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1

Mining the genetic diversity of Ehrlichia ruminantium using map genes family.  

Science.gov (United States)

Understanding bacterial genetic diversity is crucial to comprehend pathogenesis. Ehrlichia ruminantium (E. ruminantium), a tick-transmitted intracellular bacterial pathogen, causes heartwater disease in ruminants. This model rickettsia, whose genome has been recently sequenced, is restricted to neutrophils and reticulo-endothelial cells of its mammalian host and to the midgut and salivary glands of its vector tick. E. ruminantium harbors a multigene family encoding for 16 outer membrane proteins including MAP1, a major antigenic protein. All the 16 map paralogs are expressed in bovine endothelial cells and some are specifically translated in the tick or in the mammalian host. In this study, we carried out phylogenetic analyses of E. ruminantium using sequences of 6 MAP proteins, MAP1, MAP1-2, MAP1-6, MAP1-5, MAP1+1 and MAP1-14, localized either in the center or at the borders of the map genes cluster. We show that (i) map1 gene is a good tool to characterize the genetic diversity among Africa, Caribbean islands and Madagascar strains including new emerging isolates of E. ruminantium; (ii) the different map paralogs define different genotypes showing divergent evolution; (iii) there is no correlation between all MAP genotypes and the geographic origins of the strains; (iv) The genetic diversity revealed by MAP proteins is conserved whatever is the scale of strains sampling (village, region, continent) and thus was not related to the different timing of strains introduction, i.e. continuous introduction of strains versus punctual introduction (Africa versus Caribbean islands). These results provide therefore a significant advance towards the management of E. ruminantium diversity. The differential evolution of these paralogs suggests specific roles of these proteins in host-vector-pathogen interactions that could be crucial for developing broad-spectrum vaccines. PMID:19819629

Raliniaina, Modestine; Meyer, Damien F; Pinarello, Valérie; Sheikboudou, Christian; Emboulé, Loic; Kandassamy, Yane; Adakal, Hassane; Stachurski, Frédéric; Martinez, Dominique; Lefrançois, Thierry; Vachiéry, Nathalie

2010-02-10

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

Science.gov (United States)

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. PMID:16519816

Brudey, Karine; Driscoll, Jeffrey R; Rigouts, Leen; Prodinger, Wolfgang M; Gori, Andrea; Al-Hajoj, Sahal A; Allix, Caroline; Aristimuno, Liselotte; Arora, Jyoti; Baumanis, Viesturs; Binder, Lothar; Cafrune, Patricia; Cataldi, Angel; Cheong, Soonfatt; Diel, Roland; Ellermeier, Christopher; Evans, Jason T; Fauville-Dufaux, Maryse; Ferdinand, Severine; de Viedma, Dario Garcia; Garzelli, Carlo; Gazzola, Lidia; Gomes, Harrison M; Guttierez, M Cristina; Hawkey, Peter M; van Helden, Paul D; Kadival, Gurujaj V; Kreiswirth, Barry N; Kremer, Kristin; Kubin, Milan; Kulkarni, Savita P; Liens, Benjamin; Lillebaek, Troels; Ly, Ho Minh; Martin, Carlos; Martin, Christian; Mokrousov, Igor; Narvskaia, Olga; Ngeow, Yun Fong; Naumann, Ludmilla; Niemann, Stefan; Parwati, Ida; Rahim, Zeaur; Rasolofo-Razanamparany, Voahangy; Rasolonavalona, Tiana; Rossetti, M Lucia; Rusch-Gerdes, Sabine; Sajduda, Anna; Samper, Sofia; Shemyakin, Igor G; Singh, Urvashi B; Somoskovi, Akos; Skuce, Robin A; van Soolingen, Dick; Streicher, Elisabeth M; Suffys, Philip N; Tortoli, Enrico; Tracevska, Tatjana; Vincent, Veronique; Victor, Tommie C; Warren, Robin M; Yap, Sook Fan; Zaman, Khadiza; Portaels, Francoise; Rastogi, Nalin; Sola, Christophe

2006-01-01

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Recombination and Genetic Diversity  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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).

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

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 produc...

Sajduda Anna; Rüsch-Gerdes Sabine; Lucia, Rossetti M.; Rasolonavalona Tiana; Rasolofo-Razanamparany Voahangy; Rahim Zeaur; Parwati Ida; Niemann Stefan; Naumann Ludmilla; Ngeow Yun; Narvskaïa Olga; Mokrousov Igor; Martin Christian; Martin Carlos; Ly Ho

2006-01-01

5

Species diversity and genetic diversity: parallel processes and correlated patterns.  

Science.gov (United States)

Species diversity and genetic diversity may be correlated as a result of processes acting in parallel at the two levels. However, no theories predict the conditions under which different relationships between species diversity and genetic diversity might arise and therefore when one level of diversity may be predicted using the other. I used simulation models to investigate the parallel influence of locality area, immigration rate, and environmental heterogeneity on species diversity and genetic diversity. The most common pattern was moderate to strong positive species-genetic diversity correlations (SGDCs). Such correlations may be driven by any one of the three locality characteristics examined, but important exceptions and patterns emerged. Genetic diversity and species diversity were more weakly correlated when genetic diversity was measured for rare versus common species. Environmental heterogeneity not only imposes spatially varying selection on populations and communities but also causes changes in species' population sizes and therefore genetic diversity; these interacting processes can create positive, negative, or unimodal relationships of genetic diversity with species diversity. When species are considered as part of multispecies communities, predictions from single-species models of genetic diversity apply in some instances (effects of area and immigration) but often not in others (effects of environmental heterogeneity). PMID:16032574

Vellend, Mark

2005-08-01

6

Data Quality Mining using Genetic Algorithm  

Directory of Open Access Journals (Sweden)

Full Text Available Data quality mining (DQM as a new and promising data mining approach from the academic and the business point of view. Data quality is important to organizations. People use information attributes as a tool for assessing data quality. The goal of DQM is to employ data mining methods in order to detect, quantify, explain and correct data quality deficiencies in very large databases. Data quality is crucial for many applications of knowledge discovery in databases (KDD. In this work, we have considered four data qualities like accuracy, comprehensibility, interestingness and completeness. We have tried to develop Multi-objective Genetic Algorithm (GA based approach utilizing linkage between feature selection and association rule. The main motivation for using GA in the discovery of high-level prediction rules is that they perform a global search and cope better with attribute interaction that the greedy rule induction algorithms often used in data mining.

Sufal Das

2009-05-01

7

Genetic diversity revealed in human faces.  

Science.gov (United States)

From an evolutionary perspective, human facial attractiveness is proposed to signal mate quality. Using a novel approach to the study of the genetic basis of human preferences for facial features, we investigated whether attractiveness signals mate quality in terms of genetic diversity. Genetic diversity in general has been linked to fitness and reproductive success, and genetic diversity within the major histocompatibility complex (MHC) has been linked to immunocompetence and mate preferences. We asked whether any preference for genetic diversity is specific to MHC diversity or reflects a more general preference for overall genetic diversity. We photographed and genotyped 160 participants using microsatellite markers situated within and outside the MHC, and calculated two measures of genetic diversity: mean heterozygosity and standardized mean d(2). Our results suggest a special role for the MHC in female preferences for male faces. MHC heterozygosity positively predicted male attractiveness, and specifically facial averageness, with averageness mediating the MHC-attractiveness relationship. For females, standardized mean d(2) at non-MHC loci predicted facial symmetry. Thus, attractive facial characteristics appear to provide visual cues to genetic quality in both males and females, supporting the view that face preferences have been shaped by selection pressures to identify high-quality mates. PMID:18691260

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

2008-10-01

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Genetic Diversity in Irrigated Rice  

Directory of Open Access Journals (Sweden)

Full Text Available Genetic diversity of 62 genotypes of irrigated rice originating from BRRI, IRRI and China were studied through Mahalanobis D2statistic. The genotypes were grouped into five clusters. The cluster II and IV contained the highest number of genotypes (16 and the cluster I contained the lowest (7. The highest intra cluster distance was noticed for the cluster I and the lowest for cluster III. The highest inter cluster distance was observed between cluster I and cluster IV followed by cluster I and cluster V, cluster I and cluster III, cluster III and cluster IV and lowest between cluster IV and cluster V. The highest cluster means for yield and other three yield contributing characters are obtained from cluster I, six highest and two second highest means for yield contributing characters are found in cluster III but the lowest cluster mean for yield. Therefore more emphasis should be given on cluster I for selecting genotypes as parents for crossing with the genotypes of cluster III, which may produce new recombinants with desired traits.

M.R. Islam

2004-01-01

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Mining Frequent Itemsets Using Genetic Algorithm  

CERN Document Server

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.

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

2010-01-01

10

Mining disease fingerprints from within genetic pathways.  

Science.gov (United States)

Mining biological networks can be an effective means to uncover system level knowledge out of micro level associations, such as encapsulated in genetic pathways. Analysis of human disease genetic pathways can lead to the identification of major mechanisms that may underlie disorders at an abstract functional level. The focus of this study was to develop an approach for structural pattern analysis and classification of genetic pathways of diseases. A probabilistic model was developed to capture characteristic components ('fingerprints') of functionally annotated pathways. A probability estimation procedure of this model searched for fingerprints in each disease pathway while improving probability estimates of model parameters. The approach was evaluated on data from the Kyoto Encyclopedia of Genes and Genomes (consisting of 56 pathways across seven disease categories). Based on the achieved average classification accuracy of up to ~77%, the findings suggest that these fingerprints may be used for classification and discovery of genetic pathways. PMID:23304411

Nabhan, Ahmed Ragab; Sarkar, Indra Neil

2012-01-01

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The Genetic Algorithm for Truck Dispatching Problems in Surface Mine  

Directory of Open Access Journals (Sweden)

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

Xin- Ming Lu

2010-01-01

12

Does genetic diversity predict health in humans?  

Science.gov (United States)

Genetic diversity, especially at genes important for immune functioning within the Major Histocompatibility Complex (MHC), has been associated with fitness-related traits, including disease resistance, in many species. Recently, genetic diversity has been associated with mate preferences in humans. Here we asked whether these preferences are adaptive in terms of obtaining healthier mates. We investigated whether genetic diversity (heterozygosity and standardized mean d(2)) at MHC and nonMHC microsatellite loci, predicted health in 153 individuals. Individuals with greater allelic diversity (d(2)) at nonMHC loci and at one MHC locus, linked to HLA-DRB1, reported fewer symptoms over a four-month period than individuals with lower d(2). In contrast, there were no associations between MHC or nonMHC heterozygosity and health. NonMHC-d(2) has previously been found to predict male preferences for female faces. Thus, the current findings suggest that nonMHC diversity may play a role in both natural and sexual selection acting on human populations. PMID:19633717

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

2009-01-01

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Cotton genetic diversity study by AFLP markers  

Scientific Electronic Library Online (English)

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

Naveed, Murtaza.

2006-07-15

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Microbial diversity in uranium mine waste heaps  

Energy Technology Data Exchange (ETDEWEB)

Two different uranium mine waste heaps near Ronneburg, Thuringia, Germany, which contain the remains of the activity of the former uranium-mining Soviet-East German company Wismut AG, were analyzed for the occurrence of lithotropic leach bacteria. A total of 162 ore samples were taken up to a depth of 5 m. Cell counts of ferrous iron-, sulfur-, sulfur compound-, ammonia-, and nitrite-oxidizing bacteria were determined quantitatively by the most-probable-number technique. Sulfate-, nitrate-, ferric iron-, and manganese-reducing bacteria were also detected. In addition, the metabolic activity of sulfur- and iron-oxidizing bacteria was measured by microcalorimetry. Generally, all microorganisms mentioned above were detectable in heaps. Aerobic and anaerobic microorganisms thrived up to a depth of 1.5 to 2 m. Up to 99% of Thiobacillus ferrooxidans cells, the domaniant leaching bacteria, occurred to this depth. Their numbers correlated with the microbial activity measurements. Samples below 1.5 to 2 m exhibited reduced oxygen concentrations and reduced cell counts for all microorganisms. 63 refs., 3 figs.

Schippers, A.; Hallmann, R.; Wentzien, S.; Sand, W. [Universitaet Hamburg (Germany)

1995-08-01

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Assessing Plant Genetic Diversity by Molecular Tools  

Directory of Open Access Journals (Sweden)

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

Linda Mondini

2009-08-01

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Performance Analysis of Genetic Algorithm for Mining Association Rules  

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Full Text Available Association rule (AR mining is a data mining task that attempts to discover interesting patterns or relationships between data in large databases. Genetic algorithm (GA based on evolution principles has found its strong base in mining ARs. This paper analyzes the performance of GA in Mining ARs effectively based on the variations and modification in GA parameters. The recent works in the past seven years for mining association rules using genetic algorithm is considered for the analysis. Genetic algorithm has proved to generate more accurate results when compared to other formal methods available. The fitness function, crossover rate, and mutation rate parameters are proven to be the primary parameters involved in implementation of genetic algorithm. Variations and modifications introduced in primary GA parameters are found to have greater impact in increasing the accuracy of the system moderately. The speedup of the system is found to increase when the selection and fitness function are altered.

K.Indira

2012-03-01

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Fitness Uniform Selection to Preserve Genetic Diversity  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Hutter, Marcus

2001-01-01

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Genetic diversity of American wild rice species  

Scientific Electronic Library Online (English)

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

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

2011-08-01

19

Genetic diversity of American wild rice species  

Directory of Open Access Journals (Sweden)

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

Elizabeth Ann Veasey

2011-08-01

20

Great ape genetic diversity and population history  

DEFF Research Database (Denmark)

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.

Prado-Martinez, Javier; Sudmant, Peter H.

2013-01-01

 
 
 
 
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Archaeal Diversity in Waters from Deep South African Gold Mines  

Energy Technology Data Exchange (ETDEWEB)

Culture-independent molecular analysis of archaeal communities in waters collected from deep South African gold (Au) mines was performed by PCR-mediated terminal restriction fragment length polymorphism (T-RFLP) analysis of rRNA genes (rDNA) in conjunction with sequencing analysis of archaeal rDNA clone libraries. Water samples represented various environments including: deep fissure water; mine service water; and water from an overlying dolomite aquifer. T-RFLP analysis revealed that the ribotype distribution of archaea varied directly with the source of the water. The archaeal communities in the deep Au mine environments revealed a large phylogenetic diversity; the majority of members were most closely related to uncultivated species. Some archaeal rDNA clones obtained from mine service water and dolomite aquifer water samples were most closely related to the environmental rDNA clones from surface soil (Soil clones) and marine environments (Marine Group I; MGI). Other clones possessed an intermediate phylogenetic affiliation between soil clones and MGI within the Crenarchaea. Fissure water samples, derived from active or dormant geothermal environments, yielded archaeal sequences of novel phylogeny including a novel lineage of Euryarchaeota. These results suggest that deep South African Au mines harbor novel archaeal communities distinct from those observed in other environments. Based on the phylogenetic analysis of archaeal strains and rDNA clones, including these newly discovered archaeal rDNA clones, the evolutionary relationship and the phylogenetic organization of the domain Archaea is reevaluated.

Takai, Ken; Moser, Duane P.; Deflaun, Mary; Onstott, Tullis C.; Fredrickson, Jim K.

2001-12-01

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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

23

A Survey of Association Rule Mining Using Genetic Algorithm  

Directory of Open Access Journals (Sweden)

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.

Anubha Sharma

2012-08-01

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A Survey: Web Log Mining using Genetic Algorithm .  

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Full Text Available Web mining has become a vast area of Research in last few years. Web Mining Which deals with the extraction of interesting knowledge from logging information produced by web server. In this paper we present a survey generate clusters using a multi objective genetic algorithm. Genetic algorithm is also a very hot area of research. In this paper we will compare the error value between FCM(Fuzzy c-means and FCM-MOGA(Fuzzy CMeans multi objective Genetic algorithm. Genetic algorithm follows some steps and produce optimize solution. In using GA standard deviation and iteration value also affected. In this paper we have survey various paper based on Web log mining and FCM and GA.

Ranu Singhal

2013-05-01

25

Conservation of Genetic Diversity in Culture Plants  

Directory of Open Access Journals (Sweden)

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.

MAXIM A.

2010-08-01

26

Population genetic diversity and fitness in multiple environments  

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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.

McGreevy Thomas J

2010-07-01

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A genetic programming based business process mining approach  

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

Turner, Christopher James

2009-01-01

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Threat or opportunity? Landscape genetics in a coal mining area  

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Aknowledgment The area of Sveagruva have experienced several periods of coal mining. This study aim to evaluating changes in vegetation composition, species distributions and genetic structure using a combination of field and molecular analyses, to identify whether or not coal mining have effected plant life in Svea. Investigations on species and gene level were done on two Luzula species, L. confusa Lindeb. and L. nivalis (Laest.) Spreng. No direct correlation was found, and the soil...

Skottvoll, Bente Sved

2013-01-01

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Pyrosequencing and genetic diversity of microeukaryotes  

DEFF Research Database (Denmark)

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

Harder, Christoffer Bugge

2013-01-01

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

Science.gov (United States)

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.

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

2011-01-01

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Genetic diversity enhances restoration success by augmenting ecosystem services.  

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Disturbance and habitat destruction due to human activities is a pervasive problem in near-shore marine ecosystems, and restoration is often used to mitigate losses. A common metric used to evaluate the success of restoration is the return of ecosystem services. Previous research has shown that biodiversity, including genetic diversity, is positively associated with the provision of ecosystem services. We conducted a restoration experiment using sources, techniques, and sites similar to actual large-scale seagrass restoration projects and demonstrated that a small increase in genetic diversity enhanced ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). In our experiment, plots with elevated genetic diversity had plants that survived longer, increased in density more quickly, and provided more ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). We used the number of alleles per locus as a measure of genetic diversity, which, unlike clonal diversity used in earlier research, can be applied to any organism. Additionally, unlike previous studies where positive impacts of diversity occurred only after a large disturbance, this study assessed the importance of diversity in response to potential environmental stresses (high temperature, low light) along a water-depth gradient. We found a positive impact of diversity along the entire depth gradient. Taken together, these results suggest that ecosystem restoration will significantly benefit from obtaining sources (transplants or seeds) with high genetic diversity and from restoration techniques that can maintain that genetic diversity. PMID:22761681

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

2012-01-01

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Genetic diversity of human RNase 8  

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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.

Chan Calvin C

2012-01-01

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

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

Zhongping Cheng

2011-11-01

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Genetic Research: Mining for Medical Treasures  

Science.gov (United States)

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

Cathryn M. Delude (The Writing Group)

2010-07-12

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GENETIC RESOURCES AND DIVERSITY IN PAKISTANI CATTLE  

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Full Text Available Cattle in Pakistan have traditionally been raised for producing bullocks except breeds such as Sahiwal and Red Sindhi which are established milch breeds. General production system is low-input extensive system with crossbreds mainly raised under intensive high input system in the cattle/buffalo colonies to sustain the demand of milk especially during summer, the slump period in buffalo milk. Although, draft breeds are losing utility yet, it will take many generations before they are replaced due to mechanization. Efforts, however, are needed for their in situ conservation and directional selection towards beef. Institutional records indicate weak genetic control for most of the economic traits but accurate recording of performance and pedigrees can improve these estimates. Breeding policy guidelines need adoption in letter and sprit to conserve various breeds. Institutions established for breed improvement need to be restructured for achieving the goals. Adequate diversity in performance and adaptability can be exploited for actual improvement accruing to conservation and development of indigenous cattle resources.

M. SAJJAD KHAN, ZIA-UR REHMAN1 , MUQARRAB A. KHAN2 AND SOHAIL AHMAD3

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Genetic Diversity of Escherichia Coli from Sanandaj  

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Full Text Available Background and Objectives: The Escherichia coli strains are greatly important in nosocomial and community acquired infections. The aim of this study was to determine the transmission of bacterial infections using genetic analysis. Materials and Methods: Two hundred and thirty Escherichia coli strains, isolated from different clinical samples, were characterized by enterobacterial repetitive intergenic consensus (ERIC–PCR technique. The results and the similarity between the strains were determined on the basis of Jaccard similarity coefficient in the SAHN program of the NTSYS-pc software.Results:The ERIC–PCR profiles allowed typing of the 230 isolates into 205 ERIC-types which were grouped into twenty main clusters (C01–C20.The first group makes up 4.34% of the total isolates. Out of the 230 isolates, 34.2% belonged to D phylogenic group which were associated with extra-intestinal samples.Conclusion: Our results showed high diversity in E. coli isolates indicating low rate of hospital infection in our university hospitals. The majority of the isolates belonged to the D phylogenic group.

Serveh Zamani

2013-06-01

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Genetic diversity studies of Papaya meleira virus  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

2014-02-01

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Beauveria bassiana: quercetinase production and genetic diversity  

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Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

2011-03-01

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Beauveria bassiana: quercetinase production and genetic diversity  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

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

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Full Text Available 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 economically important from different regions of the world are reviewed. The genetic diversity of plant species depends on different factors i.e. ecological, geographical, breeding system & anthropogenic effects. High genetic diversity is observed at species level even in small sized population by using AFLP, SSR, & ISSR genetic markers.

Muhammad Younas Khan Barozai, Sazia Saeed

2012-03-01

 
 
 
 
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Genetic diversity of canine olfactory receptors  

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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.

Hitte Christophe

2009-01-01

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Genetic diversity in soybean genotypes with resistance to Heterodera glycines  

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

Ana Paula Oliveira Nogueira

2011-01-01

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Genetic diversity in the endangered tropical tree, Guaiacum sanctum (Zygophyllaceae).  

Science.gov (United States)

Fragmentation of tropical forests has changed continuous tropical landscapes into a network of poorly connected fragments, reducing population sizes and potentially increasing genetic isolation. This study quantifies genetic diversity within and among the 7 extant populations of the endangered tropical tree Guaiacum sanctum in Costa Rica. We describe how genetic diversity differs between populations representing continuous and fragmented habitats. Allozyme analyses were conducted on adult samples from populations representing 2 geographic regions in northwestern Costa Rica. We found high levels of genetic diversity within the species (H(es) = 0.329) and significant but relatively small differences in allele frequencies among populations (G(ST) = 0.101) and between regions (G(ST) = 0.053). We found no differences in genetic diversity between fragmented and continuous populations. Evidence for significant isolation-by-distance (IBD) was seen only when all populations were analyzed. If populations within the 2 regions were analyzed separately, IBD ceased to be significant. Our results suggest that the patterns of genetic diversity observed for G. sanctum may be caused by the ancient separation of populations into 2 disjunct geographic regions with extensive historical rates of gene flow among populations within each region. Recent forest fragmentation has not yet affected patterns of genetic diversity in this species. PMID:20142457

Fuchs, Eric J; Hamrick, James L

2010-01-01

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Genetic diversity and relationships in populations of Bordetella spp.  

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Genetic diversity in 60 strains of three nominal Bordetella species recovered from humans and other mammalian hosts was assessed by analyzing electrophoretically demonstrable allelic variation at structural genes encoding 15 enzymes. Eleven of the loci were polymorphic, and 14 distinctive electrophoretic types, representing multilocus genotypes, were identified. The population structure of Bordetella spp. is clonal, and genetic diversity is relatively limited compared with most other pathogen...

Musser, J. M.; Hewlett, E. L.; Peppler, M. S.; Selander, R. K.

1986-01-01

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Genetic diversity and genetic exchange in Trypanosoma cruzi: dual drug-resistant "progeny" from episomal transformants  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english Extensive characterisation of Trypanosoma cruzi by isoenzyme phenotypes has separated the species into three principal zymodeme groups, Z1, Z2 and Z3, and into many individual zymodemes. There is marked diversity within Z2. A strong correlation has been demonstrated between the strain clusters deter [...] mined by isoenzymes and those obtained using random amplified polymorphic DNA (RAPD) profiles. Polymorphisms in ribosomal RNA genes, in mini-exon genes, and microsatellite fingerprinting indicate the presence of at least two principal T. cruzi genetic lineages. Lineage 1 appears to correspond with Z2 and lineage 2 with Z1. Z1 (lineage 2) is associated with Didelphis. Z2 (lineage 1) may be associated with a primate host. Departures from Hardy-Weinberg equilibrium and linkage disequilibrium indicate that propagation of T. cruzi is predominantly clonal. Nevertheless, two studies show putative homozygotes and heterozygotes circulating sympatrically: the allozyme frequencies for phosphoglucomutase, and hybrid RAPD profiles suggest that genetic exchange may be a current phenomenon in some T. cruzi transmission cycles. We were able to isolate dual drug-resistant T. cruzi biological clones following copassage of putative parents carrying single episomal drug-resistant markers. A multiplex PCR confirmed that dual drug-resistant clones carried both episomal plasmids. Preliminary karyotype analysis suggests that recombination may not be confined to the extranuclear genome.

JR, Stothard; IA, Frame; MA, Miles.

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

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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

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

2014-01-01

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Autism spectrum disorder genetics: diverse genes with diverse clinical outcomes.  

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The last several years have seen unprecedented advances in deciphering the genetic etiology of autism spectrum disorders (ASDs). Heritability studies have repeatedly affirmed a contribution of genetic factors to the overall disease risk. Technical breakthroughs have enabled the search for these genetic factors via genome-wide surveys of a spectrum of potential sequence variations, from common single-nucleotide polymorphisms to essentially private chromosomal abnormalities. Studies of copy-number variation have identified significant roles for both recurrent and nonrecurrent large dosage imbalances, although they have rarely revealed the individual genes responsible. More recently, discoveries of rare point mutations and characterization of balanced chromosomal abnormalities have pinpointed individual ASD genes of relatively strong effect, including both loci with strong a priori biological relevance and those that would have otherwise been unsuspected as high-priority biological targets. Evidence has also emerged for association with many common variants, each adding a small individual contribution to ASD risk. These findings collectively provide compelling empirical data that the genetic basis of ASD is highly heterogeneous, with hundreds of genes capable of conferring varying degrees of risk, depending on their nature and the predisposing genetic alteration. Moreover, many genes that have been implicated in ASD also appear to be risk factors for related neurodevelopmental disorders, as well as for a spectrum of psychiatric phenotypes. While some ASD genes have evident functional significance, like synaptic proteins such as the SHANKs, neuroligins, and neurexins, as well as fragile x mental retardation-associated proteins, ASD genes have also been discovered that do not present a clear mechanism of specific neurodevelopmental dysfunction, such as regulators of chromatin modification and global gene expression. In its sum, the progress from genetic studies to date has been remarkable and increasingly rapid, but the interactive impact of strong-effect genetic lesions coupled with weak-effect common polymorphisms has not yet led to a unified understanding of ASD pathogenesis or explained its highly variable clinical expression. With an increasingly firm genetic foundation, the coming years will hopefully see equally rapid advances in elucidating the functional consequences of ASD genes and their interactions with environmental/experiential factors, supporting the development of rational interventions. PMID:24614762

Talkowski, Michael E; Minikel, Eric Vallabh; Gusella, James F

2014-01-01

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Predicting mining activity with parallel genetic algorithms  

Science.gov (United States)

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.

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

2005-01-01

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Keel A Data Mining Tool: Analysis With Genetic  

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Full Text Available This work is related to the KEEL (Knowledge Extraction basedon Evolutionary Learning tool, an open source software thatsupports data management and provides a platform for theanalysis of evolutionary learning for Data Mining problems ofdifferent kinds including as regression, classification,unsupervised learning. It includes a big collection of evolutionarylearning algorithms based on different approaches: Pittsburgh,Michigan. It empowers the user to perform complete analysis ofany genetic fuzzy system in comparison to existing ones, with astatistical test module for comparison.

Ms. Pooja Mittal

2012-06-01

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Analysis of Genetic Diversity in Bangladeshi Chicken using RAPD Markers  

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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...

Mollah, M. B. R.; Islam, F. B.; Islam, M. S.; Ali, M. A.; Alam, M. S.

2009-01-01

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Genetic diversity in Populus nigra plantations from west of Iran  

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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.  

Afrooz Alimohamadi

2012-12-01

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Rates of inbreeding and genetic diversity in Iranian Holstein Cattle.  

Science.gov (United States)

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

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

2014-10-01

53

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)

54

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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.

Kesinee Gatphayak

2013-01-01

55

Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly.  

Science.gov (United States)

Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations. PMID:23820582

Swaegers, J; Mergeay, J; Therry, L; Larmuseau, M H D; Bonte, D; Stoks, R

2013-11-01

56

Vietnamese chickens: a gate towards Asian genetic diversity  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. Results A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69. The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. Conclusions In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.

Bed'Hom B

2010-06-01

57

Analysis of Genetic Diversity in Bangladeshi Chicken using RAPD Markers  

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Full Text Available 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 variability for studied populations. The four primers yielded a total of 39 distinct bands, 25 of which were polymorphic. Estimation of polymorphic loci, intra-population similarity indices and Nei’s gene diversity suggested that genetic diversities within a population were high in non-descriptive, Frizzle, Naked Neck, Rhode Island Red and White Leghorn chicken populations compared to the commercial layer and broiler populations. The coefficient of gene differentiation (GST = 0.34 and gene flow (Nm = 0.98 values reflected a high level of population differences. UPGMA dendrogram segregated the chicken populations in various degree based on their genetic distance. The overall genetic distance among native chicken was relatively low comparison to the exotic populations. The results of present study might have significant impact on the breeding and conservation of native chicken genetic resources in Bangladesh.

M.B.R. Mollah

2009-01-01

58

Diversity-Oriented Synthesis as a Tool for Chemical Genetics  

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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.

Elena Lenci

2014-10-01

59

Genetic diversity and relationships of Vietnamese and European pig breeds  

International Nuclear Information System (INIS)

Indigenous resources of the Asian pig population are less defined and only rarely compared with European breeds. In this study, five indigenous pig breeds from Viet Nam (Mong Cai, Muong Khuong, Co, Meo, Tap Na), two exotic breeds kept in Viet Nam (Large White, Landrace), three European commercial breeds (Pietrain, Landrace, Large White), and European Wild Boar were chosen for evaluation and comparison of genetic diversity. Samples and data from 317 animals were collected and ten polymorphic microsatellite loci were selected according to the recommendations of the FAO Domestic Animal Diversity Information System (DAD-IS; http://www.fao.org/dad-is/). Effective number of alleles, Polymorphism Information Content (PIC), within-breed diversity, estimated heterozygosities and tests for Hardy-Weinberg equilibrium were determined. Breed differentiation was evaluated using the fixation indices of Wright (1951). Genetic distances between breeds were estimated according to Nei (1972) and used for the construction of UPGMA dendrograms which were evaluated by bootstrapping. Heterozygosity was higher in indigenous Vietnamese breeds than in the other breeds. The Vietnamese indigenous breeds also showed higher genetic diversity than the European breeds and all genetic distances had a strong bootstrap support. The European commercial breeds, in contrast, were closely related and bootstrapping values for genetic distances among them were below 60%. European Wild Boar displayed closer r60%. European Wild Boar displayed closer relation with commercial breeds of European origin than with the native breeds from Viet Nam. This study is one of the first to contribute to a genetic characterization of autochthonous Vietnamese pig breeds and it clearly demonstrates that these breeds harbour a rich reservoir of genetic diversity. (author)

60

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)

 
 
 
 
61

Genetic diversity in black howler monkeys (Alouatta pigra) from Belize.  

Science.gov (United States)

To assess the level of genetic variation in a threatened black howler monkey (Alouatta pigra) population, we examined 36 allozyme loci and restriction fragment profiles of mitochondrial DNA (mtDNA). Mean heterozygosity at allozyme loci was only 0.021 and 5.6 percent of the loci were polymorphic. Analyses of mtDNA also revealed low genetic diversity compared with other primates. F-statistics revealed no significant genetic heterogeneity among troops within the Bermudian Landing preserve, but did indicate a deficiency of heterozygotes at one of the two loci. We explore several explanations for this result, which is unexpected in a socially structured primate. Low genetic diversity in this population may reflect its history of demographic bottlenecks. PMID:9098502

James, R A; Leberg, P L; Quattro, J M; Vrijenhoek, R C

1997-03-01

62

Population genetic diversity and fitness in multiple environments  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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. Devel...

McGreevy Thomas J; Kuhn Anne; Grear Jason S; Gutjahr-Gobell Ruth; Champlin Denise M; Markert Jeffrey A; Roth Annette; Bagley Mark J; Nacci Diane E

2010-01-01

63

Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived...

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

2012-01-01

64

Genetic diversity in the interference selection limit.  

Science.gov (United States)

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 individual mutations play a relatively minor role. Instead, similar to models of quantitative genetics, molecular evolution is determined by the variance in fitness within the population, defined over an effectively asexual segment of the genome (a "linkage block"). We exploit this insensitivity in a new "coarse-grained" coalescent framework, which approximates the effects of many weakly selected mutations with a smaller number of strongly selected mutations that create the same variance in fitness. This approximation generates accurate and efficient predictions for silent site variability when interference is common. However, these results suggest that there is reduced power to resolve individual selection pressures when interference is sufficiently widespread, since a broad range of parameters possess nearly identical patterns of silent site variability. PMID:24675740

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

2014-03-01

65

Genetic diversity of noroviruses in Brazil  

Scientific Electronic Library Online (English)

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

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

2011-12-01

66

Equipment selection for working face in coal mines by genetic programming  

Energy Technology Data Exchange (ETDEWEB)

This paper introduces the basic principle and procedure of genetic programming - a new approach for optimization. It is used to predict the production and productivity as well as to select equipment for working faces in mines. The application in a Chinese coal mine shows its prospective potency in mining engineering. 3 refs., 4 figs., 3 tabs.

Yun, Q.X.; Wang, Z. [Xi' an University of Architecture and Technology, Xi' an Shaanxi Province (China)

1999-07-01

67

[Diversity of nitrogen-fixing microorganisms in biological soil crusts of copper mine wastelands].  

Science.gov (United States)

Biological soil crusts play an important role in increasing the accumulation of organic matter and nitrogen in re-vegetated mining wastelands. The diversity of nitrogen-fixing microorganisms in three types of biological soil crusts (algal crust, moss crust and algal-moss crust) from two wastelands of copper mine tailings were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis, based on the nifH gene of diazotrophs, to investigate: The diversity of nifH gene in the crusts of mine wastelands, and whether and how the nifH gene diversity in the crusts could be affected by the development of plant communities. The algal crust on the barren area displayed the highest nifH gene diversity, followed by the algal-moss crusts within vascular plant communities, and the moss crust displayed the lowest nifH gene diversity. The diversity of diazotrophs in algal-moss crust within vascular plant communities decreased with the increase of height and cover of vascular plant communities. No significant relationship was found between wasteland properties (pH, water content, contents of organic matter, nitrogen and phosphorus and heavy metal concentration) and nifH gene diversity in the crusts. Sequencing and phylogenetic analysis indicated that most nitrogen-fixing taxa in the crusts of mine wastelands belonged to Cyanobacteria, especially nonheterocystous filamentous Cyanobacteria. PMID:25223036

Zhan, Jing; Yang, Gui-De; Sun, Qing-Ye

2014-06-01

68

Maintenance of genetic diversity through plant-herbivore interactions.  

Science.gov (United States)

Identifying the factors governing the maintenance of genetic variation is a central challenge in evolutionary biology. New genomic data, methods and conceptual advances provide increasing evidence that balancing selection, mediated by antagonistic species interactions, maintains genome-wide functionally important genetic variation within species and natural populations. Because diverse interactions between plants and herbivorous insects dominate terrestrial communities, they provide excellent systems to address this hypothesis. Population genomic studies of Arabidopsis thaliana and its relatives suggest spatial variation in herbivory maintains adaptive genetic variation controlling defense phenotypes, both within and among populations. Conversely, inter-species variation in plant defenses promotes adaptive genetic variation in herbivores. Emerging genomic model herbivores of Arabidopsis could illuminate how genetic variation in herbivores and plants interact simultaneously. PMID:23834766

Gloss, Andrew D; Nelson Dittrich, Anna C; Goldman-Huertas, Benjamin; Whiteman, Noah K

2013-08-01

69

Assessment of genetic diversity in Cattleya intermedia Lindl. (Orchidaceae  

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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 study 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.

Nelson Barbosa Machado Neto

2011-10-01

70

Analysis of Genetic Diversity of Yangzhou Chicken by Microsatellite Markers  

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Full Text Available Genetic variation at 20 microsatellite loci and genetic diversity were examined for Yangzhou Chicken. Observed and effective number of alleles across the microsatellite loci varied from 2-6 with an overall mean of 3.778 and 2.404, respectively. Observed and effective heterozygosity varied from 0.129-0.755 with an average of 0.422 and 0.517, respectively. Average polymorphism information content was 0.464. The genetic structure indicated that Yangzhou Chickens have substantial genetic variation. Population showed fairly high level of inbreeding (Fis = 0.184 and global heterozygote deficit. The allele frequency distribution is displayed an L shape, suggesting that no recent bottleneck affecting the genetic variability occurred. The information generated in this study will greatly aid in the establishment of effective breeding strategies for Yangzhou Chicken and may further be utilized for studying differentiation and relationships among different chicken breeds.

G.Q. Liu

2008-01-01

71

Carassius genetic diversity investigation from Tautesti Lake (Iasi County  

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Full Text Available n this experiment we investigated the genetic diversity of Carassius gibelio Bloch, individuals, from Tautesti (Iasi County pond, using the sequencing of cytochrome b as a codominat-marker. The analysis of cytochrome b first part gene coding region has permitted to establish if there is a wild population or the pond was repopulated in the last years.

Dragos Lucian Gorgan

2010-12-01

72

Coalescence and genetic diversity in sexual populations under selection.  

Science.gov (United States)

In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting interference between linked alleles reduces the efficiency of selection and distorts patterns of genetic diversity. Inference of evolutionary history from diversity shaped by linked selection requires an understanding of these patterns. Here, we present a simple but powerful scaling analysis identifying the unit of selection as the genomic "linkage block" with a characteristic length, , determined in a self-consistent manner by the condition that the rate of recombination within the block is comparable to the fitness differences between different alleles of the block. We find that an asexual model with the strength of selection tuned to that of the linkage block provides an excellent description of genetic diversity and the site frequency spectra compared with computer simulations. This linkage block approximation is accurate for the entire spectrum of strength of selection and is particularly powerful in scenarios with many weakly selected loci. The latter limit allows us to characterize coalescence, genetic diversity, and the speed of adaptation in the infinitesimal model of quantitative genetics. PMID:24019480

Neher, Richard A; Kessinger, Taylor A; Shraiman, Boris I

2013-09-24

73

HIV Genetic Diversity and Drug Resistance  

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Full Text Available Most of the current knowledge on antiretroviral (ARV drug development and resistance is based on the study of subtype B of HIV-1, which only accounts for 10% of the worldwide HIV infections. Cumulative evidence has emerged that different HIV types, groups and subtypes harbor distinct biological properties, including the response and susceptibility to ARV. Recent laboratory and clinical data highlighting such disparities are summarized in this review. Variations in drug susceptibility, in the emergence and selection of specific drug resistance mutations, in viral replicative capacity and in the dynamics of resistance acquisition under ARV selective pressure are discussed. Clinical responses to ARV therapy and associated confounding factors are also analyzed in the context of infections by distinct HIV genetic variants.

André F. Santos

2010-02-01

74

Community genetics: resource addition has opposing effects on genetic and species diversity in a 150-year experiment.  

Science.gov (United States)

We used the Park Grass Experiment, begun in 1856, to test alternative hypotheses about the relationship between genetic diversity and plant species diversity. The niche variation hypothesis predicts that populations with few interspecific competitors and hence broader niches are expected to contain greater genetic diversity. The coexistence hypothesis predicts that genetic diversity within species favours coexistence among species and therefore species and genetic diversity should be positively correlated. Amplified Fragment Length Polymorphism (AFLP) markers were used to measure the genetic diversity of populations of Anthoxanthum odoratum growing in 10 plots of differing species richness that lie along resource and soil pH gradients. Genetic diversity in A. odoratum was positively correlated with the number of resources added to a plot, but not correlated with species richness. However, separate analyses have shown a negative correlation between resource addition and species richness at Park Grass and elsewhere, so genetic and species diversity appear to respond in opposite directions. PMID:19143828

Silvertown, Jonathan; Biss, Pamela M; Freeland, Joanna

2009-02-01

75

Review of genetic diversity in malaria vectors (Culicidae: Anophelinae).  

Science.gov (United States)

We review previous studies on the genetic diversity of malaria vectors to highlight the major trends in population structure and demographic history. In doing so, we outline key information about molecular markers, sampling strategies and approaches to investigate the causes of genetic structure in Anopheles mosquitoes. Restricted gene flow due to isolation by distance and physical barriers to dispersal may explain the spatial pattern of current genetic diversity in some Anopheles species. Nonetheless, there is noteworthy disagreement among studies, perhaps due to variation in sampling methodologies, choice of molecular markers, and/or analytical approaches. More refined genealogical methods of population analysis allowing for the inclusion of the temporal component of genetic diversity facilitated the evaluation of the contribution of historical demographic processes to genetic structure. A common pattern of past unstable demography (i.e., historical fluctuation in the effective population size) by several Anopheles species, regardless of methodology (DNA markers), mosquito ecology (anthropophilic vs zoophilic), vector status (primary vs secondary) and geographical distribution, suggests that Pleistocene environmental changes were major drivers of divergence at population and species levels worldwide. PMID:21864721

Loaiza, J R; Bermingham, E; Sanjur, O I; Scott, M E; Bickersmith, S A; Conn, J E

2012-01-01

76

GENETIC RESOURCES AND DIVERSITY IN DAIRY BUFFALOES OF PAKISTAN  

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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.

M. SAJJAD KHAN, NAZIR AHMAD1 AND MUQARRAB ALI KHAN2

2007-10-01

77

Genetic diversity and molecular genealogy of local silkworm varieties  

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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.

Zhouhe Du

2013-03-01

78

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

Directory of Open Access Journals (Sweden)

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.

Kesinee Gatphayak

2013-03-01

79

ESTIMATION OF GENETIC DIVERSITY IN LENTIL GERMPLASM  

Directory of Open Access Journals (Sweden)

Full Text Available The experiment was to determine the relation-ship between yield and yield contributing traits and select the promising genotypes. Twenty two genotypes and two check varieties were evaluated at Bangladesh Agricultural Research Institute, Joydebpur, Gazipur during Rabi season, 2008-2009 in a RCBD with three replications. Significant variation among the lentil genotypes were observed in respect of days to first flowering, days to maturity, plant height, pod/plant, 100-seed weight and yield. The genotype BLX-02009-06-3 flowered and matured earlier. Among the test entries, BLX-02009-18-3 and BLX-02009-18-1 were tall. The highest number of pod per plant was obtained in BLX-02009-04-5. The large seed size was found in LR9-130 and LR9-25. The highest yield was found in BLX-02009-04-1 followed by BLX-02009-04-5 than the two check varieties. Difference between genotypic coefficient of variation and phenotypic coefficient of variation was small for the traits as plant height, days to maturity, days to first flowering and 100-seed weight. Among different traits, grain yield had high variation both at genotypic and phenotypic level due to the differences of genetic materials and also the differences of the environment. Grain yield was found to be positively and significantly correlated with plant height, pods/plant, 100-seed weight at genotypic and phenotypic levels.

A.K.M.M. Alam

2011-06-01

80

Genetic diversity of cyanobacteria in four eutrophic lakes.  

Science.gov (United States)

Recent studies indicate genetic diversity of cyanobacteria in eutrophic lakes is not represented well by culture collections or morphology. Yet, few studies have investigated genetic richness and evenness of cyanobacteria using culture-independent methods. We compared the genetic structure of cyanobacteria supported by four neighboring eutrophic lakes during the ice-free season. The partial phycobilincpcB/A genes plus intergenic spacer (PC-IGS) was used as a genetic marker.Sequences were phylogeneticallygrouped by maximum likelihood into genotypes representing sub-genera of the major taxa. Genotypes fell into genera commonly observed by microscopy in these lakes including Microcystis, Aphanizomenon, Chroococcus, Anabaena, and Cylindrospermopsis. Only three genotypes were shared among all four lakes, despite significant water flowage between lakes.A Parsimony P-test indicated lakes were significantly (p=0.01) clustered on the maximum likelihood tree. Pairwise differences using Unifrac distance were moderately or not significant. Analysis of molecular variance (AMOVA) indicated genetic variation among all genotypes (?=0.06, p<0.001) and 94% of variability occurred within lakes rather than between lakes (6%), explaining the lack of pairwise differences between lakes. Lorenze curves of genotype abundance in each lake showed genetic structure was only moderately uneven (Gini coefficients of 0.37-0.5) indicating lakes did not support dominant genotypes. Overall, results from this study suggest diversity of cyanobacteria is shaped by heterogeneity within lakes (temporally or spatially) and relatively even population structures. PMID:21707672

Miller, Todd R; McMahon, Katherine D

2011-11-01

 
 
 
 
81

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

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Full Text Available 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 countries. NTSYS (Numerical Taxonomy and Multivariate Analy-sis System and SAS (Statistical Analysis System statistical software was used to analyse data. The number of alleles recorded per marker ranged from 1 to 16 (mean = 5. Cluster analysis showed a clear separation of cultivars from S. officinarum clones. The average of genetic similarity between sugarcane genotypes studied was 0.664, while genetic diversity analysis revealed a very different group (H: 0.973. An interesting results concerned CC 91-1880 distribu-tion very close to that of Q genotypes from Australia and also S. officinarum clones, suggesting that this cultivar would be a good candidate for further studies by breeders. The results obtained are useful for CENICAÑA's breed­ing program because, in spite of the genetic homogeneity present in today's sugarcane cultivars, it is clear that allelic variants are present in some of these cultivars and could be used in the new breeding projects. Key words: Sugarcane, genetic diversity, microsatellites, molecular markers, Saccharum officinarum.

John J. Riascos

2007-05-01

82

[Intraspecific genetic diversity: monitoring and principles of conservation].  

Science.gov (United States)

Genetic differentiation of a species, estimated on average according to the aggregate of allozyme loci, corresponds to a selectively neutral process. Such evolution is traditionally regarded as Markov's chain, in which the genetic dynamics of a population cannot be predicted for more than one generation. According to the concept of population systems, however, intraspecific differentiation can be interpreted as a process with memory, which retains information about the genetic structure of the ancestral population. This memory is maintained due to the organizing effect of gene immigration whose intensity is the higher, the lower the effective size of the local population. The ratio between intra- and inter-population components of gene diversity is maintained at a stable (optimal) level. Consequently, it can be regarded as the basic "reference point" in genetic monitoring of subdivided populations that have evolved under anthropogenic pressure. Such influences, altering established systemic links, distort the balance between differentiation and integration of the species gene pool and lead to adverse effects. Depending on the predominance of the inter- or intra-population component of gene diversity, these influences may be equivalent to outbreeding with an increased segregational load or to inbreeding, respectively. In the first case, the genetic process is adaptive, and, provided the negative influence is terminated in due time, it is possible to restore the genetic structure and normalize reproduction of gene pools in populations. In the second case, the genetic process is maladaptive and leads to degradation of populations. If one knows principles of the systemic organization of a species, it is possible to develop an approach to solving the problem of conservation of biological diversity by organizing non-exhaustive wildlife management. PMID:8543138

Altukhov, Iu P

1995-10-01

83

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

Science.gov (United States)

Oenocarpus mapora is an Amazonian palm species commonly used by native populations for food and in folk medicine. We measured genetic variability, using RAPD markers, of material kept in a germplasm bank composed of accessions sampled from the Brazilian Amazon. These included 74 individuals from 23 accessions sampled from 9 localities in three States of the Brazilian Amazon. Jaccard genetic similarities were calculated based on 137 polymorphic bands, amplified by 15 primers. Dendrograms constructed based on the genetic similarities among individuals and sample localities demonstrated genetic separation of Acre State from the States of Amazonas and Pará. Two models in three hierarchical levels were considered for AMOVA: one considering the grouping of sampling sites in each state, and the other considering sampling sites in each subgroup formed by the dendrograms. The first model showed no significant genetic variation among states. On the other hand, genetic variation among subgroups was significant. In this model, the within-sample-site genetic diversity was 47.15%, which is considered to be low, since O. mapora is allogamous. By means of Bayesian analysis, the sample sites were clustered into five groups, and their distribution was similar to what we found in the dendrograms based on genetic similarity. PMID:23212338

Moura, E F; de Oliveira, M S P

2012-01-01

84

Genetic diversity in some local chicken breeds using microsatellite markers  

Directory of Open Access Journals (Sweden)

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

M. Cassandro

2010-04-01

85

Genetic diversity affects colony survivorship in commercial honey bee colonies  

Science.gov (United States)

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.

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

2013-08-01

86

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

Science.gov (United States)

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

87

Evaluation of genetic diversity in different Pakistani wheat land races  

International Nuclear Information System (INIS)

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

88

Exploiting a wheat EST database to assess genetic diversity.  

Science.gov (United States)

Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F(2) individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01. PMID:21637582

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

2010-10-01

89

Genetic diversity and environmental associations of sacsaoul ( Haloxylon ammodendron)  

Science.gov (United States)

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

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

2003-07-01

90

[Genetic diversity of Sabina vulgaris populations at different succession stages].  

Science.gov (United States)

By means of random amplified polymorphic DNA markers, a molecular ecological study was made with Sabina vulgaris populations at 4 succession stages in Maowusu sandy grassland, aimed to reveal the relationships between molecular variation and succession stages. A total of 17 random primers were selected for amplification, and 190 repetitive loci were produced, of which, 173 were polymorphic. The data were analyzed by POPGENE 3. 2 Version 1. 31. The results showed that the genetic diversity of S. vulgaris populations was high, and changed with succession stages. The percentage of polymorphic loci in each S. vulgaris population ranged from 64.21% to 74.63%, with the highest in early succession stage Artemisia ordosica + S. vulgaris on semi-fixed sand dunes, and the lowest in sub-climax stage S. vulgaris on fixed dunes. The genetic differentiation among the populations was small (G(st) = 0.1761), and 82.39% of it was within the populations. Cluster analysis demonstrated that the populations at similar succession stage clustered together, suggesting that the genetic differentiation was closely related to succession stage. The genetic diversity indicated by Nei index ranged in 0. 2163 -0. 2564, and the gene flow (N(m) *) was 2.7972, indicating that more gene exchange occurred within the populations, which prevented the genetic differentiation among the populations at different succession stages. PMID:17269316

Hong, Yu; Wang, Lin-He; Zhang, Guosheng; Enhe, Bayaer; Liang, Xiaorong

2006-11-01

91

Mobilizing diversity: transposable element insertions in genetic variation and disease  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Transposable elements (TEs comprise a large fraction of mammalian genomes. A number of these elements are actively jumping in our genomes today. As a consequence, these insertions provide a source of genetic variation and, in rare cases, these events cause mutations that lead to disease. Yet, the extent to which these elements impact their host genomes is not completely understood. This review will summarize our current understanding of the mechanisms underlying transposon regulation and the contribution of TE insertions to genetic diversity in the germline and in somatic cells. Finally, traditional methods and emerging technologies for identifying transposon insertions will be considered.

O'Donnell Kathryn A

2010-09-01

92

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

Directory of Open Access Journals (Sweden)

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.

Deyun Wang

2013-09-01

93

Medical Association Rule Mining Using Genetic Network Programming  

Science.gov (United States)

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

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

94

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

Scientific Electronic Library Online (English)

Full Text Available SciELO South Africa | Language: English Abstract in english 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.

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

95

Genetic diversity in Brazilian tall coconut populations by microsatellite markers  

Directory of Open Access Journals (Sweden)

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

Francisco Elias Ribeiro

2013-12-01

96

Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers  

Directory of Open Access Journals (Sweden)

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.

Ermis Yanes Paz

2012-01-01

97

The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity.  

Science.gov (United States)

Flavonoids are representative plant secondary products. In the model plant Arabidopsis thaliana, at least 54 flavonoid molecules (35 flavonols, 11 anthocyanins and 8 proanthocyanidins) are found. Scaffold structures of flavonoids in Arabidopsis are relatively simple. These include kaempferol, quercetin and isorhamnetin for flavonols, cyanidin for anthocyanins and epicatechin for proanthocyanidins. The chemical diversity of flavonoids increases enormously by tailoring reactions which modify these scaffolds, including glycosylation, methylation and acylation. Genes responsible for the formation of flavonoid aglycone structures and their subsequent modification reactions have been extensively characterized by functional genomic efforts - mostly the integration of transcriptomics and metabolic profiling followed by reverse genetic experimentation. This review describes the state-of-art of flavonoid biosynthetic pathway in Arabidopsis regarding both structural and genetic diversity, focusing on the genes encoding enzymes for the biosynthetic reactions and vacuole translocation. PMID:23473981

Saito, Kazuki; Yonekura-Sakakibara, Keiko; Nakabayashi, Ryo; Higashi, Yasuhiro; Yamazaki, Mami; Tohge, Takayuki; Fernie, Alisdair R

2013-11-01

98

Peach genetic resources: diversity, population structure and linkage disequilibrium  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome...

Li, Xiong-wei; Meng, Xian-qiao; Jia, Hui-juan; Yu, Ming-liang; Ma, Rui-juan; Wang, Li-rong; Cao, Ke; Shen, Zhi-jun; Niu, Liang; Tian, Jian-bao; Chen, Miao-jin; Xie, Ming; Arus, Pere; Gao, Zhong-shan; Aranzana, Maria J.

2013-01-01

99

Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 represe...

Ermis Yanes Paz; Katia Gil; Laureano Rebolledo; Andrés Rebolledo; Daniel Uriza; Octavio Martínez; Miriam Isidrón; Leyanes Díaz; José Carlos Lorenzo; June Simpson

2012-01-01

100

Genetic diversity among isolates of stemphylium solani from cotton  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The fungus Stemphylium solani causes leaf blight of tomato (Lycopersicon esculentum) in Brazil. In recent years, severe epidemics of a new leaf blight of cotton (Gossipium hyrsutum) caused by S. solani occurred in three major cotton-growing Brazilian states (PR, MT and GO). Molecular analysis was performed to assess the genetic diversity among the S. solani isolates from cotton, and to verify their relationship with representative S. solani isolates from tomato. Random amplified polymorphic D...

Mehta, Y. R.

2001-01-01

 
 
 
 
101

Genetic diversity of Prunus rootstocks analyzed by RAPD markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have used RAPD markers to characterize Prunus rootstocks from different species, both commercial, and selected clones from the breeding program at Aula Dei Experimental Station (Zaragoza, Spain). Molecular markers were used to study the genetic variation among different species, and within species. Forty one genotypes were used in this study. They included P. amygdalo-persica, and P. persica × P. davidiana hybrids; P. cerasifera, P. domestica, and P. insititia clones, and other diverse in...

Casas Cendoya, Ana Mari?a; Igartua Arregui, Ernesto; Moreno Sa?nchez, Mari?a A?ngeles

1999-01-01

102

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)

103

Indigenous cattle in Sri Lanka: production systems and genetic diversity  

International Nuclear Information System (INIS)

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

104

Assessment of genetic diversity in cowpea (Vigna unguiculata  

Directory of Open Access Journals (Sweden)

Full Text Available Sixty six genotypes of cowpea (Vigna unguiculata (L. Walp were investigated to understand the extent of genetic diversitythrough twelve quantitative traits. Mahalanobis’s D2 analysis established the presence of wide genetic diversity among thesegenotypes by the formation of 23 clusters. Cluster I had the maximum number of genotypes i.e 22 and cluster 23 had onlyone genotype. Intra cluster distance analysis revealed that the minimum intra cluster distance was observed in the cluster II.The inter-cluster distance (D was found to be the maximum between the clusters XXII and XXIII and the same wasminimum between clusters II and V. The results indicated that grain yield per plant contributed maximum to the totaldivergence followed by 100 seed weight and days to 50% flowering. Number of branches per plant had least contribution tothe total divergence followed by petiole length. The existence of wide genetic diversity among the types chosen from thesame geographical location was obviously seen. In the present study, the variety Vellayani local had the maximum value forplant height and pod length and thereby distinguished from other varieties and it is present singly in the cluster XXIII. Henceit is proved to be widely divergent, since its yield is high, it can be used for further crossing and yield improvement. Thecluster XVIII had the highest cluster mean values for number of clusters per plant and the cluster XIV has the highest meanvalue for grain yield per plant. These two clusters may be utilized in crossing programme which may yield in a widespectrum of variability and for selection for seed yield in the subsequent generations. The clustering pattern of the varietiesin the present study clearly indicated that there was no parallelism between genetic and geographic diversities. Based on themean performance and genetic divergence, the genotypes Vellayani local, NBC 7, Lola, CP 18, CP 150, ACM 05-07 can beused for crossing and further selection.

R.M.Nagalakshmi, R. Usha Kumari and M. B. Boranayaka

2010-07-01

105

Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.).  

Science.gov (United States)

We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines 'Lynx-037DH' and 'Monty-028DH'. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

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

2012-01-01

106

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

Directory of Open Access Journals (Sweden)

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

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

2010-07-01

107

Genetic diversity for fermentable carbohydrates production in alfalfa  

Energy Technology Data Exchange (ETDEWEB)

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

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

2009-07-01

108

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

Directory of Open Access Journals (Sweden)

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.

Mohammad Naderi Dehkordi

2009-08-01

109

Genetic diversity between Piedmontese, Maremmana, and Podolica cattle breeds.  

Science.gov (United States)

One hundred twenty animals of three native Italian cattle breeds, Piedmontese, Maremmana, and Podolica, were genetically characterized at 21 microsatellite loci located on 13 chromosomes. Allele numbers ranged from 3 to 19; average gene diversity ranged from 0.206 to 0.878 (average 0.738). The breed that preserved the highest genetic variability was the Podolica, where the chosen markers show the highest gene diversity (0.741) and the highest heterozygosity (0.155). The lowest inbreeding rate (0.102) was registered by the Piedmontese. Genetic distances were 0.069 (Piedmontese versus Maremmana), 0.050 (Piedmontese versus Podolica), and 0.041 (Maremmana versus Podolica) and reflect the different phylogenetic origins of the breeds: Maremmana and Podolica originated from the Grey Steppe cattle group, while Piedmontese belongs to the Northern Italy Lowland cattle group. Observed heterozygosity was not significantly different from expected in any of the breeds, which is an indication that they maintain a random mating structure. The probabilistic assignment of all sampled individuals to three theoretical populations, on the basis of allele frequencies, indicated that 82% of Piedmontese, 66% of Maremmana, and 33% of Podolica can be assigned to the appropriate breed with a probability higher than 90%. This result very well reflects the impact of the selection activity on the breed genetic structure. The chosen microsatellites proved to be a good tool for describing the correct reality of the analyzed populations, but they are not sufficient to discriminate between breeds. PMID:15220392

Moioli, B; Napolitano, F; Catillo, G

2004-01-01

110

Characterization and genetic diversity analysis of cotton cultivars using microsatellites  

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

Cândida H.C. de Magalhães Bertini

2006-01-01

111

Genetic diversity of hydrothermal-vent barnacles in Manus Basin  

Science.gov (United States)

We evaluated mitochondrial cytochrome oxidase I genetic diversity of two barnacle species (Eochionelasmus ohtai manusensis, Vulcanolepas cf. parensis) at three sites in Manus Basin (Solwara 1, South Su, Solwara 8). There was no evidence for within-site or between-site genetic differentiation for either species. While E. ohtai manusensis showed limited genetic variation, V. cf. parensis showed greater variation, with sequences distributed between two divergent groups. Assuming the cytochrome oxidase I gene is not under selection, significantly negative Tajima's D in E. ohtai manusensis is consistent with a recent population expansion due to a bottleneck or founder effect, whereas V. cf. parensis (combined groups) did not depart from a stable effective population size. Considering the groups separately, V. cf. parensis Group 1 (but not Group 2) showed a negative Tajima's D, indicating these groups may have encountered different historical demographic conditions. Data reported here are part of a baseline study against which recovery of genetic diversity following mineral extraction at Solwara 1 can be measured.

Plouviez, Sophie; Schultz, Thomas F.; McGinnis, Gwendolyn; Minshall, Halle; Rudder, Meghan; Van Dover, Cindy L.

2013-12-01

112

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...

113

Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction  

Science.gov (United States)

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

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

114

A genetic algorithm approach to recognition and data mining  

Energy Technology Data Exchange (ETDEWEB)

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

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

1996-12-31

115

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

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Objective. To determine and evaluate the genetic diversity of six populations of red hybrid tilapia, with the purpose to assess the potential benefit of a future breeding program conducted at the Research Center for Aquaculture (Ceniacua), Colombia. Material and methods. A total of 300 individuals, representing a wide genetic variability, were genotyped using a fluorescent microsatellite marker set of 5 gene-based SSRs in 6 different farms belonging to 4 States of Colombia. Results. The resul...

Boris Briñez R; Xenia Caraballo O.; Marcela Salazar V.

2011-01-01

116

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

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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.

Dumasy Jean-François

2012-05-01

117

Genetic diversity and bottleneck studies in the Marwari horse breed.  

Science.gov (United States)

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(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 M 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. PMID:16385161

Gupta, A K; Chauhan, M; Tandon, S N

2005-12-01

118

Genetic Diversity Among Irrigated Traditional and Modern Rice Germplasm  

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

Khaleda Akter

2002-01-01

119

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

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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.

Chen Charlotte

2012-06-01

120

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: English Abstract in english 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.

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

2013-09-15

 
 
 
 
121

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

122

Genetic diversity of breeding popcorn lines determined by SSR markers  

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: English Abstract in english 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.

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

123

Feature Selection in Data-Mining for Genetics Using Genetic Algorithm  

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Full Text Available We discovered genetic features and environmental factors which were involved in multifactorial diseases. To exploit the massive data obtained from the experiments conducted at the General Hospital, Chennai, data mining tools were required and we proposed a 2-Phase approach using a specific genetic algorithm. This heuristic approach had been chosen as the number of features to consider was large (upto 3654 for biological data under our study. Collected data indicated for pairs of affected individuals of a same family their similarity at given points (locus of their chromosomes. This was represented in a matrix where each locus was represented by a column and each pairs of individuals considered by a row. The objective was first to isolate the most relevant associations of features and then to class individuals that had the considered disease according to these associations. For the first phase, the feature selection problem, we used a genetic algorithm (GA. To deal with this very specific problem, some advanced mechanisms had been introduced in the genetic algorithm such as sharing, random immigrant, dedicated genetic operators and a particular distance operator had been defined. Then, the second phase, a clustering based on the features selected during the previous phase, will use the clustering algorithm k-means.

V. N. Rajavarman

2007-01-01

124

Exploiting a wheat EST database to assess genetic diversity  

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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.

Ozge Karakas

2010-01-01

125

Origin, genetic diversity, and population structure of Chinese domestic sheep.  

Science.gov (United States)

To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions. PMID:16704910

Chen, Shan-Yuan; Duan, Zi-Yuan; Sha, Tao; Xiangyu, Jinggong; Wu, Shi-Fang; Zhang, Ya-Ping

2006-07-19

126

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

Science.gov (United States)

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

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

2012-01-01

127

Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea  

Science.gov (United States)

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

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

2014-01-01

128

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

Science.gov (United States)

The plant pathogenic bacterial genus Pectobacteirum consists of heterogeneous strains. The P. carotovorum species is a complex strain showing divergent characteristics, and a new subspecies named P. carotovorum subsp. brasiliensis has been identified recently. In this paper, we re-identified the P. carotovorum subsp. brasiliensis isolates from those classified under the subspecies carotovorum and newly isolated P. carotovorum subsp. brasiliensis strains. All isolates were able to produce plant cell-wall degrading enzymes such as pectate lyase, polygalacturonase, cellulase and protease. We used genetic and biochemical methods to examine the diversity of P. carotovorum subsp. brasiliensis isolates, and found genetic diversity within the brasiliensis subsp. isolates in Korea. The restriction fragment length polymorphism analysis based on the recA gene revealed a unique pattern for the brasiliensis subspecies. The Korean brasiliensis subsp. isolates were divided into four clades based on pulsed-field gel electrophoresis. However, correlations between clades and isolated hosts or year could not be found, suggesting that diverse brasiliensis subsp. isolates existed. PMID:25288994

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

2014-06-01

129

Limited genetic diversity preceded extinction of the Tasmanian tiger.  

Science.gov (United States)

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

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

2012-01-01

130

Genetic diversity of Gallibacterium isolates from California turkeys.  

Science.gov (United States)

The aim of the present study was to investigate the genetic diversity of Gallibacterium isolates recovered from lesions in turkeys. Gallibacterium has been isolated from various bird species including turkeys, but no large investigations have yet been made to characterize isolates from turkeys genetically. We therefore genotyped 53 Gallibacterium isolates obtained from turkeys between 1998 and 2004. Fifty isolates originated from 29 different flocks in California and the remaining three came from three German turkey flocks. All were recovered from birds with lesions, mainly in the upper respiratory tract. Five chicken isolates from California and five Gallibacterium reference strains were also included. Amplified fragment length polymorphism analysis demonstrated substantial genetic diversity among the Gallibacterium isolates. However, we also demonstrated that some Gallibacterium clones were present in consecutive rotations at the same farm during the entire 6-year observation period and were present in different flocks from different farms. Similarly, the same clone was identified from two of the three German flocks. Further investigation of the spread of Gallibacterium between turkey flocks, including infections acquired from chickens or wild birds, should be carried out. PMID:17497336

Bojesen, A M; Shivaprasad, H L

2007-06-01

131

Genetic diversity in populations of Erica andevalensis, a vulnerable metallophyte species from the Iberian Peninsula  

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Full Text Available Erica andevalensis is an endemic vulnerable species that grows in metal-polluted soils from the Iberian Pyrite Belt. The genetic diversity of six E. andevalensis populations from Portugal and Spain was studied using PCR Inter-simple sequence repeat (ISSR. The obtained data showed that a there is a very low genetic diversity within the populations from Portugal, and b the populations sampled in Portugal are genetically different from the Spanish populations. The lack of genetic diversity in the Portuguese populations suggests the existence of founder effects and subsequent genetic isolation. Plant genetic diversity was also low in the Spanish populations, although the analysis showed that the studied populations were different among them. A Mantel test of the correlation between genetic and geographic distances was significant evidencing the genetic isolation by distance of the studied populations. The distinctiveness and low genetic diversity of the Portuguse populations emphasizes the importance of taking measures for their conservation.

H. Freitas

2008-11-01

132

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

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

Abrams Elaine J

2006-03-01

133

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)

134

Genetic diversity of subgroup 1 ilarviruses from Eastern Australia.  

Science.gov (United States)

This is the first report of the genetic diversity within ilarvirus subgroup 1 from eastern Australia. It supports the separation of tobacco streak virus (TSV) strains from parthenium (Parthenium hysterophorus) and crownbeard (Verbescina encelioides) based on serology and host specificity. It has confirmed one previously described strain of TSV as a member of the species Strawberry necrotic shock virus and another as a new subgroup 1 ilarvirus, ageratum latent virus (AgLV), from Ageratum houstonianum. A multiplex RT-PCR showed that the genetically distinct strains of TSV and AgLV were commonly found in symptomless infections in virus-specific alternative weed hosts growing over a wide geographical range in eastern Australia. TSV has been one of the most damaging viruses in Australian oilseed and pulse crops in recent years, and this study has provided the taxonomic knowledge essential for the development of control programs for these viruses. PMID:23474983

Sharman, M; Thomas, J E

2013-08-01

135

Genetic diversity in populations of Gentoo penguins (Pygoscelis papua).  

Science.gov (United States)

RAPD analysis was used to examine the extent of genetic polymorphism in two populations of Gentoo penguin (Pygoscelis papua) from Antarctic Islands (Petermann and Livingston). The chosen two of three 10 mer oligonucleotide primers accordingly to preliminary results showed different levels of polymorphism in Gentoo penguins at Petermann Island (from 23.53 to 42.86%) and Livingston Island (from 52.94 to 57.14%). Nei's similarity coefficients were in range from 0.5606 (when Gentoo genome profiles were compared with RAPD profiles of two related penguin species: Pygoscelis adeliae (Adelie) and Pygoscelis antarctica (Chinstrep)) to 0.9281 among observed Gentoo penguin populations. Nei's distances values ranged from 0.0746 to 0.5787 among the populations and species. The obtained results will be used for further estimation of genetic diversity of Gentoo penguins and determination of their taxonomic status. PMID:16865990

Dranitsina, A S; Telegeev, G D; Maliuta, S S; Bezrukov, V F

2006-01-01

136

The impact of recent events on human genetic diversity.  

Science.gov (United States)

The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics. PMID:22312046

Jobling, Mark A

2012-03-19

137

Model of Serbian spruce genetic diversity conservation applying MPBS method  

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Full Text Available Multiple Population Breeding System (MPBS means that the genetic conservation population is split into subpopulations with each having an effective population size of approximately 50 individuals (Namkoong, 1984. The main reasons for development of the MPBS is the need for preparation of adequate breeding strategy which would be useful in future breeding goals and environmental conditions changing processes. MPBS is dynamic and allows for adaptation via natural selection or breeding. In contrast to hierarchical systems that require several generations of back-crossing to introduce genes into the breeding population immediate changes of breeding goals are possible in MPBS breeding. The cost of running a MPBS programme is not expected to differ much from running a breeding programme with just one large breeding population. MPBS is very appropriate conservation method for endangered species due to future environmental and breeding aims changes. In this paper suggestion for conservation and improvement of Serbian spruce genetic diversity applying MPBS has been explained.

Milovanovi? Jelena

2007-01-01

138

Genetic Diversity of the Cameroon Indigenous Chicken Ecotypes  

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Full Text Available 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, expected and unbiased frequencies of heterozygote were 0.60, 0.62 and 0.65 respectively, with the mean Shannon index of 1.21. The global inbreeding coefficient among population was 0.13. Inbreeding coefficient varied significantly with 4.27% variation observed among ecotypes. Within ecotypes the highest diversity was observed in the Bafang-Bakou population having 7.92±4.22 alleles per locus, 168.80±4.73 gene copies, 9 private alleles and 0.68±0.02 expected heterozigosity. However the same region displayed the highest inbreeding coefficient (0.13. In all the populations, 67% of the loci did not deviate significantly from the Hardy-Weinberg. The neighbor-joining tree, UPGMA cladogram as well as the Evanno’s population structure parameters revealed existence of 3 clusters in Cameroon chicken populations. The current study confirmed usefulness of microsatellites for studying genetic variation of the Cameroonian indigenous chicken. They demonstrate information on genetic variability of Cameroon local chicken populations, offer steps towards rational decision making prior to genetic improvement and conservation programs, without compromising the existence of each unique genotype.

T.C. Keambou

2014-01-01

139

[Genetic diversity of introduced natural enemy Agasicles hygrophila (Coleoptera: Chrysomelidae)].  

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Flea beetle Agasicles hygrophila Selman & Vogt, the most effective natural enemy of alligator weed Alternanthera philoxeroideis, is originated from South America, and has been introduced into China for more than 20 years to control the weed. In this study, the technique of random amplification of polymorphic DNA (RAPD) was applied to assess the genetic diversity of four A. hygrophila geographic populations in Guangzhou, Chongqing, Kunming, and Fuzhou of China, and, taking the population in Florida of US as the reference, the relationships between the genetic differentiation and geographic differentiation among and within the populations were explored at molecular level. Thirteen primers that produced clear and reproducible products were selected from 111 random primers to amplify the 25 samples of the five A. hygrophila populations. The total polymorphic rate was 42.0%, and the polymorphic rate of Florida population was significantly higher than that of four China populations. The genetic differentiation among the four China populations was 25.5%. The cluster analysis by UPGMA indicated that there was a positive correlation between the genetic distance and geographic distance of different A. hygrophila geographic populations. PMID:22303686

Han, Zheng; Zhao, Long-Long; Ma, Rui-Yan; Hao, Jiong; Jia, Dong

2011-11-01

140

Genetic diversity in tetraploid switchgrass revealed by AFLP marker polymorphisms.  

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Switchgrass (Panicum virgatum) is a perennial warm-season grass native to North America that has been identified as a dedicated cellulosic biofuel crop. We quantified genetic diversity in tetraploid switchgrass germplasm collected at Oklahoma State University and characterized genetic relatedness among the collections from distinct regions. Fifty-six tetraploid accessions, including seven upland and 49 lowland genotypes from throughout the US, were examined. The amplified fragment length polymorphism (AFLP) procedure was utilized to generate DNA profiling patterns that were scored visually. Sixteen selective AFLP primer combinations were used to amplify 452 polymorphic bands. The accessions' genetic similarity coefficients, UPGMA (unweighted pair-group method with arithmetic averaging) cluster analysis and principle coordinate analysis, were performed. The upland and lowland accessions clustered according to ecotypes, with one exception (TN104). Genetic similarity coefficients among the accessions ranged from 0.73 to 0.95. Analysis of molecular variance (AMOVA) was performed, showing significant differences between the upland and lowland genotypes. The trnL marker confirmed that TN104 was a lowland genotype, but the trnL marker identification of upland and lowland genotypes was not consistent with the AFLP analysis in two germplasms (Miami and AR4). PMID:22180031

Todd, J; Wu, Y Q; Wang, Z; Samuels, T

2011-01-01

 
 
 
 
141

Evaluation of genetic diversity and conservation priorities for Egyptian chickens  

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Full Text Available In this study, 21 microsatellite markers were used to genotype 196 Egyptian local chickens obtained from Fayoumi (n = 35, Dandarawy (n = 30, Baladi (n = 29, Sinai (n = 30, El-Salam (n = 36, and Golden Montazah (n = 36 strains. The results were compared to two pure commercial chicken populations reared in Japan-White Leghorn (n = 42 and Rhode Island Red (n = 43. A total of 162 alleles were observed, with an average of 7.7 alleles per locus. The average expected heterozygosity for the Egyptian chickens was 0.595. The closest pairwise Nei’s genetic distance was recorded between Sinai and Golden Montazah (0.038 and the smallest pairwise FST value (0.006 was observed between Baladi and Sinai. The most probable structure clustering of the eight studied populations was at K = 6. Baladi, Sinai and Golden Montazah strains were clustered together forming admixed mosaic cluster. Dandarawy ranked firstly and contributed the most to aggregate genetic diversity based on two prioritization methods. The information resulting from this study may be used as an initial guide to design further investigations for development of sustainable genetic improvement and conservation programs for the Egyptian chicken genetic resources.

Shin’ichi Ito

2012-07-01

142

Genetic diversity of Eurycoma longifolia inferred from single nucleotide polymorphisms.  

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Eurycoma longifolia Jack. is a treelet that grows in the forests of Southeast Asia and is widely used throughout the region because of its reported medicinal properties. Widespread harvesting of wild-grown trees has led to rapid thinning of natural populations, causing a potential decrease in genetic diversity among E. longifolia. Suitable genetic markers would be very useful for propagation and breeding programs to support conservation of this species, although no such markers currently exist. To meet this need, we have applied a genome complexity reduction strategy to identify a series of single nucleotide polymorphisms (SNPs) within the genomes of several E. longifolia accessions. We have found that the occurrence of these SNPs reflects the geographic origins of individual plants and can distinguish different natural populations. This work demonstrates the rapid development of molecular genetic markers in species for which little or no genomic sequence information is available. The SNP markers that we have developed in this study will also be useful for identifying genetic fingerprints that correlate with other properties of E. longifolia, such as high regenerability or the appearance of bioactive metabolites. PMID:12644679

Osman, Asiah; Jordan, Barbara; Lessard, Philip A; Muhammad, Norwati; Haron, M Rosli; Riffin, Norifiza Mat; Sinskey, Anthony J; Rha, ChoKyun; Housman, David E

2003-03-01

143

Web Log Mining Based-on Improved Double-Points Crossover Genetic Algorithm  

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Full Text Available Web log files have become important data source for discoveries of user behaviors. Analyzing web log files is one of the significant research fields of web mining. This paper proposes an improved double-points crossover genetic algorithm for mining user access patterns from web log files. Our work contains three different components. First, we design a coding rule according to pre-processed web log data. Second, a fitness function is presented by analyzing user sessions. Finally, a new genetic algorithm based on double-points crossover genetic algorithm is designed. In comparison with simple genetic algorithm, double-points crossover genetic algorithm demonstrates better convergence than the other, and it is more suitable for web log mining. We conducted an experiment to verify the effectiveness of the proposed algorithm. The results show that the proposed algorithm helps the website to easily gain access patterns.

Jin Xie

2014-06-01

144

Microsatellite markers for determining genetic identities and genetic diversity among jute cultivars  

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Full Text Available DNA fingerprint was generated using jute specific SSR markers on 10 jute cultivars from two Corchorus species (C. olitorius and C. capsularis and the genetic relatedness among the cultivars was estimated. A total of 106 alleles were identified using 23 primer pairs among the 10 cultivars with an average of 4.61 ± 1.92 alleles per locus, and a mean genetic diversity of 0.68±0.16. Four C. olitorius cultivars could be easily distinguished with 6 markers using 5 primer pairs and six C. capsularis cultivars with 7 markers using 6 primer pairs. The UPGMA analysis enabled the grouping of the cultivars into two major clusters, which matched with the known information on jute. This experiment provides proof that in spite of low levels of genetic polymorphisms among jute cultivars, SSR markers can reliably distinguish among them. This finding reinforces the utility of SSR primers for providing unique genetic identities or fingerprints of various jute cultivars.

Jesmin Akter

2008-05-01

145

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: English Abstract in english 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

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

2008-01-15

146

Prevalence and genetic diversity of klassevirus in wastewater in Japan.  

Science.gov (United States)

Klassevirus is a novel virus belonging to the family Picornaviridae. This study examined the prevalence and genetic diversity of klassevirus in wastewater. Raw sewage (100 ml) and secondary-treated sewage (2 l) were collected monthly for 14 months between January 2011 and February 2012 from a wastewater treatment plant in Japan. Klassevirus in the sample was concentrated by the electronegative membrane-vortex method, followed by qualitative detection by means of three types of reverse transcription (RT)-nested polymerase chain reactions (PCRs). Klassevirus was detected in seven of the 14 raw sewage (50 %) and four of the 14 secondary-treated sewage (29 %) samples by the RT-nested PCRs targeting the 2C and/or 3D regions. In contrast, none of the samples tested positive for the virus by the RT-nested PCR targeting the VP0/VP3 region. Based on direct nucleotide sequence analysis of the klassevirus-positive nested PCR fragments, the tested samples showed high nucleotide sequence similarities of 94.7-100.0 % and 93.2-100.0 % in the 2C and 3D regions, respectively, indicating the presence of a single klassevirus strain. To our knowledge, this is the first study evaluating seasonal prevalence and genetic diversity of klassevirus in environmental waters. PMID:23412720

Haramoto, Eiji; Otagiri, Mikie

2013-03-01

147

Ordering microbial diversity into ecologically and genetically cohesive units.  

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We propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. We discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. These show that if recombination is frequent and selection moderate, ecologically adaptive mutations or genes can spread within populations independently of their original genomic background (gene-specific sweeps). Alternatively, if the effect of recombination is smaller than selection, genome-wide selective sweeps should occur. In both cases, however, distinct units of overlapping ecological and genotypic similarity will form if microgeographic separation, likely involving ecological tradeoffs, induces barriers to gene flow. These predictions are supported by (meta)genomic data, which suggest that a 'reverse ecology' approach, in which genomic and gene flow information is used to make predictions about the nature of ecological units, is a powerful approach to ordering microbial diversity. PMID:24630527

Shapiro, B Jesse; Polz, Martin F

2014-05-01

148

On the Biological and Genetic Diversity in Neospora caninum  

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Full Text Available Neospora caninum is a parasite regarded a major cause of foetal loss in cattle. A key requirement to an understanding of the epidemiology and pathogenicity of N. caninum is knowledge of the biological characteristics of the species and the genetic diversity within it. Due to the broad intermediate host range of the species, worldwide geographical distribution and its capacity for sexual reproduction, significant biological and genetic differences might be expected to exist. N. caninum has now been isolated from a variety of different host species including dogs and cattle. Although isolates of this parasite show only minor differences in ultrastructure, considerable differences have been reported in pathogenicity using mainly mouse models. At the DNA level, marked levels of polymorphism between isolates were detected in mini- and microsatellites found in the genome of N. caninum. Knowledge of what drives the biological differences that have been observed between the various isolates at the molecular level is crucial in aiding our understanding of the epidemiology of this parasite and, in turn, the development of efficacious strategies, such as live vaccines, for controlling its impact. The purpose of this review is to document and discuss for the first time, the nature of the diversity found within the species Neospora caninum.

John T. Ellis

2010-03-01

149

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers  

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

Jordana Jordi

2001-07-01

150

Genetic diversity in a world germplasm collection of tall fescue  

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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.

Romina Cuyeu

2013-01-01

151

Genetic diversity in a world germplasm collection of tall fescue.  

Science.gov (United States)

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. PMID:23885206

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

2013-07-01

152

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

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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.

Leon Mejnartowicz

2006-03-01

153

Genetic diversity among five T4-like bacteriophages  

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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.

Bertrand Claire

2006-05-01

154

Genetic diversity and relationships among indigenous Mozambican cattle breeds  

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Full Text Available SciELO South Africa | Language: English Abstract in english 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.

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

2009-01-01

155

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

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

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

2011-12-01

156

Genetic diversity and admixture patterns in Indian populations.  

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India is a diverse land whose population holds the history of waves of human dispersal. Recent studies suggest two major ancestral contributions to most of the Indian sub-populations. However, present day Indians are thought to contain huge genetic diversity derived consequent to multiple cultural, linguistic and geographical variations. Genome-wide survey of individuals from current North (N-In) and South (S-In) India along with populations from HapMap Phase III and Indian sub-populations from HUGO Pan-Asian SNP Consortium is performed. Multivariate analysis (MDS and PCA) was carried out after merging data from the current study and other consortia. Indian sub-populations clustered separately from populations of major global geographical regions in MDS and PCA in a loose agglomeration except for two Indian subpopulations clustering near far eastern populations. F(st) values indicated diversity among Indian sub-populations which was substantiated by STRUCTURE analysis suggesting the possibility of additional admixture events. PMID:22892377

Chakrabarti, Biswaroop; Kumar, Sunil; Singh, Randeep; Dimitrova, Nevenka

2012-10-25

157

Role of telomere dysfunction in genetic intratumor diversity.  

Science.gov (United States)

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

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

2011-01-01

158

A Survey of Association Rule Mining Using Genetic Algorithm  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Anubha Sharma

2012-01-01

159

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

Directory of Open Access Journals (Sweden)

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

Flávio de Oliveira Francisco

2013-01-01

160

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

 
 
 
 
161

Indigenous cattle in Sri Lanka: Production systems and genetic diversity  

International Nuclear Information System (INIS)

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

162

Genetic diversity of storage proteins in cultivated buckwheat.  

Science.gov (United States)

Prolamin and albumn variations of the storage proteins in 76 cultivated buckwheat accessions (55 accessions of Fagopyrum tataricum, 21 accessions of F. esculentum) from 7 countries were characterized by A-PAGE and SDS-PAGE, respectively, for the purpose of evaluating the genetic diversity of cultivated buckwheat at the level of proteins. A total of 18 prolamin bands were detected, among which 88.89 % bands were polymorphic. The number of albumn bands based on SDS-PAGE observed in accessions ranged from 4 to 10. Most intense bands were in the range of molecular weights from 29 to 97.2 kDa. The average of genetic similarity coefficient based on prolamin bands was 0.784 (in F. tataricum and F. esculentum were 0.892 and 0.681, respectively), while on prolamin and albumn bands was 0.742 (in F. tataricum and F. esculentum were 0.864 and 0.633, respectively). Accessions of F. tataricum and F. esculentum showed significant interspecific variation in the A-PAGE and SDS-PAGE profile of the storage proteins. The cluster analysis indicated that all the accessions could be divided into 3 groups and 3 subgroups. The genetic variations among cultivated buckwheat accessions were associated with their geographic origins in some degree. PMID:18819616

Yang, Yu-Xia; Wu, Wei; Zheng, You-Liang; Yang, Wen-Ting; Cai, Qian-Rong

2008-07-01

163

Genetic Diversity of Storage Proteins in Cultivated Buckwheat  

Directory of Open Access Journals (Sweden)

Full Text Available Prolamin and albumn variations of the storage proteins in 76 cultivated buckwheat accessions (55 accessions of Fagopyrum tataricum, 21 accessions of F. esculentum from 7 countries were characterized by A-PAGE and SDS-PAGE, respectively, for the purpose of evaluating the genetic diversity of cultivated buckwheat at the level of proteins. A total of 18 prolamin bands were detected, among which 88.89 £¥bands were polymorphic. The number of albumn bands based on SDS-PAGE observed in accessions ranged from 4 to 10. Most intense bands were in the range of molecular weights from 29 to 97.2 kDa. The average of genetic similarity coefficient based on prolamin bands was 0.784 (in F. tataricum and F. esculentum were 0.892 and 0.681, respectively, while on prolamin and albumn bands was 0.742 (in F. tataricum and F. esculentum were 0.864 and 0.633, respectively. Accessions of F. tataricum and F. esculentum showed significant interspecific variation in the A-PAGE and SDS-PAGE profile of the storage proteins. The cluster analysis indicated that all the accessions could be divided into 3 groups and 3 subgroups. The genetic variations among cultivated buckwheat accessions were associated with their geographic origins in some degree.

YangYu -Xia

2008-01-01

164

Genetic diversity through the looking glass: Effect of enrichment bias  

Energy Technology Data Exchange (ETDEWEB)

The effect of enrichment bias on the diversity of 2,4-dichlorophenoxyacetate (2,4-D)-degrading (2,4-D{sup +}) bacteria recovered from soil was evaluated by comparing the diversity of isolates obtained by direct plating to the diversity of isolates obtained from 85 liquid batch cultures. By the two methods, a total of 159 isolates were purified from 1 g of soil and divided into populations based on repeated extragenic palindromic sequence PCR (rep-PCR) genomic fingerprints. Approximately 42% of the direct-plating isolates hybridized with the tfdA and tfdB genes from Alcaligenes eutrophus JMP134(pJP4), 27% hybridized with the tfdA and tfdB genes from Burk holderia sp. strain RASC, and 30% hybridized with none of the probes. In contrast, the enrichment isolates not only represented fewer populations than the isolates obtained by direct plating but also exhibited, almost exclusively, a single hybridization pattern with 2,4-D catabolic gene probes. Approximately 98% of the enrichment isolates possessed pJP4-type tfd4 and tfdB genes, whereas isolates containing RASC-type tfdA and tfdB genes were obtained from only 2 of the 85 enrichment cultures. The skewed occurrence of the pJP4-type genes among the isolates obtained by enrichment suggests that the competitive fitness of 2,4-D{sup +} populations during growth with 2,4-D may be influenced either by specific tfd alleles or by genetic factors linked to these alleles. Moreover, the results indicate that evaluation of the diversity and distribution of catabolic pathways in nature can be highly distorted by the use of enrichment culture techniques. 34 refs., 4 figs., 1 tab.

Dunbar, J.; Forney, L. [Michigan State Univ., East Lansing, MI (United States); White, S. [Los Alamos National Lab., NM (United States)

1997-04-01

165

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

Science.gov (United States)

The effect of enrichment bias on the diversity of 2,4-dichlorophenoxyacetate (2,4-D)-degrading (2,4-D(sup+)) bacteria recovered from soil was evaluated by comparing the diversity of isolates obtained by direct plating to the diversity of isolates obtained from 85 liquid batch cultures. By the two methods, a total of 159 isolates were purified from 1 g of soil and divided into populations based on repeated extragenic palindromic sequence PCR (rep-PCR) genomic fingerprints. Approximately 42% of the direct-plating isolates hybridized with the tfdA and tfdB genes from Alcaligenes eutrophus JMP134(pJP4), 27% hybridized with the tfdA and tfdB genes from Burkholderia sp. strain RASC, and 30% hybridized with none of the probes. In contrast, the enrichment isolates not only represented fewer populations than the isolates obtained by direct plating but also exhibited, almost exclusively, a single hybridization pattern with 2,4-D catabolic gene probes. Approximately 98% of the enrichment isolates possessed pJP4-type tfdA and tfdB genes, whereas isolates containing RASC-type tfdA and tfdB genes were obtained from only 2 of the 85 enrichment cultures. The skewed occurrence of the pJP4-type genes among the isolates obtained by enrichment suggests that the competitive fitness of 2,4-D(sup+) populations during growth with 2,4-D may be influenced either by specific tfd alleles or by genetic factors linked to these alleles. Moreover, the results indicate that evaluation of the diversity and distribution of catabolic pathways in nature can be highly distorted by the use of enrichment culture techniques. PMID:16535569

Dunbar, J; White, S; Forney, L

1997-04-01

166

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...

167

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

Science.gov (United States)

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

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

2014-06-01

168

Genetic diversity of Gallibacterium anatis isolates from different chicken flocks.  

Science.gov (United States)

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. PMID:12791918

Bojesen, Anders Miki; Torpdahl, Mia; Christensen, Henrik; Olsen, John Elmerdahl; Bisgaard, Magne

2003-06-01

169

Hierarchical cluster analysis of genetic diversity in Maize germplasm  

Directory of Open Access Journals (Sweden)

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

A. Subramanian and N. Subbaraman

2010-07-01

170

Genetic diversity of Gallibacterium anatis isolates from different chicken flocks  

DEFF Research Database (Denmark)

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.

2003-01-01

171

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

Directory of Open Access Journals (Sweden)

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

Boris Briñez R.

2011-05-01

172

Genetic diversity and molecular typing of Listeria monocytogenes in China  

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

Wang Yan

2012-06-01

173

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

Science.gov (United States)

Taenia asiatica has made a remarkable journey through the scientific literature of the past 50 years, starting with the paradoxical observation of high prevalences of T. saginata-like tapeworms in non-beef consuming populations, to the full description of its mitochondrial genome. Experimental studies conducted in the 1980s and 1990s have made it clear that the life cycle of T. asiatica is comparable to that of T. saginata, except for pigs being the preferential intermediate host and liver the preferential location of the cysts. Whether or not T. asiatica can cause human cysticercosis, as is the case for Taenia solium, remains unclear. Given the specific conditions needed to complete its life cycle, in particular the consumption of raw or poorly cooked pig liver, the transmission of T. asiatica shows an important ethno-geographical association. So far, T. asiatica has been identified in Taiwan, South Korea, Indonesia, the Philippines, Thailand, south-central China, Vietnam, Japan and Nepal. Especially this last observation indicates that its distribution is not restricted to South-East-Asia, as was thought so far. Indeed, the molecular tools developed over the last 20 years have made it increasingly possible to differentiate T. asiatica from other taeniids. Such tools also indicated that T. asiatica is related more closely to T. saginata than to T. solium, feeding the debate on its taxonomic status as a separate species versus a subspecies of T. saginata. Furthermore, the genetic diversity within T. asiatica appears to be very minimal, indicating that this parasite may be on the verge of extinction. However, recent studies have identified potential hybrids between T. asiatica and T. saginata, reopening the debate on the genetic diversity of T. asiatica and its status as a separate species. PMID:24450957

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

2014-01-01

174

Genetic diversity and molecular typing of Listeria monocytogenes in China  

Science.gov (United States)

Background Listeria monocytogenes can cause invasive diseases in humans and farm animals and is frequently isolated from dairy products and poultry. Listeriosis is uncommon in China but L. monocytogenes has been isolated from foods and food processing environments in China. However little is known of genetic diversity of Chinese L. monocytogenes isolates and their relationships with global isolates. Results Two hundred and twelve isolates of L. monocytogenes from food sources from 12 provinces/cities in China were analysed by serotyping, Pulsed Field Gel Electrophoresis (PFGE) and Multi-locus Sequence Typing (MLST). The predominant serotypes are 1/2a, 1/2b and 1/2c accounting for 90.1% of the isolates. PFGE divided the isolates into 61 pulse types (PTs). Twenty nine PTs were represented by more than one isolates with PT GX6A16.0004 containing the most number of isolates. MLST differentiated the isolates into 36 STs, among which 15 were novel. The 3 most common STs were ST9 (29.1%), ST8 (10.7%) and ST87 (9.2%), accounting for 49.0% of the isolates. Conclusions STs prevalent in other parts of the world are also prevalent in China including 7 STs (ST1-ST3, ST5, ST6, ST8, ST9) which caused maternal fetal infections or outbreaks, suggesting that these STs potentially can also cause severe human infections or outbreaks in China. Surveillance of these STs will provide important information for prevention of listeriosis. This study also enhances our understanding of genetic diversity of L. monocytogenes in China. PMID:22727037

2012-01-01

175

Diversity of surface dwelling beetle assemblages in open-cast lignite mines in Central Germany  

Energy Technology Data Exchange (ETDEWEB)

Species richness of ground dwelling beetle assemblages in two non-reclaimed lignite mines and a dump in Central Germany were investigated by means of pitfall trapping. During a period of five months, a total of 203 beetle species within 27 families represented by 4099 individuals were trapped. The number of individuals, species richness, as well as the proportions of endangered species did not differ between successional stages whereas species composition of sites could be related to a set of environmental variables. High values of beta-diversity between sites indicated that the total number of species recorded is caused by habitat diversity. From the viewpoint of nature conservation, it is concluded that postmining areas can play a key role in conservation of beetle diversity in agricultural areas since they harbour threatened species whose original habitats are now rare due to human impact.

Brandle, M.; Durka, W.; Altmoos, M. [UFZ Centre of Environmental Research, Halle (Germany). Dept. of Community Ecology

2000-07-01

176

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

Science.gov (United States)

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans. PMID:21679313

Shirk, A J; Cushman, S A

2011-09-01

177

AFLP assessment of genetic diversity among Indian Mucuna accessions.  

Science.gov (United States)

Amplified fragment length polymorphism (AFLP) marker was used to assess diversity in germplasm collection of Mucuna species which has gained tremendous attention in the recent past due to its promising nutritional, agronomic and medicinal attributes. Twenty five accessions comprising five species, collected from seven states of India were evaluated with twelve AFLP primer combinations that generated a total of 1,612 fragments with an average of 134 fragments per primer combination. The values of polymorphic information content (PIC), marker index (MI) and the resolving power (Rp) demonstrated the utility of the primer combinations used in the present study for discriminating the Mucuna accessions. UPGMA and Principal coordinate analysis (PCoA) of the genotypic data revealed clustering of accessions as per phenetic and genetic relationships. The Jaccard's similarity coefficient values suggested good variability among the M. pruriens accessions indicating their utility in breeding programs. Molecular diversity presented in this study combined with the datasets on other morphological/agronomic traits will be highly useful for selecting appropriate accessions for plant improvement through conventional as well as molecular breeding approaches and for evolving suitable conservation strategies. PMID:23573007

Sathyanarayana, N; Leelambika, M; Mahesh, S; Jaheer, Mahammad

2011-04-01

178

Genetic diversity of ITS sequences of Bursaphelenchus xylophilus.  

Science.gov (United States)

The sequence variation of internal transcribed spacer (ITS) regions of ribosomal DNA has been routinely used for species identification and species-level phylogeny of the pinewood nematode, Bursaphelenchus xylophilus. In this study, the intraspecies ITS genetic diversity of B. xylophilus was evaluated. Three pinewood nematode isolates from the United States, Japan, and Portugal were used for polymerase chain reaction (PCR) ITS region amplification and sequencing. Multiple peaks were observed in sequencing chromatograms from ITS regions of American and Japanese isolates, suggesting the presence of more than one ribosomal sequence for each isolate. PCR products were further cloned and 10 clones of each isolate were subsequently sequenced. Additionally, the ITS regions of individual nematodes from each isolate were amplified, cloned and sequenced. Among the 3 B. xylophilus isolates analyzed, an intraspecific and intra-isolate molecular variability was found. The intra-isolate ITS molecular diversity in the American isolate was higher than that in the Japanese and Portuguese isolates. However, the level of sequence variation observed within isolates was about the same as that described among ITS repeats within individuals. PMID:23096915

Cardoso, J M S; Fonseca, L; Abrantes, I

2012-01-01

179

Assessment of genetic diversity within sour cherry clones  

DEFF Research Database (Denmark)

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.

Clausen, Sabine Karin; Andersen, Sven Bode

2013-01-01

180

Genetic diversity of pestivirus isolates in cattle from Western Austria.  

Science.gov (United States)

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

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

2009-03-30

 
 
 
 
181

Genetic diversity of Leishmania infantum field populations from Brazil  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

182

Concordance between genetic and species diversity in coral reef fishes across the Pacific Ocean biodiversity gradient.  

Science.gov (United States)

The relationship between genetic diversity and species diversity provides insights into biogeography and historic patterns of evolution and is critical for developing contemporary strategies for biodiversity conservation. Although concordant large-scale clines in genetic and species diversity have been described for terrestrial organisms, whether these parameters co-vary in marine species remains largely unknown. We examined patterns of genetic diversity for 11 coral reef fish species sampled at three locations across the Pacific Ocean species diversity gradient (Australia: ?1600 species; New Caledonia: ?1400 species; French Polynesia: ?800 species). Combined genetic diversity for all 11 species paralleled the decline in species diversity from West to East, with French Polynesia exhibiting lowest total haplotype and nucleotide diversities. Haplotype diversity consistently declined toward French Polynesia in all and nucleotide diversity in the majority of species. The French Polynesian population of most species also exhibited significant genetic differentiation from populations in the West Pacific. A number of factors may have contributed to the general positive correlation between genetic and species diversity, including location and time of species origin, vicariance events, reduced gene flow with increasing isolation, and decreasing habitat area from West to East. However, isolation and habitat area, resulting in reduced population size, are likely to be the most influential. PMID:23206145

Messmer, Vanessa; Jones, Geoffrey P; Munday, Philip L; Planes, Serge

2012-12-01

183

Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings.  

Science.gov (United States)

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 approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions. PMID:24727268

Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng; Huang, Li-Nan

2014-06-01

184

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

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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.

Ming-Cheng Luo

2013-03-01

185

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

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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.

S. Dehuri

2006-01-01

186

[Genetic diversity of insular natural populations of Festuca pratensis Huds.: RAPD analysis].  

Science.gov (United States)

In natural populations of Festuca pratensis Huds. from the islands of Onega Lake, the level of genetic diversity was evaluated. In three populations variability of 64 RAPD loci was tested. The level of genetic diversity (P95% = 30.2; Hexp = 0.093) was low for a cross-pollinating plant species. Furthermore, genetic similarity between the plants from insular populations was found to be high (IN = 0.887). It was demonstrated that genetic variation among the population accounted for at most 5.3% of total genetic diversity, which, however, was higher than the FST values for continental populations (FST = 0.022). It was suggested that specific features of the genetic structure of insular population, i.e., low gene diversity within the populations along with high differentiation among the populations, were caused by the gene flow attenuation, as a result of isolation, and intensification of inbreeding. These features had negative effect on total population adaptation. PMID:19824550

Fedorenko, O M; Gritskikh, M V; Malysheva, I E; Nikolaevskaia, T S

2009-09-01

187

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 l...

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

2011-01-01

188

Diversity and Genetic structure of the Spanish collection of durum wheat (Triticum turgidum L) landraces  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The objectives of this study were to assess diversity and genetic structure of a collection of Spanish durum wheat (Triticum turgidum L) landraces, using SSRs, DArTs and gliadin-markers, and to correlate the distribution of diversity with geographic and climatic features, as well as agro-morphological traits. A high level of diversity was detected in the genotypes analyzed, which were separated into nine populations with a moderate to great genetic divergence among them. The three subspecies ...

Ruiz Valca?rcel, Magdalena; Giraldo Carbajo, Patricia; Royo, Conchita; Villegas, Dolores; Aranzana, Maria Jose?; Carrillo Becerril, Jose Maria

2012-01-01

189

Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13  

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Full Text Available Abstract Background Salmonella enterica serovar Enteritidis has emerged as a significant foodborne pathogen throughout the world and is commonly characterized by phage typing. In Canada phage types (PT 4, 8 and 13 predominate and in 2005 a large foodborne PT13 outbreak occurred in the province of Ontario. The ability to link strains during this outbreak was difficult due to the apparent clonality of PT13 isolates in Canada, as there was a single dominant pulsed-field gel electrophoresis (PFGE profile amongst epidemiologically linked human and food isolates as well as concurrent sporadic strains. The aim of this study was to perform comparative genomic hybridization (CGH, DNA sequence-based typing (SBT genomic analyses, plasmid analyses, and automated repetitive sequence-based PCR (rep-PCR to identify epidemiologically significant traits capable of subtyping S. Enteritidis PT13. Results CGH using an oligonucleotide array based upon chromosomal coding sequences of S. enterica serovar Typhimurium strain LT2 and the Salmonella genomic island 1 successfully determined major genetic differences between S. Typhimurium and S. Enteritidis PT13, but no significant strain-to-strain differences were observed between S. Enteritidis PT13 isolates. Individual loci (safA and fliC that were identified as potentially divergent in the CGH data set were sequenced in a panel of S. Enteritidis strains, and no differences were detected between the PT13 strains. Additional sequence-based typing was performed at the fimA, mdh, manB, cyaA, citT, caiC, dmsA, ratA and STM0660 loci. Similarly, no diversity was observed amongst PT13 strains. Variation in plasmid content between PT13 strains was observed, but macrorestriction with BglII did not identify further differences. Automated rep-PCR patterns were variable between serovars, but S. Enteritidis PT13 strains could not be differentiated. Conclusion None of the methods identified any significant variation between PT13 strains. Greater than 11,300 base pairs of sequence for each of seven S. Enteritidis PT13 strains were analyzed without detecting a single polymorphic site, although diversity between different phage types of S. Enteritidis was observed. These data suggest that Canadian S. Enteritidis PT13 strains are highly related genetically.

Ng Lai-King

2007-10-01

190

Genetic diversity based on morphological data in Panicum maximum hybrids  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

1975-19-01

191

Genetic Diversity in A Core Subset of Wild Barley Germplasm  

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Full Text Available Wild barley [Hordeum vulgare ssp. spontaneum (C. Koch Thell.] is a part of the primary gene pool with valuable sources of beneficial genes for barley improvement. This study attempted to develop a core subset of 269 accessions representing 16 countries from the Plant Gene Resources of Canada (PGRC collection of 3,782 accessions, and to characterize them using barley simple sequence repeat (SSR markers. Twenty-five informative primer pairs were applied to screen all samples and 359 alleles were detected over seven barley chromosomes. Analyses of the SSR data showed the effectiveness of the stratified sampling applied in capturing country-wise SSR variation. The frequencies of polymorphic alleles ranged from 0.004 to 0.708 and averaged 0.072. More than 24% or 7% SSR variation resided among accessions of 16 countries or two regions, respectively. Accessions from Israel and Jordan were genetically most diverse, while accessions from Lebanon and Greece were most differentiated. Four and five optimal clusters of accessions were obtained using STRUCTURE and BAPS programs and partitioned 16.3% and 20.3% SSR variations, respectively. The five optimal clusters varied in size from 15 to 104 and two clusters had only country-specific accessions. A genetic separation was detected between the accessions east and west of the Zagros Mountains only at the country, not the individual, level. These SSR patterns enhance our understanding of the wild barley gene pool, and are significant for conserving wild barley germplasm and exploring new sources of useful genes for barley improvement.

Yong-Bi Fu

2012-06-01

192

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

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The aim of this work was to study the genetic diversity among flue-cured tobacco cultivars. RAPD and AFLP analyses were used to assess the genetic similarity among selected accessions of flue-cured tobacco. Seventy eight RAPD and 154 AFLP polymorphic bands were obtained and used to assess the genetic diversity among 28 tobacco accessions. The cultivar relationships were estimated through the cluster analysis (UPGMA) based on RAPD data and AFLP data. The accessions were grouped into three majo...

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

2008-01-01

193

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

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Full Text Available 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 characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.

Ilga Porth

2014-04-01

194

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

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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...

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

2009-01-01

195

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

Science.gov (United States)

Primula sieboldii E. Morren is a perennial clonal herb that is widely distributed in Japan, but in danger of extinction in the wild. In a previous study, we revealed the genetic diversity of the species using chloroplast and nuclear DNA and used this information to define conservation units. However, we lacked information on adaptive genetic diversity, which is important for long-term survival and, thus, for the definition of conservation units. In order to identify adaptive traits that showed adaptive differentiation among populations, we studied the genetic variation in six quantitative traits within and among populations for 3 years in a common garden using 110 genets from five natural populations from three regions of Japan. The number of days to bud initiation was adaptive quantitative trait for which the degree of genetic differentiation among populations (QST) was considerably larger than that in eight microsatellite markers (FST). The relationship between this trait and environmental factors revealed that the number of days to bud initiation was negatively correlated, with the mean temperature during the growing period at each habitat. This suggests that adaptive differentiation in the delay before bud initiation was caused by selective pressure resulting from temperature differences among habitats. Our results suggest that based on adaptive diversity and neutral genetic diversity, the Saitama population represents a new conservation unit. PMID:19640318

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

2009-08-01

196

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

Science.gov (United States)

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.

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

2003-01-01

197

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

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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.

Gowda Cholenahalli LL

2008-10-01

198

Microbiology of diverse acidic and non-acidic microhabitats within a sulfidic ore mine.  

Science.gov (United States)

A wide variety of microhabitats within the extremely acidic abandoned underground copper mine Zlaté Hory (Czech Republic) was investigated. SSU rDNA libraries were analyzed from 15 samples representing gossan, sulfide-leaching environments in the oxidation zone, and acidic water springs in the mine galleries. Microbial analyses were extended by analyses of chemical composition of water and solid phases and identification of arising secondary minerals. The microbial communities of the three main classes of microenvironments differed in almost every aspect. Among others, ecological partitioning of Acidithiobacillus ferrooxidans and the recently described A. ferrivorans was observed. Distinct types of communities inhabiting the water springs were detected. The more extreme springs (pH 2 mS/cm) were inhabited by "Ferrovum" spp. and A. ferrivorans, whereas Gallionella sp. dominated the less extreme ones. A new role for gossan in the extremely acidic ecosystem is proposed. This zone was inhabited by a large diversity of neutrophilic heterotrophs that appeared to be continuously washed out to the acidic environments localized downstream. Five species originating in gossan were found in several acidic habitats. Here they can survive and probably serve as scavengers of dead biomass, particularly from chemoautotrophic growths. No such process has been described from acidic mine environments so far. PMID:23065060

Falteisek, Lukáš; Cepi?ka, Ivan

2012-11-01

199

Genetic diversity trends in twentieth century crop cultivars: a meta analysis  

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In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in t...

Wouw, M. J.; Hintum, T. J. L.; Kik, C.; Treuren, R.; Visser, L.

2010-01-01

200

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

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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.

Chunlai Chai

2010-09-01

 
 
 
 
201

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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.

202

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

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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.

Juliana Morini Küpper Cardoso Perseguini

2011-01-01

203

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

Science.gov (United States)

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

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

2012-09-01

204

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

Science.gov (United States)

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

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

2012-01-01

205

Genetic diversity of Guernsey population using pedigree data and gene-dropping simulations.  

Science.gov (United States)

The objectives of this study were to analyze the trend of within-breed genetic diversity and identify major causes leading to loss of genetic diversity in Guernsey breed in three countries. Pedigree files of Canadian (GCN), South African (GSA) and American (GUS) Guernsey populations containing 130 927, 18 593 and 1 851 624 records, respectively, were analyzed. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness index of GCN, GSA and GUS populations, in the most recent year (2007), was 97%, 74% and 79%, respectively, considering four generations back in the analysis. The rate of inbreeding in each population was 0.19%, 0.16% and 0.17% between 2002 and 2007, respectively. For the same period, the estimated effective population size for GCN, GSA and GUS was 46, 57 and 46, respectively. The estimated percentage of genetic diversity lost within each population over the last four decades was 8%, 3% and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the three populations was 93%, 91% and 86%, respectively. In conclusion, the results suggested that GCN and GUS have lost more genetic diversity than GSA over the past four decades, and this loss is gaining momentum due to increasing rates of inbreeding. Therefore, strategies such as optimum contribution selection and migration of genetic material are advised to increase effective population size, particularly in GCN and GUS. PMID:23032118

Melka, M G; Sargolzaei, M; Miglior, F; Schenkel, F

2013-02-01

206

Genetic diversity and differentiation of Mongolian indigenous cattle populations  

International Nuclear Information System (INIS)

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

207

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

Science.gov (United States)

Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources. PMID:25358313

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

2014-11-01

208

Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.).  

Science.gov (United States)

Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker-trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design. PMID:24668487

Dang, Xiaojing; Thi, Thu Giang Tran; Dong, Guanshan; Wang, Hui; Edzesi, Wisdom Mawuli; Hong, Delin

2014-06-01

209

Efficient Spatial Data mining using Integrated Genetic Algorithm and ACO  

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

K Sankar

2011-05-01

210

Genetic Diversity Among Monoconidial and Polyconidial Isolates of Bipolaris sorokiniana.  

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Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat in warm and humid wheat-growing regions of the world. This fungus shows a high genetic diversity and morphological and physiologic variability. In this study, 19 polysporic and 57 monosporic isolates of B. sorokiniana were characterized using universal rice primers-URP-PCR. The results obtained when the dendrogram was constructed with all the data produced with the amplification products showed very distinct clusters. However, the similarity among the isolates was low where 37 and 26.3 % of the monosporic and polysporic isolates, respectively, showed similarity above 70 %. All primers amplified multiple DNA fragments of polysporic as well as the monosporic isolates. Isolates fingerprints were constructed based on binary characters revealed by the three primers. An amplified fragment of approximately 750 bp was observed among 40 % of the isolates, when primer URP-1F was used. When primers URP-4R and URP-2R were used, a fragment of 450 and 400 bp was present in 31.5 and 29 % of the isolates, respectively. It was expected a higher similarity among the isolates since the monosporic cultures were originated from the polysporic. The dendrogram did not enable the separation of B. sorokiniana isolates by their geographic origin. This low correlation suggests that gene transfer may have occurred by parasexual combination in this fungus population. However, in spite of the research efforts for that end, it has not been possible to establish patterns that characterize the profile of B. sorokiniana. PMID:25100225

Mann, Michele B; Minotto, Elisandra; Feltrin, Thaisa; Milagre, Luciana P; Spadari, Cristina; Van Der Sand, Sueli T

2014-12-01

211

Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh.  

Science.gov (United States)

In order to determine the bacterial diversity and the identity of rhizobia nodulating lentil in Bangladesh, we performed a phylogenetic analysis of housekeeping genes (16S rRNA, recA, atpD and glnII) and nodulation genes (nodC, nodD and nodA) of 36 bacterial isolates from 25 localities across the country. Maximum likelihood (ML) and Bayesian analyses based on 16S rRNA sequences showed that most of the isolates (30 out of 36) were related to Rhizobium etli and Rhizobium leguminosarum. Only these thirty isolates were able to re-nodulate lentil under laboratory conditions. The protein-coding housekeeping genes of the lentil nodulating isolates showed 89.1-94.8% genetic similarity to the corresponding genes of R. etli and R. leguminosarum. The same analyses showed that they split into three distinct phylogenetic clades. The distinctness of these clades from closely related species was also supported by high resolution ERIC-PCR fingerprinting and phenotypic characteristics such as temperature tolerance, growth on acid-alkaline media (pH 5.5-10.0) and antibiotic sensitivity. Our phylogenetic analyses based on three nodulation genes (nodA, nodC and nodD) and cross-inoculation assays confirmed that the nodulation genes are related to those of R. leguminosarum biovar viciae, but clustered in a distinct group supported by high bootstrap values. Thus, our multi-locus phylogenetic analysis, DNA fingerprinting and phenotypic characterizations suggest that at least three different clades are responsible for lentil nodulation in Bangladesh. These clades differ from the R. etli-R. leguminosarum group and may correspond to novel species in the genus Rhizobium. PMID:22280898

Rashid, Md Harun-or; Schäfer, Holger; Gonzalez, Javier; Wink, Michael

2012-03-01

212

Concordance between vocal and genetic diversity in crested gibbons  

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

Roos Christian

2011-02-01

213

Genetic diversity and population structure of wild Dipsacus asperoides in China as indicated by ISSR markers.  

Science.gov (United States)

In order to evaluate the genetic diversity and genetic structure of wild Dipsacus asperoides, we surveyed genetic polymorphisms in 288 individuals from 12 populations using ISSR. A total of 240 bands were amplified, among which 190 were polymorphic loci. At the species level, genetic diversity was found to be abundant: PPB = 79.17%, NE = 1.2152, H = 0.1361, and Hsp = 0.2213. At the population level, genetic diversity was lower: PPB = 30.76 %, NE = 1.0786, H = 0.0897, and Hpop = 0.1375. The calculated Nei genetic differentiation coefficient was 0.3406, which is consistent with the calculated Shannon population genetic differentiation coefficient of 0.3787. This is commonly taken to indicate that most of the genetic variation existed within the populations. Gene flow was calculated as Nm = 0.9679, suggesting that gene exchange only occurred at a low level. Based on the Nei genetic distance, the 12 populations were divided into 4 categories. Our results suggest that D. asperoides has abundant genetic diversity and provides a foundation for the protection and improvement of germplasm resources. PMID:24615115

Chen, D X; Li, L Y; Zhang, X; Wang, Y; Zhang, Z

2014-01-01

214

Investigation of Web Mining Optimization Using Microbial Genetic Algorithm  

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Full Text Available In today's modern internet era peopleneed searching on the web and finding relevant information on the web to be efficient and fast. But traditional search engines like Google suppose to be more intelligent, still use the traditional crawling algorithms to find data relevant to the search query. But most of the times it returns irrelevant data as well which becomes confusing for the user. In a normal XML data the user inputs the search query in terms of a keyword or a question and the answer to the search query should be more precise and more relevant. So, using the traditional crawling algorithms over XML data would lead to irrelevant results. Genetic algorithms are the modern algorithms which replicates the Darwinian theory of the natural evolution. The genetic algorithms are best suited for the traditional search problem as the genetic algorithms always tend to return quality as solution for any domain data. It would be a good approach to investigate how the genetic algorithms would be suitable for the search over the XML data of different domains. So, this system implements a steady state tournament selection Microbial Genetic Algorithm over the XML data of the different domains. This would be an investigation of how the genetic algorithm would return accurate results over XML data of different domains.

Dipali Tungar

2014-02-01

215

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

CERN Document Server

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.

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

2013-01-01

216

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

Science.gov (United States)

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

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

2014-01-01

217

Genetic diversity in Monilinia laxa populations in stone fruit species in Hungary.  

Science.gov (United States)

The objectives of this study were firstly, to determine the genetic diversity of Monilinia laxa isolates from Hungary, using the PCR-based inter-simple sequence repeat (ISSR) and randomly amplified polymorphic DNA (RAPD) technique; secondly, to prepare genetic diversity groups based on the dendrograms; and finally, to select some relevant isolates to study their fungicide sensitivity. 55 and 77 random amplified polymorphic ISSR and RAPD markers, of which 23 and 18 were polymorphic and 32 and 59 monomorphic, respectively, were used to assess the genetic diversity and to study the structure of M. laxa populations in Hungary. 27 isolates out of 57 ones were confirmed as M. laxa from several orchards (subpopulations) in three geographical regions, in various inoculum sources and in various hosts, were used. 10 fungicides and 12 isolates selected from genetic diversity groups based on the ISSR dendrograms were used to determine the fungicide sensitivity of the selected isolates. The analysis of population structure revealed that genetic diversity within locations, inoculum sources and host (H(S)) accounted for 99 % of the total genetic diversity (H(T)), while genetic diversity among locations, inoculum sources and host represented only 1 %. The relative magnitude of gene differentiation between subpopulations (G(ST)) and the estimate of the number of migrants per generation (Nm) averaged 0.005-0.009 and 53.9-99.2, respectively, for both ISSR and RAPD data set. The results obtained in dendrograms were in accordance with the gene diversity analysis. Grouping of isolates in the dendrograms was irrespective of whether they came from the same or different geographical locations. There was no relationship between clustering among isolates from inoculum sources and hosts. In the fungicide sensitivity tests, five isolates out of 12 were partly insensitive to boscalid+piraclostrobin, cyprodinil, fenhexamid or prochloraz. Obtained results in genetic diversity of M. laxa populations are discussed together with implications for the management of brown rot. PMID:24474390

Fazekas, Mónika; Madar, Anett; Sipiczki, Matthias; Miklós, Ida; Holb, Imre J

2014-06-01

218

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

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

L. Touil

2008-01-01

219

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

Science.gov (United States)

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

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

2014-10-01

220

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

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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

Pereira Albano

2001-05-01

 
 
 
 
221

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

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

Emilia Maria Furdui

2011-05-01

222

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

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Full Text Available Background & objectives: Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3alpha (msp-3? and assessed its suitability as high-resolution genetic marker for population genetic studies. Methods: 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3?. Results: We observed three distinct PCR alleles at msp-3?, and among them allele A showed significantly high frequency (53%, ?2 = 8.22, p = 0.001. PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3? is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3? in the field isolates. Interpretation & conclusion: P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3? could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

Surendra Kumar Prajapati

2010-06-01

223

Analyses of genetic diversity in five Canadian dairy breeds using pedigree data.  

Science.gov (United States)

The issue of loss of animal genetic diversity, worldwide in general and in Canada in particular, has become noteworthy. The objective of this study was to analyze the trend in within-breed genetic diversity and identify the major causes of loss of genetic diversity in five Canadian dairy breeds. Pedigrees were analyzed using the software EVA (evolutionary algorithm) and CFC (contribution, inbreeding, coancestry), and a FORTRAN package for pedigree analysis suited for large populations (PEDIG). The average rate of inbreeding in the last generation analyzed (2003 to 2007) was 0.93, 1.07, 1.26, 1.09 and 0.80% for Ayrshire, Brown Swiss, Canadienne, Guernsey and Milking Shorthorn, respectively, and the corresponding estimated effective population sizes were 54, 47, 40, 46 and 66, respectively. Based on coancestry coefficients, the estimated effective population sizes in the last generation were 62, 76, 43, 61 and 76, respectively. The estimated percentage of genetic diversity lost within each breed over the last four decades was 6, 7, 11, 8 and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the five breeds ranged between 59.3% and 89.7%. The results indicate that each breed has lost genetic diversity over time and that the loss is gaining momentum due to increasing rates of inbreeding and reduced effective population sizes. Therefore, strategies to decrease rate of inbreeding and increase the effective population size are advised. PMID:24079800

Melka, M G; Stachowicz, K; Miglior, F; Schenkel, F S

2013-12-01

224

Application of Statistical Procedures for Analysis of Genetic Diversity in Domestic Animal Populations  

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Full Text Available Problem statement: A wide range of studies for the assessment of genetic diversity in livestock breed were conducted using genetic distance. For high-accuracy and unbiased estimation sampling methods, criteria of choosing type of DNA markers, distance measurement strategies, cluster analysis will be important for any genetic diversity projects. Approach: Main objective of this short review is focusing on application statistical procedures and methods in analysis of genetic diversity data in animals. Results: There is no simple strategy to address for best and effectively genetic diversity results by the way regarding to some important factors can make reliable results for next analysis. Conclusion: There is still a distinct need for developing comprehensive and user-friendly statistical packages that facilitate an integrated analysis of different data sets for generating reliable information about genetic relationships, genome diversity, and favorable allele variation. Equally important and perhaps more challenging, is the concerted and planned utilization of genome information in animal breeding programs on the basis of knowledge accrued from studies on genetic diversity.

M. R. Nassiry

2009-01-01

225

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

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Full Text Available 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 diversity. Analyses of a 436 base pair fragment of the mtDNA control region revealed that the endemic C. joculator exhibited high haplotype (h > 0.98 at both locations and nucleotide (Christmas p% = 3.63, Cocos p% = 9.99 diversity. Similarly, isolated populations of widespread angelfishes (C. bispinosa and C. flavicauda had high haplotype (h > 0.98 and nucleotide (p% = 2.81 and p% = 5.78%, respectively diversity. Therefore, in contrast to terrestrial patterns, endemic and isolated populations of widespread angelfishes do not have low genetic diversity, rather their haplotype and nucleotide diversities were among the highest reported for marine fishes. High genetic diversity should reduce extinction risk in these species as it could provide the evolutionary potential to adapt to the rapidly changing environmental conditions forecast for coral reefs.

Philip L. Munday

2013-02-01

226

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

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

HU Shi-jun

2013-03-01

227

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

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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.

Gangbiao Xu

2013-11-01

228

Genetic diversity in caribou linked to past and future climate change  

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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.

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

229

Mining Interesting Positive and Negative Association Rule Based on Improved Genetic Algorithm (MIPNAR_GA  

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Full Text Available Association Rule mining is very efficient technique for finding strong relation between correlated data. The correlation of data gives meaning full extraction process. For the mining of positive and negative rules, a variety of algorithms are used such as Apriori algorithm and tree based algorithm. A number of algorithms are wonder performance but produce large number of negative association rule and also suffered from multi-scan problem. The idea of this paper is to eliminate these problems and reduce large number of negative rules. Hence we proposed an improved approach to mine interesting positive and negative rules based on genetic and MLMS algorithm. In this method we used a multi-level multiple support of data table as 0 and 1. The divided process reduces the scanning time of database. The proposed algorithm is a combination of MLMS and genetic algorithm. This paper proposed a new algorithm (MIPNAR_GA for mining interesting positive and negative rule from frequent and infrequent pattern sets. The algorithm is accomplished in to three phases: a.Extract frequent and infrequent pattern sets by using apriori method b.Efficiently generate positive and negative rule. c.Prune redundant rule by applying interesting measures. The process of rule optimization is performed by genetic algorithm and for evaluation of algorithm conducted the real world dataset such as heart disease data and some standard data used from UCI machine learning repository.

Nikky Suryawanshi Rai

2014-01-01

230

Genetic diversity and relationship of chicory (Cichorium intybus L.) using sequence-related amplified polymorphism markers.  

Science.gov (United States)

Chicory is a crop with economically important roles and is cultivated worldwide. The genetic diversity and relationship of 80 accessions of chicories and endives were evaluated by sequence-related amplified polymorphism (SRAP) markers to provide a theoretical basis for future breeding programs in China. The polymorphic rate was 96.83%, and the average polymorphic information content was 0.323, suggesting the rich genetic diversity of chicory. The genetic diversity degree of chicory was higher (GS = 0.677) than that of endive (GS = 0.701). The accessions with the highest genetic diversity (effective number of alleles, NE = 1.609; Nei's genetic diversity, H = 0.372; Shannon information index, I = 0.556) were from Italy. The richest genetic diversity was revealed in a chicory line (NE = 1.478, H = 0.289, I = 0.443) among the 3 types (line, wild, and cultivar). The chicory genetic structure of 8 geographical groups showed that the genetic differentiation coefficient (GST) was 14.20% and the number of immigrants per generation (Nm) was 3.020. A GST of 6.80% and an Nm of 6.853 were obtained from different types. This observation suggests that these chicory lines, especially those from the Mediterranean region, have potential for providing rich genetic resources for further breeding programs, that the chicory genetic structure among different countries obviously differs with a certain amount of gene flow, and that SRAP markers could be applied to analyze genetic relationships and classifications of Cichorium intybus and C. endivia. PMID:25299087

Liang, X Y; Zhang, X Q; Bai, S Q; Huang, L K; Luo, X M; Ji, Y; Jiang, L F

2014-01-01

231

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

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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

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

2011-11-01

232

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

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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 ...

233

Genetic diversity in two introduced biofouling amphipods (Amphipods valida and Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversity  

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We investigated patterns of genetic diversity among invasive populations of A. valida and J. marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute...

234

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

Science.gov (United States)

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 synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful. PMID:25210204

Whitlock, Raj

2014-01-01

235

Global diversity and genetic contributions of chicken populations from African, Asian and European regions.  

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Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (FST ) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour-Net genetic clustering and structure analysis revealed two main groups of Asian and north-west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north-west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds. PMID:25315897

Lyimo, C M; Weigend, A; Msoffe, P L; Eding, H; Simianer, H; Weigend, S

2014-12-01

236

Strong intraspecific variation in genetic diversity and genetic differentiation in Daphnia magna: the effects of population turnover and population size.  

Science.gov (United States)

Theory predicts that genetic diversity and genetic differentiation may strongly vary among populations of the same species depending on population turnover and local population sizes. Yet, despite the importance of these predictions for evolutionary and conservation issues, empirical studies comparing high-turnover and low-turnover populations of the same species are scarce. In this study, we used Daphnia magna, a freshwater crustacean, as a model organism for such a comparison. In the southern/central part of its range, D. magna inhabits medium-sized, stable ponds, whereas in the north, it occurs in small rock pools with strong population turnover. We found that these northern populations have a significantly lower genetic diversity and higher genetic differentiation compared to the southern/central populations. Total genetic diversity across populations was only about half and average within-population diversity only about a third of that in southern/central populations. Moreover, an average southern population contains more genetic diversity than the whole metapopulation system in the north. We based our analyses both on silent sites and microsatellites. The similarity of our results despite the contrasting mutation rates of these markers suggests that the differences are caused by contemporary rather than by historical processes. Our findings show that variation in population turnover and population size may have a major impact on the genetic diversity and differentiation of populations, and hence may lead to differences in evolutionary processes like local adaptation, hybrid vigour and breeding system evolution in different parts of a species range. PMID:22221402

Walser, Barbara; Haag, C R

2012-02-01

237

Reduction of Negative Rules in Association Rule Mining Using Distance Security and Genetic Algorithm  

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Full Text Available The increasing rate of data is a challenging task for mined useful association rule in data mining. The classical association rulemining generate rule with various problem such as pruning pass of transaction database, negative rule generation and superiority of rule set. Time to time various researchers modified classical association rule mining with different approach. But in current scenario association rule mining suffered from superiority rule generation. The problem of superiority is solved by multi-objective association rule mining, but this process suffered continuity of rule generation. In this paper we are proposing a new algorithm distance weight optimization of association rule mining. In this method, we find the near distance of rule set that uses equalize distance formula and generate two class higher class and lower class .The validation of class checked by distance weight vector. Basically distance weight vector maintain a threshold value of rule item sets. In whole process, we used genetic algorithm for optimization of rule set. Here we set population size is 1000 and selection process validate by distance weight vector.

Girish Kumar Ameta

2013-03-01

238

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

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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.

Sarula Kang

2014-03-01

239

Genetic differentiation and diversity of Adansonia digitata L (baobab) in Malawi using microsatellite markers  

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Baobab (Adansonia digitata L) belonging to Bombacaceae family, is one of the most widely used indigenous priority tree species in sub-Saharan Africa, valued in the cosmetic industry for its seed oil, and powdery fruit pulp for juice making. Baobab has high potential for domestication in southern Africa, therefore understanding its genetic diversity and population structuring is warranted. The study investigated the level of genetic diversity and differentiation of five populations of A. digit...

Munthali, C. R. Y.; Chirwa, Paxie W.; Changadeya, W. J.; Akinnifesi, Festus K.

2012-01-01

240

Genetic diversity and differentiation in European beech (Fagus sylvatica L.) stands varying in management history  

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The impact of forest management on genetic diversity and mating was examined in European beech (Fagus sylvatica L.). Ten beech stands located in Europe were studied in pair-wise plots, differing in management intensity. The stands were genotyped with four highly polymorphic microsatellite loci. Comparison for genetic diversity measures between the stands with limited management and the high management-intensity stands (mostly shelter wood system) revealed no significant differences for alleli...

Buiteveld, J.; Vendramin, G. G.; Leonardi, S.; Kramer, K.; Geburek, T.

2007-01-01

 
 
 
 
241

'Landscape shape interpolation' for defining spatial pattern of beech genetic diversity in Serbia  

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Full Text Available Knowledge about spatial distribution of genetic diversity is very important for foresters in order to make right decisions during establishing of management plans for conservation, afforestation or reforestation. Advanced molecular technologies provide us with efficiently measured genetic information's which can be analyzed powerful statistical tools. Landscape Shape Interpolation analysis was applied on protein based marker data sets from six natural populations of Balkan beech. Results indicate existence of three genetically distinct groups: 1 Djerdap, Kopaonik, Zubin potok and Ivanjica; 2 Bor and 3 Pirot. These results were compared with results of UPGMA clustering of sampled population based on NEI original distances, Principal Coordinate Analysis and Monmonier's Maximum Difference Algorithm Analysis. Landscape Shape Interpolation analysis represent a powerful tool in spatial genetic diversity research. Combining of Landscape Shape Interpolation analysis results with digitalized maps of investigated area in some of numerous GIS applications will for certainly improve visualization of results and provide better understanding of causal factors of genetic diversity.

Iveti? Vladan

2008-01-01

242

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

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

Raul Gheorghe Radu

2014-07-01

243

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

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

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

2002-01-01

244

Bacterial phylogenetic diversity in a constructed wetland system treating acid coal mine drainage  

Energy Technology Data Exchange (ETDEWEB)

Microorganisms in acid mine drainage are typically acidophiles that mediate the oxidation of reduced compounds of iron and sulfur. However, microbial populations in wetland systems constructed to treat acid mine drainage are not well characterized. This study was to analyze bacterial diversity, using cultivation-independent molecular ecological techniques, in a constructed wetland that received acid drainage from an abandoned underground coal mine. DNA was purified from Fe(III)-precipitates from the oxidized surface zone of wetland sediments and 16S rRNA gene sequences were amplified and cloned. A total of 200 clones were analyzed by restriction fragment length polymorphism (RFLP) and 77 unique RFLP patterns were obtained with four restriction enzymes. Of these patterns, 30 most dominant unique clones were selected for sequencing of their 16S rRNA genes. Half of these 30 clones could be matched with autotrophic iron- and sulfur-oxidizing bacteria (Acidithiohacillus ferrooxidans and Acidithiobacillus thiooxidans). Several clones also formed a clade with heterotrophic iron-oxidizing bacteria (TRA2-10, TRA3-20, and TRA5-3) and heterotrophic bacteria (Stenotrophomas maltophilia, Bordetella spp., Alcalgenes sp., Alcaligenesfaecalis, and Alcaligenes xylosoxidans). Approximately 40% and 35% of the analyzed RFLP restriction patterns were consistent with A. ferrooxidans and A. thiooxidans, respectively. The relatively high frequency of acidithiobacilli is consistent with the chemical and physical characteristics of this site i.e., continuous, abundant supply of reduced iron and sulfur compounds, pH 3-4, ambient temperature, and limited organics originating from the coal seam and from vegetation or soil surrounding the inlet channel to the wetland.

Nicorarat, D.; Dick, W.A.; Dopson, M.; Tuovinen, O.H. [Ohio State University, Columbus, OH (USA)

2008-02-15

245

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

Science.gov (United States)

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

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

2014-10-01

246

Genetic Diversity and Evolution of Chinese Traditional Medicinal Fungus Polyporus umbellatus (Polyporales, Basidiomycota)  

Science.gov (United States)

Background Polyporus umbellatus is an important medicinal fungus distributed throughout most area of China. Its wide distribution may have resulted in substantial intraspecific genetic diversity for the fungus, potentially creating variation in its medical value. To date, we know little about the intraspecific genetic diversity of P. umbellatus. Methodology/Principal Findings The objective of this research was to assess genetic differences of P. umbellatus from geographically diverse regions of China based on nrDNA ITS and 28S rRNA (LSU, large subunit) sequences. Significant sequence variations in the ITS and LSU sequences were detected. All sclerotial samples were clustered into four clades based on phylogenetic analysis of ITS, LSU and a combined data set of both regions. Heterogeneity of ITS and LSU sequences was detected in 5 and 7 samples respectively. All clone sequences clustered into the same clade except for one LSU clone sequences (from Henan province) which clustered into two clades (Clade I and Clade II). Significant genetic divergence in P. umbellatus was observed and the genetic diversification was greater among sclerotial samples from Shaanxi, Henan and Gansu provinces than among other provinces. Polymorphism of ITS and LSU sequences indicated that in China, P. umbellatus may spread from a center (Shaanxi, Henan and Gansu province) to other regions. Conclusions/Significance We found sclerotial samples of P. umbellatus contained levels of intraspecific genetic diversity. These findings suggested that P. umbellatus populations in Shaanxi, Henan and Gansu are important resources of genetic diversity and should be conserved accordingly. PMID:23554929

Xing, Xiaoke; Ma, Xueting; Hart, Miranda M.; Wang, Airong; Guo, Shunxing

2013-01-01

247

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)

248

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

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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.

Özlem ÖZBEK

2013-02-01

249

Genetic diversity and differentiation of Juniperus thurifera in Spain and Morocco as determined by SSR.  

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

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

2014-01-01

250

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

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

Aiqing Ji

2014-10-01

251

Relationship between the genetic diversity of Artemisia halodendron and climatic factors  

Science.gov (United States)

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.

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

2014-02-01

252

Assessment of Genetic Diversity of Local and Exotic Brassica napus Germplasm  

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Full Text Available Estimation of genetic diversity of Brassica germplasm provides the basis for rapeseed/mustard genetic improvement. Studies were undertaken to estimate the genetic diversity of 30 lines of Brassica napus using Randomly Amplified Polymorphic DNA (RAPD primers. A total of 30 B. napus genotypes of local and exotic origin were characterized using molecular markers. Four RAPD primers were used to estimate the genetic distances among the genotypes in all the possible combinations. The genetic diversity study revealed different levels of genetic polymorphism for RAPD primers GLA05, GLA07, GLA09 and GLA10, resulting in amplification of 5.7, 3.5, 3.1 and 5.4 scorable bands (loci per genotype, respectively. Individual genetic distances observed among B. napus genotypes ranged from 6.5 to 51%. Bivariate data matrix was generated and genetic distances were calculated using Unweighted Pair Group of Arithmetic Mean (UPGMA procedure. The UPGMA cluster analyses revealed maximum genetic dissimilarity for 8966-1 and 8969-1 genotypes, closely followed by Ganyou-5, 89127-1, 89111-2 and Mlep-048. It is recommended that among the thirty B. napus genotypes, genetically distinct lines pointed out in the present study, should be used in future breeding programs for improvement of Brassica napus.

Mian Afaq Ahmad

2007-01-01

253

Genetic diversity of rhizobia from natural populations varies with the soil dilution sampled  

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Rhizobia were isolated from root nodules of three tree legumes inoculated with dilution series of two tropical soils. The diversity of the isolates obtained from different soil dilutions was assessed by PCR-RFLP analysis of the internally transcribed spacer (ITS) region between the 16S and 23S rRNA genes. In both soils there was a strong effect of dilution on the genetic diversity of the populations with apparent diversity decreasing with increasing dilution.

Bala, A.; Murphy, P.; Giller, K. E.

2001-01-01

254

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

Scientific Electronic Library Online (English)

Full Text Available SciELO South Africa | Language: English Abstract in english 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.

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

255

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Nikhil Jain, Vishal Sharma

2012-01-01

256

Parental selection of wheat lines based on phenotypic characterization and genetic diversity  

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Full Text Available Parental selection is an important step in breeding programs, and genetic variability increases the chances of obtaining variance in progenies. The objectives of this study were to phenotype 29 wheat genotypes and determine the genetic variability among them, in order to identify potential parental lines for breeding programs at Embrapa Wheat. For phenotyping, traits such as plant height, cycle and grains characteristics were assessed and the data were analyzed by the Euclidean distance. The genetic distance was estimated using 97 microsatellite molecular markers and the data were analyzed by Nei72 coefficient. The average distance observed for phenotyping was 10.1, and the genetic distance was 31 %. SSR markers were efficient for selecting genetically diverse genotypes despite their phenotypic similarity, and lines PF 9027, PF 950351, PF 030132, PF 979002, PF 040488 and IWT 04019 can be used as parental for future crosses, since they have genetic diversity and suitable agronomic traits.

Alice Casassola

2013-04-01

257

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

Science.gov (United States)

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

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

2007-12-01

258

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

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

S. A. Mohammadi

2006-10-01

259

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

Science.gov (United States)

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

Jimeno Yepes, Antonio; Verspoor, Karin

2014-01-01

260

Demography, genetic diversity, and population relationships among Argentinean Mapuche Indians  

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Full Text Available 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 indicated 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.

Goicoechea Alicia S.

2000-01-01

 
 
 
 
261

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

Science.gov (United States)

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

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

2013-04-01

262

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2010-01-01

263

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 relat...

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

2012-01-01

264

GENETIC DIVERSITY AMONG INDUCED MUTANTS OF WINTER BARLEY (HORDEUM VULGARE L.  

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Full Text Available The genetic diversity in 40 mutants of barley cultivars Perun and Emon, obtained by single and combination treatments with gamma rays and sodium azide was estimated using two multivariate analyses. A vastly genetic variability for the studied traits between mutants and parent genotypes and as well as among mutants themselves was found. Traits such as plant height, spike length, number of tillers/1m2, winter hardiness and 1000 grain weight have major contributions to the induced genetic diversity. The most promising genotypes for future hybridisation program were mutants ?48, ?27 and ?30.

Broyana DYULGEROVA

2012-06-01

265

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

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Full Text Available The genetic diversity within 29 populations, when 15 populations are local originating in the Tunisian south and 12 introduced of Italy, Austerely, France and Morocco, was analysed by ISSR markers (Inter Simple Repeat sequence. The genetic similarity between these various populations is estimated by the index of Rogers and Tanimoto. Genetic diversity is analyzed by one statistical procedure: hierarchical classification. The total number of bands varied between the various populations from 9-16. The percentage of total polymorphism is about 60%. Four large groups were obtained.

L. Touil

2008-01-01

266

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

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

Han Yao Zhang

2008-12-01

267

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

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

Gregory W. Peterson

2014-10-01

268

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

Science.gov (United States)

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

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

2014-11-13

269

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

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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.

S. Pashaei

2009-01-01

270

Low Genetic Diversity in Melanaphis sacchari Aphid Populations at the Worldwide Scale  

Science.gov (United States)

Numerous studies have examined the genetic diversity and genetic structure of invading species, with contrasting results concerning the relative roles of genetic diversity and phenotypic plasticity in the success of introduced populations. Increasing evidence shows that asexual lineages of aphids are able to occupy a wide geographical and ecological range of habitats despite low genetic diversity. The anholocyclic aphid Melanaphis sacchari is a pest of sugarcane and sorghum which originated in the old world, was introduced into the Americas, and is now distributed worldwide. Our purpose was to assess the genetic diversity and structuring of populations of this species according to host and locality. We used 10 microsatellite markers to genotype 1333 individuals (57 samples, 42 localities, 15 countries) collected mainly on sugarcane or sorghum. Five multilocus lineages (MLL) were defined, grouping multilocus genotypes (MLG) differing by only a few mutations or scoring errors. Analysis of a 658 bp sequence of mitochondrial COI gene on 96 individuals revealed five haplotypes, with a mean divergence of only 0.19 %. The distribution of MLL appeared to be strongly influenced by geography but not by host plant. Each of the five MLL grouped individuals from (A) Africa, (B) Australia, (C) South America, the Caribbean and the Indian Ocean including East Africa, (D) USA, and (E) China. The MLL A and C, with a wide geographic distribution, matched the definition of superclone. Among aphids, M. sacchari has one of the lowest known rates of genetic diversity for such a wide geographical distribution. PMID:25148510

Nibouche, Samuel; Fartek, Benjamin; Mississipi, Stelly; Delatte, Helene; Reynaud, Bernard; Costet, Laurent

2014-01-01

271

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

DEFF Research Database (Denmark)

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.

Pham, Lan Doan; Do, Duy Ngoc

2013-01-01

272

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

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

2011-01-01

273

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

Science.gov (United States)

• Premise of the study: Urbanization is one of the main factors contributing to loss of genetic diversity, as the resulting landscape fragmentation and habitat loss induce species isolation. However, studies of genetic structure and diversity in urbanized landscapes are still rare. We characterized microsatellite primers for Parietaria judaica to study this environment. • Methods and Results: Eleven microsatellite loci from P. judaica, an urban plant, were isolated using shotgun pyrosequencing, and the simple sequence repeat (SSR) markers were screened in 20 individuals of P. judaica. The loci were tested on 166 individuals from three populations in different cities. The number of alleles ranged from two to 19, and expected and observed heterozygosity values ranged from 0.019 to 0.912 and 0.019 to 0.448, respectively. • Conclusions: The markers amplified well in the species and will be useful for examining genetic diversity and population genetic structure in this urban plant.

Bossu, Angele; Bertaudiere-Montes, Valerie; Dubut, Vincent; Manel, Stephanie

2014-01-01

274

Assessment of genetic diversity in maize inbred lines using RAPD markers  

Directory of Open Access Journals (Sweden)

Full Text Available RAPD molecular markers were used to analyze genetic diversity between 16 corn lines. Twenty-two primerswere used resulting in the amplification of 265 fragments, of which 237 (84.44% were polymorphic. Using the UPGMAmethod the genetic associations obtained showed 5 distinct heterotic groups. A principal coordinates analysis also showed anassociation of lines in 5 groups, in agreement with the results observed in the dendrogram. A bootstrap procedure wasapplied to verify whether the amount of markers used was sufficient to ensure reliability of the results, the procedure showeda coefficient of variation of 8.3%, suggesting that the markers were sufficient to assess genetic diversity between the analyzedlines. The high rate of polymorphism between lines revealed by RAPD markers indicated that the method is efficient to analyzegenetic diversity in corn lines and that the genetic divergence can be used to establish consistent heterotic groups between cornlines.

Daniela Cristina Bruel

2007-01-01

275

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

276

Description and analysis of genetic diversity among squash accessions  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in portuguese 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.

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

2009-04-01

277

Description and analysis of genetic diversity among squash accessions  

Directory of Open Access Journals (Sweden)

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".

Athanasios L. Tsivelikas

2009-04-01

278

Description and analysis of genetic diversity among squash accessions  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in portuguese 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.

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

279

The stabilizing effects of genetic diversity on predator-prey dynamics  

Science.gov (United States)

Heterogeneity among prey in their susceptibility to predation is a potentially important stabilizer of predator-prey interactions, reducing the magnitude of population oscillations and enhancing total prey population abundance. When microevolutionary responses of prey populations occur at time scales comparable to population dynamics, adaptive responses in prey defense can, in theory, stabilize predator-prey dynamics and reduce top-down effects on prey abundance. While experiments have tested these predictions, less explored are the consequences of the evolution of prey phenotypes that can persist in both vulnerable and invulnerable classes. We tested this experimentally using a laboratory aquatic system composed of the rotifer Brachionus calyciflorus as a predator and the prey Synura petersenii, a colony-forming alga that exhibits genetic variation in its propensity to form colonies and colony size (larger colonies are a defense against predators). Prey populations of either low initial genetic diversity and low adaptive capacity or high initial genetic diversity and high adaptive capacity were crossed with predator presence and absence. Dynamics measured over the last 127 days of the 167-day experiment revealed no effects of initial prey genetic diversity on the average abundance or temporal variability of predator populations. However, genetic diversity and predator presence/absence interactively affected prey population abundance and stability; diversity of prey had no effects in the absence of predators but stabilized dynamics and increased total prey abundance in the presence of predators. The size structure of the genetically diverse prey populations diverged from single strain populations in the presence of predators, showing increases in colony size and in the relative abundance of cells found in colonies. Our work sheds light on the adaptive value of colony formation and supports the general view that genetic diversity and intraspecific trait variation of prey can play a vital role in the short-term dynamics and stability of planktonic predator-prey systems.

Steiner, Christopher F; Masse, Jordan

2013-01-01

280

The stabilizing effects of genetic diversity on predator-prey dynamics.  

Science.gov (United States)

Heterogeneity among prey in their susceptibility to predation is a potentially important stabilizer of predator-prey interactions, reducing the magnitude of population oscillations and enhancing total prey population abundance. When microevolutionary responses of prey populations occur at time scales comparable to population dynamics, adaptive responses in prey defense can, in theory, stabilize predator-prey dynamics and reduce top-down effects on prey abundance. While experiments have tested these predictions, less explored are the consequences of the evolution of prey phenotypes that can persist in both vulnerable and invulnerable classes. We tested this experimentally using a laboratory aquatic system composed of the rotifer Brachionus calyciflorus as a predator and the prey Synura petersenii, a colony-forming alga that exhibits genetic variation in its propensity to form colonies and colony size (larger colonies are a defense against predators). Prey populations of either low initial genetic diversity and low adaptive capacity or high initial genetic diversity and high adaptive capacity were crossed with predator presence and absence. Dynamics measured over the last 127 days of the 167-day experiment revealed no effects of initial prey genetic diversity on the average abundance or temporal variability of predator populations. However, genetic diversity and predator presence/absence interactively affected prey population abundance and stability; diversity of prey had no effects in the absence of predators but stabilized dynamics and increased total prey abundance in the presence of predators. The size structure of the genetically diverse prey populations diverged from single strain populations in the presence of predators, showing increases in colony size and in the relative abundance of cells found in colonies. Our work sheds light on the adaptive value of colony formation and supports the general view that genetic diversity and intraspecific trait variation of prey can play a vital role in the short-term dynamics and stability of planktonic predator-prey systems. PMID:25339982

Steiner, Christopher F; Masse, Jordan

2013-01-01

 
 
 
 
281

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

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

M. Julian Caley

2011-09-01

282

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)

283

Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers.  

Science.gov (United States)

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity. PMID:16734682

SanCristobal, M; Chevalet, C; Peleman, J; Heuven, H; Brugmans, B; van Schriek, M; Joosten, R; Rattink, A P; Harlizius, B; Groenen, M A M; Amigues, Y; Boscher, M-Y; Russell, G; Law, A; Davoli, R; Russo, V; Dèsautés, C; Alderson, L; Fimland, E; Bagga, M; Delgado, J V; Vega-Pla, J L; Martinez, A M; Ramos, M; Glodek, P; Meyer, J N; Gandini, G; Matassino, D; Siggens, K; Laval, G; Archibald, A; Milan, D; Hammond, K; Cardellino, R; Haley, C; Plastow, G

2006-06-01

284

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2001-09-01

285

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

Science.gov (United States)

A total of 360 Rhizobium leguminosarum bv. viciae strains was isolated from three brown-coal mining restoration fields of different age and plant cover (without and in the first and second year of alfalfa, Medicago sativa, cultivation) using two host species (Vicia hirsuta and Pisum sativum) as capture plants. The strains were genetically typed by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-generated 16S-23S ribosomal DNA intergenic spacer regions (IGS-RFLP) and characterized by plasmid profiles and RFLP analysis of amplified nodABC genes. The R. leguminosarum bv. viciae population was dominated by the same group of strains (irrespective of the trap plant used). According to type richness, the genetic diversity of indigenous R. leguminosarum in the second year of restoration was lower than in the first year and it resembled that of the fallow field, except for plasmid types, in which it was higher than that of the fallow field. Some of the less frequent nodABC genotypes were associated with distinct chromosomal IGS genotypes and symbiotic plasmids (pSyms) of different sizes, indicating that horizontal transfer and rearrangements of pSym can occur in natural environments. However, the dominant pSym and chromosomal genotypes were strictly correlated suggesting a genetically stable persistence of the prevailing R. leguminosarum bv. viciae genotypes in the absence of its host plant. PMID:11555271

Zhang, X X; Kosier, B; Priefer, U B

2001-09-01

286

Estimation of Genetic Diversity of Four Chrysanthemum Mini Cultivars Using RAPD  

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

J. Chatterjee

2005-01-01

287

Genetic Diversity among Mentha Populations in Egypt as Reflected by Isozyme Polymorphism  

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Full Text Available Isozyme polymorphism has been used to measure genetic diversity, genetic population structure and for the estimation of the amount of genetic divergence within and between populations and species of Mentha in Egypt. Ten isozyme systems revealed 31 isozyme loci and a total of 79 alleles in 32 populations of M. longifolia, five populations of M. spicata and one population of M. piperita. The examined populations of M. longifolia and M. spicata showed high levels of genetic variation that might be due to out-breeding and wide dispersal of seeds and pollen grains. Three alleles were scored in all populations; however, no diagnostic alleles at the species level were detected in the 31 isozyme loci. This suggests that the three species may be of hybrid origin or have recently been derived from an ancestor harboring high levels of genetic diversity. The tree illustrating genetic distance among the examined accessions of Mentha indicated obvious discrimination of the three species and the isolation of their populations from each other. At the infra-specific level, the geographically proximal populations exhibited higher genetic similarity than those that geographically distant, indicating environmental impact on the genetic diversity in the genus Mentha in Egypt.

Abd El-Zaher M.A. Mustafa

2005-01-01

288

Genetic diversity based on SSR analysis of the cultured snakehead fish, Channa argus, (Channidae) in China.  

Science.gov (United States)

The snakehead fish Channa argus is an important food fish in China. We identified six microsatellite loci for C. argus. These six microsatellite loci and four other microsatellite markers were used to analyze genetic diversity in four cultured populations of C. argus (SD, JX, HN, and ZJ) and determine their relationships. A total of 154 alleles were detected at the 10 microsatellite loci. The average expected and observed heterozygosities varied from 0.70-0.84 and 0.69-0.83, respectively, and polymorphism information content ranged between 0.66 and 0.82 in the four populations, indicating high genetic diversity. Population JX deviated from mutation-drift equilibrium and may have experienced a recent bottleneck. Analysis of pairwise genetic differentiation revealed FST values that ranged from 0.028 to 0.100, which indicates a moderate level of genetic differentiation. The largest distances were observed between populations HN and SD, whereas the smallest distances were obtained between populations HN and JX. Genetic clustering analysis demonstrated that the ZJ and HN populations probably share the same origin. This information about the genetic diversity within each of the four populations, and their genetic relationships will be useful for future genetic improvement of C. argus through selective breeding. PMID:24615092

Zhu, S-R; Li, J-L; Xie, N; Zhu, L-M; Wang, Q; Yue, G-H

2014-01-01

289

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

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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.

Francesca Maria Sarti

2010-01-01

290

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

Science.gov (United States)

Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America), via the analyses of 516 individuals, and asked the following questions: 1) Do populations have differing levels of within-population genetic diversity? 2) Do populations form distinct genetic clusters? 3) Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering) and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources) in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further contribute to the invasive success of P. cespitosum in its introduced range. PMID:24695495

Matesanz, Silvia; Theiss, Kathryn E; Holsinger, Kent E; Sultan, Sonia E

2014-01-01

291

Genetic analysis of rice varietal diversity for rice blast control.  

Science.gov (United States)

Two Indica hybrid rice of Shanyou63 (A) and Shanyou22 (B), two glutinous landraces of Huanghenuo (C) and Zinuo (D) and three improved Japonica rice of Hexi41 (E), Chujing12 (F) and 8126 (G) were selected and their genetic resistance relationship was estimated using resistance gene analogue (RGA). The results showed that there were similar genetic relationships between hybrid varieties at the genetic similarity (GS) of 0.86,and among improved Japonica varieties at the GS of 0.84, while highly genetic diversifications between traditional varieties, Indica and Japonica varieties, traditional and modern variety ( GS:0.45). The results also showed that clustering analysis based on RGA data were generally corresponded to known pedigrees and blast field resistances of the varieties. Based on varietal differences in RGA data and agronomic traits, plot experiments of five mixed-planting combinations of A/C, A/D, B/C, B/D and A/B and two combinations of E/C and E/F/G were conducted in Jianshui and Shiping counties ( Indica rice growing region) and Luxi County (warm Japonica region) in Yunnan Province in past two years, respectively. The results demonstrated that rice blast management was more effective in five mixed-planting combinations of varieties with different genetic backgrounds (GS: 0.45-0.77) than in two combinations with similar genetic relationships (GS: 0.84-0.90), compared with their monocultures. It is evident for the highly susceptible landraces in mixed-planting to achieve disease control, with significant decreases both in incidence and severity. The blast control efficiencies of landraces in different mixture combinations reached to 54.47%-92.18%. The control efficiencies of improved varieties varied from 15.12% to 25.54% in mixture combinations with closed genetic relationship. In addition,the total yield of 5 varietal combinations with distant genetic relationship increased 539.0-904.0 kg/ha in the mixed-planting plots, at increase rates of 5.6%-10.2%. Mixed rice varieties with similar genetic background did not achieve significant yield increase. Otherwise, the yield of E/F/G decreased 2.7%-4.0% compared with pure stand. The results can provide scientific basis of varietal combinations in diversification experiments for blast control. PMID:15473323

Zhu, You-Yong; Sun, Yan; Wang, Yun-Yue; Li, Yan; He, Yue-Qiu; He, Xia-Hong; Mundt, Christopher C; Mew, Tom W; Hei, Leung

2004-07-01

292

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

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

Azizur Rahman

2012-02-01

293

Diversity of albanian plant genetic resources inventory assesed by eurisco passport descriptors  

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Full Text Available Assessment of diversity of Albanian National Inventory is carried out using import statistics by passport descriptors from Plant Genetic Resources database. Flora of Albania identified more than 3 250 species of plants, but only 2% of them are included in the National Inventory (NI of Albania in EURISCO catalogue. Albanian National Inventory of Plant Genetic Resources in EURISCO (2% of Albanian Flora includes 33 genera, 62 species and 2111 accession, where 54% of them are collected genetic materials. Detailed analysis shows that collected genetic material is the principal source of diversity of Albanian NI in EURISCO. Principal component analysis and comparisons of diversity indices show the descriptors as TAXON, CROPNAME, COLLGEM, GEODATA, NOGEODATA, COLLDATE > Y.2000, COLLDATA Y.2000, COLLCODE-GB, SAMPSTAT-100, COLLSRC-10, COLLSRC-20 and COLLSRC-40 present higher range of diversity and were the principal source of variation that contribute more than other on diversity degree of Albanian NI of PGR in EURISCO. Multivariate correlation analysis show very high positive correlation among COLLGEM and GEODATA, NO-GEODATA, COLLDATE, COLLCODE, SAMPSTAT-100, and COLLSRC-10 passport descriptors. There were higher relationships between collected genetic materials and GEODATA descriptors (latitude, longitude, elevation, COLLDATA, COLLCODE and COLLSRC.

Belul Gixhari

2013-12-01

294

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants.  

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Detailed information about the geographic distribution of genetic and genomic variation is necessary to better understand the organization and structure of biological diversity. In particular, spatial isolation within species and hybridization between them can blur species boundaries and create evolutionary relationships that are inconsistent with a strictly bifurcating tree model. Here, we analyse genome-wide DNA sequence and genetic ancestry variation in Lycaeides butterflies to quantify the effects of admixture and spatial isolation on how biological diversity is organized in this group. We document geographically widespread and pervasive historical admixture, with more restricted recent hybridization. This includes evidence supporting previously known and unknown instances of admixture. The genome composition of admixed individuals varies much more among than within populations, and tree- and genetic ancestry-based analyses indicate that multiple distinct admixed lineages or populations exist. We find that most genetic variants in Lycaeides are rare (minor allele frequency <0.5%). Because the spatial and taxonomic distributions of alleles reflect demographic and selective processes since mutation, rare alleles, which are presumably younger than common alleles, were spatially and taxonomically restricted compared with common variants. Thus, we show patterns of genetic variation in this group are multifaceted, and we argue that this complexity challenges simplistic notions concerning the organization of biological diversity into discrete, easily delineated and hierarchically structured entities. PMID:24866941

Gompert, Zachariah; Lucas, Lauren K; Buerkle, C Alex; Forister, Matthew L; Fordyce, James A; Nice, Chris C

2014-09-01

295

Rapid increase in southern elephant seal genetic diversity after a founder event.  

Science.gov (United States)

Genetic diversity provides the raw material for populations to respond to changing environmental conditions. The evolution of diversity within populations is based on the accumulation of mutations and their retention or loss through selection and genetic drift, while migration can also introduce new variation. However, the extent to which population growth and sustained large population size can lead to rapid and significant increases in diversity has not been widely investigated. Here, we assess this empirically by applying approximate Bayesian computation to a novel ancient DNA dataset that spans the life of a southern elephant seal (Mirounga leonina) population, from initial founding approximately 7000 years ago to eventual extinction within the past millennium. We find that rapid population growth and sustained large population size can explain substantial increases in population genetic diversity over a period of several hundred generations, subsequently lost when the population went to extinction. Results suggest that the impact of diversity introduced through migration was relatively minor. We thus demonstrate, by examining genetic diversity across the life of a population, that environmental change could generate the raw material for adaptive evolution over a very short evolutionary time scale through rapid establishment of a large, stable population. PMID:24478305

de Bruyn, Mark; Pinsky, Malin L; Hall, Brenda; Koch, Paul; Baroni, Carlo; Hoelzel, A Rus

2014-03-22

296

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

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

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

2011-01-01

297

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

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

Lutz Richard A

2011-04-01

298

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

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

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

2014-01-01

299

Genetic diversity in yellow passion fruit (Passiflora edulis Sims based on RAPD  

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Full Text Available This study aimed to evaluate the genetic diversity by RAPD markers in 20 genotypes of ‘yellow’ passion fruit (Passiflora edulis Sims. The 16 primers generated 92 markers, 57 (62% of which were polymorphic. The genetic distance (gdij estimated by the complement of the Dice index (gdij = 0.19 and genotype grouping based on UPGMA algorithm showed low variability among genotypes. These results show a narrower genetic basis than reported for other Passiflora populations and the need to increase this variability by germplasm introduction. Divergent genotypes were also identified for the choice of parents for crosses for genetic gains in traits previously selected within the population studied.

Carlos Bernard Moreno Cerqueira-Silva

2010-01-01

300

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: English Abstract in english 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.

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

2008-12-01

 
 
 
 
301

Phosphorylation networks regulating JNK activity in diverse genetic backgrounds  

DEFF Research Database (Denmark)

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.

Bakal, Chris; Linding, Rune

2008-01-01

302

Genetic Diversity of Bt Resistance: Implications for Resistance Management  

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Full Text Available The bacterium Bacillus thuringiensis is the main source of insecticidal proteins in insect resistant plants. However, biochemical and genetic studies have shown that insect resistance to B. thuringiensis (Bt toxins can occur and with the advent of Bt transgenic crops this is a major concern. Several insect species have shown resistance to these toxins in the laboratory but the diamondback moth, Plutella xylostella is the only species which has evolved resistance under field conditions to date. Many studies have been done to elucidate the mode of action of the toxins and the mechanisms and genetics of resistance. In this article Bt toxins, their mode of action, mechanisms and genetics of resistance and management strategies for delaying resistance are reviewed. The emphasis is placed on examining the presently recommended high dose/refuge strategy.

Ali H. Sayyed

2002-01-01

303

Phosphorylation networks regulating JNK activity in diverse genetic backgrounds.  

Science.gov (United States)

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. PMID:18927396

Bakal, Chris; Linding, Rune; Llense, Flora; Heffern, Elleard; Martin-Blanco, Enrique; Pawson, Tony; Perrimon, Norbert

2008-10-17

304

Detection of Genetic Variation and Genetic Diversity in Two Indian Mudskipper Species (Boleophthalmus boddarti, B. dussumieri using RAPD Marker  

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Full Text Available Due to the environmental changes and habitat destruction the mudskipper fish population is decreasing in recent years. To predict the fish population structure, frequent manual survey and molecular methods are widely used. Molecular markers such as RAPD, microsatellite, allozyme, D-loop haplotype are frequently adopted to assess the population structure of an organism. In this study ten- arbitrary primers were screened to estimate the genetic relationships and diversity of two mudskipper species (Boleophthalmus boddarti and B. dussumieri in Vellar estuary, Tamilnadu, India. By this RAPD marker study, the genetic diversity (H in B. boddarti was more (0.0116 ± 0.0066 than in B. dussumieri (0.0056 ± 0.0024 in Vellar estuary (India. The genetic distance between B. boddarti and B. dussumieri was 1.7943. By observing the species specific bands and the phylogenetic analysis it is revealed that these two species clearly deviated into separate clusters emphasizing the distinct species status.

Vellaichamy RAMANADEVI

2013-05-01

305

Genetic diversity and relationships of korean chicken breeds based on 30 microsatellite markers.  

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The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (F IT) in native chicken was 0.234±0.025. Over 30.7% of F IT was contributed by within-population deficiency (F IS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds. PMID:25178290

Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu

2014-10-01

306

Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation.  

Science.gov (United States)

Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91 %) than between populations (9 %). Results suggested moderate genetic differentiation among Napier grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation. PMID:23671788

Wanjala, Bramwel W; Obonyo, Meshack; Wachira, Francis N; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A; Proud, Janice; Hanson, Jean

2013-01-01

307

Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers  

Science.gov (United States)

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (FIT) in native chicken was 0.234±0.025. Over 30.7% of FIT was contributed by within-population deficiency (FIS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds PMID:25178290

Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu

2014-01-01

308

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

309

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

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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.

Zlatko Liber

2014-09-01

310

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)

311

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

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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.

Rabinowicz Pablo D

2010-01-01

312

A comparative study of genetic diversity of peripheral and central populations of chukar partridge from Northwestern China.  

Science.gov (United States)

Although it has long been presumed that peripheral populations tend to exhibit low genetic diversity because of isolation and genetic drift, results of empirical investigation remain ambiguous. Some chukar partridge (Alectoris chukar) populations have expanded their ranges, resulting in several peripheral populations, due to recent deforestation by human beings in the Longdong Loess Plateau of northwestern China. On the basis of mitochondrial DNA control-region data, we compare the genetic diversity of two peripheral populations, Honghui and Wangxia, and six central populations. The Wangxia population possessed high levels of genetic diversity. The Honghui population, however, exhibited low genetic variation. The degree of isolation was the primary factor affecting the genetic diversity of the two peripheral populations. A peripheral population that was not isolated exhibited higher genetic diversity than did an isolated peripheral population. PMID:16382366

Huang, Zuhao; Liu, Naifa; Zhou, Tianlin

2005-12-01

313

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

Science.gov (United States)

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

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

2014-08-01

314

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)

315

Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers.  

Science.gov (United States)

The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus. PMID:21735103

Hu, Jihong; Pan, Lei; Liu, Honggao; Wang, Shuzhen; Wu, Zhihua; Ke, Weidong; Ding, Yi

2012-04-01

316

Genetic Diversity Between Two Populations of Heteropneustes fossilis (Bloch Using RAPD Profile  

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Full Text Available The present study was aimed to elucidate its genetic diversity based on RAPD markers from 6 individuals belonging to two ecological habitats i.e., upper lake and lower lake of Bhopal. Ten random 10-mer primers were scored in each of the individuals from two locations out of which three primers, which gave polymorphism, were selected for Polymerase Chain Reaction (PCR and used in the final RAPD analysis. The complementary approach of RAPD was used to evaluate the genetic diversity among all the accessions using 3 highly polymorphic primers. Using these primers, 128 scorable DNA fragments were found, of which 24 (18.75% were polymorphic. By comparing RAPD banding patterns, small variations were found between and within the populations. The present study yielded data elucidating the usefulness of complementary approaches to make diversity analysis more explanatory and purposeful for optimum genetic amelioration and effective conservation of its genotypic variability.

N.N. Mehrotra

2009-01-01

317

[Genetic diversity of natural populations of Arabidopsis thaliana (L.) Heynh. in Karelia].  

Science.gov (United States)

The genetic structure of ten natural populations of Arabidopsis thaliana (L.) Heynh. at eight isozyme loci was studied. The populations were located in the northern part of the species range, 200 km from the north to the south along the Onega Lake coast in Karelia. Considerable genetic diversity (P99% = 43.7, Hobs = 0.003) was revealed that is not typical of populations of self-pollinating plant species. A direct correlation between the proportion of polymorphic loci and geographical latitude was shown (r = 0.68; P < 0.05). It is suggested that a high polymorphism level in Karelian Arabidopsis thaliana (L.) populations increasing from the south to the north is due to extreme environmental conditions in the northern part of the species range. The distribution of genetic diversity within and between populations is typical of self-pollinating species: the larger part of the total diversity resides among populations (GST = 0.583). PMID:11253429

Fedorenko, O M; Savushkin, A I; Olimpienko, G S

2001-02-01

318

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

Science.gov (United States)

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

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

2005-01-01

319

Parallel declines in species and genetic diversity in tropical forest fragments.  

Science.gov (United States)

The potential for parallel impacts of habitat change on multiple biodiversity levels has important conservation implications. We report on the first empirical test of the 'species-genetic diversity correlation' across co-distributed taxa with contrasting ecological traits in the context of habitat fragmentation. In a rainforest landscape undergoing conversion to oil palm, we show that depauperate species richness in fragments is mirrored by concomitant declines in population genetic diversity in the taxon predicted to be most susceptible to fragmentation. This association, not seen in the other species, relates to fragment area rather than isolation. While highlighting the over-simplification of extrapolating across taxa, we show that fragmentation presents a double jeopardy for some species. For these, conserving genetic diversity at levels of pristine forest could require sites 15-fold larger than those needed to safeguard species numbers. Importantly, however, each fragment contributes to regional species richness, with larger ones tending to contain more species. PMID:21564453

Struebig, Matthew J; Kingston, Tigga; Petit, Eric J; Le Comber, Steven C; Zubaid, Akbar; Mohd-Adnan, Adura; Rossiter, Stephen J

2011-06-01

320

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

CERN Document Server

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.

Jassadapakorn, Chaiwat; 10.5121/ijcsit.2011.3409

2011-01-01

 
 
 
 
321

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

Directory of Open Access Journals (Sweden)

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

Rajora Om P

2009-12-01

322

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

323

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

2014-10-01

324

Genetic Diversity of Pandanus from West Java based on ISSR Markers  

Directory of Open Access Journals (Sweden)

Full Text Available Genetic Diversity of Pandanus from West Java based on ISSR Markers. The genetic diversity of 10 species ofPandanus from West Java was examined using inter simple sequence repeat (ISSR technique. Samples were collectedfrom different localities in West Java. Two primers (ISSR2 and ISSR7 were selected as reliable amplifying ISSRmarkers. The two primers amplified 19 band position, with amplification size ranged from 200 to 1500 bp. Geneticdistance for samples ranged from 0.267 to 0.957. Genetic distance was high (0.957 between P. pseudolais and P.spinistigmaticus, and between P. kurzii and P. pseudolais, where as genetic distance was low (0.267 between P.scabrifolius and P. bidur.

Sri Handayani

2010-11-01

325

Intraspecific genetic diversity of Oenococcus oeni as derived from DNA fingerprinting and sequence analyses.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The intraspecific genetic diversity of Oenococcus oeni, the key organism in the malolactic fermentation of wine, has been evaluated by random amplified polymorphic DNA (RAPD), ribotyping, small-plasmid content, and sequencing of RAPD markers with widespread distribution among the strains. Collection strains representing the diversity of this species have been studied together with some new isolates, many of which were obtained from wines produced by spontaneous malolactic fermentation. The RA...

Zavaleta, A. I.; Marti?nez-murcia, A. J.; Rodri?guez-valera, F.

1997-01-01

326

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

Directory of Open Access Journals (Sweden)

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.

Almeida Sabrina E. Matos

2000-01-01

327

Rapid anti-pathogen response in ant societies relies on high genetic diversity  

DEFF Research Database (Denmark)

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.

Ugelvig, Line V; Kronauer, Daniel Jan Christoph

2010-01-01

328

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

329

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

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

1097-11-01

330

Molecular characterization and genetic diversity of Prunus rootstocks  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Bouhadida, Mariem; Casas Cendoya, Ana Mari?a; Gonzalo Pascual, Mari?a Jose?; Aru?s, Pere; Moreno Sa?nchez, Mari?a A?ngeles; Gogorcena Aoiz, Yolanda

2009-01-01

331

Phylogenetic Diversity of Archaea and the Archaeal Ammonia Monooxygenase Gene in Uranium Mining-Impacted Locations in Bulgaria  

Science.gov (United States)

Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaera cluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaera cluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate that amoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity. PMID:24711725

Radeva, Galina; Kenarova, Anelia; Bachvarova, Velina; Popov, Ivan; Selenska-Pobell, Sonja

2014-01-01

332

Molecular genetic diversity of the gyeongju donggyeong dog in Korea.  

Science.gov (United States)

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 heterozygosity and expected heterozygosity ranged from 0.4706 to 0.9020 (mean 0.7657) and from 0.4303 to 0.8394 (mean 0.7266), respectively. The total exclusion probability of 10 microsatellite loci was 0.99955. Of the 10 microsatellite markers, the AHT121, AHTh260 and CXX279 markers had relatively high PIC values (?0.7). This study found that there were specific alleles, 116 allele at AHT121 in the Donggyeong dog when compared with other dog breeds. Also, the results showed two (Korean native dogs and the foreign dog breeds) distinct clusters. The closest distance (0.1184) was observed between the Donggyeong dog and Jindo dog, and the longest distance (0.3435) was observed between the Donggyeong dog and Bulgae. The Korean native dog breeds have comparatively near genetic distances between each other. PMID:25030603

Lee, Eun-Woo; Choi, Seong-Kyoon; Cho, Gil-Jae

2014-11-01

333

Genetic diversity and chemical polymorphism of some Thymus species.  

Science.gov (United States)

To ascertain whether there are chemical and genetic relationships among some Thymus species and also to determine correlation between these two sets of data, the essential-oil composition and genetic variability of six populations of Thymus including: T. daenensis ?ELAK. (two populations), T. fallax FISCH. & C.A.MEY., T. fedtschenkoi RONNIGER, T. migricus KLOKOV & DES.-SHOST., and T. vulgaris L. were analyzed by GC and GC/MS, and also by randomly amplified polymorphic DNA (RAPD). Thus, 27 individuals were analyzed using 16 RAPD primers, which generated 264 polymorphic scorable bands and volatiles isolated by distillation extraction were subjected to GC and GC/MS analyses. The yields of oils ranged from 2.1 to 3.8% (v/w), and 34 components were identified, amounting to a total percentage of 97.8-99.9%. RAPD Markers allowed a perfect distinction between the different species based on their distinctive genetic background. However, they did not show identical clustering with the volatile-oil profiles. PMID:23776024

Rustaiee, Ali Reza; Yavari, Alireza; Nazeri, Vahideh; Shokrpour, Majid; Sefidkon, Fatemeh; Rasouli, Musa

2013-06-01

334

Assessment of genetic diversity and relationships among Osmanthus fragrans cultivars using AFLP markers  

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: English Abstract in english 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.

Wang Jun, Yuan; Yuan Ji, Han; Mei Fang, Dong; Fu De, Shang.

2011-01-15

335

Population demographics and genetic diversity in remnant and translocated populations of sea otters  

Science.gov (United States)

The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter (Enhydra lutris) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Metochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size (r = -0.741, p = 0.038) and minimum population size (r = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, altough growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.

Bodkin, J.L.; Ballachey, B.E.; Cronin, M.A.; Scribner, K.T.

1999-01-01

336

Abundance and genetic diversity of aerobic anoxygenic phototrophic bacteria of coastal regions of the pacific ocean.  

Science.gov (United States)

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic microbes that are found in a broad range of aquatic environments. Although potentially significant to the microbial ecology and biogeochemistry of marine ecosystems, their abundance and genetic diversity and the environmental variables that regulate these properties are poorly understood. Using samples along nearshore/offshore transects from five disparate islands in the Pacific Ocean (Oahu, Molokai, Futuna, Aniwa, and Lord Howe) and off California, we show that AAP bacteria, as quantified by the pufM gene biomarker, are most abundant near shore and in areas with high chlorophyll or Synechococcus abundance. These AAP bacterial populations are genetically diverse, with most members belonging to the alpha- or gammaproteobacterial groups and with subclades that are associated with specific environmental variables. The genetic diversity of AAP bacteria is structured along the nearshore/offshore transects in relation to environmental variables, and uncultured pufM gene libraries suggest that nearshore communities are distinct from those offshore. AAP bacterial communities are also genetically distinct between islands, such that the stations that are most distantly separated are the most genetically distinct. Together, these results demonstrate that environmental variables regulate both the abundance and diversity of AAP bacteria but that endemism may also be a contributing factor in structuring these communities. PMID:22307290

Ritchie, Anna E; Johnson, Zackary I

2012-04-01

337

Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA.  

Science.gov (United States)

A culture-independent molecular phylogenetic analysis was carried out to study the prokaryotic diversity in two soil samples collected from the subsurface (1.34 km depth) of the former Homestake gold mine, Lead, South Dakota, USA at two sites, the Ross shaft and number 6 Winze. Microbial community analyses were performed by cloning and sequencing of 16S rRNA genes retrieved directly from soil samples. Geochemical characterization of soils revealed high amount of toxic metals such as As, Cd, Co, Cr, Cu, Ni, Pb, Zn, and U at both the sites. Phylogenetic analyses showed that soil samples were predominantly composed of phylotypes related to phylum Proteobacteria. Other phyla detected in libraries were Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and candidate divisions OP10 and TM7. The majority (>95%) of the phylotypes retrieved in the libraries were most closely related to environmental sequences from yet-uncultured bacteria representing a hitherto unidentified diversity. The archaeal communities at both the sites exhibited lower diversity and were most closely affiliated to uncultivated species within the Crenarchaeota. Results showed the existence of diverse microbial populations in deep subsurface environment of the Homestake gold mine. Statistical analyses demonstrated that each site harbored phylogenetically distinct microbial populations that were more diverse at Ross site compare to winze site. PMID:19763410

Rastogi, Gurdeep; Stetler, Larry D; Peyton, Brent M; Sani, Rajesh K

2009-08-01

338

Genetic Diversity among Barley Populations from West China Based on RAMP and RAPD Markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Using RAMP and RAPD for detecting the genetic diversity of 46 barley accessions, collected from west China. Seventeen primer combinations produced 104 discernible RAMP fragments of which 96 (91%) were polymorphic. The number of fragments per primer combination varied from 2 to 11, with the mean of 6.18. The mean of Polymorphism Information Content (PIC) for the RAMPs was 0.752. On the basis of 96 polymorphic fragments, each genotype had a unique banding profile and the Genetic Similarit...

Pu, Z. E.; Hou, Y. C.; Xu, X. X.; Yan, Z. H.; Wei, Y. M.; Lan, X. J.; Zheng, Y. L.

2009-01-01

339

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

Science.gov (United States)

Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID:24963708

Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

2014-01-01

340

Study on Seed Morphology and Genetic Diversity of Jatropha curcas L. from Different Provenances  

Directory of Open Access Journals (Sweden)

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.

Junjiao Guan

2013-02-01

 
 
 
 
341

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

342

Multilocus sequence typing reveals genetic diversity of carbapenem- or ceftazidime-nonsusceptible Pseudomonas aeruginosa in China.  

Science.gov (United States)

It is unclear whether the genetic background of drug-resistant Pseudomonas aeruginosa was disseminated from a certain clone. Thus, we performed MLST (multilocus sequence typing) of 896 P. aeruginosa isolates that were nonsusceptible to imipenem, meropenem, or ceftazidime. This revealed 254 sequence types (STs), including 104 new STs and 34 STs with novel alleles. Thirty-three clonal complexes and 404 singletons were found. In conclusion, drug-resistant P. aeruginosa clones can be developed from diverse genetic backgrounds. PMID:23939886

Ji, Jingshu; Wang, Jie; Zhou, Zhihui; Wang, Haiping; Jiang, Yan; Yu, Yunsong

2013-11-01

343

Fluorescent amplified fragment length polymorphism (fAFLP) analyses and genetic diversity in Litopenaeus vannamei (Penaeidae)  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The Pacific white shrimp, Litopenaeus vannamei (Penaeidae), represents about 95% of all Brazilian shrimp production. The Brazilian L. vannamei foundation broodstock was made up of specimens collected from different American Pacific sites, but little information was collected on the genetic structure of the broodstock. We used the fluorescence amplified fragment length polymorphism (fAFLP) method to study the genetic diversity of L. vannamei broodstock lines 03CMF1 and 03CBF1 originally produc...

Michelle Mantovani Gonçalves; Manoel Victor Franco Lemos; Pedro Manoel Galetti Junior; Patrícia Domingues de Freitas; Manuel Antonio Andrade Furtado Neto

2005-01-01

344

Diverse types of genetic variation converge on functional gene networks involved in schizophrenia  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Despite the successful identification of several relevant genomic loci, the underlying molecular mechanisms of schizophrenia remain largely unclear. We developed a computational approach (NETBAG+) that allows an integrated analysis of diverse disease-related genetic data using a unified statistical framework. The application of this approach to schizophrenia-associated genetic variations, obtained using unbiased whole-genome methods, allowed us to identify several cohesive gene networks relat...

Gilman, Sarah R.; Chang, Jonathan; Xu, Bin; Bawa, Tejdeep S.; Gogos, Joseph A.; Karayiorgou, Maria; Vitkup, Dennis

2012-01-01

345

Assessment of genetic diversity in maize inbred lines using RAPD markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

RAPD molecular markers were used to analyze genetic diversity between 16 corn lines. Twenty-two primerswere used resulting in the amplification of 265 fragments, of which 237 (84.44%) were polymorphic. Using the UPGMAmethod the genetic associations obtained showed 5 distinct heterotic groups. A principal coordinates analysis also showed anassociation of lines in 5 groups, in agreement with the results observed in the dendrogram. A bootstrap procedure wasapplied to verify whether the amount of...

Daniela Cristina Bruel; Valeria Carpentieri-Pípolo; Claudete de Fátima Ruas; Antonio Carlos Gerage; Silvia Graciele Hülse de Souza

2007-01-01

346

A Study of Genetic Diversity in Sardari Wheat Ecotypes Using AFLP Markers and Agronomic Traits  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Studying genetic diversity is important because a decrease in genetic variability might result in a reduction of the plasticity of the crops to respond to changes in climate, pathogen populations, or agricultural practices. In this study, 72 Sardari wheat (Triticum aestivum L.) ecotypes were analyzed by AFLP markers and 17 phenotypic characters. Three pairs of EcoRI/MseI primer combinations produced 1582 polymorphic bands (with mean percentage of polymorphic 73.92%). Cluster analysis using Ja...

Siosemardeh, A.; Zh, Osamny

2009-01-01

347

Estimation of Genetic Diversity in Capsicum Germplasm Using Randomly Amplified Polymorphic DNA  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Imtiaz Ahmed Khan

2010-01-01

348

Genetic diversity in passion fruit (Passiflora spp.) evaluated by RAPD markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The objective of this study was to characterize the genetic diversity within a Passiflora collection by PCR-RAPD markers. Genetic analysis was performed in 70 accessions, representing 11 species of the genus Passiflora. The use of only five primers produced 136 reproducible polymorphic bands. The hierarchical classification showed high levels of dissimilarities between and within the species studied. A clear separation was obtained among species and accessions of P. edulis and P. edulis f. fl...

Maria Lúcia Crochemore; Hugo Bruno Correa Molinari; Luiz Gonzaga Esteves Vieira

2003-01-01

349

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

Science.gov (United States)

Miscanthus is a perennial rhizomatous C4 grass native to East Asia. Endowed with great biomass yield, high ligno-cellulose composition, efficient use of radiation, nutrient and water, as well as tolerance to stress, Miscanthus has great potential as an excellent bioenergy crop. Despite of the high potential for biomass production of the allotriploid hybrid M. ×giganteus, derived from M. sacchariflorus and M. sinensis, other options need to be explored to improve the narrow genetic base of M. ×giganteus, and also to exploit other Miscanthus species, including M. sinensis (2n?=?2x?=?38), as bioenergy crops. In the present study, a large number of 459 M. sinensis accessions, collected from the wide geographical distribution regions in China, were genotyped using 23 SSR markers transferable from Brachypodium distachyon. Genetic diversity and population structure were assessed. High genetic diversity and differentiation of the germplasm were observed, with 115 alleles in total, a polymorphic rate of 0.77, Nei's genetic diversity index (He) of 0.32 and polymorphism information content (PIC) of 0.26. Clustering of germplasm accessions was primarily in agreement with the natural geographic distribution. AMOVA and genetic distance analyses confirmed the genetic differentiation in the M. sinensis germplasm and it was grouped into five clusters or subpopulations. Significant genetic variation among subpopulations indicated obvious genetic differentiation in the collections, but within-subpopulation variation (83%) was substantially greater than the between-subpopulation variation (17%). Considerable phenotypic variation was observed for multiple traits among 300 M. sinensis accessions. Nine SSR markers were found to be associated with heading date and biomass yield. The diverse Chinese M. sinensis germplasm and newly identified SSR markers were proved to be valuable for breeding Miscanthus varieties with desired bioenergy traits. PMID:24116066

Zhao, Hua; Wang, Bo; He, Junrong; Yang, Junpin; Pan, Lei; Sun, Dongfa; Peng, Junhua

2013-01-01

350

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

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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.

NikoBeerenwinkel

2012-09-01

351

Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L.  

Science.gov (United States)

Phaseolus coccineus L. is closely related to P. vulgaris and is the third most important cultivated Phaseolus species. Little is known about the patterns of its diversity. In this work, a representative collection of its worldwide diversity was initially developed. The collection includes 28 wild forms (WFs) and 52 landraces (LRs) from Mesoamerica (the crop domestication area), and 148 LRs from Europe (where the crop was introduced in the sixteenth century). The collection was studied by using 12 SSR molecular markers that were developed for the P. vulgaris genome. They were proved to be effective and reliable in P. coccineus in this work. Fourteen LRs of P. dumosus (previously identified as a subspecies of P. coccineus) were also studied. The genetic diversity, population structure and phylogenetic relationships were investigated. The results indicate that: (a) the European and Mesoamerican gene pools are clearly differentiated, (b) a certain reduction of diversity occurred with introduction into Europe, and (c) the Mesoamerican LRs (P. dumosus included) and WFs are closely related and are connected by a high gene flow. Inferences on the domestication process of P. coccineus are also presented. This study provides a picture of the genetic diversity distribution and outcomes with introduction into the Old World, which was not available before. It also underlines that the genetic diversity of both WFs and LRs is an important source for Phaseolus spp. breeding programs and deserves to be preserved in situ and ex situ. PMID:21279322

Spataro, G; Tiranti, B; Arcaleni, P; Bellucci, E; Attene, G; Papa, R; Spagnoletti Zeuli, P; Negri, V

2011-05-01

352

Understanding genetic toxicity through data mining: the process of building knowledge by integrating multiple genetic toxicity databases.  

Science.gov (United States)

ABSTRACT Genetic toxicity data from various sources were integrated into a rigorously designed database using the ToxML schema. The public database sources include the U.S. Food and Drug Administration (FDA) submission data from approved new drug applications, food contact notifications, generally recognized as safe food ingredients, and chemicals from the NTP and CCRIS databases. The data from public sources were then combined with data from private industry according to ToxML criteria. The resulting "integrated" database, enriched in pharmaceuticals, was used for data mining analysis. Structu