan rice varieties are closely related. Molecular identification of 7 Venezuelan cultivars could be done with 9 primers pairs which produced 10 genotype-specific-alleles. Although the genetic diversity was low, SSRs proved to be an efficient tool in assessing the genetic diversity of rice genotypes. Implications of the low genetic diversity detected and relatedness of Venezuelan cultivars are discussed.

  15. 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.

  16. Genetic diversity and population structure of Bretschneidera sinensis, an endangered species

    Directory of Open Access Journals (Sweden)

    Gangbiao Xu

    2013-11-01

    Full Text Available Amounts and distribution of intraspecific genetic variation provide benchmarks for developing conservation strategies. Bretschneidera sinensis is a monotypic relic species listed in the First Grade of the List of Wild Plants Under State Protection (First Batch in China. We examined the genetic diversity and genetic structure of 219 B. sinensis individuals sampled from 15 natural populations distributed in Hunan, Jiangxi, Guangdong, Guangxi, and Guizhou using inter-simple sequence repeat (ISSR markers generated by seven ISSR primers. The percentage of polymorphic bands (PPB at the species and population level was 74.42% and 38.06%, respectively. Shannon’s index (I of phenotypic diversity at the species and population level was 0.3630 and 0.2081, respectively, and Nei’s genetic diversity (He at the species and population level was 0.2397 and 0.1405, respectively. These results indicate that B. sinensis contains relatively high levels of genetic diversity. Analysis of molecular variance (AMOVA and estimates of the coefficient of genetic differentiation based on phenotypic diversity index also indicated high levels of population subdivision (GST = 0.2973; FST = 0.4267 in the species. Analysis of the ISSR data using UPGMA further revealed that populations were genetically clustered into two groups, while a Mantel test showed that genetic divergence was significantly correlated with geographical distance among populations (Mantel test; r = 0.3096, P = 0.008. We conclude from our results that B. sinensis is not endangered due to low evolutionary potential stemming from low genetic diversity, but by habitat destruction coupled with a low reproductive capacity, poor adaptability and weak competitiveness. The Mt. Yangming, Mt. Mangshan, Ruyang, and Mt. Bamianshan populations of the species with higher genetic diversity should be given priority for conservation, and inbreeding depression monitoring should be conducted.

  17. Genetic diversity in caribou linked to past and future climate change

    Science.gov (United States)

    Yannic, Glenn; Pellissier, Loïc; Ortego, Joaquín; Lecomte, Nicolas; Couturier, Serge; Cuyler, Christine; Dussault, Christian; Hundertmark, Kris J.; Irvine, R. Justin; Jenkins, Deborah A.; Kolpashikov, Leonid; Mager, Karen; Musiani, Marco; Parker, Katherine L.; Røed, Knut H.; Sipko, Taras; Þórisson, Skarphéðinn G.; Weckworth, Byron V.; Guisan, Antoine; Bernatchez, Louis; Côté, Steeve D.

    2014-02-01

    Climate-driven range fluctuations during the Pleistocene have continuously reshaped species distribution leading to populations of contrasting genetic diversity. Contemporary climate change is similarly influencing species distribution and population structure, with important consequences for patterns of genetic diversity and species' evolutionary potential. Yet few studies assess the impacts of global climatic changes on intraspecific genetic variation. Here, combining analyses of molecular data with time series of predicted species distributions and a model of diffusion through time over the past 21kyr, we unravel caribou response to past and future climate changes across its entire Holarctic distribution. We found that genetic diversity is geographically structured with two main caribou lineages, one originating from and confined to Northeastern America, the other originating from Euro-Beringia but also currently distributed in western North America. Regions that remained climatically stable over the past 21kyr maintained a high genetic diversity and are also predicted to experience higher climatic stability under future climate change scenarios. Our interdisciplinary approach, combining genetic data and spatial analyses of climatic stability (applicable to virtually any taxon), represents a significant advance in inferring how climate shapes genetic diversity and impacts genetic structure.

  18. Genetic diversity in three natural populations of Pitcairnia flammea (l.) John (Bromeliaceae) estimated by ISSR markers.

    Science.gov (United States)

    Souza-Sobreira, F B; Souza, G B; Rosado, C C G; Miranda, F D; Soares, T C B; Gontijo, A B P L

    2015-01-01

    Bromeliads are greatly represented in the Atlantic Forest, although many species are threatened with extinction owing to habitat fragmentation and intense extraction for ornamental purposes. Therefore, it is necessary to conduct studies generating knowledge about genetic diversity and the distribution of this diversity among and within natural populations to establish conservation strategies. These studies can be performed with the use of molecular markers. Molecular markers are advantageous for studies of natural populations, for conservation programs, and to aid in properly classifying plant species. This study aimed to evaluate the genetic diversity among and within natural populations of Pitcairnia flammea, occurring in three fragments of the Atlantic Forest in the southern State of Espírito Santo through the use of inter-simple sequence repeat (ISSR) markers. DNA samples from 55 individuals were amplified with 18 ISSR primers, generating 180 bands, 159 of which were polymorphic. The Shannon genetic diversity index ranged from 0.348 to 0.465, with an average of 0.412. The Bayesian approach for the molecular data indicated the existence of two genetic groups. Analysis of molecular variance indicated the existence of 90.3% diversity within the population and 9.74% among populations. The amount of genetic differentiation of populations was moderate (0.0974), indicating that gene flow rates may be enough to counteract the effects of genetic drift. Greater genetic variability found in population B indicates that this area is an important source of genetic variability. PMID:26634557

  19. Mining the human genome after Association for Molecular Pathology v. Myriad Genetics

    OpenAIRE

    Evans, Barbara J.

    2013-01-01

    The Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics portrays the human genome as a product of nature. This frames medical genetics as an extractive industry that mines a natural resource to produce valuable goods and services. Natural resource law offers insights into problems medical geneticists can expect after this decision and suggests possible solutions. Increased competition among clinical laboratories offers various benefits but threatens to in...

  20. 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 ...

  1. 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 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

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

    Science.gov (United States)

    Huff, D.D.; Miller, L.M.; Vondracek, B.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations. ?? 2010 US Government.

  3. Species-genetic diversity correlations in habitat fragmentation can be biased by small sample sizes.

    Science.gov (United States)

    Nazareno, Alison G; Jump, Alistair S

    2012-06-01

    Predicted parallel impacts of habitat fragmentation on genes and species lie at the core of conservation biology, yet tests of this rule are rare. In a recent article in Ecology Letters, Struebig et al. (2011) report that declining genetic diversity accompanies declining species diversity in tropical forest fragments. However, this study estimates diversity in many populations through extrapolation from very small sample sizes. Using the data of this recent work, we show that results estimated from the smallest sample sizes drive the species-genetic diversity correlation (SGDC), owing to a false-positive association between habitat fragmentation and loss of genetic diversity. Small sample sizes are a persistent problem in habitat fragmentation studies, the results of which often do not fit simple theoretical models. It is essential, therefore, that data assessing the proposed SGDC are sufficient in order that conclusions be robust. PMID:22860246

  4. High genetic diversity of Plasmodium vivax on the north coast of Papua New Guinea.

    Science.gov (United States)

    Arnott, Alicia; Barnadas, Celine; Senn, Nicolas; Siba, Peter; Mueller, Ivo; Reeder, John C; Barry, Alyssa E

    2013-07-01

    Despite having the highest Plasmodium vivax burden in the world, molecular epidemiological data from Papua New Guinea (PNG) for this parasite remain limited. To investigate the molecular epidemiology of P. vivax in PNG, 574 isolates collected from four catchment sites in East Sepik (N = 1) and Madang (N = 3) Provinces were genotyped using the markers MS16 and msp1F3. Genetic diversity and prevalence of P. vivax was determined for all sites. Despite a P. vivax infection prevalence in the East Sepik (15%) catchments less than one-half the prevalence of the Madang catchments (27-35%), genetic diversity was similarly high in all populations (He = 0.77-0.98). High genetic diversity, despite a marked difference in infection prevalence, suggests a large reservoir of diversity in P. vivax populations of PNG. Significant reductions in transmission intensity may, therefore, be required to reduce the diversity of parasite populations in highly endemic countries such as PNG. PMID:23690553

  5. Genetic diversity demonstrated by pulsed field gel electrophoresis of Salmonella enterica isolates obtained from diverse sources in Mexico

    Science.gov (United States)

    This study was conducted to determine the genetic diversity of Salmonella isolates recovered from a variety of sources using pulsed-field gel electrophoresis (PFGE) to assess their possible relatedness. Salmonella was isolated from ca. 52% of samples from a pepper var. Bell production system. A to...

  6. Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae).

    Science.gov (United States)

    Ellis, J S; Knight, M E; Darvill, B; Goulson, D

    2006-12-01

    Habitat fragmentation may severely affect survival of social insect populations as the number of nests per population, not the number of individuals, represents population size, hence they may be particularly prone to loss of genetic diversity. Erosion of genetic diversity may be particularly significant among social Hymenoptera such as bumblebees (Bombus spp.), as this group may be susceptible to diploid male production, a suggested direct cost of inbreeding. Here, for the first time, we assess genetic diversity and population structuring of a threatened bumblebee species (Bombus sylvarum) which exists in highly fragmented habitat (rather than oceanic) islands. Effective population sizes, estimated from identified sisterhoods, were very low (range 21-72) suggesting that isolated populations will be vulnerable to loss of genetic variation through drift. Evidence of significant genetic structuring between populations (theta = 0.084) was found, but evidence of a bottleneck was detected in only one population. Comparison across highly fragmented UK populations and a continental population (where this species is more widespread) revealed significant differences in allelic richness attributable to a high degree of genetic diversity in the continental population. While not directly related to population size, this is perhaps explained by the high degree of isolation between UK populations relative to continental populations. We suggest that populations now existing on isolated habitat islands were probably linked by stepping-stone populations prior to recent habitat loss. PMID:17107471

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

    OpenAIRE

    Malice M.; Baudoin JP.

    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...

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

    OpenAIRE

    Juan M. Montes; Frank Technow; Matthias Martin; Klaus Becker

    2014-01-01

    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 Polym...

  9. Genetic Diversity and Population Structure of Rice Pathogen Ustilaginoidea virens in China

    OpenAIRE

    Sun, Xianyun; Kang, Shu; Zhang, Yongjie; Tan, Xinqiu; Yu, Yufei; He, Haiyong; Zhang, Xinyu; Liu, Yongfeng; Wang, Shu; Sun, Wenxian; CAI, LEI; LI, SHAOJIE

    2013-01-01

    Rice false smut caused by the fungal pathogen Ustilaginoideavirens is becoming a destructive disease throughout major rice-growing countries. Information about its genetic diversity and population structure is essential for rice breeding and efficient control of the disease. This study compared the genome sequences of two U. virens isolates. Three SNP-rich genomic regions were identified as molecular markers that could be used to analyze the genetic diversity and population structure of U. vi...

  10. Genome-wide distribution of genetic diversity and linkage disequilibrium in elite sugar beet germplasm

    OpenAIRE

    Weißleder Knuth; Lühmann Ann-Katrin; Li Jinquan; Stich Benjamin

    2011-01-01

    Abstract Background Characterization of population structure and genetic diversity of germplasm is essential for the efficient organization and utilization of breeding material. The objectives of this study were to (i) explore the patterns of population structure in the pollen parent heterotic pool using different methods, (ii) investigate the genome-wide distribution of genetic diversity, and (iii) assess the extent and genome-wide distribution of linkage disequilibrium (LD) in elite sugar b...

  11. 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 differen...

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

    OpenAIRE

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

    2013-01-01

    Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is ...

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

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra; Changtragoon, Suchitra; Fady, Bruno; Kjær, Erik Dahl; Loo, Judy; Ramamonjisoa, Lolona; Vendramin, Giovanni G.

    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 managemen...

  14. Genetic diversity of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific

    OpenAIRE

    Kreike, N.; H. J. Van Eck; Lebot, V.

    2004-01-01

    The genetic diversity of 255 taro (Colocasia esculenta) accessions from Vietnam, Thailand, Malaysia, Indonesia, the Philippines, Papua New Guinea and Vanuatu was studied using AFLPs. Three AFLP primer combinations generated a total of 465 scorable amplification products. The 255 accessions were grouped according to their country of origin, to their ploidy level (diploid or triploid) and to their habitat—cultivated or wild. Gene diversity within these groups and the genetic distance between th...

  15. Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity

    OpenAIRE

    Emerson Brent C; Spillner Andreas; Nguyen Binh; Moulton Vincent

    2010-01-01

    Abstract We introduce a method to help identify how the genetic diversity of a species within a geographic region might have arisen. This problem appears, for example, in the context of identifying refugia in phylogeography, and in the conservation of biodiversity where it is a factor in nature reserve selection. Complementing current methods for measuring genetic diversity, we analyze pairwise distances between the haplotypes of a species found in a geographic region and derive a quantity, c...

  16. Genetic diversity and population structuring of Schistosoma mansoni in a Brazilian village

    OpenAIRE

    Thiele, E.A.; Sorensen, R.E.; A Gazzinelli; Minchella, D.J.

    2007-01-01

    The digenean trematode Schistosoma mansoni is responsible for chronic schistosomiasis worldwide and in Brazil alone an estimated 35 million people are at risk. To evaluate epidemiological patterns among human definitive hosts, we assessed genetic diversity and population subdivision of S. mansoni infrapopulations in human hosts from the highly endemic village of Virgem das Graças in the state of Minas Gerais, Brazil. We believe this is the largest such survey to date. Genetic diversity of par...

  17. Genetic Diversity Analysis of Highly Incomplete SNP Genotype Data with Imputations: An Empirical Assessment

    OpenAIRE

    Fu, Yong-Bi

    2014-01-01

    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 gen...

  18. Genetic diversity in Silene sennenii Pau (Caryophyllaceae) assayed through DNA-based techniques

    OpenAIRE

    López-Vinyallonga, Sara; López-Pujol, Jordi; Martinell, M. C.; Massó, S.; Blanché, C.

    2012-01-01

    [EN]Genetic diversity in Silene sennenii Pau (Caryophylaceae) asayed through DNA-based techniques.— Silene sennenii is a narrow endemic species from the NE of the Iberian Peninsula. It is considered as EN (“Endangered”) according to the IUCN criteria and is under legal protection in Catalonia. In the present work we report an assay using three different approaches for surveying the genetic diversity in this rare, endangered campion: analysis of chloroplast haplotypes, AFLPs and transferabilit...

  19. 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.; Richardson, J E; J.C. Weber; 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...

  20. 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...

  1. 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; 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 ...

  2. 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.

  3. 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.

  4. 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.

  5. Relationship between the genetic diversity of Artemisia halodendron and climatic factors

    Science.gov (United States)

    Huang, Wenda; Zhao, Xueyong; Zhao, Xin; Li, Yuqiang; Lian, Jie; Yun, Jianying

    2014-02-01

    Artemisia halodendron (Asteraceae) is a dominant sand-fixing semi-shrub species native to the Horqin Sandy Land of northeastern China. In this study, we evaluated levels of genetic variation within and among sampled A. halodendron populations from two different hydrothermal regions of the Horqin Sandy Land using inter-simple sequence repeat (ISSR) markers. We also investigated possible relationships between genetic diversity of this species and climatic factors. Our analysis revealed that A. halodendron is highly genetically diverse, with populations from a low hydrothermal level region having higher genetic diversity index values than those from a high hydrothermal level region. An analysis of molecular variation (AMOVA) revealed relatively high levels (>89.83%) of within-population genetic variation. Based on cluster analysis, the 13 studied A. halodendron populations can be clustered into two clades. Genetic diversities of all populations have been influenced by many climatic factors, and Nei's genetic diversity (h) is strongly correlated with annual temperature range (ART). These results have important implications for restoration and management of degraded ecosystems in arid and semi-arid areas.

  6. 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.

  7. 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)

  8. Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii).

    Science.gov (United States)

    Morris, Katrina M; Wright, Belinda; Grueber, Catherine E; Hogg, Carolyn; Belov, Katherine

    2015-08-01

    The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction due to the spread of devil facial tumour disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in diversity at immune loci in wild species have almost exclusively focused on genes of the major histocompatibility complex (MHC); however, these genes only account for a fraction of immune gene diversity. Devils lack diversity at functionally important immunity loci, including MHC and Toll-like receptor genes. Whether there are polymorphisms at devil immune genes outside these two families is unknown. Here, we identify polymorphisms in a wide range of key immune genes, and develop assays to type single nucleotide polymorphisms (SNPs) within a subset of these genes. A total of 167 immune genes were examined, including cytokines, chemokines and natural killer cell receptors. Using genome-level data from ten devils, SNPs within coding regions, introns and 10 kb flanking genes of interest were identified. We found low polymorphism across 167 immune genes examined bioinformatically using whole-genome data. From this data, we developed long amplicon assays to target nine genes. These amplicons were sequenced in 29-220 devils and found to contain 78 SNPs, including eight SNPS within exons. Despite the extreme paucity of genetic diversity within these genes, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining diversity may hold adaptive potential. The low functional diversity may leave devils highly vulnerable to infectious disease, and therefore, monitoring and preserving remaining diversity will be critical for the long-term management of this species. Examining genetic variation in diverse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad-scale immunogenetic diversity analysis in threatened species. PMID:26119928

  9. 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.

  10. 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

  11. Analysis of Fungicide Sensitivity and Genetic Diversity among Colletotrichum Species in Sweet Persimmon

    OpenAIRE

    Gang, Geun-Hye; Cho, Hyun Ji; Kim, Hye Sun; Kwack, Yong-Bum; Kwak, Youn-Sig

    2015-01-01

    Anthracnose, caused by Colletotrichum gloeosporioides (C. gloeosporioides; Teleomorph: Glomerella cingulata), is the most destructive disease that affects sweet persimmon production worldwide. However, the biology, ecology, and genetic variations of C. gloeosporioides remain largely unknown. Therefore, in this study, the development of fungicide resistance and genetic diversity among an anthracnose pathogen population with different geographical origins and the exposure of this population to ...

  12. 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.

  13. 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’ individu...

  14. 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 elimi...

  15. SELF-ADAPTATION MECHANISM TO CONTROL THE DIVERSITY OF THE POPULATION IN GENETIC ALGORITHM

    OpenAIRE

    Chaiwat Jassadapakorn; Prabhas Chongstitvatana

    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 expli...

  16. An Analysis of Genetic Diversity Across the Maize Genome Using Microsatellites

    OpenAIRE

    Vigouroux, Yves; Mitchell, Sharon; Matsuoka, Yoshihiro; Hamblin, Martha; Kresovich, Stephen; Smith, J Stephen C; Jaqueth, Jennifer; Smith, Oscar S (Howie); Doebley, John

    2005-01-01

    How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative defi...

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

    Science.gov (United States)

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

    2012-01-01

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

  18. 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.

  19. Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers

    OpenAIRE

    Ilga Porth; El-Kassaby, Yousry A.

    2014-01-01

    Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characterist...

  20. 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...

  1. High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks

    OpenAIRE

    Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Alvares Serrão, Ester

    2013-01-01

    The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing...

  2. High Genetic Diversity and Structured Populations of the Oriental Fruit Moth in Its Range of Origin

    OpenAIRE

    Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; DORN, SILVIA; Chen, Maohua

    2013-01-01

    The oriental fruit moth Grapholita (?=?Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected through...

  3. 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; Deeming, D C; Holm, Lars-Erik

    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...

  4. Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi.

    Science.gov (United States)

    Pombert, Jean-François; Xu, Jinshan; Smith, David R; Heiman, David; Young, Sarah; Cuomo, Christina A; Weiss, Louis M; Keeling, Patrick J

    2013-04-01

    Microsporidia from the Encephalitozoonidae are obligate intracellular parasites with highly conserved and compacted nuclear genomes: they have few introns, short intergenic regions, and almost identical gene complements and chromosome arrangements. Comparative genomics of Encephalitozoon and microsporidia in general have focused largely on the genomic diversity between different species, and we know very little about the levels of genetic diversity within species. Polymorphism studies with Encephalitozoon are so far restricted to a small number of genes, and a few genetically distinct strains have been identified; most notably, three genotypes (ECI, ECII, and ECIII) of the model species E. cuniculi have been identified based on variable repeats in the rRNA internal transcribed spacer (ITS). To determine if E. cuniculi genotypes are genetically distinct lineages across the entire genome and at the same time to examine the question of intraspecies genetic diversity in microsporidia in general, we sequenced de novo genomes from each of the three genotypes and analyzed patterns of single nucleotide polymorphisms (SNPs) and insertions/deletions across the genomes. Although the strains have almost identical gene contents, they harbor large numbers of SNPs, including numerous nonsynonymous changes, indicating massive intraspecies variation within the Encephalitozoonidae. Based on this diversity, we conclude that the recognized genotypes are genetically distinct and propose new molecular markers for microsporidian genotyping. PMID:23291622

  5. Genetic diversity of Heterobasidion spp. in Scots pine, Norway spruce and European silver fir stands

    Directory of Open Access Journals (Sweden)

    Piotr ?akomy

    2013-12-01

    Full Text Available Investigations of genetic diversity of Heterobasidion spp. in Scots pine, Norway spruce and European silver fir stands indicated that almost all of identified genets occurring in those stands were small and occupied only a single stump. In some cases two, three or even four genets could effectively exist in an individual stump. Genetic similarity of H. annosum s.s. genets varied from 0% to 62%, H. parviporum from 0% to 38% and H. abietinum from 0% to 55%. The oldest and biggest genet was found in laying fir log and overgrew the wood for at least 14 years. This genet belonged to H. abietinum. The size of genets was related to thinning operation, spore dispersal, age of stand or competition in wood colonization.

  6. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron.

    Science.gov (United States)

    Wu, Fu Qin; Shen, Shi Kang; Zhang, Xin Jun; Wang, Yue Hua; Sun, Wei Bang

    2014-01-01

    Comprehensive studies on the genetic diversity and structure of endangered species are urgently needed to promote effective conservation and management activities. The big tree rhododendron, Rhododendron protistum var. giganteum, is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. Unfortunately, limited information is available regarding the population genetics of this species. Therefore, we conducted amplified fragment length polymorphism (AFLP) analysis to characterize the genetic diversity and variation of this species within and between remaining populations. Twelve primer combinations of AFLP produced 447 unambiguous and repetitious bands. Among these bands, 298 (66.67 %) were polymorphic. We found high genetic diversity at the species level (percentage of polymorphic loci = 66.67 %, h = 0.240, I = 0.358) and low genetic differentiation (Gst = 0.110) between the two populations. Gene flow between populations (Nm) was relatively high at 4.065. Analysis of molecular variance results revealed that 22 % of the genetic variation was partitioned between populations and 78 % of the genetic variation was within populations. The presence of moderate to high genetic diversity and low genetic differentiation in the two populations can be explained by life history traits, pollen dispersal and high gene flow (Nm = 4.065). Bayesian structure and principal coordinate analysis revealed that 56 sampled trees were clustered into two groups. Our results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes. These results will assist with the design of conservation and management programmes, such as in situ and ex situ conservation, seed collection for germplasm conservation and reintroduction. PMID:25477251

  7. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    Science.gov (United States)

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  8. Genetic Diversity in Mazandaranian Native Cattle: A Comparison with Holstein Cattle, using ISSR Marker

    Directory of Open Access Journals (Sweden)

    S. Pashaei

    2009-01-01

    Full Text Available This study was carried out to investigate genetic diversity in Mazandaranian native cattle population comparised to the Holstein breed, using Inter Simple Sequence Repeats (ISSR marker. A total of 175 animals, including 71 native and 104 cattle of Holstein breed were screened. The extraction of DNA samples were carried out, using modified salting out method. A 19-mer oligonucleotide, (GA9C, was used as primer in PCR reactions. The PCR products showed 15 different fragments with length ranged from 120 to1600 bp in the two breeds.. Genetic variation indexes, including effective number of alleles, Shannon index, Nei’s gene diversity and standard genetic distance were estimated, using POPGene software. Generally, the estimated genetic variation indexes showed low levels of diversity in the two breeds. However, Nei's gene diversity and Shannon index estimation was observed almost two folds in native cattle compared to Holstein breed. Less levels of diversity in Holstein cattle may be because of applying intensive selection programs. Conversely, native cattle have been less affected by selection. Therefore, it seems that Mazandaranian native cattle probably are better for breeding programs than Holstein cattle. Results showed that ISSR Markers are reliable and can be used in genetic diversity investigations.

  9. 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.

  10. 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.

  11. 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].

  12. 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.

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

    Science.gov (United States)

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

    2015-10-01

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

  14. Endemic and widespread coral reef fishes have similar mitochondrial genetic diversity.

    Science.gov (United States)

    Delrieu-Trottin, Erwan; Maynard, Jeffrey; Planes, Serge

    2014-12-22

    Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability. PMID:25355471

  15. Genetic diversity in natural populations of Theobroma subincanum Mart. in the Brazilian Amazon.

    Science.gov (United States)

    Rivas, L H; Giustina, L D; Luz, L N; Karsburg, I V; Pereira, T N S; Rossi, A A B

    2013-01-01

    The genus Theobroma, recently reclassified in the family Malvaceae, comprises some species with high economic potential, including the cupuí, Theobroma subincanum Mart., which has not yet been domesticated, and whose genetics and population structure are mostly unknown. This study aimed to assess the population structure and genetic diversity in natural populations of T. subincanum Mart., using inter-simple sequence repeat (ISSR) markers. A total of 59 individuals were sampled in three geographically separate populations, CFA, CMN, and CPT. Nei's genetic distance was estimated to characterize populations with the use of 13 polymorphic primers. The analysis of molecular variance revealed that the variability between populations (51.71%) was higher than that within populations (48.29%). Among the three populations, CPT showed the highest diversity index and percentage of polymorphism. The ISSR molecular markers were efficient and presented sufficient polymorphism to estimate genetic diversity in populations of T. subincanum Mart. PMID:24301761

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

    Directory of Open Access Journals (Sweden)

    Toraj KHABIRI

    2013-02-01

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

  17. 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.

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

    Science.gov (United States)

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

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

  20. Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.

    Science.gov (United States)

    Pacioni, Carlo; Hunt, Helen; Allentoft, Morten E; Vaughan, Timothy G; Wayne, Adrian F; Baynes, Alexander; Haouchar, Dalal; Dortch, Joe; Bunce, Michael

    2015-12-01

    The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000-4000 years in association with a dramatic population decline. In addition, we obtained near-complete 11-loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of 'new' microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current-day conservation strategies. PMID:26497007

  1. 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

  2. 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.

  3. Induced genetic diversity in mungbean (Vigna radiata L. Wilczek)

    International Nuclear Information System (INIS)

    Variability and genetic divergence for 8 economically important metric traits were studied in 34 micromutants of mungbean and 2 base genotypes. Primary branches, pods per cluster and clusters per plant showed high heritability with high genetic advance. On the basis of D2-values, micromutants could be grouped into 9 clusters, indicating that mutation is effective in creating genetic divergence. Primary branches, pods per cluster and days to maturity contributed maximum to the divergence of the micromutants. Thus hybridization among the selected micro-mutants would have maximum chance for generation of variability with transgressive segregants of partical utility. (author). 5 tabs., 6 refs

  4. Description and analysis of genetic diversity among squash accessions

    Directory of Open Access Journals (Sweden)

    Athanasios L. Tsivelikas

    2009-04-01

    Full Text Available 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.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 agricultores 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".

  5. 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.

  6. Population structure and genetic diversity in Gynaikothrips uzeli (Thysanoptera: Phlaeothripidae): is there a correlation between genetic and geographic proximity?

    Science.gov (United States)

    Mascarenhas, A L S; Waldschmidt, A M; Silva, J C

    2015-01-01

    Gynaikothrips uzeli (Thysanoptera: Phlaeothripidae) is a minuscule insect species, which forms galls, is subsocial, and parthenogenetic. It is associated with Ficus benjamina L. (Moraceae) and has a pantropical occurrence. The paucity of genetic studies on the order Thysanoptera led us to use inter-simple sequence repeat molecular marker to assess intra- and inter-gall, as well as intra- and inter-site, genetic variability and population structure of G. uzeli. Analyses indicated low genetic variability, probably related to haplodiploidy, genetic drift, the galling habit, and the low dispersal ability of G. uzeli. Populations were highly structured, with higher variation within populations than among them. Geographic distance does not appear to affect structure and genetic diversity, the latter being influenced by G. uzeli's bioecological traits, by numerous introductions during a short period, and by a possible recent, common ancestry. PMID:26345912

  7. Assessing the Genetic Diversity in Crops with Molecular Markers: Theory and Experimental Results with CIMMYT Wheat and Maize Elite Germplasm and Genetic Resources

    OpenAIRE

    Reif, Jochen Christoph

    2004-01-01

    Genetic diversity is a valuable natural resource and plays a key role in future breeding progress. Germplasm collections as a source of genetic diversity must be well-characterized for an efficient management and effective exploitation. The advent of PCR-based molecular markers such as sim-ple sequence repeats (SSRs) has created an opportunity for fine-scale genetic characterization of germplasm collections. The objective of this research was to optimize the utilization of genetic re-sources ...

  8. 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.

  9. 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...

  10. 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.

  11. Molecular Genetic Diversity of the Gyeongju Donggyeong Dog in Korea

    OpenAIRE

    Lee, Eun-Woo; CHOI, Seong-Kyoon; CHO, Gil-Jae

    2014-01-01

    The present study was conducted to analyze the genetic characteristics of the Donggyeong dog and establish parentage conservation systems for it by using 10 microsatellite markers recommended by the International Society for Animal Genetics (ISAG). A total of 369 dogs from 12 dog breeds including the Donggyeong dog were genotyped using 10 microsatellite loci. The number of alleles per locus varied from 5 to 10 with a mean value of 7.6 in the Donggyeong dog. The observed hete...

  12. Genetic diversity of Sardinian goat population based on microsatellites

    Directory of Open Access Journals (Sweden)

    A. Carta

    2010-01-01

    Full Text Available During the last century, the selection for production traits of the main livestock species has led to a reduction in number of local populations with consequent loss of genetic variability. In Sardinia, the genetic improvement strategy has been based on selection for the local pure breed in sheep, whereas in the other species (cattle, swine and goat, an often unplanned crossbreeding with improved breeds has been applied.

  13. Genetic diversity among sugarcane (Saccharum spp.) varieties using molecular markers

    OpenAIRE

    John J. Riascos; Jorge I. Victoria; Fernando Angel

    2007-01-01

    The genetic base of today's sugarcane cultivars appears to be narrow and could be the reason for current slow progress in improving sugarcane crops. Sixty-three primer pairs (producing 263 polymorphic fragments) flanking simple sequence repeats or micro-satellites were used for assessing the genetic variability of five S. officinarum clones and 33 sugarcane cultivars used in CENICAÑA breeding projects, selected for their economic and agronomic im-portance in several Central and South-American...

  14. Molecular markers and genetic diversity of Plasmodium vivax

    OpenAIRE

    Cristiana Ferreira Alves de Brito; Marcelo Urbano Ferreira

    2011-01-01

    Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable molecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers...

  15. Genetic diversity in mutated and non-mutated rice varieties.

    Science.gov (United States)

    Naeem, M; Ghouri, F; Shahid, M Q; Iqbal, M; S Baloch, F; Chen, L; Allah, S; Babar, M; Rana, M

    2015-01-01

    We studied the genetic variability due to mutation induced by ?-rays (10, 15, and 20 Kr) on various traits of twelve rice genotypes. Mutated and non-mutated seeds were sown in the field between July 2013 and 2014 using a split plot design. Yield and yield-related trait data was recorded, which showed significant (P genetic variability in the existing germplasm. PMID:26681058

  16. Spectrum of genetic diversity and networks of clonal organisms

    OpenAIRE

    Rozenfeld, Alejandro F.; Arnaud-Haond, Sophie; Hernández-García, Emilio; Eguíluz, Víctor M; Matías, Manuel A; Serrão, Ester A.; Duarte, Carlos M.

    2007-01-01

    Clonal reproduction characterizes a wide range of species including clonal plants in terrestrial and aquatic ecosystems, and clonal microbes, such as bacteria and parasitic protozoa, with a key role in human health and ecosystem processes. Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models a...

  17. 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.

  18. 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)

  19. Genetic diversity in different populations of sloths assessed by DNA fingerprinting

    Directory of Open Access Journals (Sweden)

    MORAES N.

    2002-01-01

    Full Text Available In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 ± 0.07 to 0.87 ± 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations.

  20. 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.

  1. Species and genetic diversity in the genus Drosophila inhabiting the Indian subcontinent

    Indian Academy of Sciences (India)

    Bashisth N. Singh

    2015-06-01

    Biodiversity is the sum total of all living things on the earth with particular reference to the profound variety in structure, function and genetic constitution. It includes both number and frequency of species or genes in a given assemblage and the variety of resulting ecosystems in a region. It is usually considered at three different levels: genetic, species and ecological diversities. Genus Drosophila belongs to the family Drosophilidae (class Insecta, order Diptera), characterized by rich species diversity at global level and also in India, which is a megadiverse country. At global level, more than 1500 species have been described and several thousands estimated. Hawaiian Islands are particularly rich in species diversity with more than 500 species which provides a unique opportunity to study evolution in genus Drosophila. About 150 species of Drosophila have been reported from India. Certain species of Drosophila found in India have been investigated for genetic diversity within the species. In this regard, Drosophila ananassae is noteworthy. It is a cosmopolitan and domestic species with common occurrence in India and is endowed with many genetic peculiarities. Population genetics and evolutionary studies in this species have revealed as to how genetic diversity within a species play an important role in adaptation of populations to varying environments. In addition, the work carried on D. melanogaster, D. nasuta, D. bipectinata and certain other species in India has shown that these species vary in degree and pattern of genetic diversity, and have evolved different mechanisms for adjusting to their environments. The ecological adaptations to various kinds of stress studied in certain species of Drosophila inhabiting the Indian subcontinent are also discussed.

  2. The Systems Genetics Resource: A Web Application to Mine Global Data for Complex Disease Traits

    OpenAIRE

    Van Nas, Atila; Pan, Calvin; Ingram-Drake, Leslie A; Ghazalpour, Anatole; Drake, Thomas A; Sobel, Eric M.; Papp, Jeanette C; Lusis, Aldons J

    2013-01-01

    The Systems Genetics Resource (SGR) (http://systems.genetics.ucla.edu) is a new open-access web application and database that contains genotypes and clinical and intermediate phenotypes from both human and mouse studies. The mouse data include studies using crosses between specific inbred strains and studies using the Hybrid Mouse Diversity Panel. SGR is designed to assist researchers studying genes and pathways contributing to complex disease traits, including obesity, diabetes, atherosclero...

  3. 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.

  4. 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.

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

    Science.gov (United States)

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

    2009-07-01

    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. PMID:21637518

  6. 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.

  7. Demographic history and the low genetic diversity in Dipteryx alata (Fabaceae) from Brazilian Neotropical savannas.

    Science.gov (United States)

    Collevatti, R G; Telles, M P C; Nabout, J C; Chaves, L J; Soares, T N

    2013-08-01

    Genetic effects of habitat fragmentation may be undetectable because they are generally a recent event in evolutionary time or because of confounding effects such as historical bottlenecks and historical changes in species' distribution. To assess the effects of demographic history on the genetic diversity and population structure in the Neotropical tree Dipteryx alata (Fabaceae), we used coalescence analyses coupled with ecological niche modeling to hindcast its distribution over the last 21?000 years. Twenty-five populations (644 individuals) were sampled and all individuals were genotyped using eight microsatellite loci. All populations presented low allelic richness and genetic diversity. The estimated effective population size was small in all populations and gene flow was negligible among most. We also found a significant signal of demographic reduction in most cases. Genetic differentiation among populations was significantly correlated with geographical distance. Allelic richness showed a spatial cline pattern in relation to the species' paleodistribution 21?kyr BP (thousand years before present), as expected under a range expansion model. Our results show strong evidences that genetic diversity in D. alata is the outcome of the historical changes in species distribution during the late Pleistocene. Because of this historically low effective population size and the low genetic diversity, recent fragmentation of the Cerrado biome may increase population differentiation, causing population decline and compromising long-term persistence. PMID:23591520

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    2009-01-01

    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. PMID:21637518

  10. Multiple factors affect diversity and abundance of ammonia-oxidizing microorganisms in iron mine soil.

    Science.gov (United States)

    Xing, Yi; Si, Yan-Xiao; Hong, Chen; Li, Yang

    2015-07-01

    Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. In this study, four soil samples collected from a desert zone in an iron-exploration area and others from farmland and planted forest soil in an iron mine surrounding area. We analyzed the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in iron-mining area near the Miyun reservoir using ammonia monooxygenase. A subunit gene (amoA) as molecular biomarker. Quantitative polymerase chain reaction was applied to explore the relationships between the abundance of AOA and AOB and soil physicochemical parameters. The results showed that AOA were more abundant than AOB and may play a more dominant role in the ammonia-oxidizing process in the whole region. PCR-denaturing gradient gel electrophoresis was used to analyze the structural changes of AOA and AOB. The results showed that AOB were much more diverse than AOA. Nitrosospira cluster three constitute the majority of AOB, and AOA were dominated by group 1.1b in the soil. Redundancy analysis was performed to explore the physicochemical parameters potentially important to AOA and AOB. Soil characteristics (i.e. water, ammonia, organic carbon, total nitrogen, available phosphorus, and soil type) were proposed to potentially contribute to the distributions of AOB, whereas Cd was also closely correlated to the distributions of AOB. The community of AOA correlated with ammonium and water contents. These results highlight the importance of multiple drivers in microbial niche formation as well as their affect on ammonia oxidizer composition, both which have significant consequences for ecosystem nitrogen functioning. PMID:25860433

  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. Global and local genetic diversity at two microsatellite loci in Plasmodium vivax parasites from Asia, Africa and South America

    DEFF Research Database (Denmark)

    Schousboe, Mette L; Ranjitkar, Samir; Rajakaruna, Rupika S; Amerasinghe, Priyanie H; Konradsen, Flemming; Morales, Francisco; Ord, Rosalyn; Pearce, Richard; Leslie, Toby; Rowland, Mark; Gadalla, Nahla; Bygbjerg, Ib C; Alifrangis, Michael; Roper, Cally

    2014-01-01

    BACKGROUND: Even though Plasmodium vivax has the widest worldwide distribution of the human malaria species and imposes a serious impact on global public health, the investigation of genetic diversity in this species has been limited in comparison to Plasmodium falciparum. Markers of genetic diversity are vital to the evaluation of drug and vaccine efficacy, tracking of P. vivax outbreaks, and assessing geographical differentiation between parasite populations. METHODS: The genetic diversity of ...

  13. Genetic diversity analysis of sugarcane ( Saccharum sp.) clones using simple sequence repeat markers of sugarcane and rice

    OpenAIRE

    G.Banumathi , V.Krishnasamy, M.Maheswaran, R.Samiyappan, P.Govindaraj and N.Kumaravadivel

    2010-01-01

    Molecular markers are powerful tools, which help in differentiating plant varieties at the DNA level and have been widelyused for genetic diversity studies in a number of crop species'. Understanding the genetic diversity of available clones of S.officinarum and S. spontaneum will be helpful in breeding programs. In the present study, a set of 48 sugarcane clones fromNational Hybridization Garden, Sugarcane Breeding Institute, Coimbatore was subjected to genetic diversity analysisinvolving 40...

  14. 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...

  15. Reduction of Negative and Positive Association Rule Mining and Maintain Superiority of Rule Using Modified Genetic Algorithm

    OpenAIRE

    Nikhil Jain,Vishal Sharma,Mahesh Malviya

    2012-01-01

    Association rule mining play important rule inmarket data analysis and also in medical diagnosisof correlated problem. For the generation ofassociation rule mining various technique are usedsuch as Apriori algorithm, FP-growth and treebased algorithm. Some algorithms are wonderperformance but generate negative association ruleand also suffered from Superiority measureproblem. In this paper we proposed a multi-objectiveassociation rule mining based on genetic algorithmand Euclidean distance fo...

  16. Impact of mutation type and amplicon characteristics on genetic diversity measures generated using a high-resolution melting diversity assay.

    Science.gov (United States)

    Cousins, Matthew M; Donnell, Deborah; Eshleman, Susan H

    2013-01-01

    We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology. PMID:23178437

  17. 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.

  18. Genetic diversity and population structure of Siberian apricot (Prunus sibirica L.) in China.

    Science.gov (United States)

    Li, Ming; Zhao, Zhong; Miao, Xingjun; Zhou, Jingjing

    2014-01-01

    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. PMID:24384840

  19. Suitability of blood protein polymorphisms in assessing genetic diversity in indigenous sheep in Kenya

    International Nuclear Information System (INIS)

    Knowledge of genetic diversity is important as it forms the basis for designing breeding programmes and making rational decisions on sustainable utilization of animal genetic resources. This study was designed to assess the efficiency of blood protein polymorphism as a rapid tool for assessing genetic diversity, using seven blood proteins (transferrin, albumin, haemoglobin, esterase A, esterase C, carbonic anhydrase and X-protein) and 457 indigenous fat-tailed (351) and fat-rumped (106) hair sheep in Kenya from 7 populations, with 40 Merino as controls. Transferrin was analysed using polyacrylamide gel electrophoresis and starch gel electrophoresis was used to analyse the other six loci. Of the seven loci analysed, two - carbonic anhydrase and X-protein - could not be interpreted. The five interpretable markers, however, showed low levels of polymorphism in allele numbers and heterozygosity. Multilocus mean FST values of 0.083 indicated a moderate genetic differentiation between the populations analysed. The Dm and Da genetic distance estimates showed the indigenous sheep populations in Kenya to be closely related genetically, with the dendrogram failing to resolve indigenous sheep into fat-tailed sheep and fat-rumped hair sheep. Due to its costs and modest equipment demands, blood protein polymorphism can be used as a rapid tool to assess genetic diversity and prioritize breeds to be analysed by microsatellite DNA markers. (author)

  20. Phosphorylation networks regulating JNK activity in diverse genetic backgrounds

    DEFF Research Database (Denmark)

    Bakal, Chris; Linding, Rune

    2008-01-01

    Cellular signaling networks have evolved to enable swift and accurate responses, even in the face of genetic or environmental perturbation. Thus, genetic screens may not identify all the genes that regulate different biological processes. Moreover, although classical screening approaches have succeeded in providing parts lists of the essential components of signaling networks, they typically do not provide much insight into the hierarchical and functional relations that exist among these components. We describe a high-throughput screen in which we used RNA interference to systematically inhibit two genes simultaneously in 17,724 combinations to identify regulators of Drosophila JUN NH(2)-terminal kinase (JNK). Using both genetic and phosphoproteomics data, we then implemented an integrative network algorithm to construct a JNK phosphorylation network, which provides structural and mechanistic insights into the systems architecture of JNK signaling.

  1. Effect of Genetically Modified Poplars on Soil Microbial Communities during the Phytoremediation of Waste Mine Tailings?†

    OpenAIRE

    Hur, Moonsuk; Kim, Yongho; Song, Hae-Ryong; Kim, Jong Min; Choi, Young Im; Yi, Hana

    2011-01-01

    The application of transgenic plants to clean up environmental pollution caused by the wastes of heavy metal mining is a promising method for removing metal pollutants from soils. However, the effect of using genetically modified organisms for phytoremediation is a poorly researched topic in terms of microbial community structures, despite the important role of microorganisms in the health of soil. In this study, a comparative analysis of the bacterial and archaeal communities found in the rh...

  2. 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 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)

  3. 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 utilisable 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. The improvement of crops that lack botanical seeds necessitate therefore 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 the economies of time and space 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 the 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 cellular and tissue biology to achieve homozygosity, minimise or eliminate chimeras, and significantly shorten the duration of the generation of mutants. Additionally, the 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, contributes 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 the tagging of mutation events in the genomes of vegetatively propagated crops are also discussed. (author)

  4. Genetic diversity in Algerian sheep breeds, using microsatellite markers

    International Nuclear Information System (INIS)

    Two breeds - Ouled-Djellal and Hamra (85 animals) - were genotyped for 12 microsatellites using PCR and sequencing. Allele number and frequency were calculated, and 141 different alleles were found for these microsatellites, reflecting high genetic variability within these breeds. This study is being extended to other Algerian breeds to estimate variability and genetic distances between them. In parallel, blood samples from the various breeds are being collected to build up a DNA bank. The results should support establishment of a strategy to promote the use and development of locally adapted sheep resources. (author)

  5. The Loss of Genetic Diversity: An Impending Global Issue.

    Science.gov (United States)

    Pierce, James P.

    Definitions of biosphere and ecosystem are provided as the basis for understanding a problem that threatens to become (or already is) a global issue, namely, human activity which results in reducing the diversity of life forms present in the biosphere as an ecosystem. Two aspects of this problem are: (1) the growth of human populations worldwide…

  6. 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.

  7. 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.

  8. 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.

  9. Reconstruction time of a mine through reliability analysis and genetic algorithms

    Scientific Electronic Library Online (English)

    M., Kumral.

    2009-05-01

    Full Text Available A mining system consists of many sub-systems such as drilling, blasting, loading, hauling, ventilation, hoisting and supporting. During mining operation, these sub-systems may experience various problems that stop the operation because of possible environmental, equipment and safety issues. In order [...] to ensure delivery contracts in the required quality and safe mining medium, the operation should be, at least, performed in the specified reliability level of the system. If the system reliability decreases below the specified level, there will be safety and financial losses for the mining company. Therefore, the mine should be maintained by a reconstruction procedure to guarantee the operation continuity. Given that each sub-system has a different reliability function and maintenance cost, the determination of reconstruction time will be a complicated decision making problem. In this paper, the determination of reconstruction time is formulated as a nonlinear optimization problem and solved by genetic algorithms (GA). A case study was conducted to demonstrate the performance of the approach for an underground operation. The results showed that the approach could be used to determine the best action time.

  10. Bovine coronaviruses from the respiratory tract: Antigenic and genetic diversity

    Science.gov (United States)

    Bovine corona viruses (BoCV) isolated from respiratory tract, nasal swab and broncho alveolar washing fluid samples were evaluated for genetic and antigenic differences. These BoCV from the respiratory tract of healthy and clinically ill cattle with BRD signs were compared to reference and vaccine ...

  11. Glacial refugia and modern genetic diversity of 22 western North American tree species.

    Science.gov (United States)

    Roberts, David R; Hamann, Andreas

    2015-04-01

    North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711

  12. Genetic diversity of Tunisian figs (Ficus carica L.) as revealed by nuclear microsatellites.

    Science.gov (United States)

    Saddoud, O; Chatti, K; Salhi-Hannachi, A; Mars, M; Rhouma, A; Marrakchi, M; Trifi, M

    2007-09-01

    The present study portrays the achievement of the genetic polymorphism surveying and the establishment of an ecotypes identification key on the basis of simple sequence repeats data. Seventy-two Tunisian fig ecotypes in situ and ex situ conserved were analyzed using six microsatellite loci. A total of 58 alleles and 124 genotypes were revealed and permitted to evidence high degree of genetic diversity mainly explained at the intra group level. Cluster analysis based on genetic distances proved that a typical continuous genetic diversity characterizes the local germplasm. In addition, the microsatellite multilocus genotyping has permitted to unambiguously distinguish 70 well-defined ecotypes (resolving power of 97.22%). Data are discussed in relation with the reliability of the used markers to check the conformity of the plant material and to rationally manage the conservation of this crop. PMID:17850599

  13. Genetic Diversity of Pancreatic Ductal Adenocarcinoma and Opportunities for Precision Medicine.

    Science.gov (United States)

    Knudsen, Erik S; O'Reilly, Eileen M; Brody, Jonathan R; Witkiewicz, Agnieszka K

    2016-01-01

    Patients with pancreatic ductal adenocarcinoma (PDA) have a poor prognosis despite new treatments; approximately 7% survive for 5 years. Although there have been advances in systemic, primarily cytotoxic, therapies, it has been a challenge to treat patients with PDA using targeted therapies. Sequence analyses have provided a wealth of information about the genetic features of PDA and have identified potential therapeutic targets. Preclinical and early-phase clinical studies have found specific pathways could be rationally targeted; it might also be possible to take advantage of the genetic diversity of PDAs to develop therapeutic agents. The genetic diversity and instability of PDA cells have long been thought of as obstacles to treatment, but are now considered exploitable features. We review the latest findings in pancreatic cancer genetics and the promise of targeted approaches in PDA therapy. PMID:26385075

  14. 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.

    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 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.

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

    OpenAIRE

    Aiqing Ji; Yina Wang; Guoliang Wu; Wenjiang Wu; Hongyan Yang; Qihai Wang

    2014-01-01

    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...

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

    OpenAIRE

    Tang, G Q; Xue, J.; Lian, M. J.; R. F. Yang; Liu, T. F.; Z. Y. Zeng; Jiang, A. A.; Jiang, Y.Z.; L. Zhu; L. Bai; 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...

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Almeida Sabrina E. Matos

    2000-01-01

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

  19. 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.

  20. Assessment of genetic diversity of Haloxylon salicornicum genotypes, a native plant of Kuwait

    OpenAIRE

    F. AL-SALAMEEN; H. AL-HASHASH; S. AL-AMAD

    2013-01-01

    ABSTRACT Haloxylon salicornicum is one of the most important native desert flora scattered in Kuwait. Despite its ecological and economical importance, H. salicornicum is endangered by severe loss. Unless great attention is paid towards its protection and documentation, it faces the danger of extinction. Due to lack of information on the genetic diversity of H. salicornicum, this study attempts to analyse samples collected from nine representative locations from the Kuwait desert. Diversity a...

  1. 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

  2. Genetic diversity of anaplasma species major surface proteins and implications for anaplasmosis serodiagnosis and vaccine development

    OpenAIRE

    De La Fuente, J; Lew, A.; Lutz, H; Meli, M. L.; Hofmann-Lehmann, R; Shkap, V; Molad, T.; Mangold, A J; Almazán, C; Naranjo,V.; Gortázar, C; Torina, A; S. Caracappa; García-Pérez, A L; Barral, M

    2005-01-01

    The genus Anaplasma (Rickettsiales: Anaplasmataceae) includes several pathogens of veterinary and human medical importance. An understanding of the diversity of Anaplasma major surface proteins (MSPs), including those MSPs that modulate infection, development of persistent infections, and transmission of pathogens by ticks, is derived in part, by characterization and phylogenetic analyses of geographic strains. Information concerning the genetic diversity of Anaplasma spp. MSPs will likely in...

  3. The Effect of Board Directors from Countries with Different Genetic Diversity Levels on Corporate Performance

    OpenAIRE

    Delis, Manthos; Gaganis, Chrysovalantis; Hasan, Iftekhar; Pasiouras, Fotios

    2015-01-01

    We link genetic diversity in the country of origin of firms’ board members with corporate performance via board members’ nationality. We hypothesize that our approach captures deep-rooted differences in cultural, institutional, social, psychological, physiological, and other traits that cannot be captured by other recently measured indices of diversity. Using a panel of firms listed in the North American and U.K. stock markets, we find that adding board directors from countries with different...

  4. Characterization of genetic resources of onion (Allium cepa L.) from the Spanish secondary centre of diversity

    OpenAIRE

    Mallor Giménez, Cristina; Carravedo Fantova, Miguel; Estopañán Muñoz, Gloria; Mallor, F.

    2011-01-01

    Onions are the second most-valuable vegetable in the world. Despite its global culinary and economic significance, the knowledge of genetic diversity and resources is limited. The aim of this study was to morphologically and physico-chemically characterize eighty-six onion landraces from Spain, part of the secondary Mediterranean Centre of diversity. The evaluated traits in the bulb included: weight, shape, firmness, soluble solids content (SSC), pungency and sugars content (gluco...

  5. Genetic and morphological diversity of the genus Lampetra (Petromyzontidae) in Europe

    OpenAIRE

    Mateus, Catarina Sofia Pereira

    2013-01-01

    This study aims at contributing to the knowledge on genetic and morphological diversity of European Lampetra. Mitochondrial DNA was used to infer the phylogeography of this genus, and further define conservation units in the Iberian Peninsula. Morphological data was then combined to describe three new species endemic to Portugal. These results support evidence of the high diversity of the Iberian Peninsula, a region that acted as glacial refugium during the Pleistocene glaciations. The analys...

  6. Patterns of genetic and eco-geographical diversity in Spanish barleys

    OpenAIRE

    Yahiaoui, Samia; igartua Arregui, Ernesto; Moralejo, María Ángeles; Ramsay, L.; Molina-Cano, José Luis; Ciudad, Francisco J.; Lasa Dolhagaray, José Manuel; Gracia Gimeno, María Pilar; Casas Cendoya, Ana María

    2008-01-01

    The pool of Western Mediterranean landraces has been under-utilised for barley breeding so far. The objectives of this study were to assess genetic diversity in a core collection of inbred lines derived from Spanish barley landraces to establish its relationship to barleys from other origins, and to correlate the distribution of diversity with geographical and climatic factors. To this end, 64 SSR were used to evaluate the polymorphism among 225 barley (Hordeum vulgare ssp. vulgare) genotypes...

  7. SPAR profiles and genetic diversity amongst pomegranate (Punica granatum L.) genotypes

    OpenAIRE

    Ranade, S. A.; Rana, T. S.; Narzary, D.

    2009-01-01

    We are interested in studying the distribution and range of diversity amongst the pomegranates in India. Single Primer Amplification Reaction (SPAR) profiling using Random Amplified Polymorphic DNA (RAPD) and Directed Amplification of Minisatellite DNA (DAMD) methods enabled the determination of the genetic diversity amongst a total of 64 Indian pomegranate genotypes including 15 wild, 34 semi-wild and 14 cultivated types. SPAR profile data were scored for the computation of pairwise distance...

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

    DEFF Research Database (Denmark)

    Pham, Lan Doan; Do, Duy Ngoc; Binh, Nguyen Trong; Nam, Le Quang; Ba, Nguyen Van; Thuy, Tran Thi Thu; Hoan, Tran Xuan; Cuong, Vu Chi; Kadarmideen, Haja

    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 o...

  9. Intraspecific genetic diversity and composition modify species-level diversity-productivity relationships

    OpenAIRE

    Schöb, Christian; Kerle, Sarah; Karley, Alison J.; Morcillo, Luna; Pakeman, Robin J; Newton, Adrian C.; Brooker, Rob W

    2015-01-01

    Biodiversity regulates ecosystem functions such as productivity, and experimental studies of species mixtures have revealed selection and complementarity effects driving these responses. However, the impacts of intraspecific genotypic diversity in these studies are unknown, despite it forming a substantial part of the biodiversity. In a glasshouse experiment we constructed plant communities with different levels of barley (Hordeum vulgare) genotype and weed species diversity and assessed thei...

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

    Directory of Open Access Journals (Sweden)

    Geo Coppens d’Eeckenbrugge

    2011-12-01

    Full Text Available 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’ individual motivations and actions, and overlooking the effects of farmer’s social organization per se. After reviewing common shortcomings in studies on sorghum and maize, this article analyzes how social anthropology, through the analysis of intermarriage, residence and seed inheritance practices, can contribute to studies on crop genetic diversity in situ. Crop varieties are thus considered social objects and socially based sampling strategies can be developed. Such an approach is justified because seed exchange is built upon trust and as such seed systems are embedded in a pre-existing social structure and centripetally oriented as a function of farmers’ social identity. The strong analogy between farmers’ cultural differentiation and crop genetic differentiation, both submitted to the same vertical transmission processes, allows proposing a common methodological framework for social anthropology and crop population genetics, where the classical interaction between genetic and environmental factors, G × E, is replaced by a three-way interaction G × E × S, where “S” stands for the social differentiation factors.

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

    Science.gov (United States)

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

    2015-01-01

    Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security. PMID:25468001

  12. 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

  13. Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago.

    Science.gov (United States)

    Bottin, L; Verhaegen, D; Tassin, J; Olivieri, I; Vaillant, A; Bouvet, J M

    2005-06-01

    We present a study of the genetic diversity and structure of a tropical tree in an insular system. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. A total of 431 individuals over 17 populations were analysed for eight polymorphic microsatellite loci. The number of alleles per locus ranged from 3 to 33 and the observed heterozygosity per population ranged from 0.01 in Mare to 0.74 in Ile des Pins. The genetic diversity was lowest in the most recent islands, the Loyautes, and highest in the oldest island, Grande Terre, as well as the nearby small Ile des Pins. Significant departures from panmixia were observed for some loci-population combinations (per population FIS = 0-0.03 on Grande-Terre and Ile des Pins, and 0-0.67 on Loyautes). A strong genetic differentiation among all islands was observed (FST = 0.22), and the amount of differentiation increased with geographic distance in Iles Loyaute and in Grande Terre. At both population and island levels, island age and isolation seem to be the main factors influencing the amount of genetic diversity. In particular, populations from recent islands had large average FIS that could not be entirely explained by null alleles or a Wahlund effect. This result suggests that, at least in some populations, selfing occurred extensively. Conclusively, our results indicate a strong influence of insularity on the genetic diversity and structure of Santalum austrocaledonicum. PMID:15910320

  14. 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.

  15. Identifying Genetic Hotspots by Mapping Molecular Diversity of Widespread Trees: When Commonness Matters.

    Science.gov (United States)

    Souto, Cintia P; Mathiasen, Paula; Acosta, María Cristina; Quiroga, María Paula; Vidal-Russell, Romina; Echeverría, Cristian; Premoli, Andrea C

    2015-01-01

    Conservation planning requires setting priorities at the same spatial scale at which decision-making processes are undertaken considering all levels of biodiversity, but current methods for identifying biodiversity hotspots ignore its genetic component. We developed a fine-scale approach based on the definition of genetic hotspots, which have high genetic diversity and unique variants that represent their evolutionary potential and evolutionary novelties. Our hypothesis is that wide-ranging taxa with similar ecological tolerances, yet of phylogenetically independent lineages, have been and currently are shaped by ecological and evolutionary forces that result in geographically concordant genetic patterns. We mapped previously published genetic diversity and unique variants of biparentally inherited markers and chloroplast sequences for 9 species from 188 and 275 populations, respectively, of the 4 woody dominant families of the austral temperate forest, an area considered a biodiversity hotspot. Spatial distribution patterns of genetic polymorphisms differed among taxa according to their ecological tolerances. Eight genetic hotspots were detected and we recommend conservation actions for some in the southern Coastal Range in Chile. Existing spatially explicit genetic data from multiple populations and species can help to identify biodiversity hotspots and guide conservation actions to establish science-based protected areas that will preserve the evolutionary potential of key habitats and species. PMID:26245788

  16. Genetic diversity of high-elevation populations of an endangered medicinal plant

    OpenAIRE

    Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

    2015-01-01

    Despite its wide distribution across the entire Himalayan range, the current status of Podophyllum hexandrum, a highly important anti-cancerous herb, remains endangered. Genetic diversity characterization of 24 populations comprising of 209 individuals representing the whole of the Indian Himalayas revealed that regardless of geographic location, all of the populations are intermixed and are composed broadly of two types of genetic populations. Our findings also suggested that these populatio...

  17. Molecular and agronomic assessment of genetic diversity and hybrid breeding in triticale

    OpenAIRE

    Tams, Swenja H.

    2006-01-01

    Knowledge of the genetic diversity of a species is of paramount importance for the choice of crossing parents in line and hybrid breeding. Genetic distance (GD) estimates based on molecular markers proved to be well suited for direct exploration of the relationship within a germplasm pool. Triticale hybrid breeding and heterosis have received increasing attention in recent years. Hybrid seed production is highly attractive for autogamous species because of the built-in variety protection of h...

  18. Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy

    OpenAIRE

    Navascués, M.; Emerson, B. C.

    2009-01-01

    Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated popu...

  19. Optimization of combined genetic gain and diversity for collection and deployment of seed orchards crops.

    Czech Academy of Sciences Publication Activity Database

    Funda, T.; Lstib?rek, M.; Lachout, Petr; Klápšt?, J.; El-Kassaby, Y. A.

    2009-01-01

    Ro?. 5, ?. 4 (2009), s. 583-593. ISSN 1614-2942 Grant ostatní: GA ?R(CZ) GA201/08/0486 Institutional research plan: CEZ:AV0Z10750506 Keywords : Genetic Gain * Seed orchard * Optimization Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 2.018, year: 2009 http://library.utia.cas.cz/separaty/2009/SI/lachout-optimization of combined genetic gain and diversity for collection and deployment of seed orchards crops.pdf

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

    OpenAIRE

    Sofalian, Omid; Rasool ASGHARI-ZAKARIA; Nasser ZARE; Toraj KHABIRI

    2013-01-01

    Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ? type of geliadins...

  1. 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.

  2. Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed

    OpenAIRE

    Berthouly-Salazar, Cécile; Thévenon, Sophie; Van, Thu Nhu; Nguyen, Binh Trong; Pham, Lan Doan; Chi, Cuong Vu; Maillard, Jean-Charles

    2012-01-01

    The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H’mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H’mong pig population from Ha ...

  3. High levels of genetic diversity in Penaeus monodon populations from the east coast of India

    OpenAIRE

    Khedkar, Gulab Dattarao; Reddy, A Chandrashekar; Ron, Tetszuan Benny; Haymer, David

    2013-01-01

    Quality production of the shrimp Penaeus monodon in hatchery operations depends heavily on the evaluation of genetic diversity and population structure of brood stocks. Mitochondrial DNA (mtDNA) sequences have been widely used to study genetic variability and relationships in many crustacean groups, and these same markers may be incorporated into evaluation studies of shrimp broods and populations. For this purpose we looked at variation in mitochondrial D-loop sequences as an indicator of ge...

  4. 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

  5. Methodological framework for projecting the potential loss of intraspecific genetic diversity due to global climate change

    OpenAIRE

    Pfenninger Markus; Bálint Miklós; Pauls Steffen U

    2012-01-01

    Abstract Background While research on the impact of global climate change (GCC) on ecosystems and species is flourishing, a fundamental component of biodiversity – molecular variation – has not yet received its due attention in such studies. Here we present a methodological framework for projecting the loss of intraspecific genetic diversity due to GCC. Methods The framework consists of multiple steps that combines 1) hierarchical genetic clustering methods to define comparable units of infer...

  6. Founder events predict changes in genetic diversity during human-mediated range expansions

    OpenAIRE

    Uller, T; Leimu, R.

    2011-01-01

    Intentional or accidental introduction of species to new locations is predicted to result in loss of genetic variation and increase the likelihood of inbreeding, thus reducing population viability and evolutionary potential. However, multiple introductions and large founder numbers can prevent loss of genetic diversity and may therefore facilitate establishment success and range expansion. Based on a meta-analysis of 119 introductions of 85 species of plants and animals, we here show a quanti...

  7. 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...

  8. 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

  9. 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.

  10. Genetic diversity of fungi closely associated with common reed

    OpenAIRE

    Wirsel, Stefan G. R.; Leibinger, Wolfgang; Ernst, Michael; Mendgen, Kurt

    2001-01-01

    Variation in endophytic fungal diversity closely associated with roots, stems and leaves of common reed (Phragmites australis) is reported at sites with different oxygen conditions. Fungi isolated from surface-sterilized reed tissue were identified and characterized by morphological and molecular methods including internal transcribed spacer (ITS)sequence analysis from two dry and two flooded sites at Lake Constance (Germany). Most isolates were ascomycetes, some basidiomycetes. There were di...

  11. Genetic and molecular diversity in nondeletion Hb H disease

    OpenAIRE

    1982-01-01

    Restriction endonuclease mapping of nondeletion alpha-thalassemia determinants from a variety of racial groups showed no detectable abnormalities within a 40-kilobase region of the zeta-alpha globin gene cluster. By using a zeta-specific probe, we defined three different types of interactions that give rise to Hb H disease, each involving a nondeletion alpha-thalassemia haplotype. mRNA analysis showed further diversity within these groups, indicating that there are at least three nondeletion ...

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

    OpenAIRE

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

    2011-01-01

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a mor...

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

    DEFF Research Database (Denmark)

    Bojesen, A.M.; Torpdahl, Mia; Christensen, H.; Olsen, J.E.; Bisgaard, M.

    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 charact...

  14. 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).

  15. 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.

  16. Genetic diversity of Lagerstroemia (Lythraceae) species assessed by simple sequence repeat markers.

    Science.gov (United States)

    He, D; Liu, Y; Cai, M; Pan, H T; Zhang, Q X; Wang, X Y; Wang, X J

    2012-01-01

    Lagerstroemia (crape myrtle) are famous ornamental plants with large pyramidal racemes, long flower duration, and diverse colors. However, little is known about the genetic structure and diversity of germplasm in Lagerstroemia. We genotyped 81 L. indica cultivars, five other species of Lagerstroemia, and 10 interspecific hybrids using 30 simple sequence repeat markers; 275 alleles were generated with a mean of nine alleles per locus. The mean polymorphism information content value, a measure of gene diversity, was 0.63, with a range from 0.25 to 0.86. The mean observed heterozygosity (0.51) tended to be lower than the mean expected heterozygosity (0.67). The mean F-statistics (F(ST), F(IS), and F(IT)) were 0.05, 0.20, and 0.24, respectively, indicating a high level of genetic variation among cultivars. Clustering analysis based on genetic distance divided the 96 genotypes into three distinct groups, which corresponded with their genetic backgrounds and geographic regions. L. indica cultivars and the other five L. species were grouped into different sub-clusters. Chinese and North American cultivars were divided into different clusters. These data about the genetic relationship among cultivars demonstrated the potential value of L. indica cultivars and other Lagerstroemia species for widening the genetic basis of breeding programs for this ornamental flower. PMID:23079847

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

    International Nuclear Information System (INIS)

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

  18. 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 it

  19. Y genetic variation and phenotypic diversity in health and disease

    OpenAIRE

    Case, Laure K; Teuscher, Cory

    2015-01-01

    Sexually dimorphic traits arise through the combined effects of sex hormones and sex chromosomes on sex-biased gene expression, and experimental mouse models have been instrumental in determining their relative contribution in modulating sex differences. A role for the Y chromosome (ChrY) in mediating sex differences outside of development and reproduction has historically been overlooked due to its unusual genetic composition and the predominant testes-specific expression of ChrY-encoded gen...

  20. GENETIC DIVERSITY OF FLEXIVIRUSES INFECTING POME FRUIT TREES

    OpenAIRE

    Gadiou, S; Kundu, JK; Paunovic, S; Garcia-Diez, P; Komorowska, B.; Gospodaryk, A; Handa, A.; Massart, S.; Birisik, N; Takur, PD; Polischuk, V

    2010-01-01

    Three amplicons corresponding to the variable genome regions of Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV) and Apple stem pitting virus (ASPV) were sequenced from different apple cultivars and geographic areas in Europe and Asia. Multiple alignments of nucleotide sequence of these isolates with those from databases showed a very high divergence. Genetic variability at the nucleotide level among ACSLV and ASPV isolates was very high, ranging from 83.5 to 85.0% an...

  1. 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...

  2. Molecular characterization and genetic diversity of Prunus rootstocks

    OpenAIRE

    Bouhadida, Mariem; Casas Cendoya, Ana María; Gonzalo Pascual, María José; Arús, Pere; Moreno Sánchez, María Ángeles; Gogorcena Aoiz, Yolanda

    2009-01-01

    Twenty microsatellite primer pairs, previously developed in peach, were used to characterize and to explore genetic relationships among 44 clones, representing three groups of rootstocks defined as: (1) Peach-based rootstocks (Prunus dulcis x P. persica, P. persica x P. davidiana); (2) Myrobalan - Marianna plums (P. cerasifera, and interspecific hybrids having P. cerasifera as a parent); and (3) Slow growing plums (P. insititia, P. domestica, and P. domestica x P. spinosa). Eighteen SSR marke...

  3. 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)

  4. Diversity, Epidemiology, and Genetics of Class D  -Lactamases

    OpenAIRE

    2009-01-01

    Class D ?-lactamase-mediated resistance to ?-lactams has been increasingly reported during the last decade. Those enzymes also known as oxacillinases or OXAs are widely distributed among Gram negatives. Genes encoding class D ?-lactamases are known to be intrinsic in many Gram-negative rods, including Acinetobacter baumannii and Pseudomonas aeruginosa, but play a minor role in natural resistance phenotypes. The OXAs (ca. 150 variants reported so far) are characterized by an important genetic ...

  5. 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...

  6. 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

  7. Development of molecular tools for characterization and genetic diversity analysis in Tunisian fig (Ficus carica) cultivars.

    Science.gov (United States)

    Chatti, Khaled; Baraket, Ghada; Ben Abdelkrim, Ahmed; Saddoud, Olfa; Mars, Messaoud; Trifi, Mokhtar; Salhi Hannachi, Amel

    2010-10-01

    Fig, Ficus carica L., is a useful genetic resource for commercial cultivation. In this study, RAPD (60), ISSR (48), RAMPO (63), and SSR (34) markers were compared to detect polymorphism and to establish genetic relationships among Tunisian fig tree cultivars. The statistical procedures conducted on the combined data show considerable genetic diversity, and the tested markers discriminated all fig genotypes studied. The identification key established on the basis of SSR permitted the unambiguous discrimination of cultivars and confirmed the reliability of SSR for fingerprinting fig genotypes. The study findings are discussed in relation to the establishment of a national reference collection that will aid in the conservation of Tunisian fig resources. PMID:20628809

  8. Nature and Extent of Genetic Diversity of Dengue Viruses Determined by 454 Pyrosequencing

    Science.gov (United States)

    Choudhury, Md Abu; Lott, William B; Banu, Shahera; Cheng, Anthony Youzhi; Teo, Yik-Ying; Ong, Rick Twee-Hee; Aaskov, John

    2015-01-01

    Dengue virus (DENV) populations are characteristically highly diverse. Regular lineage extinction and replacement is an important dynamic DENV feature, and most DENV lineage turnover events are associated with increased incidence of disease. The role of genetic diversity in DENV lineage extinctions is not understood. We investigated the nature and extent of genetic diversity in the envelope (E) gene of DENV serotype 1 representing different lineages histories. A region of the DENV genome spanning the E gene was amplified and sequenced by Roche/454 pyrosequencing. The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene. A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences, and the sequences of each constructed haplotype showed that the haplotypes segregated with the Sanger consensus sequence of the population from which they were drawn. Haplotypes determined through pyrosequencing identified a recombinant DENV genome that could not be identified through Sanger sequencing. Nucleotide level sequence diversities of DENV-1 populations determined from SNP analysis were very low, estimated from 0.009–0.01. There were also no stop codon, frameshift or non-frameshift mutations observed in the E genes of any lineage. No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5). Although our hypothesis that accumulation of deleterious mutations over time led to the extinction and replacement of DENV lineages was ultimately not supported by the data, our data does highlight the significant technical issues that must be resolved in the way in which population diversity is measured for DENV and other viruses. The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations. PMID:26566128

  9. 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.

  10. A molecular study of genetic diversity in shisham (Dalbergia Sissoo) plantation of NWFP, Pakistan

    International Nuclear Information System (INIS)

    Genetic diversity of 22 accessions of Dalbergia sissoo that were collected from the canal, road and farmer's field and forest sites of N.W.F.P, Pakistan has been studied, by using a finger printing technique 'RAPD' (Random Amplified Polymorphism DNA). Out of 20 primers OPA-2 was the primer that allows distinguishing the diseased and healthy accessions. The selected primer was used for identification and for establishing a profiling system to estimate genetic relationships and to evaluate the genetic variability among the accessions. A total of 126 DNA bands or fragments were amplified by using the primers. The UPGMA cluster analysis revealed 2 main clusters among 22 accessions of Dalbergia sissoo based on coefficient of similarity and dissimilarity. Overall 72% similarity and 98% dissimilarity were observed. Low level of genetic variation and high level of genetic relatedness occurred among the canal, road, farmer's field and forest sites. The accessions were closely related with each other and showed mix pattern of genetic diversity. Thus RAPD markers have the potential to characterize and establish genetic relationships among the accessions of Dalbergia sissoo. (author)

  11. 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.

  12. 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.

  13. Molecular Markers for Genetic Diversity Studies of European Hare (Lepus europaeus Pallas, 1778 Populations

    Directory of Open Access Journals (Sweden)

    Noémi Soós

    2015-05-01

    Full Text Available The purpose of this article is to give an overview of different molecular techniques which have been used in studies concerning population genetic issues of Lepus species and specifically of L. europaeus. The importance of these researches is ever-growing as the European populations of the brown hare have suffered several falloffs as a consequent upon both natural and anthropogenic effects. With developing tools and techniques molecular genetics have become the centrepiece of population genetics and conservation biology. Nucleic acid methods based on both bi- and uniparentally inherited DNA (allozymes, microsatellites, Y chromosome, mtDNA are often used to study genetic structure, diversity and phylogeography of different species’ populations due to their effectiveness in identifying genetic variability

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

    Science.gov (United States)

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

    2013-06-01

    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 previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers' management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change. PMID:23531982

  15. 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...

  16. Genetic Diversity and Zoonotic Potential of Cryptosporidium parvum Causing Foal Diarrhea?

    OpenAIRE

    Grinberg, A.; Learmonth, J; Kwan, E.; Pomroy, W.; Lopez Villalobos, N.; Gibson, I; Widmer, G.

    2008-01-01

    Cryptosporidium isolates from diarrheic foals in New Zealand (n = 9) were identified as C. parvum, subtyped at two polymorphic loci, and compared with human (n = 45) and bovine (n = 8) isolates. Foal C. parvum isolates were genetically diverse, markedly similar to human and bovine isolates, and carried GP60 IIaA18G3R1 alleles, indicating a zoonotic potential.

  17. Clonal diversity and fine-scale genetic structure in a high andean treeline population.

    Czech Academy of Sciences Publication Activity Database

    Peng, Y.; Macek, P.; Macková, Jana; Romoleroux, K.; Hensen, I.

    2015-01-01

    Ro?. 47, ?. 1 (2015), s. 59-65. ISSN 0006-3606 Grant ostatní: GA AV ?R(CZ) IAA601110702; GA MŠk(CZ) LM2010009 Institutional support: RVO:60077344 Keywords : AFLP * clonal diversity * clonal propagation * fine-scale genetic structure * Polylepis reticulata * treeline Impact factor: 2.084, year: 2014

  18. 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...

  19. High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region

    OpenAIRE

    Douaihy, Bouchra; Vendramin, Giovanni G.; Boraty?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.

  20. Assessment of genetic diversity and relatedness among Tunisian almond germplasm using SSR markers.

    Science.gov (United States)

    Gouta, H; Ksia, E; Buhner, T; Moreno, M A; Zarrouk, M; Mliki, A; Gogorcena, Y

    2010-12-01

    Genetic diversity of 50 Tunisian almond (Prunus dulcis Mill.) genotypes and their relationships to European and American cultivars were studied. In total 82 genotypes were analyzed using ten genomic SSRs. A total of 159 alleles were scored and their sizes ranged from 116 to 227 bp. The number of alleles per locus varied from 12 to 23 with an average of 15.9 alleles per locus. Mean expected and observed heterozygosities were 0.86 and 0.68, respectively. The total value for the probability of identity was 4 × 10(-13) . All SSRs were polymorphic and they were able all together to distinguish unambiguously the 82 genotypes. The Dice similarity coefficient was calculated for all pair wise and was used to construct an UPGMA dendrogram. The results demonstrated that the genetic diversity within local almond cultivars was important, with clear geographic divergence between the northern and the southern Tunisian cultivars. The usefulness of SSR markers for almond fingerprinting, detection of synonyms and homonyms and evaluation of the genetic diversity in the Tunisian almond germplasm was also discussed. The results confirm the potential value of genetic diversity preservation for future breeding programs. PMID:21166798

  1. 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.

  2. ASSESSMENT OF GENETIC DIVERSITY IN BULB ONION (ALLIUM CEPA L.) USING SIMPLE SEQUENCE REPEAT MARKERS

    Science.gov (United States)

    Onions are the second most-valuable vegetable in the world, following only tomato. Despite their economic significance, knowledge of onion genetic diversity and resources is limited, owing to a paucity of public marker and germplasm resources and their out-breeding, biennial habit. The unusually l...

  3. Evaluation of genetic diversity in fig accessions by using microsatellite markers.

    Science.gov (United States)

    do Val, A D B; Souza, C S; Ferreira, E A; Salgado, S M L; Pasqual, M; Cançado, G M A

    2013-01-01

    Fig (Ficus carica L.) is a fruit of great importance worldwide. Its propagation is carried out with stem cuttings, a procedure that favors the occurrence of synonymy among specimens. Thus, molecular markers have become an important tool for studies of DNA fingerprinting, germplasm characterization, and genetic diversity evaluation in this plant species. The aim of this study was the analysis of genetic diversity among accessions of fig and the detection of synonyms among samples using molecular markers. Five microsatellite markers previously reported as polymorphic to fig were used to characterize 11 fig cultivars maintained in the germplasm bank located in Lavras, Minas Gerais. A total of 21 polymorphic DNA fragments were amplified, with an average of 4.2 alleles per locus. The average allelic diversity and polymorphic information content were 0.6300 and 0.5644, respectively, whereas the total value for the probability of identity was 1.45 x 10(-4). The study allowed the identification of 10 genotypes and 2 synonymous individuals. The principal coordinate analysis showed no defined clusters despite the formation of groups according to geographical origin. However, neighbor-joining analysis identified the same case of synonymy detected using principal coordinate analysis. The data also indicated that the fig cultivars analyzed constitute a population of individuals with high genetic diversity and a broad range of genetic variation. PMID:23661461

  4. Genetic diversity of avian paramyxovirus type 1: defining Newcastle disease virus genotypes

    Science.gov (United States)

    All Newcastle disease virus (NDV) isolates belong to a single serotype of avian paramyxovirus type-1 (APMV-1); however, significant genetic diversity is recognized between different NDV isolates. Historically, two systems have been used to classify NDV into lineages or genotypes, with both systems ...

  5. 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

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

    Directory of Open Access Journals (Sweden)

    M. Faisal Anwar Malik

    2009-03-01

    Full Text Available 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 peptides. Ten major bands were recorded out of total 26 bands detected, while 50% of total were polymorphic. Dendrogram constructed using Ward’s method divided the accessions in two main groups consisting of four clusters. The results of cluster analysis indicated that genetic diversity between Pakistani and US or AVRDC accessions is much larger that the genetic diversity between Pakistani and North Korean or Japanese accessions. Although cluster analysis completely separated most of the Pakistani accessions from USA and AVRDC accessions, but could not distinguish between the accessions from Japan and North Korea. As the accessions from various sources differed considerably, it was difficult to establish any relationship between origin and clustering pattern.

  7. 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.

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

    OpenAIRE

    Mériaux Jean-Claude; Verrier Etienne; Callède Lucille; Leroy Grégoire; Ricard Anne; Danchin-Burge Coralie; Rognon Xavier

    2009-01-01

    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.

  9. Unusually high genetic diversity in COI sequences of Chimarra obscura (Trichoptera: Philopotamidae)

    Science.gov (United States)

    Chimarra obscura (Walker 1852) is a philopotamid caddisfly found throughout much of North America. Using the COI DNA barcode locus, we have found unexpectedly high amounts of genetic diversity and distances within C. obscura. Of the approximately 150 specimens sampled, we have fo...

  10. Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea.

    Science.gov (United States)

    Kim, Hye Ri; Park, Yung Chul

    2015-11-10

    The aim of this study was to investigate the genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae in Korea. The Korean A. a. coreae is characterized by high levels of haplotype diversity (Hd=0.967) and low levels of nucleotide diversity (?=0.00683). Haplogroup 1 is well separated from the haplotypes of the neighboring regions of the Korean Peninsula, while the other haplogroups are closely related to those from the Russian Far East. Thus, further investigations are required to confirm the validity of the subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations present in the Korean Peninsula and its neighboring countries. Haplogroup 1 includes most Korean haplotypes and forms a star-like haplotype network structure, which reveals relatively low levels of sequence divergence and high frequency of unique mutations (only few mutations are shared in most of the haplotype nodes). The results indicate that the haplotypes of Haplogroup 1 might have experienced population expansion since their migration into Korea, which was further corroborated with negative results of neutrality tests for Korean population of A. a. coreae. PMID:26263836

  11. 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)

  12. Evidence of two genetic clusters of manatees with low genetic diversity in Mexico and implications for their conservation.

    Science.gov (United States)

    Nourisson, Coralie; Morales-Vela, Benjamín; Padilla-Saldívar, Janneth; Tucker, Kimberly Pause; Clark, Annmarie; Olivera-Gómez, Leon David; Bonde, Robert; McGuire, Peter

    2011-07-01

    The Antillean manatee (Trichechus manatus manatus) occupies the tropical coastal waters of the Greater Antilles and Caribbean, extending from Mexico along Central and South America to Brazil. Historically, manatees were abundant in Mexico, but hunting during the pre-Columbian period, the Spanish colonization and throughout the history of Mexico, has resulted in the significantly reduced population occupying Mexico today. The genetic structure, using microsatellites, shows the presence of two populations in Mexico: the Gulf of Mexico (GMx) and Chetumal Bay (ChB) on the Caribbean coast, with a zone of admixture in between. Both populations show low genetic diversity (GMx: N(A) = 2.69; H(E) = 0.41 and ChB: N(A) = 3.0; H(E) = 0.46). The lower genetic diversity found in the GMx, the largest manatee population in Mexico, is probably due to a combination of a founder effect, as this is the northern range of the sub-species of T. m. manatus, and a bottleneck event. The greater genetic diversity observed along the Caribbean coast, which also has the smallest estimated number of individuals, is possibly due to manatees that come from the GMx and Belize. There is evidence to support limited or unidirectional gene flow between these two important areas. The analyses presented here also suggest minimal evidence of a handful of individual migrants possibly between Florida and Mexico. To address management issues we suggest considering two distinct genetic populations in Mexico, one along the Caribbean coast and one in the riverine systems connected to the GMx. PMID:21681472

  13. Assessment of genetic diversity in Horse gram (Dolichos uniflorus

    Directory of Open Access Journals (Sweden)

    V Sandeep Varma, K Kanaka Durga and R Ankaiah

    2013-06-01

    Full Text Available Twenty three horse gram accessions were studied during spring seasons of 2008-09 and 2010-11. The results indicated significant differences among the 23 accessions for all characters studied, indicating the presence of sufficient genetic variation. Mahalanobis D2 statistics grouped all the 23 cultivars of horse gram into seven clusters. Cluster I had 11 genotypes, Cluster II had 7 genotypes while clusters III, IV, V, VI and VII contributed as solitary germplasms. Among the seed yield components, test weight (8.7 % followed by seed yield per plant (5.5 % and pod length (2.4 % contributed maximum towards the divergence. Among seed quality parameters, seedling dry weight (50.99 % contributed the maximum to the genetic divergence. The maximum intra cluster distance ranged from 0 (clusters III, IV, V, VI and VII to 8.15 (cluster I?. The maximum inter cluster distance (24.89 was noticed between cluster V (HG 18 and cluster VII (AK 38 indicating that the genotypes included in these clusters had maximum divergence and may be used as promising parents for hybridization programme to obtain better segregants in hose gram.

  14. Genetic diversity among mandarins in fruit-quality traits.

    Science.gov (United States)

    Goldenberg, Livnat; Yaniv, Yossi; Kaplunov, Tatiana; Doron-Faigenboim, Adi; Porat, Ron; Carmi, Nir

    2014-05-28

    A detailed phenotypic analysis of fruit-quality traits was conducted among 46 mandarin varieties within the Israeli Citrus breeding collection, belonging to genetically different natural subgroups, including common mandarin (C. reticulata Blanco), clementine (C. clementina Hort. ex. Tan), satsuma (C. unshiu Marcovitch), Mediterranean mandarin (C. deliciosa Tenore), King mandarin (C. nobilis Loureiro), and mandarin hybrids, such as tangor (C. reticulata × C. sinensis) and tangelo (C. reticulata × C. paradisi). Evaluated qualities included physical attributes (size, shape, color, peel thickness, and seed number); physiological properties (ripening period, peelability, and segmentation); nutritional and biochemical composition (vitamin C, phenol, flavonoid, and carotenoid contents and total antioxidant activity); and sensory attributes (total soluble solids and acid levels, flavor preference, sweetness, sourness, and fruitiness). The results indicated wide genetic variability in fruit-quality traits among mandarin varieties and natural subgroups, and statistical and hierarchical clustering analysis revealed multiple correlations among attributes. Such phenomic analysis is an obligatory requirement for identification of molecular markers for distinct fruit-quality traits and for selection of appropriate parents for future breeding programs. PMID:24828369

  15. Molecular markers and genetic diversity of Plasmodium vivax

    Scientific Electronic Library Online (English)

    Cristiana Ferreira Alves de, Brito; Marcelo Urbano, Ferreira.

    2011-08-01

    Full Text Available Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable mol [...] ecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers under selective pressure, for instance, antigen-coding polymorphic genes, and markers that are not under strong natural selection, such as most minisatellite and microsatellite loci. First, we review data obtained using genes encoding for P. vivax antigens: circumsporozoite protein, merozoite surface proteins 1 and 3?, apical membrane antigen 1 and Duffy binding antigen. We next address neutral or nearly neutral molecular markers, especially microsatellite loci, providing a complete list of markers that have already been used in P. vivax populations studies. We also analyse the microsatellite loci identified in the P. vivax genome project. Finally, we discuss some practical uses for P. vivax genotyping, for example, detecting multiple-clone infections and tracking the geographic origin of isolates.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    DEFF Research Database (Denmark)

    Topping, Christopher John; Østergaard, Siri

    2003-01-01

    Altering environmental conditions affects the genetic composition of populations via demographic and selective responses by creating of variety of population substructuring types. Classical genetic approaches can predict the genetic composition of populations under long-term or structurally stable conditions, but exclude factors such as animal behaviour, environmental structure, and breeding biology, all of which influence genetic diversity. Most populations are unique in some of these characteristics, and therefore may be unsuitable for the classical approach. Here, an alternative approach using a genetically explicit individual-based model (IBM) coupled to a dynamic landscape model was used to obtain measures for the genetic status of simulated vole populations. The rate of loss of expected heterozygosity (He) was calculated for simulated populations using two levels of spatial and temporal heterogeneity. Results showed that both spatial and temporal heterogeneity exerted an influence on the rate of loss ofgenetic diversity, but the precise effect was a balance between the effects of population sub-structuring, the frequency of founder effects and population size. These were in turn related to habitat availability and their influence on vole behaviour. Interaction between spatial and temporal dynamics altered the ratio of effective population size to census size. This indicates an altered reproductive potential, crucial in conservation biology applications. However, when the loss of heterozygosity was corrected for the harmonic mean of the population size, the rate of loss was almost identical in the four scenarios. Unlike classical genetic models, IBMs are flexible enough to mimic real population processes under a range of environmental and behavioural conditions. We conclude that IBMs incorporating explicit genetics provide a promising new approach to the evaluation of the effect of animal behaviour, and random and man-induced events on the genetic composition of populations. They also provide a new platformfrom which to investigate the implication of real world deviations from assumptions of traditional genetic models.

  18. Genetic diversity of wild soybean populations in Dongying, China, by simple sequence repeat analysis.

    Science.gov (United States)

    Wang, Y H; Zhang, X J; Fan, S J

    2015-01-01

    Annual wild soybean (Glycine soja Sieb. et Zucc.), the ancestor of cultivated soybean (G. max), is believed to be a potential gene source for further improvement of soybean to cope with environmental stress. In this study, 10 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population genetic structure in five wild soybean populations using 195 accessions collected from Dongying, China. Ten SSR markers yielded 90 bands, with an average of nine bands per marker. The percentage of polymorphic loci (P) was 97.78%, the distribution of expected heterozygosity (HE) was 0.1994-0.4460 with an average of 0.3262, and the distribution from Shannon's information index (I) was 0.3595-0.6506 with an average of 0.5386. The results showed that wild soybean had a high degree of genetic diversity at the species level. Nei's differentiation coefficient (FST) was 0.1533, and gene flow (Nm) was 1.3805, which indicated that genetic variation mainly existed within populations and that there was a certain level of gene exchange between populations. Some genetic differentiation occurred among populations, although this was not significant. Cluster analysis indicated that there was no significant correlation between the genetic structure of wild soybean populations and their geographic distribution, and the clustering results may be relatively consistent with the habitats of the accessions. In the present study, the genetic diversity of wild soybeans showed a broad genetic base and enables suggestions for the conservation of this plant to be made. PMID:26436402

  19. Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity

    OpenAIRE

    Burle, Marília Lobo; Fonseca, Jaime Roberto; Kami, James A.; Gepts, Paul

    2010-01-01

    Brazil is the largest producer and consumer of common bean (Phaseolus vulgaris L.), which is the most important source of human dietary protein in that country. This study assessed the genetic diversity and the structure of a sample of 279 geo-referenced common bean landraces from Brazil, using molecular markers. Sixty-seven microsatellite markers spread over the 11 linkage groups of the common bean genome, as well as Phaseolin, PvTFL1y, APA and four SCAR markers were used. As expected, the s...

  20. Genetic diversity of Cosmos species revealed by RAPD and ISSR markers.

    Science.gov (United States)

    Rodríguez-Bernal, A; Piña-Escutia, J L; Vázquez-García, L M; Arzate-Fernández, A M

    2013-01-01

    The genus Cosmos is native of America and is constituted by 34 species; 28 of them are endemic of Mexico. The cosmos are used as a nematicide, antimalarial, and antioxidative agent. The aim of this study was to estimate the genetic diversity among 7 cosmos species based on random amplified polymorphic DNA (RAPD) and inter-simple sequences repeats (ISSR) markers. With RAPD markers, the obtained polymorphism was 91.7 % and the genetic diversity was 0.33, whereas these values were 65.6%, and 0.22 from ISSR markers, respectively, indicating the presence of high genetic diversity among the Cosmos species that were analyzed. The unweighted pair group method with arithmetic mean dendrograms that were obtained with both markers were notably similar, revealing 2 clusters and indicating a clear genetic differentiation among the Cosmos species that were assessed. The first cluster comprised the species Cosmos sulphureus, Cosmos pacificus, and Cosmos diversifolius, while the second cluster included the species Cosmos purpureus, Cosmos crithmifolius, Cosmos bipinnatus, and Cosmos parviflorus. Besides this, the Cosmos species were clustered according to their collection sites. The Mantel test corroborates the correlation between the genetic distance and the geographic altitude of each Cosmos species. The results suggest that it is necessary to preserve the Cosmos species in their natural habitat in addition to the germoplasm collection for ex situ conservation. PMID:24338421

  1. Genetic diversity between and within populations of Handroanthus heptaphyllus (Vell. Mattos using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Neide Tomita Mori

    2012-03-01

    Full Text Available Handroanthus heptaphyllus (Vell. Mattos, popularly known as ipê-roxo, is a species of the family Bignoneaceae much appreciated for its beauty, excellent quality wood which is used for making medicinal products and also in reforestation programs of degraded areas, as well as landscaping and restoration. The aim of this study was to investigate the genetic diversity between and within populations of H. heptaphyllus using microsatellite markers. The 192 seedlings were produced from seeds collected on 30 trees into the two populations of natural forest fragments in Botucatu region, São Paulo, Brazil. Eight microsatellite loci were analyzed, with allelic polymorphism varying from six alleles for locus TAU22 to 14 alleles for loci TAU12, TAU30, and TAU31, with an expected mean number of alleles per locus (Ae of 4.9. The mean expected heterozygosity (He for the two populations was 0.785, the mean observed heterozygosity (Ho was 0.609, and the fixation index (F was low between populations, with a mean of 0.222. The gene differentiation between the two populations (Gst was 0.100. We concluded that the higher genetic diversity is within populations; therefore, as far as germplasm collection programs in Botucatu region are concerned, it is recommended that a larger sampling of individuals should be considered within populations, thereby providing good genetic representativeness. The populations have enough genetic diversity to support genetic improvement and germplasm preservation programs.

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

    Science.gov (United States)

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

    2013-08-01

    Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/]. PMID:23977990

  3. Genetic diversity in wild diploid wheats Triticum monococcum var. boeoticum and T. urartu (Poaceae).

    Science.gov (United States)

    Smith-Huerta, N L; Huerta, A J; Barnhart, D; Waines, J G

    1989-08-01

    The genetic diversity of two wild diploid wheat species, Triticum monococcum var. boeoticum and T. urartu, was assessed using starch gel electrophoresis. Genetic diversity is uniformly low in both species. Number of alleles per locus was very low with a mean of 1.22 for T. monococcum var. boeoticum and 1.19 in T. urartu. Percentage of polymorphic loci was also low, with a mean of 19.71 for T. monococcum var. boeoticum and a mean of 18.35 for T. urartu. Mean gene diversity was low with a mean of 0.052 in populations of T. monococcum var. boeoticum and a mean of 0.040 in populations of T. urartu. Genetic affinities of the species and of populations were computed using Nei's identity index (NI). Overall genetic affinities of the two species are NI=0.697. The genetic affinities of different populations of a species are uniformly high with NIs ranging from 0.894 to 1.000 in T. monococcum var. boeoticum and from 0.898 to 1.000 in T. urartu. PMID:24227153

  4. Genetic diversity of sesame (sesamum indicum L.) germplasm from Pakistan using RAPD markers

    International Nuclear Information System (INIS)

    Genetic diversity among 20 sesame (Sesamum indicum L.) accessions was examined at DNA level by means of random amplified polymorphic DNA (RAPD) analysis. Ten primers used produced a total of 93 RAPD fragments, of which 70 (75%) were polymorphic. Each primer generated 5 to 17 amplified fragments with an average of 9.3 bands per primer. Based on pair-wise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were computed to assess the associations among the accessions. Pair-wise similarity indices varied from 0.65 to 0.91. A UPGMA cluster analysis based on these genetic similarities located most of the accessions far apart from one another, showing a high level of polymorphism. Genetically, all the genotypes were classified into two major groups and six subgroups or clusters. A single accession (22243) was relatively distinct from rest of the accessions and created independent cluster. In conclusion, even with the use of a limited set of primers, RAPD technique revealed a high level of genetic variation among sesame accessions collected from diverse ecologies of Pakistan. This high level of genetic diversity among the genotypes suggested that RAPD technique is valuable for sesame systematic, and can be helpful for the upholding of germplasm banks and the competent choice of parents in breeding programs. (author)

  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. Effect of habitat fragmentation on levels and patterns of genetic diversity in natural populations of the peat moss Polytrichum commune.

    Science.gov (United States)

    Wilson, Pamela J; Provan, Jim

    2003-04-22

    Peat bogs represent unique ecosystems that are under particular threat from fragmentation due to peat harvesting, with only 38% of the original peatland in Europe remaining intact and unaffected by peat cutting, drainage and silviculture. In this study, we have used microsatellite markers to determine levels and patterns of genetic diversity in both cut and uncut natural populations of the peat moss Polytrichum commune. Overall diversity levels suggest that there is more genetic variation present than had previously been assumed for bryophytes. Despite this, diversity values from completely cut bogs were found to be lower than those from uncut peatlands (average 0.729 versus 0.880). In addition, the genetic diversity was more highly structured in the cut populations, further suggesting that genetic drift is already affecting genetic diversity in peat bogs subjected to fragmentation. PMID:12737668

  7. Genetic diversity and taxonomic status of Pinus tabulaeformis f. shekanensis revealed by ISSR markers.

    Science.gov (United States)

    Liu, Z-H; Xie, Q; Li, Z-Q

    2015-01-01

    Pinus tabulaeformis f. shekanensis is a rare taxon endemic in the Ziwuling Loess Plateau, of which only one population is known. Inter-simple sequence repeat molecular markers were employed to compare the taxon's genetic diversity with its 4 nearest wild relatives (P. tabulaeformis, P. tabulaeformis var. mukdensis, P. massoniana, and P. henryi) to assess the taxonomic status of P. tabulaeformis f. shekanensis. Inter-simple sequence repeat marker data revealed higher genetic diversity in the P. tabulaeformis f. shekanensis population than in the other populations. Population genetic analysis (neighbor-joining cluster analysis, principal coordinate analysis, and structure clustering) revealed that P. tabulaeformis f. shekanensis and P. tabulaeformis are likely conspecific (the former may be a variety of the latter). Strategies are also proposed for the conservation of P. tabulaeformis f. shekanensis. PMID:25730043

  8. 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.

  9. 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.

  10. 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)

  11. 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)

  12. GAPDH gene diversity in spirochetes: a paradigm for genetic promiscuity.

    Science.gov (United States)

    Figge, R M; Cerff, R

    2001-12-01

    In this study we have determined gap sequences from nine different spirochetes. Phylogenetic analyses of these sequences in the context of all other available eubacterial and a selection of eukaryotic Gap sequences demonstrated that the eubacterial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene diversity encompasses at least five highly distinct gene families. Within these gene families, spirochetes show an extreme degree of sequence divergence that is probably the result of several lateral gene transfer events between spirochetes and other eubacterial phyla, and early gene duplications in the eubacterial ancestor. A Gap1 sequence from the syphilis spirochete Treponema pallidum has recently been shown to be closely related to GapC sequences from Euglenozoa. Here we demonstrate that several other spirochetal species are part of this cluster, supporting the conclusion that an interkingdom gene transfer from spirochetes to Euglenozoa must have occurred. Furthermore, we provide evidence that the GAPDH genes present in the protists Parabasalia may also be of spirochetal descent. PMID:11719573

  13. 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.

  14. Genetic diversity of Rhizoctonia solani associated with potato tubers in France.

    Science.gov (United States)

    Fiers, Marie; Edel-Hermann, Véronique; Héraud, Cécile; Gautheron, Nadine; Chatot, Catherine; Le Hingrat, Yves; Bouchek-Mechiche, Karima; Steinberg, Christian

    2011-01-01

    The soilborne fungus Rhizoctonia solani is a pathogen of many plants and causes severe damage in crops around the world. Strains of R. solani from the anastomosis group (AG) 3 attack potatoes, leading to great yield losses and to the downgrading of production. The study of the genetic diversity of the strains of R. solani in France allows the structure of the populations to be determined and adapted control strategies against this pathogen to be established. The diversity of 73 French strains isolated from tubers grown in the main potato seed production areas and 31 strains isolated in nine other countries was assessed by phylogenetic analyses of (i) the internal transcribed spacer sequences (ITS1 and ITS2) of ribosomal RNA (rRNA), (ii) a part of the gene tef-1? and (iii) the total DNA fingerprints of each strain established by amplified fragment length polymorphism (AFLP). The determination of the AGs of R. solani based on the sequencing of the ITS region showed three different AGs among our collection (60 AG 3 PT, 8 AG 2-1 and 5 AG 5). Grouping of the strains belonging to the same AG was confirmed by sequencing of the gene tef-1? used for the first time to study the genetic diversity of R. solani. About 42% of ITS sequences and 72% of tef-1? sequences contained polymorphic sites, suggesting that the cells of R. solani strains contain several copies of ITS and the tef-1? gene within the same nucleus or between different nuclei. Phylogenetic trees showed a greater genetic diversity within AGs in tef-1? sequences than in ITS sequences. The AFLP analyses showed an even greater diversity among the strains demonstrating that the French strains of R. solani isolated from potatoes were not a clonal population. Moreover there was no relationship between the geographical origins of the strains or the variety from which they were isolated and their genetic diversity. PMID:21642342

  15. Analysis of genetic diversity in the Oryza officinalis complex

    Scientific Electronic Library Online (English)

    María Teresa, Federici; Andrei B., Shcherban; Fabián, Capdevielle; Marta, Francis; Duncan, Vaughan.

    2002-08-15

    Full Text Available The genetic relationships among 34 accessions of wild rice from Asia, Africa, America and Australia were analysed using RFLP technique. After southern blotting, DNA digestion pattern was hybridised with a highly repetitive DNA sequence of a retrotransposon from a gypsy family of mobile elements. A d [...] endrogram was constructed from RFLP data in which the species clustered according to their genome designation (CC, BB, BBCC and CCDD genomes). Some species did not appear in the same group, for example, O. eichingeri from Africa and Sri Lanka clustered separately from each other. The same situation was observed for the accessions from China of O. officinalis, which cluster together showing a close relationship with O. rhizomatis, and O. eichingeri (both of CC genome). Also, the tetraploid BBCC from India of O. officinalis appears in the same cluster of O. eichingeri and O. punctata (both from Africa) suggesting close phylogenetic relationship with the African genomes BB, CC and BBCC.

  16. 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

  17. Annotation and genetic diversity of the chicken collagenous lectins

    DEFF Research Database (Denmark)

    Hamzic, Edin; Pinard-van der Laan, Marie-Hélène

    2015-01-01

    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 structureacross 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.

  18. 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

  19. Genetic diversity in peripheral and subcentral populations of corrigiola litoralis L. (Illecebraceae)

    Science.gov (United States)

    Durka

    1999-10-01

    Genetic diversity and differentiation were studied in Corrigiola litoralis L., an annual plant species growing on seasonally flooded river banks. Plant species that are restricted to river systems may consist of highly isolated populations. For this species, pronounced genetic differentiation among rivers was expected. Plants were sampled from the river Loire (France) representing subcentral populations and the rivers Rhine, Weser and Elbe (Germany) representing peripheral ones. Allozyme electrophoresis revealed 17 putative loci in 11 enzyme systems. At the species level, percentage polymorphic loci, mean number of alleles, observed heterozygosity and expected heterozygosity were P=29%, A=1.5 +/- 0.2, Ho=0.007 +/- 0.005 and He=0.065 +/- 0.035, respectively. Peripheral populations were smaller in number and showed decreased levels of genetic diversity relative to central populations. Corrigiola litoralis was highly inbreeding as indicated by a mean FIS of 0.755. Genetic differentiation among populations was high with a mean FST-value of 0.585. Hierarchical F-statistics revealed that genetic variability was partitioned at 57% among sites, 52% among countries and 11% among sites within countries. Genetic distances between French and German populations were 0.08, indicative of considerable differentiation at the intraspecific level. The overall low level of allozyme diversity is attributed to the breeding system and to habitat conditions homogenized by regular flooding. The decrease in diversity from subcentral to peripheral populations is considered to be a result of drift and founder effects during postglacial recolonization. Peripheral populations were characterized by a single fixed allele at locus IDH, thus representing an evolutionarily significant unit. PMID:10583550

  20. 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...

  1. Genetic diversity and association mapping in a collection of selected Chinese soybean accessions based on SSR marker analysis

    OpenAIRE

    Y. H. Li; Smulders, M.J.M.; Chang, R.Z.; Qiu, L.J.

    2011-01-01

    For broadening the narrow genetic base of modern soybean cultivars, 159 accessions were selected from the Chinese soybean collection which contained at least one of seven important agronomic traits: resistance to soybean cyst nematode (SCN) or soybean mosaic virus (SMV), tolerance to salt, cold, or drought, high seed oil content or high protein content. Genetic diversity evaluation using 55 microsatellite loci distributed across the genome indicated that a large amount of genetic diversity (0...

  2. Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

    OpenAIRE

    Laidò, Giovanni; Mangini, Giacomo; Taranto, Francesca; Gadaleta, Agata; Blanco, Antonio; Cattivelli, Luigi; Marone, Daniela; Mastrangelo, Anna M; Papa, Roberto; Vita, Pasquale De

    2013-01-01

    Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K?=?2), both of the sets of molecular markers distinguished t...

  3. Genetic Diversity of Pseudomonas aeruginosa Strains Isolated from Ventilated Patients with Nosocomial Pneumonia, Cancer Patients with Bacteremia, and Environmental Water

    OpenAIRE

    Ruimy, Raymond; Genauzeau, Emmanuel; Barnabe, Christian; Beaulieu, Arnaud; Tibayrenc, Michel; Andremont, Antoine

    2001-01-01

    Random amplified polymorphic DNA typing was used to study the genetic diversity of Pseudomonas aeruginosa strains from (i) ventilated patients with nosocomial pneumonia who were hospitalized in intensive care units, (ii) cases of bacteremia in cancer patients with severe neutropenia, and (iii) rivers and swimming pools. Genetic diversity was determined by three phylogenetic methods and by statistical analysis of population genetics. The population studied undergoes epidemic clonality with a h...

  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. The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers.

    Science.gov (United States)

    Yang, Shi Ying; Saxena, Rachit K; Kulwal, Pawan L; Ash, Gavin J; Dubey, Anuja; Harper, John D I; Upadhyaya, Hari D; Gothalwal, Ragini; Kilian, Andrzej; Varshney, Rajeev K

    2011-04-01

    With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F(2) mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology. PMID:21677394

  6. The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

    Indian Academy of Sciences (India)

    Shi Ying Yang; Rachit A. Saxena; Pawan L. Kulwal; Gavin J. Ash; Anuja Dubey; John D. I. Harper; Hari D. Upadhyaya; Ragini Gothalwal; Andrzej Kilian; Rajeev K. Varshney

    2011-04-01

    With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F2 mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% ($P \\gt 0.001$) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology.

  7. Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum)

    Indian Academy of Sciences (India)

    Ashok Badigannavar; Gerald O. Myers

    2015-03-01

    Cottonseed contains 16% seed oil and 23% seed protein by weight. High levels of palmitic acid provides a degree of stability to the oil, while the presence of bound gossypol in proteins considerably changes their properties, including their biological value. This study uses genetic principles to identify genomic regions associated with seed oil, protein and fibre content in upland cotton cultivars. Cotton association mapping panel representing the US germplasm were genotyped using amplified fragment length polymorphism markers, yielding 234 polymorphic DNA fragments. Phenotypic analysis showed high genetic variability for the seed traits, seed oil range from 6.47–25.16%, protein from 1.85–28.45% and fibre content from 15.88–37.12%. There were negative correlations between seed oil and protein content. With reference to genetic diversity, the average estimate of ST was 8.852 indicating a low level of genetic differentiation among subpopulations. The AMOVA test revealed that variation was 94% within and 6% among subpopulations. Bayesian population structure identified five subpopulations and was in agreement with their geographical distribution. Among the mixed models analysed, mixed linear model (MLM) identified 21 quantitative trait loci for lint percentage and seed quality traits, such as seed protein and oil. Establishing genetic diversity, population structure and marker trait associations for the seed quality traits could be valuable in understanding the genetic relationships and their utilization in breeding programmes.

  8. 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.

  9. 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. 

  10. 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.

  11. Evidence for extensive genetic diversity and substructuring of the Babesia bovis metapopulation.

    Science.gov (United States)

    Flores, D A; Minichiello, Y; Araujo, F R; Shkap, V; Benítez, D; Echaide, I; Rolls, P; Mosqueda, J; Pacheco, G M; Petterson, M; Florin-Christensen, M; Schnittger, L

    2013-11-01

    Babesia bovis is a tick-transmitted haemoprotozoan and a causative agent of bovine babesiosis, a cattle disease that causes significant economic loss in tropical and subtropical regions. A panel of nineteen micro- and minisatellite markers was used to estimate population genetic parameters of eighteen parasite isolates originating from different continents, countries and geographic regions including North America (Mexico, USA), South America (Argentina, Brazil), the Middle East (Israel) and Australia. For eleven of the eighteen isolates, a unique haplotype was inferred suggesting selection of a single genotype by either in vitro cultivation or amplification in splenectomized calves. Furthermore, a high genetic diversity (H = 0.780) over all marker loci was estimated. Linkage disequilibrium was observed in the total study group but also in sample subgroups from the Americas, Brazil, and Israel and Australia. In contrast, corresponding to their more confined geographic origin, samples from Israel and Argentina were each found to be in equilibrium suggestive of random mating and frequent genetic exchange. The genetic differentiation (F(ST)) of the total study group over all nineteen loci was estimated by analysis of variance (?) and Nei's estimation of heterozygosity (G(ST')) as 0.296 and 0.312, respectively. Thus, about 30% of the genetic diversity of the parasite population is associated with genetic differences between parasite isolates sampled from the different geographic regions. The pairwise similarity of multilocus genotypes (MLGs) was assessed and a neighbour-joining dendrogram generated. MLGs were found to cluster according to the country/continent of origin of isolates, but did not distinguish the attenuated from the pathogenic parasite state. The distant geographic origin of the isolates studied allows an initial glimpse into the large extent of genetic diversity and differentiation of the B. bovis population on a global scale. PMID:24589113

  12. High genetic diversity declines towards the geographic range periphery of Adonis vernalis, a Eurasian dry grassland plant.

    Science.gov (United States)

    Hirsch, H; Wagner, V; Danihelka, J; Ruprecht, E; Sánchez-Gómez, P; Seifert, M; Hensen, I

    2015-11-01

    Genetic diversity is important for species' fitness and evolutionary processes but our knowledge on how it varies across a species' distribution range is limited. The abundant centre hypothesis (ACH) predicts that populations become smaller and more isolated towards the geographic range periphery - a pattern that in turn should be associated with decreasing genetic diversity and increasing genetic differentiation. We tested this hypothesis in Adonis vernalis, a dry grassland plant with an extensive Eurasian distribution. Its life-history traits and distribution characteristics suggest a low genetic diversity that decreases and a high genetic differentiation that increases towards the range edge. We analysed AFLP fingerprints in 28 populations along a 4698-km transect from the geographic range core in Russia to the western range periphery in Central and Western Europe. Contrary to our expectation, our analysis revealed high genetic diversity (range of proportion of polymorphic bands = 56-81%, He = 0.168-0.238) and low genetic differentiation across populations (?ST  = 0.18). However, in congruence with the genetic predictions of the ACH, genetic diversity decreased and genetic differentiation increased towards the range periphery. Spanish populations were genetically distinct, suggesting a divergent post-glacial history in this region. The high genetic diversity and low genetic differentiation in the remaining A. vernalis populations is surprising given the species' life-history traits and points to the possibility that the species has been widely distributed in the studied region or that it has migrated from a diverse source in an East-West direction, in the past. PMID:26122089

  13. Genetic diversity for mycorrhizal symbiosis and phosphate transporters in rice.

    Science.gov (United States)

    Jeong, Kwanho; Mattes, Nicolas; Catausan, Sheryl; Chin, Joong Hyoun; Paszkowski, Uta; Heuer, Sigrid

    2015-11-01

    Phosphorus (P) is a major plant nutrient and developing crops with higher P-use efficiency is an important breeding goal. In this context we have conducted a comparative study of irrigated and rainfed rice varieties to assess genotypic differences in colonization with arbuscular mycorrhizal (AM) fungi and expression of different P transporter genes. Plants were grown in three different soil samples from a rice farm in the Philippines. The data show that AM symbiosis in all varieties was established after 4 weeks of growth under aerobic conditions and that, in soil derived from a rice paddy, natural AM populations recovered within 6 weeks. The analysis of AM marker genes (AM1, AM3, AM14) and P transporter genes for the direct Pi uptake (PT2, PT6) and AM-mediated pathway (PT11, PT13) were largely in agreement with the observed root AM colonization providing a useful tool for diversity studies. Interestingly, delayed AM colonization was observed in the aus-type rice varieties which might be due to their different root structure and might confer an advantage for weed competition in the field. The data further showed that P-starvation induced root growth and expression of the high-affinity P transporter PT6 was highest in the irrigated variety IR66 which also maintained grain yield under P-deficient field conditions. PMID:26466747

  14. Mining the human genome after Association for Molecular Pathology v. Myriad Genetics.

    Science.gov (United States)

    Evans, Barbara J

    2014-07-01

    The Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics portrays the human genome as a product of nature. This frames medical genetics as an extractive industry that mines a natural resource to produce valuable goods and services. Natural resource law offers insights into problems medical geneticists can expect after this decision and suggests possible solutions. Increased competition among clinical laboratories offers various benefits but threatens to increase fragmentation of genetic data resources, potentially causing waste in the form of lost opportunities to discover the clinical significance of particular gene variants. The solution lies in addressing legal barriers to appropriate data sharing. Sustainable discovery in the field of medical genetics can best be achieved through voluntary data sharing rather than command-and-control tactics, but voluntary mechanisms must be conceived broadly to include market-based approaches as well as donative and publicly funded data commons. The recently revised Health Insurance Portability and Accountability Act Privacy Rule offers an improved--but still imperfect--framework for market-oriented data sharing. This article explores strategies for addressing the Privacy Rule's remaining defects. America is close to having a legal framework that can reward innovators, protect privacy, and promote needed data sharing to advance medical genetics. PMID:24357850

  15. 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.

  16. Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds.

    Science.gov (United States)

    Hall, S J G; Lenstra, J A; Deeming, D C

    2012-06-01

    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. PMID:22583326

  17. 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.

    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.

  18. 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.

  19. 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

  20. Genetic diversity of stilbene metabolism in Vitis sylvestris.

    Science.gov (United States)

    Duan, Dong; Halter, David; Baltenweck, Raymonde; Tisch, Christine; Tröster, Viktoria; Kortekamp, Andreas; Hugueney, Philippe; Nick, Peter

    2015-06-01

    Stilbenes, as important secondary metabolites of grapevine, represent central phytoalexins and therefore constitute an important element of basal immunity. In this study, potential genetic variation in Vitis vinifera ssp. sylvestris, the ancestor of cultivated grapevine, was sought with respect to their output of stilbenes and potential use for resistance breeding. Considerable variation in stilbene inducibility was identified in V. vinifera ssp. sylvestris. Genotypic differences in abundance and profiles of stilbenes that are induced in response to a UV-C pulse are shown. Two clusters of stilbene 'chemovars' emerged: one cluster showed quick and strong accumulation of stilbenes, almost exclusively in the form of non-glycosylated resveratrol and viniferin, while the second cluster accumulated fewer stilbenes and relatively high proportions of piceatannol and the glycosylated piceid. For all 86 genotypes, a time dependence of the stilbene pattern was observed: piceid, resveratrol, and piceatannol accumulated earlier, whereas the viniferins were found later. It was further observed that the genotypic differences in stilbene accumulation were preceded by differential accumulation of the transcripts for chalcone synthase (CHS) and stilbene-related genes: phenylalanine ammonium lyase (PAL), stilbene synthase (StSy), and resveratrol synthase (RS). A screen of the population with respect to susceptibility to downy mildew of grapevine (Plasmopara viticola) revealed considerable variability. The subpopulation of genotypes with high stilbene inducibility was significantly less susceptible as compared with low-stilbene genotypes, and for representative genotypes it could be shown that the inducibility of stilbene synthase by UV correlated with the inducibility by the pathogen. PMID:25873669