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

Directory of Open Access Journals (Sweden)

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

Sajduda Anna

2006-03-01

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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)

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 numeric...

Gazzola, Lidia

2006-01-01

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XML Mining Using Genetic Algorithm  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Soumadip Ghosh

2011-01-01

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Genetic diversity in experimental metapopulations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Bakker, Johanna

2008-01-01

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XML Mining Using Genetic Algorithm  

Directory of Open Access Journals (Sweden)

Full Text Available In recent years XML documents have became very popular for representing semi-structured data and a standard for data exchange over the web. Mining XML data from the web is becoming increasingly important as well. In general frequent item sets are generated from large data sets by applying association rule mining algorithms like Apriori, Partition, Pincer-Search, Incremental, Border algorithm etc., which take too much computer time to compute all the frequent item sets. By using Genetic Algorithm (GA we can improve the scenario. The major advantage of using GA in the discovery of frequent item sets is that they perform global search and its time complexity is less compared to other algorithms as the genetic algorithm is based on the greedy approach. The main aim of this paper is to find all the frequent item sets from XML database using genetic algorithm.

Soumadip Ghosh

2011-06-01

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Genetic diversity among Bolivian arenaviruses?  

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Machupo virus and Chapare virusare members of the Tacaribe serocomplex (virus family Arenaviridae) and etiological agents of hemorrhagic fever in humans in Bolivia. The nucleotide sequences of the complete Z genes, a large fragment of the RNA-dependent RNA polymerase genes, the complete glycoprotein precursor genes, and the complete nucleocapsid protein genes of 8 strains of Machupo virus were determined to increase our knowledge of the genetic diversity among the Bolivian arenaviruses. The r...

Cajimat, Maria N. B.; Milazzo, Mary Louise; Rollin, Pierre E.; Nichol, Stuart T.; Bowen, Michael D.; Ksiazek, Thomas G.; Fulhorst, Charles F.

2009-01-01

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Evidence of population genetic effects in Peromyscus melanophrys chronically exposed to mine tailings in Morelos, Mexico.  

Science.gov (United States)

Effects of environmental chemical pollution can be observed at all levels of biological organization. At the population level, genetic structure and diversity may be affected by exposure to metal contamination. This study was conducted in Huautla, Morelos, Mexico in a mining district where the main contaminants are lead and arsenic. Peromyscus melanophrys is a small mammal species that inhabits Huautla mine tailings and has been considered as a sentinel species. Metal bioaccumulation levels were examined by inductively coupled plasma mass spectrometry and genetic analyses were performed using eight microsatellite loci in 100 P. melanophrys individuals from 3 mine tailings and 2 control sites. The effect of metal bioaccumulation levels on genetic parameters (population and individual genetic diversity, genetic structure) was analyzed. We found a tissue concentration gradient for each metal and for the bioaccumulation index. The highest values of genetic differentiation (Fst and Rst) and the lowest number of migrants per generation (Nm) were registered among the exposed populations. Genetic distance analyses showed that the most polluted population was the most genetically distant among the five populations examined. Moreover, a negative and significant relationship was detected between genetic diversity (expected heterozygosity and internal relatedness) and each metal concentration and for the bioaccumulation index in P. melanophrys. This study highlights that metal stress is a major factor affecting the distribution and genetic diversity levels of P. melanophrys populations living inside mine tailings. We suggest the use of genetic population changes at micro-geographical scales as a population level biomarker. PMID:23108757

Mussali-Galante, Patricia; Tovar-Sánchez, Efraín; Valverde, Mahara; Valencia-Cuevas, Leticia; Rojas, E

2013-11-01

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Genetic diversity of American wild rice species  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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) w...

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

2011-01-01

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Genetic diversity in a crop metapopulation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Heerwaarden, J.; Eeuwijk, F. A.; Ross-ibarra, J.

2010-01-01

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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

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[Genetic diversity of human Erythroviruses].  

Science.gov (United States)

B19 Parvovirus (B19V) has been considered for a long period of time as the unique human virus belonging to the genus Erythrovirus. The genetic diversity of B19V isolates has been shown to be very low (13% nucleotide divergence) led to specify the classification of this virus family. Phylogenetic analysis of partial sequences of V9-related isolates combined with Erythrovirus sequences in sequences banks indicates an organization into three well-individualized genotypes. Analysis of the nearly full-length genome sequences show an ancient separation between the three genotypes lineages. Genotype 3 (the most ancient lineage) could have originated in Africa. The functional regions of major proteins are conserved in the three genotypes. The frequency of these genotypes is various according to studies. Genotype 1 is predominant, except in Ghana where all the described isolates were genotype 3. A prospective French study performed between 1999 and 2001 indicated that genotypes 2 and 3 viruses circulated with a significant frequency (10%). Pathogenic properties might not differ according to the genotype. PMID:18387751

Servant-Delmas, A; Laperche, S; Mercier, M; Lefrère, J-J

2009-03-01

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Biodiversity assessment in forests - from genetic diversity to landscape diversity  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Assessing biodiversity in forests requires a reliable and sustainable monitoring concept, which must include all levels of diversity, the genetic, the species and the landscape level. Diversity studies should not be reduced to quantitative analysis, but qualitative interpretations are an important part for the understanding of the results. Also, the linkage of terrestrial data and remote sensing data as well the implementation of abiotic and biotic data collected on existing monitoring system...

Granke O; Kenter B; Wu, Kriebitzsch; Kohl M; Kohler R; Olschofsky K

2009-01-01

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Genetic diversity in farm animals - a review  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2010-01-01

14

Genetic diversity in farm animals -- a review.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2010-01-01

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Biodiversity assessment in forests - from genetic diversity to landscape diversity  

Directory of Open Access Journals (Sweden)

Full Text Available Assessing biodiversity in forests requires a reliable and sustainable monitoring concept, which must include all levels of diversity, the genetic, the species and the landscape level. Diversity studies should not be reduced to quantitative analysis, but qualitative interpretations are an important part for the understanding of the results. Also, the linkage of terrestrial data and remote sensing data as well the implementation of abiotic and biotic data collected on existing monitoring systems are useful sources to analyse cause-effect relationships and interactions between the different aspects of diversity.

Granke O

2009-01-01

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The Genetic Algorithm for Truck Dispatching Problems in Surface Mine  

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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

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The Genetic Algorithm for Truck Dispatching Problems in Surface Mine  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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.

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

2010-01-01

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Genetic Diversity and Recombination of Porcine Sapoviruses  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Sapoviruses (SaVs) are emerging enteric pathogens that cause diarrhea in humans and animals. Human SaVs are genetically variable and have been classified into four genogroups (GI, -II, -IV, and -V). To date, only two genetically similar porcine SaV strains have been reported that belong to GIII. To investigate the genetic diversity of porcine SaVs and their genetic relatedness to human strains, we sequenced 286 nucleotides (nt) of the RNA-dependent RNA polymerase (RdRp) region of nine porcine...

Wang, Qiu-hong; Han, Myung Guk; Funk, Julie A.; Bowman, Gary; Janies, Daniel A.; Saif, Linda J.

2005-01-01

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Genetic diversity of Rhodopirellula strains.  

Science.gov (United States)

Rhodopirellula baltica SH1(T) is a marine planctomycete with 7,325 genes in its genome. Ten strains of the genus Rhodopirellula were studied in whole genome microarray experiments to assess the extent of their genetic relatedness to R. baltica SH1(T). DNA of strains which were previously affiliated with the species R. baltica (OTU A) hybridized with 3,645-5,728 genes of the type strain on the microarray. Strains SH398 and 6C (OTU B), representing a closely related species with an average nucleotide identity of 88 %, showed less hybridization signals: 1,816 and 3,302 genes gave a hybridization signal, respectively. Comparative genomics of eight permanent draft genomes revealed the presence of over 4,000 proteins common in R. baltica SH1(T) and strains of OTU A or B. The genus Rhodopirellula is characterized by large genomes, with over 7,000 genes per genome and a core genome of around 3000 genes. Individual Rhodopirellula strains have a large portion of strain-specific genes. PMID:23975513

Frank, Carsten S; Klockow, Christine; Richter, Michael; Glöckner, Frank Oliver; Harder, Jens

2013-10-01

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Performance Analysis of Genetic Algorithm for Mining Association Rules  

Directory of Open Access Journals (Sweden)

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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Assessing Plant Genetic Diversity by Molecular Tools  

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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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Limited Genetic Diversity of Brucella spp.  

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

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

2001-01-01

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Chemical and genetic diversity of Cremanthodium lineare.  

Science.gov (United States)

Chemical constituents and evolutionally neutral DNA sequences of six samples of Cremanthodium lineare Maxim., collected in the Sichuan Province of China, were studied. Three samples produced furanoeremophilanes and the other three, eremophilan-8-ones. The chemotypes were found to be correlated with DNA sequence types, suggesting that the chemical diversity observed has a genetic origin. Production of furanoeremophilanes by a Cremanthodium species suggests an evolutionary relationship between Cremanthodium and Ligularia species, and possibly to related genera. PMID:24119572

Saito, Yoshinori; Ichihara, Mayu; Takiguchi, Koji; Tanio, Yui; Okamoto, Yasuko; Hanai, Ryo; Kuroda, Chiaki; Kawahara, Takayuki; Gong, Xun; Tori, Motoo

2013-12-01

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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

25

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.

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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 88.8â??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

27

A Survey: Web Log Mining using Genetic Algorithm .  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

2013-01-01

28

Limited Genetic Diversity in the Endophytic Sugarcane Bacterium Acetobacter diazotrophicus  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Acetobacter diazotrophicus isolates that originated from different sugarcane cultivars growing in diverse geographic regions of Mexico and Brazil were shown to have limited genetic diversity. Measurements of polymorphism in the electrophoretic mobilities of metabolic enzymes revealed that the mean genetic diversity per enzyme locus (among the four electrophoretic types distinguished) was 0.064. The results of the genetic analysis indicate that the genetic structure of A. diazotrophicus is clo...

Caballero-mellado, Jesus; Martinez-romero, Esperanza

1994-01-01

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2010-01-01

30

Genetic diversity of Ehrlichia canis in Brazil.  

Science.gov (United States)

Canine monocytic ehrlichiosis is a highly prevalent disease in Brazil, where the genetic diversity of Ehrlichia canis remains undefined. In this study, we used the TRP36 gene to examine the genetic diversity of E. canis strains from naturally infected dogs residing in five distinct geographic regions in Brazil. E. canis DNA was detected in 82/126 (65%) dogs by dsb-specific PCR and E. canis was isolated in cell culture from 13 dogs. Sequences obtained from dsb genes amplified from the isolates were identical to the US E. canis strain. An extended molecular characterization based on the TRP36 gene identified two major genogroups based on differences among eight isolates. Isolates with tandem repeat amino acid sequence (TEDSVSAPA) identical to the previously reported TRP36 sequence were found in the midwest, northeast and southeast regions of Brazil, and classified into the US genogroup. A novel Brazilian genotype with a different tandem repeat sequence (ASVVPEAE) was also identified in midwest, northern and southern regions. Similarity in the N-terminal sequence of a US genogroup member with the Brazilian genogroup suggested that genomic recombination between the two genogroups may have occurred. Other subtypes within the Brazilian genogroup were also identified using C-terminal amino acid divergence. We identified two distinct major Brazilian genogroups and several subtypes based on analysis of TRP36, and such information will be useful for further genotyping and possible associations with disease severity, understanding of the genetic and antigenic variability of E. canis, and for developing strain-specific vaccines and diagnostic methods based on TRP36. PMID:23490559

Aguiar, D M; Zhang, X; Melo, A L T; Pacheco, T A; Meneses, A M C; Zanutto, M S; Horta, M C; Santarém, V A; Camargo, L M A; McBride, J W; Labruna, M B

2013-06-28

31

A Survey: Web Log Mining using Genetic Algorithm .  

Directory of Open Access Journals (Sweden)

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

32

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

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High genetic diversity is not essential for successful introduction.  

Science.gov (United States)

Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive. PMID:24340190

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

2013-11-01

34

High genetic diversity is not essential for successful introduction  

Science.gov (United States)

Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive.

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

2013-01-01

35

Genetic diversity and relationships among Italian and Spanish hazelnut cultivars  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this work, 22 Italian and 36 Spanish accessions from various germplasm repositories were studied at 16 microsatellite markers in order to study: (1) the genetic diversity in the Italian cultivars and (2) their genetic relationships with Spanish cultivated varieties.

Botta, Roberto; Boccacci, Paolo; Torello Marinoni, Daniela

2009-01-01

36

Population genetic diversity and fitness in multiple environments  

Directory of Open Access Journals (Sweden)

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

37

Threat or opportunity? Landscape genetics in a coal mining area  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 pH ex...

2013-01-01

38

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

39

A genetic algorithm-based approach to data mining  

Energy Technology Data Exchange (ETDEWEB)

Most data mining systems to date have used variants of traditional machine-learning algorithms to tackle the task of directed knowledge discovery. This paper presents an approach which, as well as being useful for such directed data mining, can also be applied to the further tasks of undirected data mining and hypothesis refinement. This approach exploits parallel genetic algorithms as the search mechanism and seeks to evolve explicit {open_quotes}rules{close_quotes} for maximum comprehensibility. Example rules found in real commercial datasets are presented.

Flockhart, I.W.; Radcliffe, N.J. [Univ. of Edinburgh (United Kingdom)

1996-12-31

40

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

 
 
 
 
41

An assessment of the Central-China pig genetic diversity using Weitzman approach  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The genetic diversity of livestock breeds plays an important role in livestock production, but the significant loss of breeds is threatening genetic diversity of farm animal genetic resources (AnGR). The Weitzman approach which was accepted as a framework for assessment of genetic diversity on AnGR was exploited. In this study, several measurement indexes of genetic diversity, involving total genetic diversity, contributions of each breed to the total diversity, marginal diversities, conserva...

2010-01-01

42

Molecular genetics of human pigmentation diversity.  

Science.gov (United States)

The genetic basis underlying normal variation in the pigmentary traits of skin, hair and eye colour has been the subject of intense research directed at understanding the diversity seen both between and within human populations. A combination of approaches have been used including comparative genomics of candidate genes and the identification of regions of the human genome under positive selection, together with genome-wide and specific allele association studies. Independent selection for different pigmentation gene sets has been found between Asian, European and African populations. Several genome-wide association studies for pigmentation have now been conducted and identified single nucleotide polymorphism (SNP) markers in known, TYR, TYRP1, OCA2, SLC45A2, SLC24A5, MC1R, ASIP, KITLG and previously unknown SLC24A4, IRF4, TPCN2, candidate genes. The contribution of SNP polymorphisms present in populations from South Asia have been tested and alleles found at TYR, SLC45A2 and SLC24A5 can largely account for differences between those of darkest and lightest skin reflectance using a simple additive model. Skin and hair colour associations in Europeans are found within a range of pigmentation gene alleles, whereas blue-brown eye colour can be explained by a single SNP proposed to regulate OCA2 expression. Functional testing of variant alleles has begun to connect phenotype correlations with biological differences. Variant MC1R alleles show direct correlations between the biochemical signalling properties of the encoded receptor and the red-hair fair skin pigmentation phenotype. Direct testing of a range of clonal melanocyte cultures derived from donor skin tissue characterized for three causal SNPs within SLC45A2, SLC24A5 and OCA2 has assessed their impact on melanin content and tyrosinase enzyme activity. From a culmination of genetic and functional studies, it is apparent that a number of genes impacting melanosome biogenesis or the melanin biosynthetic pathway are candidates to explain the diversity seen in human pigmentation. PMID:19297406

Sturm, Richard A

2009-04-15

43

Genetic Diversity of Tunisian Date Palm Germplasm Using ISSR Markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Aim of the study is the analysis of the genetic diversity among a set of Tunisian date palm varieties. We used different genetic markers generated from selected ISSR primers. Inter Simple Sequence Repeat (ISSR) markers involve Polymerase Chain Reaction (PCR) amplification of DNA using a single primer composed of a microsatellite sequence. ISSR technology rapidly reveals high polymorphic fingerprints and determines genetic diversity. Seven primers were used to cluster 10 date palm varieties an...

Karim, K.; Chokri, B.; Amel, S.; Wafa, H.; Richid, H.; Nouredine, D.

2010-01-01

44

Genetic diversity of Plasmodium vivax malaria in China and Myanmar  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Genetic diversity and population structure of Plasmodium vivax parasites are valuable to the prediction of the origin and spread of novel variants within and between populations, and to the program evaluation of malaria control measures. Using two polymorphic genetic markers, the merozoite surface protein genes PvMSP-3? and PvMSP-3?, we investigated the genetic diversity of four Southeast Asian P. vivax populations, representing both subtropical and temperate strains with dramatically diver...

Zhong, Daibin; Bonizzoni, Mariangela; Zhou, Guofa; Wang, Guangze; Chen, Bin; Vardo-zalik, Anne; Cui, Liwang; Yan, Guiyun; Zheng, Bin

2011-01-01

45

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely ...

Lv, J.; Qi, J.; Shi, Q.; Shen, D.; Zhang, S.; Shao, G.; Li, H.; Sun, Z.; Weng, Y.; Shang, Y.; Gu, X.; Li, X.; Zhu, X.; Zhang, J.; Treuren, R.

2012-01-01

46

Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.)  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely ...

Lv, Jing; Qi, Jianjian; Shi, Qiuxiang; Shen, Di; Zhang, Shengping; Shao, Guangjin; Li, Hang; Sun, Zhanyong; Weng, Yiqun; Shang, Yi; Gu, Xingfang; Li, Xixiang; Zhu, Xiaoguo; Zhang, Jinzhe; Treuren, Robbert

2012-01-01

47

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.

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

48

Beauveria bassiana: quercetinase production and genetic diversity  

Directory of Open Access Journals (Sweden)

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

Eula Maria de M. B Costa

2011-03-01

49

GENETIC RESOURCES AND DIVERSITY IN PAKISTANI CATTLE  

Directory of Open Access Journals (Sweden)

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

50

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

Directory of Open Access Journals (Sweden)

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

51

Intelligence Service Of Web Mining With Genetic Algorithm  

Directory of Open Access Journals (Sweden)

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

Kolli Prabhakara Rao

2013-10-01

52

Limited intra-genetic diversity in Dientamoeba fragilis housekeeping genes.  

Science.gov (United States)

Dientamoeba fragilis is a common intestinal parasite of unsettled clinical significance. Differences in clinical outcome of parasitic infections may reflect parasite genetic diversity, and so tools to study intra-genetic diversity that could potentially reflect differences in clinical phenotypes are warranted. Here, we show that genetic analysis of three D. fragilis housekeeping genes enables clear distinction between the two known genotypes, but that integration of housekeeping genes in multi-locus sequencing tools for D. fragilis may have limited epidemiological and clinical value due to no further added genetic resolution. PMID:23681023

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

2013-08-01

53

Nested core collections maximizing genetic diversity in Arabidopsis thaliana  

DEFF Research Database (Denmark)

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

McKhann, Heather I; Camilleri, Christine

2004-01-01

54

Genetic diversity among fourteen different Fusarium species using RAPD marker  

Directory of Open Access Journals (Sweden)

Full Text Available Bonde SR, Gade AK, Rai MK. 2012. Genetic diversity among fourteen different Fusarium species using RAPD marker. Biodiversitas 13: 55-60. We report genetic diversity of total fourteen different Fusarium species by RAPD-PCR analysis using 25 random primers. The genus Fusarium is food borne pathogen responsible for T-2 toxin production which affects human and animal health. In the present study, total 14-different species of Fusarium were analyzed on the basis of genetic diversity using RAPD method. A dendrogram was developed by UPGMA method. RAPD analysis was carried out by using 25 different universal primers each of them consisted of 10 bases. Genetic similarity coefficients between pair wise varied from 0.00 to 0.9 based on an unweighted paired group method of arithmetic average (UPGMA cluster analysis. RAPD-PCR technique can be used as an important tool for the genetic differentiation Fusarium species.

ANIKET K. GADE

2013-10-01

55

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

Science.gov (United States)

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

56

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

57

Mining protein networks for synthetic genetic interactions  

Directory of Open Access Journals (Sweden)

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

Zhao Shan

2008-10-01

58

Genetic diversity in Populus nigra plantations from west of Iran  

Directory of Open Access Journals (Sweden)

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

Afrooz Alimohamadi

2012-11-01

59

Great ape genetic diversity and population history  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Most great ape genetic variation remains uncharacterized1,2; however, its study is critical for understanding population history3–6, recombination7, selection8 and susceptibility to disease9,10.Herewe 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 speci...

Prado-martinez, Javier; Lorente-galdo?s, Bele?n; Santpere, Gabriel; Casals, Ferran; Laayouni, Hafid; Hernandez, Jessica; Hernando-herraez, Irene; Pybus, Marc; Petit-marty, Natalia; Fernandez-callejo, Marcos; Dabad, Marc; Carvalho, Tiago; Mele?, Marta; Comas, David; Navarro, Arcadi

2013-01-01

60

Great ape genetic diversity and population history  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Most great ape genetic variation remains uncharacterized(1,2); however, its study is critical for understanding population history(3-6), recombination(7), selection(8) and susceptibility to disease(9,10). 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, signa...

Prado-martinez, Javier; Lorente-galdo?s, Bele?n; Santpere, Gabriel; Casals, Ferran; Laayouni, Hafid; Hernandez, Jessica; Hernando-herraez, Irene; Pybus, Marc; Petit-marty, Natalia; Fernandez-callejo, Marcos; Dabad, Marc; Carvalho, Tiago; Mele?, Marta; Comas, David; Navarro, Arcadi

2013-01-01

 
 
 
 
61

GENETIC DIVERSITY IN ALBANIAN SHEEP BREEDS ESTIMATED BY AFLP MARKERS  

Directory of Open Access Journals (Sweden)

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

Vilson Bozgo

2010-08-01

62

Genetic diversity in Hemileia vastatrix based on RAPD markers.  

Science.gov (United States)

Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs. PMID:16396347

Gouveia, M Manuela C; Ribeiro, Ana; Várzea, Vítor M P; Rodrigues, Carlos J

2005-01-01

63

Polishing the craft of genetic diversity creation in directed evolution.  

Science.gov (United States)

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

Tee, Kang Lan; Wong, Tuck Seng

2013-12-01

64

Evaluation of genetic diversity in Pampus argenteus using SSR markers.  

Science.gov (United States)

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

Qin, Y; Shi, G; Sun, Y

2013-01-01

65

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 betwe...

Dumasy, Jean-franc?ois; Daniaux, C.; Donnay, Isabelle; Baret, Philippe

2012-01-01

66

[Genetic diversity of DNA microsatellite for Tibetan Yak].  

Science.gov (United States)

To assess the genetic diversity and relationship of the Tibetan yak breeds. The genetic diversity and phylogenies of a total of 480 individual from 11 Tibetan yak groups were analyzed using PCR and multiplex gel electrophoresis of silver staining technology with eight pairs of microsatellite markers.The result showed that these markers were highly polymorphic loci with rich genetic diversity in the Tibetan yak populations.The average polymorphic information content (PIC) in 11 groups of yak were higher than 0.5. The highest HEL13 was 0.8496, and the lowest TGLA57 was 0.7349. Among them, the PICof Dingqing yak was minimum (0.7505), indicating that the group is relatively pure.Sangri Yak had the highest PIC value (0.7949) indicating greater genetic variationwithinthe groups. Among the 11 groups examined, the order of heterozygosity size wasSangri(0.8193)>Jiangda(0.8190)>Sangsang(0.8157)>Baqing(0.8150)>Kangbu(0.8123)> Jiali(0.8087)>Gongbujiangda(0.8054)>Sibu(0.8041)>Leiwuqi(0.8033)>Pali(0.8031)>Dingqing(0.7831). The groups from eastern Tibet had grater genetic diversity than those from Western Tibet, which indicate that Tibet may be one of the cradles of the yak.According to the genetic distance, the cluster relationship constructed with UPGMA and NJ methods showed that 11 yak groups in Tibet could be divided into three forms. In summary,Tibet yak has abundant genetic diversity and the selected microsatellite markers can be used to evaluategenetic diversity of Tibetan yak. PMID:23448930

Li, Duo; Chai, Zhi-Xin; Ji, Qiu-Mei; Zhang, Cheng-Fu; Xin, Jin-Wei; Zhong, Jin-Cheng

2013-02-01

67

Genetic diversity analysis of common beans based on molecular markers  

Directory of Open Access Journals (Sweden)

Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Homar R. Gill-Langarica

2011-01-01

68

Genetic diversity analysis of common beans based on molecular markers  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collecti [...] on (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

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

69

Archaeal Diversity in Waters from Deep South African Gold Mines  

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A culture-independent molecular analysis of archaeal communities in waters collected from deep South African gold mines was performed by performing a PCR-mediated terminal restriction fragment length polymorphism (T-RFLP) analysis of rRNA genes (rDNA) in conjunction with a sequencing analysis of archaeal rDNA clone libraries. The water samples used represented various environments, including deep fissure water, mine service water, and water from an overlying dolomite aquifer. T-RFLP analysis ...

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

2001-01-01

70

Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras  

Directory of Open Access Journals (Sweden)

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

Lopez Ana

2012-11-01

71

Genetic diversity among five T4-like bacteriophages  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Nolan James M; Petrov Vasiliy; Bertrand Claire; Krisch Henry M; Karam Jim D

2006-01-01

72

How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Major histocompatibility complex (MHC) genes have been put forward as a model for studying how genetic diversity is maintained in wild populations. Pathogen-mediated selection (PMS) is believed to generate the extraordinary levels of MHC diversity observed. However, establishing the relative importance of the three proposed mechanisms of PMS (heterozygote advantage, rare-allele advantage and fluctuating selection) has proved extremely difficult. Studies have attempted to differentiate between...

2010-01-01

73

The population genetics of mimetic diversity in Heliconius butterflies  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Kronforst, Marcus R.; Gilbert, Lawrence E.

2008-01-01

74

Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger  

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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

75

Genetic diversity and relationships of Vietnamese and European pig breeds  

International Nuclear Information System (INIS)

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

2003-10-06

76

Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a reg...

Esko, To?nu; Mezzavilla, Massimo; Nelis, Mari; Borel, Christelle; Debniak, Tadeusz; Jakkula, Eveliina; Julia, Antonio; Karachanak, Sena; Khrunin, Andrey; Kisfali, Peter; Krulisova, Veronika; Aus?rele? Kuc?inskiene?, Zita; Rehnstro?m, Karola; Traglia, Michela; Nikitina-zake, Liene

2013-01-01

77

Genetic diversity of Actinobacillus lignieresii isolates from different hosts.  

Science.gov (United States)

Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacillus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies. PMID:21303512

Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

2011-01-01

78

Landscape, population structure and genetic diversity of Stomoxys calcitrans.  

Science.gov (United States)

To investigate whether different landscapes could affect genetic diversity and structure of the cosmopolitan diptera Stomoxys calcitrans, populations from Gabon and southern France were studied using dominant amplified fragment length polymorphism (AFLP) markers. Gabon is characterized by a forested closed landscape, and southern France by an open Mediterranean landscape. The genetic diversity between Gabon and France populations did not differ significantly (P > 0.05). Contrary to our expectation, this study shows a moderate level of genetic differentiation between these two distant countries (Fst = 0.0979) and a low genetic structure among Gabonese and French populations (Fst = 0.0291 and 0.0275 respectively). This result could indicate the capacities of S. calcitrans populations to sustain a high level of gene flow, despite geographic distance and isolation. PMID:19353950

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

2009-03-01

79

Mapping viral functional domains for genetic diversity in plants.  

Science.gov (United States)

Cucumber mosaic virus (CMV) comprises numerous isolates with various levels of in-host diversity. Subgroup-distinctive features of the Fny and LS strains provided us with a platform to genetically map the viral control elements for genetic variation in planta. We found that both RNAs 1 and 2 controlled levels of genetic diversity, and further fine mapping revealed that the control elements of mutation frequency reside within the first 596 amino acids (aa) of RNA 1. The 2a/2b overlapping region of the 2a protein also contributed to control of viral genetic variation. Furthermore, the 3' nontranslated region (NTR) of RNA 3 constituted a hot spot of polymorphism, where the majority of fixed mutations found in the population were clustered. The 2b gene of CMV, a viral suppressor of gene silencing, controls the abundance of the fixed mutants in the viral population via a host-dependent mechanism. PMID:23115283

Pita, Justin S; Roossinck, Marilyn J

2013-01-01

80

Genetic diversity measures of the Croatian Spotted goat  

Directory of Open Access Journals (Sweden)

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

Pavi? Vesna

2011-01-01

 
 
 
 
81

Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis  

Science.gov (United States)

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

Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; Liu, Xinyue; Melake-Berhan, Admasu; Huot Creasy, Heather; Puiu, Daniela; Rosovitz, M. J.; Khouri, Hoda M.; Beckstrom-Sternberg, Stephen M.; Allan, Gerard J.; Keim, Paul; Ravel, Jacques; Rabinowicz, Pablo D.

2011-01-01

82

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)

2010-06-01

83

Soybean parent selection based on genetic diversity  

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Thirty-four soybean lines were assessed for twelve traits. The genetic distances were estimates using multivariate techniques, to identify parents to be included in breeding programs for hybridization. Grouping by the Tocher method, from generalized Mahalanobis distances, divided the 34 lines into four groups. The most important agronomic traits, weight of seeds per plot, plant height, height of first pod and days to maturity were considered when recommending for crossing. The following cross...

Valéria Carpentieri-Pípolo; Antônio Eduardo Pípolo; Flávio André Martins da Silva; Marcos Rafael Petek

2000-01-01

84

Characterization and genetic diversity analysis of cotton cultivars using microsatellites  

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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 S...

Magalha?es Bertini, Ca?ndida H. C.; Ivan Schuster; Tocio Sediyama; Everaldo Gonçalves de Barros; Maurílio Alves Moreira

2006-01-01

85

Genetic diversity and differentiation of Mongolian and Russian yak populations.  

Science.gov (United States)

In this study we examined the genetic diversity of yak populations in the northernmost part of their current global distribution. Five Mongolian and one Russian yak populations as well as one Chinese yak population from the Qinghai-Tibetan Plateau, the putative centre of yak domestication, were analysed with 15 microsatellite loci to determine the level of genetic variation within populations as well as the genetic differentiation and relationship between populations. A total of 116 microsatellite alleles were identified. The mean number of alleles per locus (MNA) across populations was 7.73 +/- 1.98 and the mean expected heterozygosity (HE) was 0.696 +/- 0.026. The relative magnitude of gene differentiation (F(ST)) among populations was 4.1%, and all genetic differentiations (F(ST)) between populations were significant (p yak (p yak populations in Mongolia and Russia have maintained high genetic diversity within populations and a low, although significant, genetic differentiation between populations. Both phylogenetic and principal component analyses support a close genetic relationship between the Gobi Altai, south Gobi and north Hangai populations, and between the Hovsgol and Buryatia populations respectively. Our results indicate that these yak populations should be considered as distinct genetic entities in respect of conservation and breeding programmes. PMID:16130478

Xuebin, Q; Jianlin, H; Lkhagva, B; Chekarova, I; Badamdorj, D; Rege, J E O; Hanotte, O

2005-04-01

86

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

Science.gov (United States)

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

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

2013-08-01

87

[The genetic diversity of Cymbidium by ISSR].  

Science.gov (United States)

ISSR was applied to detect the relationship between 16 Cymbidium species, and 836 bands were amplified with 15 primers, including 227 polymorphic bands. The polymorphic percentage is 27.2%. UPGMA results showed that the genetic distance were closest between C.goeringii (Rchb.f.) Rchb.f. and C. goeringii var. longibracteatum, and C.lancifolium Hook. was far away from the other 15 species. This result is quite similar to the traditional classification, indicating that the technique could supplement some information to traditional taxonomy in the molecular level. PMID:18487154

Wu, Zhen-Xing; Wang, Hui-Zhong; Shi, Nong-Nong; Zhao, Yan

2008-05-01

88

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.

89

Genetic diversity of noroviruses in Brazil  

Directory of Open Access Journals (Sweden)

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

Julia Monassa Fioretti

2011-12-01

90

Genetic diversity in farm animals--a review.  

Science.gov (United States)

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology. PMID:20500753

Groeneveld, L F; Lenstra, J A; Eding, H; Toro, M A; Scherf, B; Pilling, D; Negrini, R; Finlay, E K; Jianlin, H; Groeneveld, E; Weigend, S

2010-05-01

91

Genetic diversity and conservation in a small endangered horse population.  

Science.gov (United States)

The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy-Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population. PMID:23649723

Janova, Eva; Futas, Jan; Klumplerova, Marie; Putnova, Lenka; Vrtkova, Irena; Vyskocil, Mirko; Frolkova, Petra; Horin, Petr

2013-08-01

92

Assessment of Genetic Diversity in Tea Genotypes Through RAPD Primers  

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

Habib Ahmad

2007-01-01

93

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

94

Assessment of Genetic Diversity in Tea Genotypes Through RAPD Primers  

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

2007-01-01

95

Soybean parent selection based on genetic diversity  

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Full Text Available Thirty-four soybean lines were assessed for twelve traits. The genetic distances were estimates using multivariate techniques, to identify parents to be included in breeding programs for hybridization. Grouping by the Tocher method, from generalized Mahalanobis distances, divided the 34 lines into four groups. The most important agronomic traits, weight of seeds per plot, plant height, height of first pod and days to maturity were considered when recommending for crossing. The following crosses were recommended based on the genetic divergence and the key agronomic traits: lines 23, 10, 2, 27 and 25 (group I with genotype 6 (group II and genotype 16 (group III. Thus only ten crosses would be made, representing only 2% of the total crosses which could be made in the partial diallel among the 34 lines assessed, which would allow up to 561 combinations.Trinta e quatro linhagens de soja foram avaliadas para doze características. As distâncias genéticas foram estimadas utilizando técnicas multivariadas com objetivo de identificar parentais a serem incluidos em um programa de melhoramento envolvendo hibridação. O agrupamento pelo método de Tocher, a partir das distâncias generalizadas de Mahalanobis, dividiu as 34 linhagens em 4 grupos. As caracterísiticas agronômicas mais importantes, peso de sementes por parcela, altura de planta, altura da primeira vagem e dias para maturação foram consideradas para a recomendação dos cruzamentos. Os seguintes cruzamentos foram recomendados baseado na divergência genética e nas características agronômicas chave: linhagens 23, 10, 2, 27 e 25 (grupo I com genótipo 6 (grupoII e com o genótipo 16 (grupo III. Portanto somente 10 cruzamentos poderiam ser realizados representando somente 2% do total de cruzamentos qu poderiam ser realizados em um dialelo parcial entre as 34 linhagens avaliadas as quais admitiriam até 561 combinações.

Valéria Carpentieri-Pípolo

2000-01-01

96

Utilizing the genetic diversity within rice cultivars.  

Science.gov (United States)

Plant breeding of rice emphasizes improvement in yield, disease resistance, and milling quality. Numerous other traits (e.g., bran carotenoids) that historically have not been selected for could provide added value in expanding niche markets, as well as be useful tools for understanding the genetic control of these traits. Residual heterozygosity is present in many rice cultivars; therefore, it is possible to select for different alleles within an existing cultivar. By identifying and using cultivars with high levels of variability for a trait, we were able to develop separate lines from single cultivars that showed high and low levels of that trait. The rice cultivar RU9101001 and the warm- and cold-sprouting lines that were derived from it were used to demonstrate that residual heterozygosity was present within a cultivar and that the original heterozygosity was separated in the derived lines. Rice simple sequence repeat markers were heterozygous in the parent RU9101001 cultivar, but the cold-sprouting lines were homozygous for one set of alleles and the warm-sprouting lines were homozygous for the other set. Through detailed phenotypic screening, we developed lines that exhibited low and high levels of the following traits in the specified cultivars: cold-sprouting from RU9101001 and Bonnet 73, postharvest yellowing from Tominishiki, early tillering from Hei Jaio and Tominishiki, and bran carotenoid levels from Spring. If variability exists in a cultivar, then utilization of residual heterozygosity may provide a quicker and more efficient means to develop lines with special characteristics using cultivars that are already agronomically valuable or to develop near isogenic lines for genetic and biochemical investigations. PMID:22183122

Belefant-Miller, Helen; Miller, Gordon H; Moldenhauer, Karen A K

2012-03-01

97

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

98

Bacterial Diversity in a Mine Water Treatment Plant? †  

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We investigated the microbial community in a pilot plant for treatment of acid mine water by biological ferrous iron oxidation using clone library analysis and calculated statistical parameters for further characterization. The microbial community in the plant was conspicuously dominated by a group of Betaproteobacteria affiliated with “Ferribacter polymyxa”.

2009-01-01

99

Assessment of Genetic Diversity in Iranian Fennels Using ISSR Markers  

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

Kaivan Bahmani

2012-07-01

100

Molecular genetic diversity of Satureja bachtiarica.  

Science.gov (United States)

Fifty-seven genotypes from eight population of Satureja bachtiarica was evaluated using fifteen ISSR and eleven RAPD markers. DNA profiling using RAPD primers amplified 84 loci, among which 81 were polymorphic with an average of 7.36 polymorphic fragments per locus. Also, using RAPD markers maximum and minimum polymorphic bands observed for Semyrom (77.38 %) and Farsan (40.48 %) populations, respectively. Semyrom population recorded the highest unbiased expected heterozygosity (0.259) and Shannon's Indices (0.38). While, the lowest values of unbiased expected heterozygosity (0.172) and Shannon's Index (0.245) were recorded for Eghlid and Farsan populations, respectively. On the other hand, ISSR primers produced 136 bands, from which 134 were polymorphic with an average of 9.06 polymorphic fragments per primer (98.52 %). The ISSR markers evaluation revealed that maximum and minimum polymorphic bands observed for Semyrom (66.18 %) and Farsan (31.62 %), respectively. Shahrekorud population recorded the highest unbiased expected heterozygosity (0.211) and Shannon's Indices (0.301). While, the lowest value of unbiased expected heterozygosity (0.175) observed for Farsan and Yazd populations and the lowest Shannon's Index (0.191) recorded by Farsan population. The overall results of the study revealed that both ISSR and RAPD markers were effective for evaluation of genetic variation of S. bachtiarica. PMID:24096911

Saidi, Mehdi; Movahedi, Khavar; Mehrabi, Ali Ashraf; Kahrizi, Danial

2013-11-01

 
 
 
 
101

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

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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

102

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

103

Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection.  

Science.gov (United States)

A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D(2) from 14 traits. Both dendrograms built by Fst and D(2) reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D(2) matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort. PMID:21080033

Li, Xiaobai; Yan, Wengui; Agrama, Hesham; Hu, Biaolin; Jia, Limeng; Jia, Melissa; Jackson, Aaron; Moldenhauer, Karen; McClung, Anna; Wu, Dianxing

2010-12-01

104

Genetic Diversity in Brassica Species Using SDS-PAGE Analysis  

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

Rahman Md. Mukhlesur

2004-01-01

105

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

106

Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations  

DEFF Research Database (Denmark)

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

Pham, L. D.; Do, Duy Ngoc

2014-01-01

107

Genetic Diversity among Botulinum Neurotoxin-Producing Clostridial Strains?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore-forming rod-shaped bacteria that have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and death in humans and other animal species. A collection of 174 C. botulinum strains was examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine the genetic diversity within ...

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

2007-01-01

108

Genetic Diversity of Tunisian Date Palm Germplasm Using ISSR Markers  

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Full Text Available Aim of the study is the analysis of the genetic diversity among a set of Tunisian date palm varieties. We used different genetic markers generated from selected ISSR primers. Inter Simple Sequence Repeat (ISSR markers involve Polymerase Chain Reaction (PCR amplification of DNA using a single primer composed of a microsatellite sequence. ISSR technology rapidly reveals high polymorphic fingerprints and determines genetic diversity. Seven primers were used to cluster 10 date palm varieties and 82 polymorphic markers were sufficient to identify all of the studied varieties. These discrete molecular markers were used to estimate genetic distances among the 10 accessions and to examine their genetic relationships. Data analysis identified phenetic groups that were in agreement with those obtained according to agronomic traits and random amplified polymorphic DNA (RAPD markers. Among the 12 Simple Sequence Repeat (SSR motifs tested, the most abundant were AG. Present result provides evidence of divergence between Tunisian varieties that are organized in clusters. However, we are unable to identify all tested genotypes as mono varietal groups.

D. Nouredine

2010-01-01

109

Genetic diversity in Brazilian tall coconut populations by microsatellite markers  

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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

110

GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage? †  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines i...

Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Nostrand, Joy D.; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou

2011-01-01

111

Genetic Diversity of Cryptosporidium spp. in Captive Reptiles  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The genetic diversity of Cryptosporidium in reptiles was analyzed by PCR-restriction fragment length polymorphism and sequence analysis of the small subunit rRNA gene. A total of 123 samples were analyzed, of which 48 snake samples, 24 lizard samples, and 3 tortoise samples were positive for Cryptosporidium. Nine different types of Cryptosporidium were found, including Cryptosporidium serpentis, Cryptosporidium desert monitor genotype, Cryptosporidium muris, Cryptosporidium parvum bovine and ...

2004-01-01

112

Genetic Diversity within Cryptosporidium parvum and Related Cryptosporidium Species  

Digital Repository Infrastructure Vision for European Research (DRIVER)

To assess the genetic diversity in Cryptosporidium parvum, we have sequenced the small subunit (SSU) rRNA gene of seven Cryptosporidium spp., various isolates of C. parvum from eight hosts, and a Cryptosporidium isolate from a desert monitor. Phylogenetic analysis of the SSU rRNA sequences confirmed the multispecies nature of the genus Cryptosporidium, with at least four distinct species (C. parvum, C. baileyi, C. muris, and C. serpentis). Other species previously defined by biologic characte...

1999-01-01

113

Genetic Diversity of Storage Proteins in Cultivated Buckwheat  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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-...

YangYu -Xia; Wu Wei; ZhengYou- Liang; Cai Qian-Rong

2008-01-01

114

Genetic Diversity among Xanthomonas campestris Strains Pathogenic for Small Grains  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A collection of 51 Xanthomonas campestris strains from throughout the world was studied to detect and assess genetic diversity among pathogens of small grains. Isolates from barley, bread wheat, bromegrass, canary grass, cassava, maize, orchard grass, rice, rough-stalked meadow grass, rye, timothy, and triticale were analyzed by pathogenicity tests on bread wheat cv. Alondra and barley cv. Corona, indirect immunofluorescence, and restriction fragment length polymorphism (RFLP). Three probes w...

Bragard, C.; Verdier, V.; Maraite, H.

1995-01-01

115

Assessment of Genetic Diversity in Iranian Fennels Using ISSR Markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2012-01-01

116

Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2011-01-01

117

Genetic diversity among isolates of Phaeomoniella chlamydospora on grapevines  

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Phaeomoniella chlamydospora is one of the main causal agents of Petri disease and esca of grapevines. Although it is known to have a coelomycete synanamorph, no teleomorph has thus far been reported for P. chlamydospora, and its disease cycle remains largely unknown. The present study compared the genetic diversity of P. chlamydospora isolates from different grapevine-growing countries using amplified fragment length polymorphisms. Sixty-three isolates from South Africa and 25 from grapevine ...

2006-01-01

118

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...

1999-01-01

119

Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers  

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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...

2012-01-01

120

Genetic diversity of Plasmodium vivax in Kolkata, India  

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Full Text Available Abstract Background Plasmodium vivax malaria accounts for approximately 60% of malaria cases in Kolkata, India. There has been limited information on the genotypic polymorphism of P. vivax in this malaria endemic area. Three highly polymorphic and single copy genes were selected for a study of genetic diversity in Kolkata strains. Methods Blood from 151 patients with P. vivax infection diagnosed in Kolkata between April 2003 and September 2004 was genotyped at three polymorphic loci: the P. vivax circumsporozoite protein (pvcs, the merozoite surface protein 1 (pvmsp1 and the merozoite surface protein 3-alpha (pvmsp3-alpha. Results Analysis of these three genetic markers revealed that P. vivax populations in Kolkata are highly diverse. A large number of distinguishable alleles were found from three genetic markers: 11 for pvcs, 35 for pvmsp1 and 37 for pvmsp3-alpha. These were, in general, randomly distributed amongst the isolates. Among the 151 isolates, 142 unique genotypes were detected the commonest genotype at a frequency of less than 2% (3/151. The overall rate of mixed genotype infections was 10.6%. Conclusion These results indicate that the P. vivax parasite population is highly diverse in Kolkata, despite the low level of transmission. The genotyping protocols used in this study may be useful for differentiating re-infection from relapse and recrudescence in studies assessing of malarial drug efficacy in vivax malaria.

Day Nick PJ

2006-08-01

 
 
 
 
121

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)

2011-10-01

122

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

123

Could contaminant induced mutations lead to a genetic diversity overestimation?  

Science.gov (United States)

Contaminant driven genetic erosion reported through the inspection of selectable traits can be underestimated using neutral markers. This divergence was previously reported in the aquatic system of an abandoned pyrite mine. The most sensitive genotypes of the microcrustacean cladoceran Daphnia longispina were found to be lacking in the impacted reservoir near the entrance of the metal rich acid mine drainage (AMD). Since that divergence could be, at least partially, accounted for by mutagenicity and genotoxicity of the AMD, the present study aimed at providing such a characterization. The Allium cepa chromosomal aberration assay, using root meristematic cells, was carried out, by exposing seeds to 100, 10, 1, and 0.1 % of the local AMD. Chromosomal aberrations, cell division phases and cell death were quantified after the AMD exposure and after 24 and 48 h recovery periods. The AMD revealed to be mutagenic and genotoxic, even after diluting it to 1 and 0.1 %. Dilutions within this range were previously found to be below the lethality threshold and to elicit sublethal effects on reproduction of locally collected D. longispina clonal lineages Significant mutagenic effects (micronuclei and chromosomal breaks) were also found at 0.1 % AMD, supporting that exposure may induce permanent genetic alterations. Recovery tests showed that AMD genotoxic effects persisted after the exposure. PMID:23686739

Sobral, Olímpia; Marin-Morales, Maria Aparecida; Ribeiro, Rui

2013-07-01

124

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

125

Characterization and genetic diversity analysis of cotton cultivars using microsatellites  

Directory of Open Access Journals (Sweden)

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

126

Characterization and genetic diversity analysis of cotton cultivars using microsatellites  

Scientific Electronic Library Online (English)

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

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

127

Genetic Diversity in Natural Populations of New World Leishmania  

Scientific Electronic Library Online (English)

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

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

128

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

129

[Genetic diversity in goat breeds based on microsatellite analysis].  

Science.gov (United States)

Fluorescence PCR was applied to investigate the genetic diversities of 9 indigenous Chinese goat breeds and 1 exotic breed with 10 microsatellite DNA markers recommended by the Food and Agriculture Organization of the United Nations and the International Livestock Research Institute of Animal Genetics, which provide data for the preservation and utilization of indigenous goat breeds genetic resource. We found that the 7 breeds were high polymorphic while 3 breeds were moderate polymorphic. We also detected 119 alleles, and the effective allele number ranged from 1.4641 to 9.2911. The average heterozygosity of loci and breeds respectively varied from 0.2618 to 0.7672 and from 0.5196 to 0.7024. As well as SRCRSP23 site and Hexi cashmere goat had the highest average heterozygosity. Then we analyzed the phylogenetic trees (NJ and UPGMA), and found both of them were generally in accordance with their original breeding history and localities. PMID:20684301

Xu, Limei; Liu, Chousheng; Zhang, Liping; Wang, Zhigang; Han, Xu; Li, Xiaoxia; Chang, Shuang

2010-05-01

130

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...

131

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

132

Characterisation of the genetic diversity of Brucella by multilocus sequencing  

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

MacMillan Alastair P

2007-04-01

133

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

The genetic diversity and genetic structure of three Chinese silkworm species Bombyx mori L., Antheraea pernyi Guérin-Meneville and Samia cynthia ricini Donovan were comparatively assessed based on RAPD markers. At the species level, A. pernyi and B. mori showed high levels of genetic diversity, whereas S. cynthia ricini showed low level of genetic diversity. However, at the strain level, A. pernyi had relatively highest genetic diversity and B. mori had lowest genetic diversity. Analysis of...

2010-01-01

134

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.

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

135

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

136

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

137

Indigenous cattle in Sri Lanka: production systems and genetic diversity  

International Nuclear Information System (INIS)

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

2009-06-08

138

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

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

139

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

140

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

Directory of Open Access Journals (Sweden)

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

 
 
 
 
141

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

142

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)

2003-10-06

143

Host range, prevalence, and genetic diversity of adenoviruses in bats.  

Science.gov (United States)

Bats are the second largest group of mammals on earth and act as reservoirs of many emerging viruses. In this study, a novel bat adenovirus (AdV) (BtAdV-TJM) was isolated from bat fecal samples by using a bat primary kidney cell line. Infection studies indicated that most animal and human cell lines are susceptible to BtAdV-TJM, suggesting a possible wide host range. Genome analysis revealed 30 putative genes encoding proteins homologous to their counterparts in most known AdVs. Phylogenetic analysis placed BtAdV-TJM within the genus Mastadenovirus, most closely related to tree shrew and canine AdVs. PCR analysis of 350 bat fecal samples, collected from 19 species in five Chinese provinces during 2007 and 2008, indicated that 28 (or 8%) samples were positive for AdVs. The samples were from five bat species, Hipposideros armiger, Myotis horsfieldii, M. ricketti, Myotis spp., and Scotophilus kuhlii. The prevalence ranged from 6.25% (H. armiger in 2007) to 40% (M. ricketti in 2007). Comparison studies based on available partial sequences of the pol gene demonstrated a great genetic diversity among bat AdVs infecting different bat species as well as those infecting the same bat species. This is the first report of a genetically diverse group of DNA viruses in bats. Our results support the notion, derived from previous studies based on RNA viruses (especially coronaviruses and astroviruses), that bats seem to have the unusual ability to harbor a large number of genetically diverse viruses within a geographic location and/or within a taxonomic group. PMID:20089640

Li, Yan; Ge, Xingyi; Zhang, Huajun; Zhou, Peng; Zhu, Yan; Zhang, Yunzhi; Yuan, Junfa; Wang, Lin-Fa; Shi, Zhengli

2010-04-01

144

Genetic Diversity among Coconut (Cocos nucifera L. Genotypes Using Isozymes  

Directory of Open Access Journals (Sweden)

Full Text Available The study was aimed at characterizing and analyzing the genetic diversity at the isozyme level of thirty coconut cultivars. Ten enzyme systems viz., Alcohol Dehydrogenase, Glutamate Oxaloacetate Transaminase, Glucose-6 Phosphate Dehydrogenase, Peroxidase, Esterase, ?-Amylase, Phosphorylase, Malate Dehydrogenase, Super Oxide Dismutase and Acid Phosphatase were studied using discontinuous polyacrylamide gel electrophoresis. Twenty loci and 40 alleles were observed, of which, 14 loci were polymorphic. Seven loci were heterozygous. Null alleles were observed for ACP, ADH and MDH. Greater heterozygosity was observed for Glucose-6 Phosphate Dehydrogenase and least for Super Oxide Dismutase. Among the cultivars, Nadora Tall and Calangute Tall showed maximum heterozygosity while Kulasekharam Green Dwarf showed least heterozygosity.

P. Geethalakshmi

2005-01-01

145

Genetic Diversity of Walnut Revealed by AFLP and RAPD Markers  

Digital Repository Infrastructure Vision for European Research (DRIVER)

AFLP and RAPD methods were used to investigate the genetic diversity of walnuts in western Sichuan plateau and Qinba mountainous regions. 35 samples were collected from 8 different regions, and 32 RAPD primers and 28 AFLP primer combinations were identified with polymorphism bands among the entire. 324 and 2155 fragments were respectively produced by RAPD and AFLP makers, and 86.1 % of RAPD bands and 57.2% of AFLP bands showed polymorphic with the size of 180~2000 bp and 50~1800 bp, ...

Zheng Xu; Tingxing Hu; Fan Zhang

2012-01-01

146

Genetic Diversity within Human Erythroviruses: Identification of Three Genotypes  

Digital Repository Infrastructure Vision for European Research (DRIVER)

B19 virus is a human virus belonging to the genus Erythrovirus. The genetic diversity among B19 virus isolates has been reported to be very low, with less than 2% nucleotide divergence in the whole genome sequence. We have previously reported the isolation of a human erythrovirus isolate, termed V9, whose sequence was markedly distinct (>11% nucleotide divergence) from that of B19 virus. To date, the V9 isolate remains the unique representative of a new variant in the genus Erythrovirus, and ...

Servant, Annabelle; Laperche, Syria; Lallemand, Francis; Marinho, Vale?rie; Saint Maur, Guillemette; Meritet, Jean Franc?ois; Garbarg-chenon, Antoine

2002-01-01

147

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

148

Comparative molecular analysis of the prokaryotic diversity of two salt mine soils in southwest China.  

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While much is known about the microbial diversity in some hypersaline environments, little is known about those of salt mine tunnel soils. The objective of this study was to conduct a comprehensive phylogenetic comparison of the archaeal and bacterial communities present in Yipinglang salt mine (YPL) and Qiaohou salt mine (QH) tunnels differing in salinity and salt composition using 16S rRNA gene clone libraries. Two hundred twenty-eight sequences for QH and 182 sequences for YPL were analyzed by amplified ribosomal DNA-restriction analysis. Libraries revealed 44 bacterial and 57 archaeal different operational taxonomic units belonging to at least 8 bacterial and 3 archaeal divisions, but not all divisions were observed in both salt mines. The bacterial community affiliated with the Bacteroidetes was the most abundant (60% of clones) in QH, while the community in YPL was dominated by ?-Proteobacteria (45% of clones). All archaeal clones from QH were affiliated with Halobacteriaceae. In contrast, in the YPL library, 49% of clones belonged to Halobacteriaceae, 31% of clones related to unclassified archaea, and 21% of clones belonged to Crenarchaeota. Bioinformatic analysis and comparisons showed that the clone libraries were significantly different between two salt mines. PMID:23457089

Xiao, Wei; Wang, Zhi-Gang; Wang, Yong-Xia; Schneegurt, Mark A; Li, Zhi-Ying; Lai, Yong-Hong; Zhang, Shi-Ying; Wen, Meng-Liang; Cui, Xiao-Long

2013-11-01

149

Centennial olive trees as a reservoir of genetic diversity  

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

Diez, Concepcion M.; Trujillo, Isabel; Barrio, Eladio; Belaj, Angjelina; Barranco, Diego; Rallo, Luis

2011-01-01

150

Diversity and genetic structure among subpopulations of Gossypium mustelinum (Malvaceae).  

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Gossypium mustelinum is the only cotton species native to Brazil; it is endemic to the semi-arid region of the northeast. The populations are found near perennial and semi-perennial sources of water, such as ponds or pools in intermittent streams. Problems with in situ conservation derive from human interference in its habitat, mainly because of excessive cattle grazing and deforestation. Establishing efficient strategies for in situ conservation requires knowledge of the genetic structure of the populations. We evaluated the structure and genetic variability of populations of G. mustelinum in the Tocó and Capivara Rivers (State of Bahia). Two hundred and eighteen mature G. mustelinum plants were genotyped with SSR markers. The molecular data were used to estimate the allelic frequencies, the heterozygosity, the F statistics, and the genetic distance among the populations and among individuals. We found high genetic diversity among the populations. The FST indexes for each population were also high and strongly correlated with physical distance. The high estimated level of endogamy and the low observed heterozygosity are indicative that the populations reproduce mainly by self-fertilization and crosses between related individuals. Consequently, strategies for in situ preservation should include at least three occurrence sites of G. mustelinum from each population. For ex situ conservation, the collections should include as many sites as possible. PMID:23512677

Alves, M F; Barroso, P A V; Ciampi, A Y; Hoffmann, L V; Azevedo, V C R; Cavalcante, U

2013-01-01

151

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

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The cyanobionts isolated from 10 Azolla accessions belonging to 6 species (Azolla mexicana, A. microphylla, A. rubra, A. caroliniana, A. filiculoides, A. pinnata) were cultured under laboratory conditions and analyzed on the basis of whole cell protein profiles and molecular marker dataset generated using repeat sequence primers (STRR(mod) and HipTG). The biochemical and molecular marker profiles of the cyanobionts were compared with those of the free-living cyanobacteria and symbiotic Nostoc strains from Anthoceros sp., Cycas sp. and Gunnera monoika. Cluster analysis revealed the genetic diversity among the selected strains, and identified 3 distinct clusters. Group 1 included cyanobionts from all the 10 accessions of Azolla, group 2 comprised all the symbiotic Nostoc strains, while group 3 included the free-living cyanobacteria belonging to the genera Nostoc and Anabaena. The interrelationships among the Azolla cyanobionts were further revealed by principal component analysis. Cyanobionts from A. caroliniana-A. microphylla grouped together while cyanobionts associated with A. mexicana-A. filiculoides along with A. pinnata formed another group. A. rubra cyanobionts had intermediate relationship with both the subgroups. This is the first study analyzing the diversity existing among the cultured cyanobionts of diverse Azolla species through the use of biochemical and molecular profiles and also the genetic distinctness of these free-living cyanobionts as compared to cyanobacterial strains of the genera Anabaena and Nostoc. PMID:18481216

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

2008-01-01

152

The loss of genetic diversity in Sichuan taimen as revealed by DNA fingerprinting.  

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Species endangerment often derives from the "endangerment" of genetic diversity, thus loss of genetic diversity is an important cause of species extinction. Since historical specimens were unavailable, previous studies mainly described the genetic diversity status in the current population rather than the loss of genetic variation over time. In this study, we collected samples during 1998-1999 and obtained historical specimens from 1957 to 1958. Based on the two sets of fish, we determined the changes in genetic diversity of Sichuan taimen using DNA fingerprinting. The differences in genetic parameters between the present samples and historical taimens revealed their loss of genetic variation. As a result, the existing populations have lower viability, and proper management has to be implemented to preserve genetic diversity. PMID:16944294

Wu, Xue-Chang

2006-06-01

153

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

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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

154

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

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

Dongsheng Liu

2010-11-01

155

Neural network and genetic algorithm technology in data mining of manufacturing quality information  

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Data Mining of Manufacturing Quality Information (MQI) is the key technology in Quality Lead Control. Of all the data mining methods, Neural Network and Genetic Algorithm is widely used for their strong advantages, such as non-linear, collateral, veracity etc. But if you singly use them, there will be some limitations preventing your research, such as convergence slowly, searching blindness etc. This paper combines their merits and use Genetic BP Algorithm in Data Mining of MQI. It has been successfully used in the key project of Natural Science Foundation of China (NSFC) - Quality Control and Zero-defect Engineering (Project No. 59735120).

Song, Limei; Qu, Xing-Hua; Ye, Shenghua

2002-03-01

156

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

157

Genetic diversity within Cryptosporidium parvum and related Cryptosporidium species.  

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To assess the genetic diversity in Cryptosporidium parvum, we have sequenced the small subunit (SSU) rRNA gene of seven Cryptosporidium spp., various isolates of C. parvum from eight hosts, and a Cryptosporidium isolate from a desert monitor. Phylogenetic analysis of the SSU rRNA sequences confirmed the multispecies nature of the genus Cryptosporidium, with at least four distinct species (C. parvum, C. baileyi, C. muris, and C. serpentis). Other species previously defined by biologic characteristics, including C. wrairi, C. meleagridis, and C. felis, and the desert monitor isolate, clustered together or within C. parvum. Extensive genetic diversities were present among C. parvum isolates from humans, calves, pigs, dogs, mice, ferrets, marsupials, and a monkey. In general, specific genotypes were associated with specific host species. A PCR-restriction fragment length polymorphism technique previously developed by us could differentiate most Cryptosporidium spp. and C. parvum genotypes, but sequence analysis of the PCR product was needed to differentiate C. wrairi and C. meleagridis from some of the C. parvum genotypes. These results indicate a need for revision in the taxonomy and assessment of the zoonotic potential of some animal C. parvum isolates. PMID:10427023

Xiao, L; Morgan, U M; Limor, J; Escalante, A; Arrowood, M; Shulaw, W; Thompson, R C; Fayer, R; Lal, A A

1999-08-01

158

Genetic Diversity in Bread Wheat (Triticum aestivum L. Genotypes  

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Full Text Available Wheat is one most important cereal crops grown in Ethiopia. Yet, keeping in view insufficient information on exotic bread wheat genotypes is limiting the access to useful traits present among the genotypes in the Somali region of Ethiopia. The aim of the study was to assess the extent of genetic diversity among bread wheat genotypes. Twenty six bread wheat (Triticum aestivum L. genotypes obtained from ICARDA-CIMMYT were tested at Gode and Kelafo research sites at three cropping seasons (2009/10, 2010/11 and 2011/12 under irrigation. The experiment was conducted in randomized complete block design with three replications. Ten agronomic traits were included in the study. The mean values, ranges and the coefficient of variation of the 10 characters indicated the existence of sufficient variability among genotypes. Multivariate techniques were used to classify 26 bread wheat genotypes. Principal component analysis showed that the first six principal components explained about 91.87% of the total variation. D2 analysis showed the 26 bread wheat genotypes grouped into six clusters. This made to become moderate diversity among the genotypes. The crosses between genotypes selected from cluster-III with cluster-VI and cluster V with cluster VI are expected to produce better genetic recombination and segregation in their progenies. Therefore, these bread wheat genotypes need to be crossed and selected to develop high yielding pure line variety.

S. Alamerew

2013-01-01

159

Genetic diversity of caprine Blastocystis from Peninsular Malaysia.  

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Blastocystis sp. is a common intestinal parasite found in humans and animals. The possibility of zoonotic transmission to humans from livestock especially goats led us to investigate the genetic diversity of caprine Blastocystis sp. obtained from five different farms in Peninsular Malaysia. Moreover, there is a lack of information on the prevalence as well as genetic diversity of Blastocystis sp. in goat worldwide. Results showed that 73/236 (30.9 %) of the goats were found to be positive for Blastocystis infection. The most predominant Blastocystis sp. subtype was ST1 (60.3 %) followed by ST7 (41.1 %), ST6 (41.1 %), and ST3 (11.0 %) when amplified by PCR using sequenced-tagged site (STS) primers. Four farms had goats infected only with ST1 whereas the fifth showed mixed infections with multiple STs. The proximity of the fifth farm to human dwellings, nearby domesticated animals and grass land as opposed to a sterile captive environment in the first four farms may account for the multiple STs seen in the fifth farm. Since ST1, ST3, ST6 and ST 7 were previously reported in human infection worldwide in particular Malaysia, the potential of the zoonotic transmission of blastocystosis should not be disregarded. The implications of different farm management systems on the distribution of Blastocystis sp. STs are discussed. PMID:22961236

Tan, Tian Chye; Tan, Peng Chiang; Sharma, Reuben; Sugnaseelan, Sumita; Suresh, Kumar Govind

2013-01-01

160

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

 
 
 
 
161

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers  

Science.gov (United States)

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 < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA 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.

Aranguren-Mendez, Jose; Jordana, Jordi; Gomez, Mariano

2001-01-01

162

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

163

Effects of the interaction between genetic diversity and UV-B radiation on wood frog fitness.  

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Genetic diversity may buffer amphibian populations against environmental vicissitudes. We hypothesized that wood frogs (Rana sylvatica)from populations with lower genetic diversity are more susceptible to ultraviolet-B (UV-B) radiation than those from populations with higher diversity. We used RAPD markers to obtain genetic diversity estimates for 12 wood frog populations. We reared larval wood frogs from these populations and exposed experimental groups of eggs and larvae to one of three treatments: unfiltered sunlight, sunlight filtered through a UM-B-blocking filter (Mylar), and sunlight filtered through a UV-B-transmitting filter (acetate). In groups exposed to UVB, larval mortality and deformity rates increased significantly, but egg mortality did not. We found a significant negative relationship between genetic diversity and egg mortality, larval mortality, and deformity rates. Furthermore, the interaction between UV-B treatment and genetic diversity significantly affected larval mortality. Populations with low genetic diversity experienced higher larval mortality rates when exposed to UVB than did populations with high genetic diversity. This is the first time an interaction between genetic diversity and an environmental stressor has been documented in amphibians. Differences in genetic diversity among populations, coupled with environmental stressors, may help explain patterns of amphibian decline. PMID:16909573

Weyrauch, Shauna L; Grubb, Thomas C

2006-06-01

164

[Temporal evolution of the genetic diversity of Chaerophyllum bulbosum: Consequences on the genetic resources management].  

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To increase the germplasm necessary for varietal improvement of tuberous-rooted chervil, a food apiaceae of increasing importance, two successive surveys of wild populations were carried out in Germany, in the Rhine and the Weser River basins. These mainly riparian populations are likely to be shaped by changes in hydrographic networks that characterize their habitat. Molecular studies have shown a strong structuration between wild populations (GST?32 %), but did not reveal any structuring effect of the hydrographic network on diversity or any global phenomenon of genetic erosion. A discussion about the strategy for maintaining the diversity of this species on a long-term period is proposed. PMID:24841963

Le Clerc, Valérie; Suel, Anita; Geoffriau, Emmanuel; Huet, Sébastien; Briard, Mathilde

2014-05-01

165

Genetic diversity in widespread species is not congruent with species richness in alpine plant communities.  

Science.gov (United States)

The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies. PMID:23006492

Taberlet, Pierre; Zimmermann, Niklaus E; Englisch, Thorsten; Tribsch, Andreas; Holderegger, Rolf; Alvarez, Nadir; Niklfeld, Harald; Coldea, Gheorghe; Mirek, Zbigniew; Moilanen, Atte; Ahlmer, Wolfgang; Marsan, Paolo Ajmone; Bona, Enzo; Bovio, Maurizio; Choler, Philippe; Cie?lak, El?bieta; Colli, Licia; Cristea, Vasile; Dalmas, Jean-Pierre; Frajman, Božo; Garraud, Luc; Gaudeul, Myriam; Gielly, Ludovic; Gutermann, Walter; Jogan, Nejc; Kagalo, Alexander A; Korbecka, Gra?yna; Küpfer, Philippe; Lequette, Benoît; Letz, Dominik Roman; Manel, Stéphanie; Mansion, Guilhem; Marhold, Karol; Martini, Fabrizio; Negrini, Riccardo; Niño, Fernando; Paun, Ovidiu; Pellecchia, Marco; Perico, Giovanni; Pi?ko?-Mirkowa, Halina; Prosser, Filippo; Pu?ca?, Mihai; Ronikier, Micha?; Scheuerer, Martin; Schneeweiss, Gerald M; Schönswetter, Peter; Schratt-Ehrendorfer, Luise; Schüpfer, Fanny; Selvaggi, Alberto; Steinmann, Katharina; Thiel-Egenter, Conny; van Loo, Marcela; Winkler, Manuela; Wohlgemuth, Thomas; Wraber, Tone; Gugerli, Felix; Vellend, Mark

2012-12-01

166

Indigenous cattle in Sri Lanka: Production systems and genetic diversity  

International Nuclear Information System (INIS)

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

2009-06-08

167

Microbial diversity in acid mineral bioleaching systems of dongxiang copper mine and Yinshan lead-zinc mine.  

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To understand the composition and structure of microbial communities in acid mineral bioleaching systems, the molecular diversity of 16S rDNA genes was examined using a PCR-based cloning approach. A total of 31 Operational Taxonomic Units (OTUs) were obtained from the four samples taken from four different bioleaching sites in Yinshan lead-zinc mine and Dongxiang copper mine in Jiangxi Province, China. The percentages of overlapping OTUs between sites ranged from 22.2 to 50.0%. Phylogenetic analysis revealed that the bacteria present at the four bioleaching sites fell into six divisions, alpha-Proteobacteria (1.1%), beta-Proteobacteria (2.3%), gamma-Proteobacteria (30.8%), Firmicutes (15.4%), Actinobacteria (0.3%) and Nitrospira (50.1%). Organisms of genera Leptospirillum, Acidithiobacillus, and Sulfobacillus, which were in Nitrospira, gamma-Proteobacteria, and Firmicutes divisions, respectively, were the most dominant. The results of principal component analysis based on the six phylogenetic divisions and biogeochemical data indicated that the microbial community structure of a site was directly related to the biogeochemical characteristic of that site. It follows therefore that sites with similar biogeochemical characteristics were comprised of similar microbial community structures. The results in our study also suggest that the elements copper and arsenic appear to be the key factors affecting the compositions and structures of microbial community in the four bioleaching sites. PMID:18157706

He, Zhiguo; Xiao, Shengmu; Xie, Xuehui; Hu, Yuehua

2008-03-01

168

Genetic diversity revealed by AFLP markers in Albanian goat breeds  

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

Hoda Anila

2012-01-01

169

Genetic diversity of Plasmodium vivax isolates from Azerbaijan  

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

Majori Giancarlo

2004-11-01

170

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

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Background With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity. Methods A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from th...

Engelsma, K. A.; Calus, M. P. L.; Bijma, P.; Windig, J. J.

2010-01-01

171

Inter simple sequence repeat fingerprints for assess genetic diversity of tunisian garlic populations  

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Garlic (Allium sativum L.) that is cultivated in Tunisia is heterogeneous and unclassified with no registered local cultivars. At present, the level of genetic diversity in Tunisian garlic is almost unknown. Inter Simple Sequence Repeats (ISSR) genetic markers were therefore used to assess the genetic diversity and its distribution in 31 Tunisian garlic accessions with 4 French classified clones used as control. It was the first time that ISSR markers were used to detect diversity in garlic. ...

2011-01-01

172

Genetic diversity assessment and individual identification of gyrfalcon (Falco rusticolus) in Iceland  

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The Icelandic gyrfalcon (Falco rusticolus) is a small and isolated non-migratory population and its ecological status has been carefully monitored for the last three decades. Lack of genetic diversity within isolated bird populations has been linked to greater susceptibility to environmental threats; therefore, estimates of the degree of genetic diversity in endangered species can be crucial. This study set out to complement the current existing ecological data with genetic diversity assessme...

Lára Guðmundsdóttir

2011-01-01

173

Genetic diversity of Hepatitis B Virus in Indonesia: epidemiological and clinical significance  

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Hepatitis B virus (HBV) infection remains a major public health problem particularly in Asia and Pacific that belongs to hepatitis B endemic regions. With high genetic diversity of the entire genome, this DNA virus has been classified into eight genotypes, genotype A to H, and recently two new genotypes, I and J, has been found in Asia. Interestingly, distribution of HBV genetic diversity is geographically specific worldwide. Further, distribution of HBV genetic diversity in Indonesia is asso...

Thedja, M. D.

2012-01-01

174

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

175

Invertebrates or iron: does large-scale opencast mining impact invertebrate diversity in ephemeral wetlands?  

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Full Text Available Disturbance has been offered as explanatory mechanism in structuring the variation of species across a landscape. In this study, we investigated the effect of the impact by Kolomela Iron Mine on the variation of species occurring in temporary pans. Using a novel null model approach to partitioning two sets of data (from before and after the establishment of the mine into independent alpha (? and beta (? components, we determined that the mining practices have had little to no impact on the invertebrate diversity. This suggests that these communities were more resilient than previously assumed. The results were, however, confounded by the fact that the resting eggs of pan inhabitants could remain dormant in the sediment for decades; suggesting that observed diversity patterns were possibly remnants of unknown past events. To ensure that the effect of present day impacts are assessed, continuous monitoring was recommended. Similarly, the preservation of conservation areas and a landscape wide management system were proposed to ensure that large scale ecological process are not jeopardised by the gradual fragmentation of the pan metacommunity.

Falko Theo Buschke

2013-03-01

176

Inadequacy of diversity indices in discerning metal mine drainage effects on a steam invertebrate community  

Energy Technology Data Exchange (ETDEWEB)

The benthic invertebrates of the Dolores River in southwest Colorado were sampled during three seasons in an area of historic mine drainage. Benthic density exhibited significantly lower values below the mine drainage. However, the number of species did not decrease significantly, indicating that the effect of the mine drainage was primarily non-selective (i.e. favoring no one taxon). This pattern was seasonal with the least effects evident in summer and the greatest effects found in spring. Diversity indices used to assess the effects of this stress on the invertebrate community were Margalef's, Simpson's, Shannon-Weaver's, Brillouin's, and the Biotic Condition Index. None of the indices tested adequately responded to a decreasing trend in the benthic density when number of species remained constant. The indices did respond to a combination of low density and number of species or to the predominant representation by one species. The Biotic Condition Index actually increased at the stations with the lowest density and number of species. Diversity indices appear to be inadequate in assessing a non-selective stress.

Chadwick, J.W.; Canton, S.P.

1984-02-01

177

Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity.  

Science.gov (United States)

Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate. PMID:23249956

Esko, Tõnu; Mezzavilla, Massimo; Nelis, Mari; Borel, Christelle; Debniak, Tadeusz; Jakkula, Eveliina; Julia, Antonio; Karachanak, Sena; Khrunin, Andrey; Kisfali, Peter; Krulisova, Veronika; Aušrelé Ku?inskiené, Zita; Rehnström, Karola; Traglia, Michela; Nikitina-Zake, Liene; Zimprich, Fritz; Antonarakis, Stylianos E; Estivill, Xavier; Glava?, Damjan; Gut, Ivo; Klovins, Janis; Krawczak, Michael; Ku?inskas, Vaidutis; Lathrop, Mark; Macek, Milan; Marsal, Sara; Meitinger, Thomas; Melegh, Béla; Limborska, Svetlana; Lubinski, Jan; Paolotie, Aarno; Schreiber, Stefan; Toncheva, Draga; Toniolo, Daniela; Wichmann, H-Erich; Zimprich, Alexander; Metspalu, Mait; Gasparini, Paolo; Metspalu, Andres; D'Adamo, Pio

2013-06-01

178

Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity  

Science.gov (United States)

Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145?000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate.

Esko, Tonu; Mezzavilla, Massimo; Nelis, Mari; Borel, Christelle; Debniak, Tadeusz; Jakkula, Eveliina; Julia, Antonio; Karachanak, Sena; Khrunin, Andrey; Kisfali, Peter; Krulisova, Veronika; Ausrele Kucinskiene, Zita; Rehnstrom, Karola; Traglia, Michela; Nikitina-Zake, Liene; Zimprich, Fritz; Antonarakis, Stylianos E; Estivill, Xavier; Glavac, Damjan; Gut, Ivo; Klovins, Janis; Krawczak, Michael; Kucinskas, Vaidutis; Lathrop, Mark; Macek, Milan; Marsal, Sara; Meitinger, Thomas; Melegh, Bela; Limborska, Svetlana; Lubinski, Jan; Paolotie, Aarno; Schreiber, Stefan; Toncheva, Draga; Toniolo, Daniela; Wichmann, H-Erich; Zimprich, Alexander; Metspalu, Mait; Gasparini, Paolo; Metspalu, Andres; D'Adamo, Pio

2013-01-01

179

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

Science.gov (United States)

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

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

2004-09-01

180

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

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

Malice M.

2009-01-01

 
 
 
 
181

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...

182

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

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

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

2010-07-01

183

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

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The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, drau...

Leroy, Gre?goire; Calle?de, Lucille; Verrier, Etienne; Me?riaux, Jean-claude; Ricard, Anne; Danchin-burge, Coralie; Rognon, Xavier

2009-01-01

184

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

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

Caser, M.; Scariot, V.; Arens, P.

2010-01-01

185

Hitchhiker’s guide to genetic diversity in socially structured populations  

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When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking. A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration. Under conditions in which genetic and cultural variants are transmitted symmetrically, neutral genes may also...

2012-01-01

186

Genetic diversity of marine animals in China: a summary and prospectiveness  

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Genetic diversity can reflect the origin and evolution of species. It can also inform the practices of genetic conservation, breeding and genetic improvement, even stabilization of marine ecosystem. In the past two decades, accumulating studies have focused on the genetic diversity of major marine fish and shellfish in China. Here we summarize the achievements of this area and its application to taxonomy, germplasm identification, phylogenetic evolutionary biology, analysis of population gene...

2011-01-01

187

Genetic diversity of Cryptosporidium spp. in captive reptiles.  

Science.gov (United States)

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

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

2004-02-01

188

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

189

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

190

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

191

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

Science.gov (United States)

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

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

2014-05-01

192

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

193

Genetic Diversity within Human Erythroviruses: Identification of Three Genotypes  

Science.gov (United States)

B19 virus is a human virus belonging to the genus Erythrovirus. The genetic diversity among B19 virus isolates has been reported to be very low, with less than 2% nucleotide divergence in the whole genome sequence. We have previously reported the isolation of a human erythrovirus isolate, termed V9, whose sequence was markedly distinct (>11% nucleotide divergence) from that of B19 virus. To date, the V9 isolate remains the unique representative of a new variant in the genus Erythrovirus, and its taxonomic position is unclear. We report here the isolation of 11 V9-related viruses. A prospective study conducted in France between 1999 and 2001 indicates that V9-related viruses actually circulate at a significant frequency (11.4%) along with B19 viruses. Analysis of the nearly full-length genome sequence of one V9-related isolate (D91.1) indicates that the D91.1 sequence clusters together with but is notably distant from the V9 sequence (5.3% divergence) and is distantly related to B19 virus sequences (13.8 to 14.2% divergence). Additional phylogenetic analysis of partial sequences from the V9-related isolates combined with erythrovirus sequences available in GenBank indicates that the erythrovirus group is more diverse than thought previously and can be divided into three well-individualized genotypes, with B19 viruses corresponding to genotype 1 and V9-related viruses being distributed into genotypes 2 and 3.

Servant, Annabelle; Laperche, Syria; Lallemand, Francis; Marinho, Valerie; De Saint Maur, Guillemette; Meritet, Jean Francois; Garbarg-Chenon, Antoine

2002-01-01

194

Genetic diversity of symbiotic cyanobacteria in Cycas revoluta (Cycadaceae).  

Science.gov (United States)

The diversity of cyanobacterial species within the coralloid roots of an individual and populations of Cycas revoluta was investigated based on 16S rRNA gene sequences. Sixty-six coralloid roots were collected from nine natural populations of cycads on Kyushu and the Ryukyu Islands, covering the entire distribution range of the species. Approximately 400 bp of the 5'-end of 16S rRNA genes was amplified, and each was identified by denaturing gradient gel electrophoresis. Most coralloid roots harbored only one cyanobiont, Nostoc, whereas some contained two or three, representing cyanobiont diversity within a single coralloid root isolated from a natural habitat. Genotypes of Nostoc within a natural population were occasionally highly diverged and lacked DNA sequence similarity, implying genetic divergence of Nostoc. On the other hand, Nostoc genotypes showed no phylogeographic structure across the distribution range, while host cycads exhibited distinct north-south differentiation. Cycads may exist in symbiosis with either single or multiple Nostoc strains in natural soil habitats. PMID:22537413

Yamada, Shuntaro; Ohkubo, Satoshi; Miyashita, Hideaki; Setoguchi, Hiroaki

2012-09-01

195

Structural diversity in Salmonella O antigens and its genetic basis.  

Science.gov (United States)

This review covers the structures and genetics of the 46 O antigens of Salmonella, a major pathogen of humans and domestic animals. The variation in structures underpins the serological specificity of the 46 recognized serogroups. The O antigen is important for the full function and virulence of many bacteria, and the considerable diversity of O antigens can confer selective advantage. Salmonella O antigens can be divided into two major groups: those which have N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine (GalNAc) and those which have galactose (Gal) as the first sugar in the O unit. In recent years, we have determined 21 chemical structures and sequenced 28 gene clusters for GlcNAc-/GalNAc-initiated O antigens, thus completing the structure and DNA sequence data for the 46 Salmonella O antigens. The structures and gene clusters of the GlcNAc-/GalNAc-initiated O antigens were found to be highly diverse, and 24 of them were found to be identical or closely related to Escherichia coli O antigens. Sequence comparisons indicate that all or most of the shared gene clusters were probably present in the common ancestor, although alternative explanations are also possible. In contrast, the better-known eight Gal-initiated O antigens are closely related both in structures and gene cluster sequences. PMID:23848592

Liu, Bin; Knirel, Yuriy A; Feng, Lu; Perepelov, Andrei V; Senchenkova, Sof'ya N; Reeves, Peter R; Wang, Lei

2014-01-01

196

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

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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

197

Genetic diversity of Leishmania infantum field populations from Brazil.  

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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 methods, 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. PMID:22310534

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

2012-02-01

198

Genetic diversity and relationships of endangered Spanish cattle breeds.  

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Information on the genetic structure and variability of autochthonous livestock breeds is essential for effective conservation programs. Here we present a molecular characterization on the basis of 30 microsatellite markers of 5 Spanish endangered cattle breeds Betizu (BET), Mallorquina (MAL), Menorquina, Monchina (MON), and Serrana de Teruel (ST) and of 2 fighting bull populations, Casta Navarra (CN) and Casta Vistahermosa. The feral and critically endangered BET is divided into 2 subpopulations, one of which has exceptionally low diversity values. A low number of alleles was also observed in the island population MAL. Although the small population size and genetic drift have caused a considerable divergence between the breeds, phylogenetic analysis is in accordance with historical and geographical data. The 2 northern Spanish feral breeds BET and MON cluster together. The local fighting breed CN is relatively close to the more inbred Casta Vistahermosa, which is the progenitor of most other fighting bulls in Spain. Comparison with nonendangered breeds suggests admixture of Alpine and/or Pyrenean mountain cattle in the ST, which may contribute to the high level of linkage disequilibrium in this population. PMID:17986470

Martín-Burriel, Inmaculada; Rodellar, Clementina; Lenstra, Johannes A; Sanz, Arianne; Cons, Carmen; Osta, Rosarsio; Reta, Miguel; De Argüello, Santos; Sanz, Albina; Zaragoza, Pilar

2007-01-01

199

Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.  

Science.gov (United States)

Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia. PMID:23411374

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

2013-09-01

200

Genetic diversity analysis of groundnut genotypes using SSR markers  

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Full Text Available Groundnut (Arachis hypogaea L., an important oilseed crop is a rich source of oil and protein. Molecular marker technologies are the effectivetools and they are used for the assessment of genetic variability because they are not influenced by the environment. Among the molecularmarkers, Simple Sequence Repeat (SSR has proved to be the most powerful tool for variety identification in groundnut and has much potential ingenetic and breeding studies. Among the 17 SSR primer pairs used for assessing the genetic diversity, 6 primer pairs (24.0 per cent werepolymorphic. The genotype TMV 2 was susceptible to rust and late leaf spot diseases and it was separately clustered in the dendrogram andamong the eleven foliar disease resistant genotypes, the genotypes viz., COG 0423, COG 0436 and COG 0432 were distantly clustered fromTMV 2. Hence, by using the genotypes viz., TMV 2, COG 0423, COG 0436 and COG 0432, three combinations viz., TMV 2 x COG 0423, TMV2 x COG 0436 and TMV 2 x C0G 0432 could be made for further studies.

D. Shoba, N. Manivannan and P.Vindhiyavarman

2010-12-01

 
 
 
 
201

Assessment of genetic diversity within sour cherry clones  

DEFF Research Database (Denmark)

Harvested yields of sour cherry (Prunus cerasus) cultivar â??Stevnsbaerâ?? 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 â??Stevnsbaerâ?? clone â??Birgitteâ?? and clone â??Vikiâ?? have consistently produced higher yields. A number of these selections were evaluated for yield and genomic differences to investigate variation between and within the â??Birgitteâ?? and â??Vikiâ?? clones. Variation in yield was mainly found at the clonal level. The clone â??Vikiâ?? was found to be the highest yielding with an average of 20 kg/tree compared to only 7.0 kg/tree from clone â??Birgitteâ??. The selected trees derived from within clone â??Birgitteâ?? had a significantly higher, average yield over 7 years compared to the original â??Birgitteâ??, 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

202

Assessment of Genetic Diversity across differentially adopted rice ecotypes  

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Full Text Available Rice is an important staple food and a rich source of carbohydrates for 90% of South and Southeast Asians. Geneticdiversity of naturally adopted upland lines along with few germplasm collections in Karnataka were studied basedon 13 SSR loci on chromosome 1. A total of 24 individuals belonging to 3 differentially adopted groups [Upland(8, landraces (8 and cultivated varieties (8] had a moderate to high level of genetic variability at groups level withnumber of alleles ranging from 5 to 23 (average 11.5 and PIC from 0.51 to 0.94 (average 0.79. The heterozygosityvaried from 0.39 to as high as 0.70. Over all genetic diversity of 0.81 was revealed indicating a high level of geneticvariation among these individuals. At the similarity coefficient of 7, all the lines were clearly grouped in 3 clusters.All cultivated types grouped in one cluster (cluster 1 except Rasi and CTH 1 which were included in cluster 2 andcluster 3 respectively. Cluster 1 contained 9 cultivated genotypes, where as cluster 2 contained 11 land races andcluster 3 had 4 upland lines. Out of 4 upland lines one line (AC-35341 intermixed, with C1 and three lines (PS-229,JBT-37/4 and AC-35310 with C3. The study of SSR markers on chromosome 1 facilitated the classification of theselines according to their adaptability. The information about the genetics of these populations will be for specificchromosomes and will be very useful for rice breeding programs, especially for gene mapping and ultimately formarker assisted selection programs.

Sridevi, G1., Raju, B.R2., Mohankumar, M.V2* and Sheshshayee, M, S.

2012-03-01

203

Genetic diversity in wild Dipsacus chinensis populations from China based on ISSR markers.  

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Wild Dipsacus chinensis plants in China have become endangered owing to over-harvesting and habitat fragmentation. We examined the genetic diversity and genetic structure of 90 individuals from three populations using inter-simple sequence repeat markers and found that 106 of 173 bands amplified by 22 informative and reliable primers were polymorphic. These findings correspond to a medium level of genetic diversity. At the species level, the estimates of parameters of genetic diversity were as follows: polymorphic loci (61.27%); effective number of alleles (1.3873); Nei's genetic diversity (0.2202); Shannon's information index (0.3235). At the population level, the estimates were polymorphic loci (9.53%); effective number of alleles (1.0419); Nei's genetic diversity (0.0258); Shannon's information index (0.0402). Nei's coefficient of genetic differentiation was 0.8829, which is consistent with Shannon's coefficient of genetic differentiation (0.8757). Most of the genetic variation existed among populations, and some differentiation may have resulted from habitat fragmentation and barriers to gene flow (gene flow = 0.0663). Combining our results with those of on-site field investigation, we conclude that the present genetic diversity and genetic structure of natural populations of D. chinensis have been strongly affected by harvesting and habitat fragmentation. We also propose strategies for the conservation of this plant. PMID:23661445

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

2013-01-01

204

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

205

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

206

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

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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

207

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

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

G. Marimuthu

2006-01-01

208

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

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

VIVI YUSKIANTI

2012-09-01

209

Association Rule Mining: A Multi-objective Genetic Algorithm Approach Using Pittsburgh Technique  

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Full Text Available Association rules [4] usually found out the relationship between different data entities in given data set and moreover it is very much important task of data mining. Basically, association rule mining is a multi-objective problem, instead of a single objective problem. A multi-objective genetic algorithm approach using Pittsburgh technique is introduced in this paper for discovering the interesting association rules with multiple criteria i.e. support, confidence and simplicity and complexity With Genetic Algorithm. In this paper we have discussed the results on various datasets and show effectiveness of the new proposed algorithm.

PG Scholar Ms. Sonia Sharma

2013-09-01

210

Comparative Analysis of Stability-Genetic Diversity in Seagrass (Posidonia oceanica) Meadows Yields Unexpected Results  

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The diversity–stability relationship is the subject of a long-standing debate in ecology, but the genetic component of diversity has seldom been explored. In this study, we analyzed the interplay between genetic diversity and demographic responses to environmental pressures. This analysis included 30 meadows formed by the Mediterranean endemic seagrass, Posidonia oceanica, showing a wide range of population dynamics ranging from a near equilibrium state to steep decline due to strong enviro...

Arnaud-haond, Sophie; Marba?, Nu?ria; Di?az Almela, Elena; Serra?o, Ester A.; Duarte, Carlos M.

2009-01-01

211

Comparison of AFLP and SSR for Genetic Diversity Analysis of Brassica napus Hybrids  

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Full Text Available The AFLP and SSR markers were used to estimate the genetic diversity of 25 Brassica napus hybrids attending Guizhou regional test. The fingerprints obtained with both the AFLP and SSR markers revealed high levels of heterozygosity. Nine AFLP primer combinations produced 16 loci, while 11 SSR primer pairs generated 22 loci. The mean of expected heterozygosity, Shannon’s information index, and genetic differentiation obtained by SSR were higher than those by AFLP, indicating that the SSR methodology evaluated genetic diversity among B. napus more efficiently than the AFLP approach. The higher level of genetic diversity detected by SSR markers was contributed to the lower genetic similarity estimates based on SSR markers (mean 0.69 as compared to AFLP markers (mean 0.73. While the AFLP technique was suitable for identification and DNA fingerprinting of B. napus germplasm. Based on AFLP and SSR analysis, it was concluded that B. napus hybrids had high level genetic diversity.

Li Li

2011-09-01

212

Prevalence and genetic diversity of pneumococcal serogroup 6 in Australia.  

Science.gov (United States)

The prevalence of the newly discovered pneumococcal serotype 6C has increased in some countries since the introduction of seven-valent conjugate pneumococcal vaccine (PCV7). The distribution of invasive serogroup 6 serotypes, in Australia, including 6C and 6D, has not been reported previously. During the period 1999 to 2008, 6097 isolates were referred to the New South Wales Pneumococcal Reference Laboratory for serotyping. Of these, 847 were identified by Quellung reaction as belonging to serogroup 6 and 702 were available for further study. Serotypes were determined by serotype-specific PCR as follows: 6A, 197 (28.1%); 6B, 452 (64.4%); 6C, 52 (7.4%) and one 6D. The average numbers of invasive serogroup 6 isolates, per annum, fell from 62.2 before (2000-2005) to 49.7 after (2006-2008) the introduction of PCV7. The proportions of invasive 6B fell (from 72.4% to 47.3%, p 0.03), those of 6C rose (from 3.3% to 17%, p 0.02) significantly and those of 6A remained fairly constant (24.3% vs 27%, p 0.69) between the two periods. All 6C and 6D and selected 6A and 6B isolates were further characterized by multilocus sequence typing and sequence analysis of cps genes cpsA-cpsB (wzg-wzh) and wchA-wciN(beta) -wciO, wciP. Results showed considerable diversity within serotype 6C, apparently as a result of both mutation and recombination. Sequence typing indicates that, in Australia, 6C has been largely derived from 6A. The genetic diversity and rapid increase in incidence of serotype 6C causing invasive pneumococcal disease has potential implications for vaccine efficacy. PMID:20950338

Zhuo, F; Xiao, M; Kong, F; Oftadeh, S; Zhou, F; Zhang, J; Gilbert, G L

2011-08-01

213

Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains  

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

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

2006-07-06

214

Genetic diversity among Botulinum Neurotoxin-producing clostridial strains.  

Science.gov (United States)

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore-forming rod-shaped bacteria that have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and death in humans and other animal species. A collection of 174 C. botulinum strains was examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine the genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT/A to BoNT/G). Analysis of the16S rRNA gene sequences confirmed previous identifications of at least four distinct genomic backgrounds (groups I to IV), each of which has independently acquired one or more BoNT genes through horizontal gene transfer. AFLP analysis provided higher resolution and could be used to further subdivide the four groups into subgroups. Sequencing of the BoNT genes from multiple strains of serotypes A, B, and E confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven toxin genes of the serotypes were compared and showed various degrees of interrelatedness and recombination, as was previously noted for the nontoxic nonhemagglutinin gene, which is linked to the BoNT gene. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for the treatment of botulism. PMID:17114256

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

2007-02-01

215

Genetic Diversity among Botulinum Neurotoxin-Producing Clostridial Strains?  

Science.gov (United States)

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

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

2007-01-01

216

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

217

Genetic algorithm optimization of a large U.K. coal mine ventilation network  

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This paper reports on results of an application of a genetic algorithm to the optimization of a large UK Coal Mine Ventilation Network. The genetic algorithm technique has been developed into a computer program for minimizing the total network operating fan power costs. The application of booster fans may become an attractive alternative for ventilation engineers to provide an adequate supply of fresh air around the working areas in some deep and/or extensive mines. The objective of this research is to minimize the total power consumption of a ventilation system by determining the optimum combinations of (1) main fan and booster fans ratings and (2) booster fan position(s). A modular computer program, which combines the application of the genetic algorithm optimization technique together with a ventilation network simulator, has been developed using the C++ language. The ventilation network simulator uses the standard hardy-cross iterative scheme implicit within the VNET mine ventilation software that was developed at the University of Nottingham. This paper presents detail of a study on an extensive UK coal mine ventilation network. The ventilation of this network is investigated using various configurations--a single main surface fan, or a main surface fan with either a single, two or three underground booster fans. The paper highlights the major genetic operators that are used to evolve the optimum solution. It is concluded that the genetic algorithm approach is an efficient and flexible solution method.

Yang, Z.Y.; Lowndes, I.S.; Denby, B.

1999-07-01

218

Genetic diversity among isolates of stemphylium solani from cotton  

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Full Text Available 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 DNA (RAPD markers and internal transcribed spacers of ribosomal DNA (rDNA were used to compare 33 monosporic isolates of S. solani (28 from cotton and five from tomato. An isolate of Alternaria macrospora from cotton was also used for comparison. RAPD analysis showed the presence of polymorphism between the genera and the species. The A. macrospora and the S. solani isolates from cotton and tomato were distinct from each other, and fell into separate groups. Variation by geographic region was observed for the tomato isolates but not for the cotton isolates. Amplifications of the ITS region using the primer pair ITS4/ITS5 resulted in a single PCR product of approximately 600 bp for all the isolates. Similarly, when amplified fragments were digested with eight restriction enzymes, identical banding patterns were observed for all the isolates. Hence, rDNA analysis revealed no inter-generic or intra-specific variation. The genetic difference observed between the cotton and the tomato isolates provides evidence that S. solani attacking cotton in Brazil belongs to a distinct genotype.

MEHTA Y.R.

2001-01-01

219

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

220

Genetic diversity of Phytophthora infestans in the Northern Andean region  

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

Grünwald Niklaus J

2011-02-01

 
 
 
 
221

Genetic Diversity of Pandanus from West Java based on ISSR Markers  

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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...

2010-01-01

222

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

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

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

2012-01-01

223

AFRICAN GENETIC DIVERSITY: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping  

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Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evol...

2008-01-01

224

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

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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 it...

Surendra Kumar Prajapati; Hema Joshi; Neena Valecha

2010-01-01

225

Inter simple sequence repeat fingerprints for assess genetic diversity of tunisian garlic populations  

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Garlic (Allium sativum L.) that is cultivated in Tunisia is heterogeneous and unclassified with no registered local cultivars. At present, the level of genetic diversity in Tunisian garlic is almost unknown. Inter Simple Sequence Repeats (ISSR) genetic markers were therefore used to assess the genetic diversity and its distribution in 31 Tunisian garlic accessions with 4 French classified clones used as control. It was the first time that ISSR markers were used t...

2011-01-01

226

Genetic diversity between herds of Alpine and Saanen dairy goats and the naturalized Brazilian Moxotó breed  

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Brazilian naturalized goat breeds are adapted to the semiarid conditions prevalent in the Northeast region of the country (which has the largest Brazilian goat heard) and represent an as yet uninvestigated source of genetic diversity. Currently, imported goat breeds are crossed with Brazilian naturalized goat breeds, endangering the genetic potential of the naturalized breeds. We used 11 microsatellite markers to determine the genetic diversity among imported (non-naturalized) dairy Alpine an...

Adriana Mello de Araújo; Simone Eliza Facioni Guimarães; Thea Mírian Medeiros Machado; Paulo Sávio Lopes; Carmen Silva Pereira; Francisco Luiz Ribeiro da Silva; Marcelo Teixeira Rodrigues; Virgínia de Souza Columbiano; Cleusa Graça da Fonseca

2006-01-01

227

Genetic diversity and malaria vaccine design, testing, and efficacy: Preventing and overcoming “vaccine resistant malaria”  

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The development of effective malaria vaccines may be hindered by extensive genetic diversity in the surface proteins being employed as vaccine antigens. Understanding of the extent and dynamics of genetic diversity in vaccine antigens is needed to guide rational vaccine design and to interpret the results of vaccine efficacy trials conducted in malaria endemic areas. Molecular epidemiological, population genetic, and structural approaches are being employed to try to identify immunologically ...

Takala, Shannon L.; Plowe, Christopher V.

2009-01-01

228

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

229

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

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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

230

Genetic diversity of blastocystis in livestock and zoo animals.  

Science.gov (United States)

Blastocystis is a common unicellular anaerobic eukaryote that inhabits the large intestine of many animals worldwide, including humans. The finding of Blastocystis in faeces in mammals and birds has led to proposals of zoonotic potential and that these hosts may be the source of many human infections. Blastocystis is, however, a genetically diverse complex of many distinct organisms (termed subtypes; STs), and sampling to date has been limited, both geographically and in the range of hosts studied. In order to expand our understanding of host specificity of Blastocystis STs, 557 samples were examined from various non-primate animal hosts and from a variety of different countries in Africa, Asia and Europe. STs were identified using 'barcoding' of the small subunit rRNA gene using DNA extracted either from culture or directly from faeces. The host and geographic range of several STs has thereby been greatly expanded and the evidence suggests that livestock is not a major contributor to human infection. Two new STs were detected among the barcode sequences obtained; for these, and for three others where the data were incomplete, the corresponding genes were fully sequenced and phylogenetic analysis was undertaken. PMID:23770574

Alfellani, Mohammed A; Taner-Mulla, Derya; Jacob, Alison S; Imeede, Christine Atim; Yoshikawa, Hisao; Stensvold, C Rune; Clark, C Graham

2013-07-01

231

Assessment of genetic diversity in germplasm of linseed  

International Nuclear Information System (INIS)

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

232

Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity  

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The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second–nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth–nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.

Muller, Romy; Roberts, Charlotte A.; Brown, Terence A.

2014-01-01

233

Genetic Diversity Analysis of Indian Mustard (Brassica juncea L.  

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Full Text Available Genetic diversity using Mahalanobis D² statistics was studied in 46 genotypes of Indian mustard in both protected (againstdiseases and pests and unprotected conditions for seed yield and its components. The 46 genotypes were grouped into sevenclusters based on D² analysis in both conditions. Cluster III was the largest with 18 genotypes followed by cluster IV (12and cluster I (5 in protected condition. In unprotected condition, cluster II comprised of 19 genotypes followed by cluster III(10 and cluster I, IV (5. The contribution of genotypes in different clusters was almost same in both the conditions whichstrengthened the conformation of formation of clusters. For both the conditions, it was observed that the same character,number of primary branches per plant exhibited maximum percentage towards divergence. The study revealed that theclusters I and VII possessing high mean values for the most of the desirable traits in both the conditions are desired to becrossed with cluster II and V for exploiting heterosis.

R.Doddabhimappa, B.Gangapur, G. Prakash and Channayya. P. Hiremath

2010-07-01

234

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

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

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

2004-12-01

235

Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop.  

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Cassava (Manihot esculenta) is an allogamous, vegetatively propagated, Neotropical crop that is also widely grown in tropical Africa and Southeast Asia. To elucidate genetic diversity and differentiation in the crop's primary and secondary centers of diversity, and the forces shaping them, SSR marker variation was assessed at 67 loci in 283 accessions of cassava landraces from Africa (Tanzania and Nigeria) and the Neotropics (Brazil, Colombia, Peru, Venezuela, Guatemala, Mexico and Argentina). Average gene diversity (i.e., genetic diversity) was high in all countries, with an average heterozygosity of 0.5358 +/- 0.1184. Although the highest was found in Brazilian and Colombian accessions, genetic diversity in Neotropical and African materials is comparable. Despite the low level of differentiation [F(st)(theta) = 0.091 +/- 0.005] found among country samples, sufficient genetic distance (1-proportion of shared alleles) existed between individual genotypes to separate African from Neotropical accessions and to reveal a more pronounced substructure in the African landraces. Forces shaping differences in allele frequency at SSR loci and possibly counterbalancing successive founder effects involve probably spontaneous recombination, as assessed by parent-offspring relationships, and farmer-selection for adaptation. PMID:12856084

Fregene, M A; Suarez, M; Mkumbira, J; Kulembeka, H; Ndedya, E; Kulaya, A; Mitchel, S; Gullberg, U; Rosling, H; Dixon, A G O; Dean, R; Kresovich, S

2003-10-01

236

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

237

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

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

Naouel Jabbes

2011-11-01

238

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.

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

239

Bacteria diversity and arsenic mobilization in rock biofilm from an ancient gold and arsenic mine.  

Science.gov (United States)

In this paper we characterize the biofilm community from an ancient Z?oty Stok gold and arsenic mine. Bacterial diversity was examined using a culture-independent technique based on 16S rRNA gene amplification, cloning and sequencing. We show that unexpectedly the microbial diversity of this community was extremely high (more than 190 OTUs detected), with the most numerous members from Rhizobiales (?-Proteobacteria). Although the level of rock biofilm diversity was similar to the microbial mat community we have previously characterized in the same adit, its taxonomic composition was completely different. Detailed analysis of functional arrA and aioA genes, chemical properties of siderophores found in pore water as well as the biofilm chemical composition suggest that the biofilm community contributes to arsenic pollution of surrounding water in a biogeochemical cycle similar to the one observed in bacterial mats. To interpret our results concerning the biological arsenic cycle, we applied the theory of ecological pyramids of Charles Elton. PMID:23743145

Tomczyk-?ak, Karolina; Kaczanowski, Szymon; Drewniak, ?ukasz; Dmoch, ?ukasz; Sklodowska, Aleksandra; Zielenkiewicz, Urszula

2013-09-01

240

High genetic diversity in Sarracenia leucophylla(Sarraceniaceae), a carnivorous wetland herb.  

Science.gov (United States)

Eighteen allozyme loci were used to examine genetic diversity in 10 natural populations of Sarracenia leucophylla Raf., a pitcher plant restricted to the southeastern United States. One ex situ population propagated for restoration in Georgia was also analyzed. S. leucophylla is an insect-pollinated, outcrossing perennial wetland herb that is threatened over much of its geographic range. Fifteen loci (83.3%) were polymorphic, with a mean number of alleles of 3.33. Compared to species having similar life-history traits and to previously analyzed Sarracenia species, S. leucophylla displayed unexpectedly high genetic diversity. For example, genetic diversity within the species (Hes) was 0.224 and mean population genetic diversity (Hep) was 0.183. Although small S. leucophylla populations maintained less genetic diversity than larger ones, these differences were not statistically significant. Nonetheless, this suggests that small populations may have lost rare alleles. Statistically significant genetic differentiation among populations was found (theta = 0.192, P < .01), although it was not atypical considering the species' life-history characteristics. A significant correlation (P < .01) between genetic and geographic distance was found, indicating an isolation-by-distance effect. However, the correlation coefficient for this relationship was low (r = 0.46), suggesting that factors other than gene flow play a prominent role in the geographic distribution of genetic diversity within the species. The ex situ population captured most of the allozyme variation found in its source population. PMID:15220390

Wang, Z-F; Hamrick, J L; Godt, M J W

2004-01-01

 
 
 
 
241

Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research.  

Science.gov (United States)

The historical origins of classical laboratory mouse strains have led to a relatively limited range of genetic and phenotypic variation, particularly for the study of behavior. Many recent efforts have resulted in improved diversity and precision of mouse genetic resources for behavioral research, including the Collaborative Cross and Diversity Outcross population. These two populations, derived from an eight way cross of common and wild-derived strains, have high precision and allelic diversity. Behavioral variation in the population is expanded, both qualitatively and quantitatively. Variation that had once been canalized among the various inbred lines has been made amenable to genetic dissection. The genetic attributes of these complementary populations, along with advances in genetic and genomic technologies, makes a systems genetic analyses of behavior more readily tractable, enabling discovery of a greater range of neurobiological phenomena underlying behavioral variation. PMID:24272351

Chesler, Elissa J

2014-02-01

242

The effect of multiple paternity on genetic diversity during and after colonisation  

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In metapopulations, genetic variation of local populations is influenced by the genetic content of the founders, and of migrants following establishment. We analyse the effect of multiple paternity on genetic diversity using a model in which the highly promiscuous marine snail Littorina saxatilis expands from a mainland to colonise initially empty islands of an archipelago. Migrant females carry a large number of eggs fertilised by 1 - 10 mates. We quantify the genetic diver...

Rafajlovic, M.; Eriksson, A.; Rimark, A.; Saltin, S. H.; Charrier, G.; Panova, M.; Andre?, C.; Johannesson, K.; Mehlig, B.

2012-01-01

243

Genetic Diversity in Introduced Golden Mussel Populations Corresponds to Vector Activity  

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We explored possible links between vector activity and genetic diversity in introduced populations of Limnoperna fortunei by characterizing the genetic structure in native and introduced ranges in Asia and South America. We surveyed 24 populations: ten in Asia and 14 in South America using the mitochondrial cytochrome c oxidase subunit I (COI) gene, as well as eight polymorphic microsatellite markers. We performed population genetics and phylogenetic analyses to investigate population genetic...

Ghabooli, Sara; Zhan, Aibin; Sardin?a, Paula; Paolucci, Esteban; Sylvester, Francisco; Perepelizin, Pablo V.; Briski, Elizabeta; Cristescu, Melania E.; Macisaac, Hugh J.

2013-01-01

244

Diversity of arbuscular mycorrhizal fungi in a gypsum mining impacted semiarid area Diversidade de fungos micorrízicos arbusculares em áreas impactadas por mineração gesseira no semiarido  

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The aim of this work was to evaluate the impact of gypsum mining on the occurrence and diversity of arbuscular mycorrhizal fungi (AMF). Soil samples were collected in the rainy and dry periods in four areas of a gypsum mine: native preserved "caatinga" (NC); mine vicinity (MS); reject area (RA); interface between the reject area and an area of "caatinga" degraded by mining (IN). Forty two plant species were identified in these areas; some were not found in both collection periods. Thirty six ...

Adália Cavalcanti do Espírito Santo Mergulhão; Hélio Almeida Burity; Bruno Tomio Goto; Leonor Costa Maia

2010-01-01

245

Genetic diversity of the toxic cyanobacterium Microcystis in Lake Mikata.  

Science.gov (United States)

The aim of the present study was to clarify the bloom dynamics and community composition of hepatotoxin microcystin-producing and non-microcystin-producing Microcystis genotypes in the environment. In Lake Mikata (Fukui, Japan) from April 2003 to January 2004, seasonal variation in the number of cells with microcystin (mcy) genotypes and the genetic diversity of the total population were investigated using quantitative competitive PCR and a 16S rDNA clone library, respectively. Using competitive PCR, cells with mcyA genotypes were quantified in August and October, and the ratio of the number of these mcyA genotypes to colony-forming Microcystis cells was 0.37 and 2.37, respectively. The 16S rDNA clones obtained could be divided into 12 ribotypes: a-l. Sixty-one Microcystis strains isolated from Lake Mikata during the sampling period were subjected to toxicity tests using HPLC and ELISA, PCR-based detection of the mcyA gene, and sequence analysis of the 16S rDNA. All isolates could be differentiated into 11 ribotypes (a, b, d, f, h, i, and m-q). Ribotypes b, f, i, m, n, and p had at least one strain that was a microcystin producer. In natural communities ribotypes b and f accounted for 85% of the 16S rDNA clones in August, and ribotypes b and i accounted for 24% of the clones in October. Thus, in some bloom stages the presence of microcystin genotypes identified using the 16S rDNA clone library correlated with that of mcy genotypes determined using competitive PCR. PMID:15892077

Yoshida, Mitsuhiro; Yoshida, Takashi; Takashima, Yukari; Kondo, Ryuji; Hiroishi, Shingo

2005-06-01

246

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

247

Genetic diversity in Brazilian populations of Aedes albopictus  

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Full Text Available Random amplified polymorphic DNA (RAPD analysis technique was undertaken in Aedes albopictus populations from three states in Brazil, Rio de Janeiro (RJ, Minas Gerais (MG and Pernambuco (PE, to estimate the level of genetic variability and levels of genetic exchange between populations. Allele and genotype frequencies were measured on 47 RAPD loci. Average observed heterozigosity (Ho ranged from 0.282 in MG to 0.355 in Casa Forte (PE population. Genetic distances estimates indicated that RJ and MG were more genetically similar than populations from PE. Genetic variation observed in local Brazilian populations was attributed to genetic drift associated with restricted gene flow in recently established populations.

Ayres CFJ

2002-01-01

248

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

249

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

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

Jae Geun Kim*

2012-03-01

250

Genetic diversity and gene flow in the endangered dwarf bear poppy, Arctomecon humilis (Papaveraceae).  

Science.gov (United States)

Arctomecon humilis is a critically endangered species endemic to the Moenkopi shale of Washington County, Utah. Recovery plans for the species would be improved by an understanding of genetic diversity and gene flow among its remaining populations. Ten variable isozyme loci were used to calculate genetic diversity statistics for study populations. Westerly populations possessed higher levels of genetic variability than other populations at the same isozyme loci. Three of the populations exhibited significant deviations from Hardy-Weinberg expectations. No correlation existed between genetic distance and geographic distance. Most of the genetic diversity was distributed among populations with little gene flow between populations, suggesting that observed genetic differences may arise from genetic drift. For the westerly populations, similar genotypes were observed in the seedling and old age classes, while intermediate age classes typically possessed an alternate set of genotypes at Pgi-2. Mean heterozygosity increased with age class across populations. Westerly populations of A. humilis shared more alleles with the nearest geographic population of A. californica than other populations. Since the westerly populations contained more genetic variability and more alleles in common with a near relative, they may be relictual. Other populations may contain less genetic diversity due to founder effects and/or genetic drift. PMID:21685011

Allphin, L; Windham, M D; Harper, K T

1998-09-01

251

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

252

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

253

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

254

Amplified fragment length polymorphism analysis of genetic diversity of Haemonchus contortus during selection for drug resistance.  

Science.gov (United States)

For the first time we used amplified fragment length polymorphism on individual nematode parasites to analyse the genetic diversity between and within isolates during consecutive stages of increased benzimidazole resistance and of increased levamisole resistance of Haemonchus contortus. The genetic diversity of the H. contortus genome turned out to be unusually high, within and between the isolates. The difference between individuals of an isolate could be as high as between individuals of two different mammalian species that do not interbreed. During benzimidazole selection the genetic constitution of the population was changed, but did not lead to a decrease in the genetic diversity. The selection for levamisole resistance resulted in a limited reduction of the genetic diversity only after the first selection step. The extensive genetic diversity apparently has allowed a fast and flexible response of H. contortus to drug selection as shown by the appearance of drug resistant isolates. This selection however has little or no effect on the extent of the genetic diversity of these resistant isolates. Implications for more sustainable control methods are discussed. PMID:11429180

Otsen, M; Hoekstra, R; Plas, M E; Buntjer, J B; Lenstra, J A; Roos, M H

2001-08-01

255

Life history influences how fire affects genetic diversity in two lizard species.  

Science.gov (United States)

'Fire mosaics' are often maintained in landscapes to promote successional diversity in vegetation with little understanding of how this will affect ecological processes in animal populations such as dispersal, social organization and re-establishment. To investigate these processes, we conducted a replicated, spatiotemporal landscape genetics study of two Australian woodland lizard species [Amphibolurus norrisi (Agamidae) and Ctenotus atlas (Scincidae)]. Agamids have a more complex social and territory structure than skinks, so fire might have a greater impact on their population structure and thus genetic diversity. Genetic diversity increased with time since fire in C. atlas and decreased with time since fire in A. norrisi. For C. atlas, this might reflect its increasing population size after fire, but we could not detect increased gene flow that would reduce the loss of genetic diversity through genetic drift. Using landscape resistance analyses, we found no evidence that postfire habitat succession or topography affected gene flow in either species and we were unable to distinguish between survival and immigration as modes of postfire re-establishment. In A. norrisi, we detected female-biased dispersal, likely reflecting its territorial social structure and polygynous mating system. The increased genetic diversity in A. norrisi in recently burnt habitat might reflect a temporary disruption of its territoriality and increased male dispersal, a hypothesis that was supported with a simulation experiment. Our results suggest that the effects of disturbance on genetic diversity will be stronger for species with territorial social organization. PMID:24750427

Smith, Annabel L; Bull, C Michael; Gardner, Michael G; Driscoll, Don A

2014-05-01

256

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

257

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

258

Genetic diversity and differentiation of Mongolian indigenous cattle populations  

International Nuclear Information System (INIS)

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

2003-10-06

259

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

260

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

 
 
 
 
261

Culture-independent molecular analysis of bacterial diversity in uranium-ore/-mine waste-contaminated and non-contaminated sites from uranium mines  

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Soil, water and sediment samples collected from in and around Jaduguda, Bagjata and Turamdih mines were analyzed for physicochemical parameters and cultured, and yet to be cultured microbial diversity. Culturable fraction of microbial community measured as Colony Forming Unit (CFU) on R2A medium revealed microbes between 104 and 109 CFU/g sample. Community DNA was extracted from all the samples; 16S rRNA gene amplified, cloned and subject to Amplified Ribosomal DNA Restriction Analysis. Clon...

2011-01-01

262

Tetraploid Wheat Landraces in the Mediterranean Basin: Taxonomy, Evolution and Genetic Diversity  

Science.gov (United States)

The geographic distribution of genetic diversity and the population structure of tetraploid wheat landraces in the Mediterranean basin has received relatively little attention. This is complicated by the lack of consensus concerning the taxonomy of tetraploid wheats and by unresolved questions regarding the domestication and spread of naked wheats. These knowledge gaps hinder crop diversity conservation efforts and plant breeding programmes. We investigated genetic diversity and population structure in tetraploid wheats (wild emmer, emmer, rivet and durum) using nuclear and chloroplast simple sequence repeats, functional variations and insertion site-based polymorphisms. Emmer and wild emmer constitute a genetically distinct population from durum and rivet, the latter seeming to share a common gene pool. Our population structure and genetic diversity data suggest a dynamic history of introduction and extinction of genotypes in the Mediterranean fields.

Oliveira, Hugo R.; Campana, Michael G.; Jones, Huw; Hunt, Harriet V.; Leigh, Fiona; Redhouse, David I.; Lister, Diane L.; Jones, Martin K.

2012-01-01

263

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

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

Mériaux Jean-Claude

2009-01-01

264

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

Science.gov (United States)

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

265

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

Science.gov (United States)

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

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

2010-01-01

266

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

International Nuclear Information System (INIS)

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

1998-05-17

267

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Grapputo Alessandro; Kumpulainen Tomi; Mappes Johanna; Parri Silja

2005-01-01

268

Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Kohat District, Pakistan  

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Malaria is one of the serious diseases threatening human health in Pakistan and contributes to a large proportion of the total malaria deaths in South Asia. However, little is known about the nature and extent of genetic diversity of the malarial parasites circulating in Pakistan. This study was designed to assess the infection status of Plasmodium and the genetic diversity of Plasmodium vivax and Plasmodium falciparum by analyzing msp-3?, msp-3? and msp-1, msp-2 genes respectively ...

Lubna Khatoon; Inam Ullah Khan; Shahid Ali Shah; Muhammad Ishtiaq Jan; Farhat Ullah; Salman Akbar Malik

2012-01-01

269

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

270

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

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

2012-01-01

271

Evaluation of Genetic Diversity of Spelt Breeding Materials Based on AFLP and Quality Analyses  

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The genetic diversity of cultivated spelt (Triticum aestivum ssp. spelta) presently is narrow. Evaluation of germplasm collections of spelt on quality level supplemented with DNA analysis is, therefore, of great importance. This study was designed to help the evaluation process for the selection of new spelt varieties with a support of molecular characterization. A total of 30 genotypes, including two common wheat varieties, were included in the evaluation of genetic diversity on quality and ...

Gulyas, G.; Rakszegi, M.; Bognar, Z.; Lang, L.; Bedo, Z.

2012-01-01

272

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

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Abstract Background Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range. Results We demonstrate that: (1) lower genetic diversity was c...

Vandewoestijne Sofie; Schtickzelle Nicolas; Baguette Michel

2008-01-01

273

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

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

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

2011-01-01

274

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

BACKGROUND: Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range. RESULTS: We demonstrate that: (1) lower genetic diversity was coupled to a sharp decrease in adult li...

Vandewoestijne, Sofie; Schtickzelle, Nicolas; Baguette, Michel

2008-01-01

275

GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage.  

Science.gov (United States)

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems. PMID:21097602

Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Van Nostrand, Joy D; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou

2011-02-01

276

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

277

Genetic diversity within and among sinai populations of three Ballota species (Lamiaceae).  

Science.gov (United States)

Ballota undulata, Ballota kaiseri, and Ballota saxatilis are very rare (and endemic--B. kaiseri), threatened species growing in St. Catherine Protectorate, southern Sinai, Egypt. They are subjected to a number of threats that have caused populations to decline in both number and size. For the long-term survival of these species, an appropriate conservation strategy for the maintenance of their genetic variation should be developed. This study measures genetic diversity within and among populations of these Ballota species and determines the conservation implications of the results. The genetic analyses demonstrated that the three Ballota species maintain relatively high levels of genetic diversity (He = 0.195-0.317) and that most of the their genetic diversity was found within populations (GST = 0.045-0.099). Indirect estimates of historical gene flow for B. undulata and B. saxatilis were relatively high (Nm(W) = 5.25 and 3.37, respectively) but suggest that there is somewhat less gene movement among B. kaiseri populations (Nm(W) = 2.29). The levels of genetic diversity maintained within populations of the three Ballota species indicate that an appropriate sampling design for ex situ safeguarding should capture the majority of the genetic diversity found within these taxa. PMID:16407527

Zaghloul, M S; Hamrick, J L; Moustafa, A A; Kamel, W M; El-Ghareeb, R

2006-01-01

278

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Nemati, Zahra; Tehranifar, Ali; Farsi, Mohammad; Mirshamsi Kakhki, Amin; Nemati, Hossein; Khayat, Mehdi

2012-01-01

279

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

280

High Genetic Diversity and Low Differentiation of Michelia coriacea (Magnoliaceae), a Critically Endangered Endemic in Southeast Yunnan, China  

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Michelia coriacea, a critically endangered tree, has a restricted and fragmented distribution in Southeast Yunnan Province, China. The genetic diversity, genetic structure and gene flow in the three extant populations of this species were detected by 10 inter-simple sequence repeat (ISSR) markers and 11 simple sequence repeat (SSR) markers. Examination of genetic diversity revealed that the species maintained a relatively high level of genetic diversity at the species level (percentage of pol...

2012-01-01

 
 
 
 
281

Genetic diversity and structure in two species of Leavenworthia with self-incompatible and self-compatible populations  

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Self-fertilization is a common mating system in plants and is known to reduce genetic diversity, increase genetic structure and potentially put populations at greater risk of extinction. In this study, we measured the genetic diversity and structure of two cedar glade endemic species, Leavenworthia alabamica and L. crassa. These species have self-incompatible (SI) and self-compatible (SC) populations and are therefore ideal for understanding how the mating system affects genetic diversity and...

2011-01-01

282

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.

283

High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks  

Science.gov (United States)

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

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

2013-01-01

284

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

285

Genetic structure and diversity of animal populations exposed to metal pollution.  

Science.gov (United States)

Studying the genetic diversity of wild populations that are affected by pollution provides a basis for estimating the risks of environmental contamination to both wildlife, and indirectly to humans. Such research strives to produce both a better understanding of the underlying mechanisms by which genetic diversity is affected,and the long-term effects of the pollutants involved.In this review, we summarize key aspects of the field of genetic ecotoxicology that encompasses using genetic patterns to examine metal pollutants as environmental stressors of natural animal populations. We address genetic changes that result from xenobiotic exposure versus genetic alterations that result from natural ecological processes. We also describe the relationship between metal exposure and changes in the genetic diversity of chronically exposed populations, and how the affected populations respond to environmental stress. Further, we assess the genetic diversity of animal populations that were exposed to metals, focusing on the literature that has been published since the year 2000.Our review disclosed that the most common metals found in aquatic and terrestrial ecosystems were Cd, Zn, Cu and Pb; however, differences in the occurrence between aquatic (Cd=Zn>Cu>Pb>Hg) and terrestrial (Cu>Cd>Pb>Zn>Ni)environments were observed. Several molecular markers were used to assess genetic diversity in impacted populations, the order of the most common ones of which were SSR's > allozyme > RAPD's > mtDNA sequencing> other molecular markers.Genetic diversity was reduced for nearly all animal populations that were exposed to a single metal, or a mixture of metals in aquatic ecosystems (except in Hyalella azteca, Littorina littorea, Salmo trutta, and Gobio gobio); however, the pattern was less clear when terrestrial ecosystems were analyzed.We propose that future research in the topic area of this paper emphasizes seven key areas of activity that pertain to the methodological design of genetic ecotoxicological studies. Collectively, these points are designed to provide more accurate data and a deeper understanding of the relationship between alterations in genetic diversity of impacted populations and metal exposures. In particular, we believe that the exact nature of all tested chemical pollutants be clearly described, biomarkers be included, sentinel organisms be used, testing be performed at multiple experimental sites, reference populations be sampled in close geographical proximity to where pollution occurs, and genetic structure parameters and high-throughput technology be more actively employed. Furthermore, we propose a new class of biomarkers,termed "biomarkers of permanent effect," which may include measures of genetic variability in impacted populations. PMID:24158580

Mussali-Galante, Patricia; Tovar-Sánchez, Efraín; Valverde, Mahara; Rojas, Emilio

2014-01-01

286

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

287

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

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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. ...

2005-01-01

288

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

289

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

290

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

291

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

292

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

Science.gov (United States)

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

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

2008-01-01

293

Effect of fluoride pollution on genetic diversity of a medicinal tree, Syzygium cumini.  

Science.gov (United States)

Syzygium cumini Linn. (Myrtaceae) is a medicinal tree (Jamun) used worldwide in treatment of diabetes. However, no molecular data is available on genetic polymorphism and its relationship, if any with fluoride pollution. In the present study, the genetic variability of two populations of S. cumini growing in fluoride rich soils and normal soils located in Rajasthan and Haryana regions of India, respectively was determined using random amplified polymorphic DNA (RAPD) markers. Different measures of diversity in Rajasthan populations: Shannon's index of phenotypic diversity (I) = 0.440; Nei's genetic diversity (h) = 0.292; effective number of alleles per locus (Ne) = 1.497; total species diversity (Hsp) = 0.307 and within population diversity (Hpop) = 0.158 showed high diversity in comparison to Haryana populations. Thus, it seems that Rajasthan population responds with increased genetic variation resulting possibly from new mutation that affect allele frequencies as a consequence of adaptation to contaminated environment. This may imply that the increased diversity levels may act as a buffer to combat fluoride stress. Cluster analysis and principal component analysis (PCA) results showed mixing between the populations. PMID:23360002

Khan, Suphiya; Baunthiyal, Mamta; Kumari, Alka; Sharma, Vinay

2012-07-01

294

Hitchhiker’s guide to genetic diversity in socially structured populations  

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

L. S. PREMO

2012-02-01

295

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

Science.gov (United States)

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

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

2009-01-01

296

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

297

Genetic diversity among the land races of sorghum collected in Tamil Nadu  

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Full Text Available Sixty three local land races of sorghum (Sorghum bicolor L. collected from different parts of Tamil Nadu were evaluated fortheir genetic diversity based on nine characters. The genotypes were grouped into 14 clusters indicating high genetic divergenceamong them. The study indicated no definite relationship between geographic and genetic diversity and geographic diversitycannot be used as an index of genetic diversity. Based on the inter cluster distance and cluster mean for various characters itcould be seen that the clusters VI, X, XII were the most divergent from the other clusters. The genotypes from these parentspossibly be utilized for hybridization programme. Days to flowering, plant height, ear head length and grain weight contributed

K. Ganesamurthy D. Punitha and M. Elangovan

2010-12-01

298

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

Science.gov (United States)

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

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

2013-01-01

299

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.

300

Description and analysis of genetic diversity among squash accessions  

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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

 
 
 
 
301

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

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

William B. Sherwin

2010-07-01

302

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

1991-09-01

303

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)

2010-12-01

304

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

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

Bourguiba Hedia

2012-04-01

305

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

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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

306

Genetic diversity of Callosobruchus maculatus (Fab.) (Coleoptera: Bruchidae) populations  

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Variations in esterase pattern and genetic similarity of six populations (Madurai, Nagapattinam, Coimbatore, Thiruvannamalai, Chennai and Vellore) of Callosobruchus maculatus were assessed. Among the populations studied, esterase pattern of the Coimbatore population is distinctly different then the other populations. PCR-DNA analysis showed similar patterns of DNA expression in all the 6 different populations. However, the genetic similarity index generated based on PCR results showed differe...

Raja, M.; John William, S.; Jahir Hussain, K.

2009-01-01

307

Spectrum of genetic diversity and networks of clonal organisms  

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

Rozenfeld, Alejandro F.; Arnaud-haond, Sophie; Herna?ndez-garci?a, Emilio; Egui?luz, Vi?ctor M.; Mati?as, Manuel A.; Serra?o, Ester A.; Duarte, Carlos M.

2007-01-01

308

Genetic diversity analysis of Bt cotton genotypes in Pakistan using simple sequence repeat markers.  

Science.gov (United States)

The popularity of genetically modified insect resistant (Bt) cotton has promoted large scale monocultures, which is thought to worsen the problem of crop genetic homogeneity. Information on genetic diversity among Bt cotton varieties is lacking. We evaluated genetic divergence among 19 Bt cotton genotypes using simple sequence repeat (SSR) markers. Thirty-seven of 104 surveyed primers were found informative. Fifty-two primers selected on the basis of reported intra-hirsutum polymorphism in a cotton marker database showed a high degree of polymorphism, 56% compared to 13% for randomly selected primers. A total of 177 loci were amplified, with an average of 1.57 loci per primer, generating 38 markers. The amplicons ranged in size from 98 to 256 bp. The genetic similarities among the 19 genotypes ranged from 0.902 to 0.982, with an average of 0.947, revealing a lack of diversity. Similarities among genotypes from public sector organizations were higher than genotypes developed by private companies. Hybrids were found to be more distant compared to commercial cultivars and advanced breeding lines. Cluster analysis grouped the 19 Bt cotton genotypes into three major clusters and two independent entries. Cultivars IR-3701, Ali Akbar-802 and advanced breeding line VH-259 grouped in subcluster B2, with very narrow genetic distances despite dissimilar parentage. We found a very high level of similarity among Pakistani-bred Bt cotton varieties, which means that genetically diverse recurrent parents should be included to enhance genetic diversity. The intra-hirsutum polymorphic SSRs were found to be highly informative for molecular genetic diversity studies in these cotton varieties. PMID:22535395

Ullah, I; Iram, A; Iqbal, M Z; Nawaz, M; Hasni, S M; Jamil, S

2012-01-01

309

Effects of Medicago truncatula Genetic Diversity, Rhizobial Competition, and Strain Effectiveness on the Diversity of a Natural Sinorhizobium Species Community?  

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We investigated the genetic diversity and symbiotic efficiency of 223 Sinorhizobium sp. isolates sampled from a single Mediterranean soil and trapped with four Medicago truncatula lines. DNA molecular polymorphism was estimated by capillary electrophoresis-single-stranded conformation polymorphism and restriction fragment length polymorphism on five loci (IGSNOD, typA, virB11, avhB11, and the 16S rRNA gene). More than 90% of the rhizobia isolated belonged to the Sinorhizobium medicae species ...

Rangin, Ce?cile; Brunel, Brigitte; Cleyet-marel, Jean-claude; Perrineau, Marie-mathilde; Be?na, Gilles

2008-01-01

310

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

311

Studies on Genetic Diversity in Pakistani Wheat Varieties using Randomly Amplified Polymorphic DNA  

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Full Text Available To improve yield and quality of wheat, presence of genetic diversity is an important prerequisite. To estimate the extent of genetic variability, DNA markers including Randomly Amplified Polymorphic DNA (RAPD have been widely used in various crops of agronomic importance. During present study, RAPDs were used to estimate genetic relationship among 10 Pakistani wheat varieties and to identify genetically diverse genotypes which can be used in future breeding programs. RAPD primers used during present study produced an average of 1.9 alleles per primer. Size of scorable fragments ranged from 250-1000 bp. A high level of genetic dissimilarity (GD = up to 63% was estimated among the wheat varieties. Ten wheat varieties were grouped in 3 clusters using dendrogram analysis. Clusters A, B and C comprised land races, derivatives of Mexi-Pak and elite lines having alien gene, respectively.

Aisha Naz

2006-01-01

312

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

313

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

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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.

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

2014-01-01

314

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

315

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

Science.gov (United States)

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

316

Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data.  

Science.gov (United States)

The hermaphroditic nematode Pristionchus pacificus is an established model system for comparative studies with Caenorhabditis elegans in developmental biology, ecology, and population genetics. In this study, we present whole-genome sequencing data of 104 P. pacificus strains and the draft assembly of the obligate outcrossing sister species P. exspectatus. We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. P. pacificus is 10 times more diverse than C. elegans and exhibits substantial population structure that allows us to probe its evolution on multiple timescales. Consistent with reduced effective recombination in this self-fertilizing species, we find haplotype blocks that span several megabases. Using the P. exspectatus genome as an outgroup, we polarized variation in P. pacificus and found a site frequency spectrum (SFS) that decays more rapidly than expected in neutral models. The SFS at putatively neutral sites is U shaped, which is a characteristic feature of pervasive linked selection. Based on the additional findings (i) that the majority of nonsynonymous variation is eliminated over timescales on the order of the separation between clades, (ii) that diversity is reduced in gene-rich regions, and (iii) that highly differentiated clades show very similar patterns of diversity, we conclude that purifying selection on many mutations with weak effects is a major force shaping genetic diversity in P. pacificus. PMID:24443445

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

2014-04-01

317

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

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

Blaney Kate M

2008-12-01

318

Genetic Diversity Analysis of CIMMYT Bread Wheat (Triticum aestivum L. Lines by SRAP Markers  

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Full Text Available Genetic diversity is one of the key factors for the improvement of many crop plants including wheat. Many wheat scientistshave studied genetic diversity in wheat germplasm using different molecular markers which have provided a powerfulapproach to analyze genetic relationships among wheat germplasms. In this study, genetic diversity of CIMMYT(International maize and wheat improvement center bread wheat lines collected from Russia was evaluated using 30sequence-related amplified polymorphism (SRAP primer combinations. 686 DNA band was obtained from the 23 primercombinations and approximately 90% of them were found to be polymorphic. Ratio of polymorphic loci, Shannon'sdiversity index and gene diversity were found 82.61%, 0.39 and 0.26 respectively. The three main clusters were found byusing UPGMA (Unweighted Pair Group Method with Arithmetic Mean cluster analysis method and the average rate ofgenetic similarity with 0.462. Two main clusters were shown in principal component analysis (PCA which is consistentwith the result of UPGMA. It can be concluded that SRAP markers can be used for wheat genetic diversity studies and havepotential linkage mapping, molecular characterizations and marker assisted selection (MAS breeding.

Ertugrul FILIZ

2012-12-01

319

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

320

Population Structure and Genetic Diversity of Native and Invasive Populations of Solanum rostratum (Solanaceae)  

Science.gov (United States)

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

Zhao, Jiali; Solis-Montero, Lislie; Lou, Anru; Vallejo-Marin, Mario

2013-01-01

 
 
 
 
321

Genetic Diversity Among Botulinum Neurotoxin-Producing Clostridial Strains.  

Science.gov (United States)

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore-forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and death...

B. T. Foley C. H. Helma K. K. Hill L. O. Ticknor T. J. Smith

2007-01-01

322

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

323

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

324

Genetic diversity in different populations of sloths assessed by DNA fingerprinting  

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

MORAES N.

2002-01-01

325

Genetic diversity of Plantago ovata Forsk. through RAPD markers  

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Full Text Available Genetic variability of 15 sets of Plantago ovata Forsk. studied using 11 arbitrary oligonucleotide primers. Among the 90 DNAfragments produced 71 fragments were found to be polymorphic. The mean number of polymorphic bands per primer among 15Plantago ovata genotypes was 6.45 . The higher polymorphism (90.00 % was exhibited by primer OPF-17, while the lowerpolymorphism (60.00 % was detected by OPF-2. The genetic similarity matrix from RAPD data for 15 genotypes was calculatedbased on Jaccard’s coefficients of similarity ranged from 0.45 to 0.80. UPGMA cluster analysis reveals that the 15 genotypeswere clustered in to three clusters. Genetically distinct genotypes identified using RAPD markers could be potential sources ofgermplasm for Isabgol improvement.

Ashish G Vala1*, R.S.Fougat1 and G.C.Jadeja

2011-12-01

326

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

327

Enhancing genetic diversity through induced mutagenesis in vegetatively propagated plants  

International Nuclear Information System (INIS)

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

2008-08-12

328

Enhancing Genetic Diversity Through Induced Mutagenesis in Vegetatively Propagated Plants  

International Nuclear Information System (INIS)

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

2008-08-12

329

Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia.  

Science.gov (United States)

Disused tin-mining ponds make up a significant amount of water bodies in Malaysia particularly at the Kinta Valley in the state of Perak where tin-mining activities were the most extensive, and these abundantly available water sources are widely used in the field of aquaculture and agriculture. However, the natural ecology and physicochemical conditions of these ponds, many of which have been altered due to secondary post-mining activities, remains to be explored. As ammonia-oxidizing bacteria (AOB) are directly related to the nutrient cycles of aquatic environments and are useful bioindicators of environmental variations, the focus of this study was to identify AOBs associated with disused tin-mining ponds that have a history of different secondary activities in comparison to ponds which were left untouched and remained as part of the landscape. The 16S rDNA gene was used to detect AOBs in the sediment and water sampled from the three types of disused mining ponds, namely ponds without secondary activity, ponds that were used for lotus cultivation and post-aquaculture ponds. When the varying pond types were compared with the sequence and phylogenetic analysis of the AOB clone libraries, both Nitrosomonas and Nitrosospira-like AOB were detected though Nitrosospira spp. was seen to be the most ubiquitous AOB as it was present in all ponds types. However, AOBs were not detected in the sediments of idle ponds. Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture indicated the highest richness of AOBs. Canonical correspondence analysis indicated that among the physicochemical properties of the pond sites, TAN and nitrite were shown to be the main factors that influenced the community structure of AOBs in these disused tin-mining ponds. PMID:24078113

Sow, S L S; Khoo, G; Chong, L K; Smith, T J; Harrison, P L; Ong, H K A

2014-02-01

330

Genetic diversity of natural populations of Machilus thunbergii, an endangered tree species in eastern China, determined with ISSR analysis.  

Science.gov (United States)

The genetic diversity of 10 Machilus thunbergii populations in eastern China was analyzed using inter-simple sequence repeat markers. The populations showed high genetic diversity, with an overall population genetic diversity of 0.2343. Genetic diversity varied largely among populations, and populations with the highest genetic diversity were mainly from the eastern and western parts of the natural distribution area. Small populations, lack of effective gene flow, and fragmentation of habitats have led to greater genetic differentiation among populations, with 41.18% of genetic variation existing among populations. Unweighted pair-group method with arithmetic mean cluster analysis indicated that populations distributed between latitudes 25° and 31°N were clustered together and should be prioritized for in situ conservation. Northern, eastern, and southern populations were located in peripheral areas of the distribution range and were clustered separately. Collection of distinctive germplasm from peripheral populations should be promoted and ex situ conservation of elite germplasm should be implemented. PMID:23546979

Liu, J; Sun, H G; Jiang, J M; Shao, W H; Luan, Q F

2013-01-01

331

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

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

2012-01-01

332

Chytrid epidemics may increase genetic diversity of a diatom spring-bloom.  

Science.gov (United States)

Contrary to expectation, populations of clonal organisms are often genetically highly diverse. In phytoplankton, this diversity is maintained throughout periods of high population growth (that is, blooms), even though competitive exclusion among genotypes should hypothetically lead to the dominance of a few superior genotypes. Genotype-specific parasitism may be one mechanism that helps maintain such high-genotypic diversity of clonal organisms. Here, we present a comparison of population genetic similarity by estimating the beta-dispersion among genotypes of early and peak bloom populations of the diatom Asterionella formosa for three spring-blooms under high or low parasite pressure. The Asterionella population showed greater beta-dispersion at peak bloom than early bloom in the 2 years with high parasite pressure, whereas the within group dispersion did not change under low parasite pressure. Our findings support that high prevalence parasitism can promote genetic diversification of natural populations of clonal hosts. PMID:23657362

Gsell, Alena S; de Senerpont Domis, Lisette N; Verhoeven, Koen J F; van Donk, Ellen; Ibelings, Bastiaan W

2013-10-01

333

Microsatellite markers based genetic diversity and bottleneck studies in Zanskari pony.  

Science.gov (United States)

Genetic diversity in Zanskari pony breed was evaluated at 48 microsatellite loci using fifty adult, healthy and unrelated animals. Allele frequency data was used to detect genetic diversity and bottleneck. The estimated average number of alleles (±s.e.) was 8.5208±2.5010 with a total of 409 alleles. A high level of genetic diversity within this breed was observed in terms of number of alleles, observed heterozygosity (0.6763±0.1704), expected Leven's heterozygosity (0.7724±0.795), expected Nei's heterozygosity (0.7644±0.0787) and polymorphism information content (>0.5). In-breeding coefficient (F(is)) was 0.115±0.0209, suggesting moderately high in-breeding in Zanskari breed. Although analysis of bottleneck revealed no bottleneck in recent past but population of Zanskari ponies has decreased drastically and only a few thousand pure-bred animals are left. The information is useful for proposing effective population management strategies for future. PMID:22445609

Gupta, A K; Chauhan, Mamta; Bhardwaj, Anuradha; Tandon, S N

2012-05-15

334

Simplified process model discovery based on role-oriented genetic mining.  

Science.gov (United States)

Process mining is automated acquisition of process models from event logs. Although many process mining techniques have been developed, most of them are based on control flow. Meanwhile, the existing role-oriented process mining methods focus on correctness and integrity of roles while ignoring role complexity of the process model, which directly impacts understandability and quality of the model. To address these problems, we propose a genetic programming approach to mine the simplified process model. Using a new metric of process complexity in terms of roles as the fitness function, we can find simpler process models. The new role complexity metric of process models is designed from role cohesion and coupling, and applied to discover roles in process models. Moreover, the higher fitness derived from role complexity metric also provides a guideline for redesigning process models. Finally, we conduct case study and experiments to show that the proposed method is more effective for streamlining the process by comparing with related studies. PMID:24616618

Zhao, Weidong; Liu, Xi; Dai, Weihui

2014-01-01

335

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

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

C. Suwannapoom

2012-08-01

336

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

Science.gov (United States)

The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow, and largely attributable to the cross-pollination and self-incompatibility reproductive system. A STRUCTURE (model-based program) analysis revealed that the 21 populations can be divided into two main groups, mainly based on geographic differences and genetic exchanges. The entire wild Siberia apricot population in China could be divided into two subgroups, including 107 accessions in subgroup (SG) 1 and 147 accessions in SG 2. A Mantel test revealed a significant positive correlation between genetic and geographic distance matrices, and there was a very significant positive correlation among three marker datasets. Overall, we recommend a combination of conservation measures, with ex situ and in situ conservation that includes the construction of a core germplasm repository and the implement of in situ conservation for populations HR, MY, and ZY. PMID:24384840

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

2014-01-01

337

Microsatellite Markers based Genetic Diversity Analysis in Damani and Nachi Goat Breeds of Pakistan  

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Full Text Available The genetic variation in two indigenous Pakistani goat breeds (Damani and Nachi was studied with 9 microsatellite markers in order to determine the genetic diversity between them. A total number of 50 non relative individuals of Damani (25 and Nachi (25 were sampled to explore genetic polymorphisms and relationship between these two important goat breeds. Result revealed considerable level of genetic diversity in both breeds and a total number of 53 alleles were identified with mean of 3.2 in Damani and 4.6 in Nachi. The genetic diversity in both breeds ranged from 0.51(Nachi to 0.73 (Damani. High level of genetic differentiation (FST = 0.20 and low level of gene flow (Nm=0.95 found could be due to their divergent or expanded geographical locations. Heterozygote across two populations (FIT was found to be 0.15. The mean Polymorphic Information Content (PIC was 0.70 ranging from 0.54 (MAF33 to 0.83 (ILSTS011, revealed the high level of polymorphism for studied microsatellite markers set in this study. The measures of genetic variation revealed that there is good scope for effective improvement, conservation and designing national breeding policies for goat breeds in future.

Tanveer Hussain*1, Masroor Ellahi Babar2, Haleema Sadia1, Misbah Shaheen1, Asif Nadeem1, Akhtar Ali1, Abdul Wajid1 and Sajjad Ali Shah1

2013-11-01

338

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

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

Ming Li

2013-12-01

339

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)

2003-10-06

340

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

Science.gov (United States)

Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854), high allelic richness (R = 16.7-19.5), low inbreeding co-efficients (FIS = 0.013-0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency <1%). However, spatial genetic structure (SGS) analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss. PMID:24367531

Noreen, Annika M E; Webb, Edward L

2013-01-01

 
 
 
 
341

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

342

Genetic diversity in introduced golden mussel populations corresponds to vector activity.  

Science.gov (United States)

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

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

2013-01-01

343

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

CERN Multimedia

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

344

Genetic Diversity of Gallibacterium anatis Isolates from Different Chicken Flocks  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 char...

2003-01-01

345

Genetic diversity of fungi closely associated with common reed  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

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

2001-01-01

346

Genetic Code: Four Diversity Types of Protein Amino Acids  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper presents, for the first time, four diversity types of protein amino acids. The first type includes two amino acids (G, P), both without standard hydrocarbon side chains; the second one four amino acids, as two pairs [(A, L), (V, I)], all with standard hydrocarbon side chains; the third type comprises the six amino acids, as three pairs [(F, Y), (H, W), (C, M)], two aromatic, two hetero aromatic and two "hetero" non-aromatic); finally, the fourth type consists of e...

Rakocevic, Miloje M.

2011-01-01

347

Genetic Diversity and Abundance of Flavobacterial Proteorhodopsin in China Seas? †  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Proteorhodopsin (PR) genes related to Flavobacteria were found to be highly diverse in the East and South China seas and displayed a distinct geographic pattern, which appeared to reflect cold versus warm adaptation when Global Oceanic Sampling database metagenomic data were included. Flavobacterial PR genes were more abundant offshore than nearshore, implying that inheritance of the PR gene could be important for Flavobacteria living in the oligotrophic environment.

Zhao, Meiru; Chen, Feng; Jiao, Nianzhi

2009-01-01

348

Genetic diversity of Plasmodium falciparum infections : Influence on protective malaria immunity  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Detailed knowledge of the interaction between the human host and the antigenic and genetic diversity of Plasmodium falciparum infections is a prerequisite for understanding the mechanisms underlying acquisition of immunity to malaria. This thesis assessed the diversity of P. falciparum by genotyping the highly polymorphic vaccine candidate antigen merozoite surface protein 2 (msp2 ) gene in different transmission areas. Factors influencing the number of genotypes and the rel...

Bereczky, Sa?ndor

2005-01-01

349

Study of the genetic diversity of almond seedling populations in Morocco: application of chemometric approach  

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Almond (Prunus amygdalus Batsch) in Morocco is still propagated by farmers mostly from seed, generating a large genetic diversity. Evaluation of the almond diversity in Morocco from the point of view of kernel quality, oil and protein contents, and major fatty acid composition were determined. Principal component analysis (PCA) was used to compare the kernel components among 46 genotypes selected from different production regions, as well as five introduced cultivars. Oil and protein contents...

Kodad, Ossama; Socias I Company, Rafel; Estopan?a?n Mun?oz, Gloria; Juan Esteban, Teresa; Oukabli, A.; Mamouni, A.

2011-01-01

350

Genetic diversity and ecosystem functioning in the face of multiple stressors  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Species diversity is important for a range of ecosystem processes and properties, including the resistance to single and multiple stressors. It has been suggested that genetic diversity may play a similar role, but empirical evidence is still relatively scarce. Here, we report the results of a microcosm experiment where four strains of the marine diatom Skeletonema marinoi were grown in monoculture and in mixture under a factorial combination of temperature and salinity stress. The strains di...

Roger, Fabian; Godhe, Anna; Gamfeldt, Lars

2012-01-01

351

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

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

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

2009-01-01

352

Within-Host Genetic Diversity of Endemic and Emerging Parvoviruses of Dogs and Cats ?  

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Viral emergence can result from the adaptation of endemic pathogens to new or altered host environments, a process that is strongly influenced by the underlying sequence diversity. To determine the extent and structure of intrahost genetic diversity in a recently emerged single-stranded DNA virus, we analyzed viral population structures during natural infections of animals with canine parvovirus (CPV) or its ancestor, feline panleukopenia virus (FPV). We compared infections that occurred shor...

Hoelzer, Karin; Shackelton, Laura A.; Holmes, Edward C.; Parrish, Colin R.

2008-01-01

353

Organelle Genetic Diversity and Phylogeography of Scots Pine (Pinus sylvestris L.)  

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The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles’ diversity represents an important criterion which could be later applied in planning for future forest management...

Floran, Valentina; Sestras, Radu E.; Garci?a Gil, Mari?a Rosario

2011-01-01

354

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

355

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

356

Genetic Diversity in Colletotrichum gloeosporioides from Stylosanthes spp. at Centers of Origin and Utilization.  

Science.gov (United States)

ABSTRACT Using molecular markers, this work compares the genetic diversity in Colletotrichum gloeosporioides infecting species of the tropical forage legume Stylosanthes at the center of origin in Brazil and Colombia with that of Australia, China, and India, where Stylosanthes spp. have been introduced for commercial use. There was extensive diversity in the pathogen population from Brazil, Colombia, China, and India. The Australian pathogen population was least diverse probably due to its geographical isolation and effective quarantine. The extensive diversity in China and India means that threats from exotic pathogen races to Stylosanthes pastures can potentially come from countries outside the South American center of origin. In Brazil and India, both with native Stylosanthes populations, a high level of genetic differentiation in the pathogen population was associated with sites where native or naturalized host population was widely distributed. There was limited genetic diversity at germplasm evaluation sites, with a large proportion of isolates having identical haplotypes. This contrasts recent pathogenicity results for 78 of the Brazilian isolates that show hot spots of complex races are more common around research stations where host germplasm are tested, but few are found at sites containing wild host populations. For a pathogen in which the same races arise convergently from different genetic backgrounds, this study highlights the importance of using both virulence and selectively neutral markers to understand pathogen population structure. PMID:18943132

Weeds, P L; Chakraborty, S; Fernandes, C D; d'A Charchar, M J; Ramesh, C R; Kexian, Y; Kelemu, S

2003-02-01

357

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

Directory of Open Access Journals (Sweden)

Full Text Available The genetic diversity among seven Xanthomonas isolates representing four species was assessed using RAPD and ISSR PCR-based techniques. Both techniques revealed high degrees of polymorphisms among the studied isolates. A cluster dendrogram based on the combined data of RAPD and ISSR showed that genetic diversity exists in local isolates of Xanthomonas. In terms of percentage similarity values, the genomic variation was found to be in the range of 29.29% - 100% among the isolates. X. campestris (Mangifera indica remained unclustered in cluster dendrogram and revealed a unique genomic profile compared to other isolates used in this study.

Fatima Sabin

2012-01-01

358

Genetic Diversity in a Bacillus anthracis Historical Collection (1954 to 1988)?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Bacillus anthracis, the etiologic agent of anthrax, has been widely described as a genetically monomorphic species. We used both multiple-locus variable-number tandem-repeat analysis (MLVA) and pagA gene sequencing to determine the genetic diversity of a historical collection of B. anthracis isolates collected from the 1950s to the 1980s from various geographic locations and sources. We sequenced the pagA gene of 124 diverse B. anthracis isolates and found all previously identified B. anthrac...

Sue, David; Marston, Chung K.; Hoffmaster, Alex R.; Wilkins, Patricia P.

2007-01-01

359

Characterization of sorghum genotypes for yield and other agronomic traits through genetic variability and diversity analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Studies on the genetic variability and diversity analysis were carried out with 39 sorghum genotypes for nine quantitativecharacters. The Shannon-Weaver diversity index (H'), a measure of dissimilarity was found to be highest for number ofleaves per plant, plant height and leaf width and these characters had high heritability coupled with high genetic advance.Of the 36 correlations, 24 were significant at P=0.05 and 21 were significant at 0.01 and 14 were found to be of usefulcorrelations (r>...

2013-01-01

360

Invertebrates or iron: does large-scale opencast mining impact invertebrate diversity in ephemeral wetlands?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Disturbance has been offered as explanatory mechanism in structuring the variation of species across a landscape. In this study, we investigated the effect of the impact by Kolomela Iron Mine on the variation of species occurring in temporary pans. Using a novel null model approach to partitioning two sets of data (from before and after the establishment of the mine) into independent alpha (?) and beta (?) components, we determined that the mining practices have had lit...

Falko Theo Buschke

2013-01-01

 
 
 
 
361

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

362

Genetic diversity in the oral pathogen Porphyromonas gingivalis: molecular mechanisms and biological consequences.  

Science.gov (United States)

Porphyromonas gingivalis is a Gram-negative anaerobic bacterium that colonizes the human oral cavity. It is implicated in the development of periodontitis, a chronic periodontal disease affecting half of the adult population in the USA. To survive in the oral cavity, these bacteria must colonize dental plaque biofilms in competition with other bacterial species. Long-term survival requires P. gingivalis to evade host immune responses, while simultaneously adapting to the changing physiology of the host and to alterations in the plaque biofilm. In reflection of this highly variable niche, P. gingivalis is a genetically diverse species and in this review the authors summarize genetic diversity as it relates to pathogenicity in P. gingivalis. Recent studies revealing a variety of mechanisms by which adaptive changes in genetic content can occur are also reviewed. Understanding the genetic plasticity of P. gingivalis will provide a better framework for understanding the host-microbe interactions associated with periodontal disease. PMID:23642116

Tribble, Gena D; Kerr, Jennifer E; Wang, Bing-Yan

2013-05-01

363

Genetic Diversity among Ocimum Populations in Egypt as Reflected by Morphological, Seed Proteins and Isozyme Polymorphism  

Directory of Open Access Journals (Sweden)

Full Text Available Seven populations of two species of Ocimum were analyzed using data from morphological and biochemical (seed proteins and isozymes characters to measure genetic variation within and between populations and species of Ocimum in Egypt. Ten isozyme systems revealed 23 loci and a total of 49 alleles in the studied Ocimum populations. The constructed trees based on variation in morphological, seed proteins or isozyme data clearly demonstrated the existence of genetic diversity among and within populations of Ocimum that might be related to natural hybridization and fluctuations in environmental conditions. Seed proteins and isozyme polymorphism exhibited validity for studying genetic diversity and taxonomic relationships in Ocimum at both species and infra-specific levels. Moreover, Ocimum kilimandscharicum exhibited higher levels of genetic variation and also higher number of unique alleles than Ocimum basilicum.

Abd El-Zaher M.A. Mustafa

2006-01-01

364

Gene Flow and Maintenance of Genetic Diversity in Invasive Mosquitofish (Gambusia holbrooki)  

Science.gov (United States)

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

Diez-del-Molino, David; Carmona-Catot, Gerard; Araguas, Rosa-Maria; Vidal, Oriol; Sanz, Nuria; Garcia-Berthou, Emili; Garcia-Marin, Jose-Luis

2013-01-01

365

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

Science.gov (United States)

Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki) that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations. PMID:24358194

Díez-del-Molino, David; Carmona-Catot, Gerard; Araguas, Rosa-Maria; Vidal, Oriol; Sanz, Nuria; García-Berthou, Emili; García-Marín, Jose-Luis

2013-01-01

366

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

367

Microsatellite analysis of the genetic diversity in the Black Slavonian pig  

Directory of Open Access Journals (Sweden)

Full Text Available This research is focused on the genetic diversity and population structure of the Black Slavonian pig, with the aim of assessing the situation regarding the endangerment of genetic diversity, and defining the further role of this breed in the preseration of its genetic diversity. Genetic population parameters were assessed in 42 animals at 8 microsatellite loci. On three of the observed loci there was a deviation from the Hardy-Weinberg (HW equilibrium with P<0.01, one locus showed P<0.05, and in all of them the stated deviation resulted from a deficiency of heterozygous animals. The entire population's deviation from the HW equilibrium, with _ 2=92.8, Df=16, and P<0.0001 was also significant. Average PIC value for all 8 loci was 0.368. The average number of detected allelic variants was 2.50, with a standard deviation of 0.76 alleles. Such a small number of detected allelic variants, as well as the significant deviation from the HW equilibrium in four loci caused by a deficiency of heterozygotes, can be taken as one of the indicators of the reduced genetic diversity of the breed.

Bradi? Martina

2007-01-01

368

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

Directory of Open Access Journals (Sweden)

Full Text Available A better knowledge of factors organizing crop genetic diversity in situ increases the efficiency of diversity analyses and conservation strategies, and requires collaboration between social and biological disciplines. Four areas of anthropology may contribute to our understanding of the impact of social factors on crop diversity: ethnobotany, cultural, cognitive and social anthropology. So far, most collaborative studies have been based on ethnobotanical methods, focusing on farmers’ individual motivations and actions, and overlooking the effects of farmer’s social organization per se. After reviewing common shortcomings in studies on sorghum and maize, this article analyzes how social anthropology, through the analysis of intermarriage, residence and seed inheritance practices, can contribute to studies on crop genetic diversity in situ. Crop varieties are thus considered social objects and socially based sampling strategies can be developed. Such an approach is justified because seed exchange is built upon trust and as such seed systems are embedded in a pre-existing social structure and centripetally oriented as a function of farmers’ social identity. The strong analogy between farmers’ cultural differentiation and crop genetic differentiation, both submitted to the same vertical transmission processes, allows proposing a common methodological framework for social anthropology and crop population genetics, where the classical interaction between genetic and environmental factors, G × E, is replaced by a three-way interaction G × E × S, where “S” stands for the social differentiation factors.

Geo Coppens d’Eeckenbrugge

2011-12-01

369

Bovine coronaviruses from the respiratory tract: antigenic and genetic diversity.  

Science.gov (United States)

BoCV isolated from respiratory tract, nasal swab and broncho alveolar washing fluid samples were evaluated for genetic and antigenic differences. These BoCV from the respiratory tract of healthy and clinically ill cattle with BRD signs were compared to reference and vaccine strains based on Spike protein coding sequences and VNT using convalescent antisera. Based on this study, the BoCV isolates belong to one of two genomic clades (clade 1 and 2) which can be differentiated antigenically. The respiratory isolates from Oklahoma in this study were further divided by genetic differences into three subclades, 2a, 2b, and 2c. Reference enteric BoCV strains and a vaccine strain were in clade 1. Currently available vaccines designed to control enteric disease are based on viruses from one clade while viruses isolated from respiratory tracts, in this study, belong to the other clade. PMID:23246548

Fulton, R W; Ridpath, J F; Burge, L J

2013-01-30

370

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

Science.gov (United States)

The Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics portrays the human genome as a product of nature. This frames medical genetics as an extractive industry that mines a natural resource to produce valuable goods and services. Natural resource law offers insights into problems medical geneticists can expect after this decision and suggests possible solutions. Increased competition among clinical laboratories offers various benefits but threatens to increase fragmentation of genetic data resources, potentially causing waste in the form of lost opportunities to discover the clinical significance of particular gene variants. The solution lies in addressing legal barriers to appropriate data sharing. Sustainable discovery in the field of medical genetics can best be achieved through voluntary data sharing rather than command-and-control tactics, but voluntary mechanisms must be conceived broadly to include market-based approaches as well as donative and publicly funded data commons. The recently revised Health Insurance Portability and Accountability Act Privacy Rule offers an improved-but still imperfect-framework for market-oriented data sharing. This article explores strategies for addressing the Privacy Rule's remaining defects. America is close to having a legal framework that can reward innovators, protect privacy, and promote needed data sharing to advance medical genetics.Genet Med 16 7, 504-509. PMID:24357850

Evans, Barbara J

2014-07-01

371

Bringing genetic diversity to the forefront of conservation policy and management  

DEFF Research Database (Denmark)

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

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

2013-01-01

372

Morphoagronomic genetic diversity in american wild rice species  

Digital Repository Infrastructure Vision for European Research (DRIVER)

To characterize the genetic variability among species and populations of South American wild rice, eleven populations of Oryza glumaepatula, seven of O. grandiglumis, four of O. latifolia and one of O. alta, from Brazil and Argentina, were evaluated. A greenhouse experiment was conducted in completely randomized blocks with 23 treatments. Twenty morphoagronomic traits were assessed. Univariate analyses were performed with 16 quantitative traits with the partitioning of populations within spec...

Elizabeth Ann Veasey; Edson Ferreira da Silva; Eliana Aparecida Schammass; Giancarlo Conde Xavier Oliveira; Akihiko Ando

2008-01-01