WorldWideScience

Sample records for genetic diversity mining

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

    Sajduda Anna

    2006-03-01

    Full Text Available Abstract Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1 Unique Events Polymorphism (UEP (2 Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown

  2. Genetic diversity in populations

    Martínková, Natália; Zemanová, Barbora

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

  3. Genetic diversity in Entamoeba histolytica

    C Graham Clark; Mehreen Zaki; Ibne Karim Md Ali

    2002-11-01

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

  4. Human Capital and Genetic Diversity

    Sequeira, Tiago; Santos, Marcelo,; Ferreira-Lopes, Alexandra

    2013-01-01

    The determinants of human capital have been studied sparsely in the literature. Although there is a huge literature on the determinants of schooling linked with the quality of schooling, there are not many contributions that explore the deep determinants of investment in, quantity and quality of human capital. This paper investigates the relationship between human capital and the ancestral genetic diversity of populations. It highlights a strong hump-shaped relationship between genetic divers...

  5. Genetic diversity in Trichomonas vaginalis.

    Meade, John C; Carlton, Jane M

    2013-09-01

    Recent advances in genetic characterisation of Trichomonas vaginalis isolates show that the extensive clinical variability in trichomoniasis and its disease sequelae are matched by significant genetic diversity in the organism itself, suggesting a connection between the genetic identity of isolates and their clinical manifestations. Indeed, a high degree of genetic heterogeneity in T vaginalis isolates has been observed using multiple genotyping techniques. A unique two-type population structure that is both local and global in distribution has been identified, and there is evidence of recombination within each group, although sexual recombination between the groups appears to be constrained. There is conflicting evidence in these studies for correlations between T vaginalis genetic identity and clinical presentation, metronidazole susceptibility, and the presence of T vaginalis virus, underscoring the need for adoption of a common standard for genotyping the parasite. Moving forward, microsatellite genotyping and multilocus sequence typing are the most robust techniques for future investigations of T vaginalis genotype-phenotype associations. PMID:23702460

  6. Genetic selection and conservation of genetic diversity*.

    Blackburn, H D

    2012-08-01

    For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development. PMID:22827378

  7. Allele mining and enhanced genetic recombination for rice breeding.

    Leung, Hei; Raghavan, Chitra; Zhou, Bo; Oliva, Ricardo; Choi, Il Ryong; Lacorte, Vanica; Jubay, Mona Liza; Cruz, Casiana Vera; Gregorio, Glenn; Singh, Rakesh Kumar; Ulat, Victor Jun; Borja, Frances Nikki; Mauleon, Ramil; Alexandrov, Nickolai N; McNally, Kenneth L; Sackville Hamilton, Ruaraidh

    2015-12-01

    Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources. PMID:26606925

  8. Do species conservation assessments capture genetic diversity?

    Malin C. Rivers

    2014-12-01

    Our results support the view that current threat thresholds of the IUCN Red List criteria reflect genetic diversity, and hence evolutionary potential; although the genetic diversity distinction between threatened categories was less evident. Thus, by supplementing conventional conservation assessments with genetic data, new insights into the biological robustness of IUCN Red List assessments for targeted conservation initiatives can be achieved.

  9. Genetic Diversity and Societally Important Disparities.

    Rosenberg, Noah A; Kang, Jonathan T L

    2015-09-01

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

  10. Personalized medicine and human genetic diversity.

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

    2014-09-01

    Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more modern studies including genome-wide association studies (GWAS) and next-generation sequencing. We introduce several examples, such as sickle cell anemia and Tay-Sachs disease that are caused by rare mutations and are more frequent in certain geographical populations, and common treatment responses that are caused by common variants, such as hepatitis C infection. We conclude with comments about the continued relevance of human genetic diversity in medical genetics and personalized medicine more generally. PMID:25059740

  11. Mining Frequent Itemsets Using Genetic Algorithm

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

    2010-01-01

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

  12. Performance Analysis of Genetic Algorithm for Mining Association Rules

    Indira, K.; Kanmani, S.

    2012-01-01

    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. Ge...

  13. Genetic diversity and structure of livestock breeds

    Wilkinson, Samantha

    2012-01-01

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

  14. How does ecological disturbance influence genetic diversity?

    Banks, Sam C; Cary, Geoffrey J; Smith, Annabel L; Davies, Ian D; Driscoll, Don A; Gill, A Malcolm; Lindenmayer, David B; Peakall, Rod

    2013-11-01

    Environmental disturbance underpins the dynamics and diversity of many of the ecosystems of the world, yet its influence on the patterns and distribution of genetic diversity is poorly appreciated. We argue here that disturbance history may be the major driver that shapes patterns of genetic diversity in many natural populations. We outline how disturbance influences genetic diversity through changes in both selective processes and demographically driven, selectively neutral processes. Our review highlights the opportunities and challenges presented by genetic approaches, such as landscape genomics, for better understanding and predicting the demographic and evolutionary responses of natural populations to disturbance. Developing this understanding is now critical because disturbance regimes are changing rapidly in a human-modified world. PMID:24054910

  15. Bacterial diversity in soils around a lead and zinc mine

    HU Qing; QI Hong-yan; ZENG Jing-hai; ZHANG Hong-xun

    2007-01-01

    Five samples of soil collected from a lead and zinc mine were used to assess the effect of combined contamination of heavy metals on soil bacterial communities using a polyphasic approach including characterization of isolates by culture method, community level catabolic profiling in BIOLOG GN microplates, and genetic community fingerprinting by denaturing gradient gel electrophoresis of 16S rDNA fragments amplified by PCR from community DNA (PCR-DGGE). The structure of the bacterial community was affected to a certain extent by heavy metals. The PCR-DGGE analysis of 16S rRNA genes showed that there were significant differences in the structure of the microbial community among the soil samples, which were related to the contamination levels. The number of bacteria and the number of denaturing gradient gel electrophoresis (DGGE) bands in the soils increased with increasing distance from the lead and zinc mine tailing, whereas the concentration of lead (Pb) and cadmium (Cd) was decreased. Heavily polluted soils could be characterized by a community that differs from those of lightly polluted soils in richness and structure of dominating bacterial populations. The clustering analysis of the DGGE profiles showed that the bacteria in all the five samples of soil belonged to three clusters. The data from the BIOLOG analysis also showed the same result. This study showed that heavy metal contamination decreased both the biomass and diversity of the bacterial community in soil.

  16. Fungal diversity in major oil-shale mines in China.

    Jiang, Shaoyan; Wang, Wenxing; Xue, Xiangxin; Cao, Chengyou; Zhang, Ying

    2016-03-01

    As an insufficiently utilized energy resource, oil shale is conducive to the formation of characteristic microbial communities due to its special geological origins. However, little is known about fungal diversity in oil shale. Polymerase chain reaction cloning was used to construct the fungal ribosomal deoxyribonucleic acid internal transcribed spacer (rDNA ITS) clone libraries of Huadian Mine in Jilin Province, Maoming Mine in Guangdong Province, and Fushun Mine in Liaoning Province. Pure culture and molecular identification were applied for the isolation of cultivable fungi in fresh oil shale of each mine. Results of clone libraries indicated that each mine had over 50% Ascomycota (58.4%-98.9%) and 1.1%-13.5% unidentified fungi. Fushun Mine and Huadian Mine had 5.9% and 28.1% Basidiomycota, respectively. Huadian Mine showed the highest fungal diversity, followed by Fushun Mine and Maoming Mine. Jaccard indexes showed that the similarities between any two of three fungal communities at the genus level were very low, indicating that fungi in each mine developed independently during the long geological adaptation and formed a community composition fitting the environment. In the fresh oil-shale samples of the three mines, cultivable fungal phyla were consistent with the results of clone libraries. Fifteen genera and several unidentified fungi were identified as Ascomycota and Basidiomycota using pure culture. Penicillium was the only genus found in all three mines. These findings contributed to gaining a clear understanding of current fungal resources in major oil-shale mines in China and provided useful information for relevant studies on isolation of indigenous fungi carrying functional genes from oil shale. PMID:26969053

  17. Implications of recurrent disturbance for genetic diversity.

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

    2016-02-01

    Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes. PMID:26839689

  18. Structural and genetic diversity in antibody repertoires from diverse species.

    de los Rios, Miguel; Criscitiello, Michael F; Smider, Vaughn V

    2015-08-01

    The antibody repertoire is the fundamental unit that enables development of antigen specific adaptive immune responses against pathogens. Different species have developed diverse genetic and structural strategies to create their respective antibody repertoires. Here we review the shark, chicken, camel, and cow repertoires as unique examples of structural and genetic diversity. Given the enormous importance of antibodies in medicine and biological research, the novel properties of these antibody repertoires may enable discovery or engineering of antibodies from these non-human species against difficult or important epitopes. PMID:26188469

  19. Nephronophthisis: A Genetically Diverse Ciliopathy

    Roslyn J. Simms

    2011-01-01

    Full Text Available Nephronophthisis (NPHP is an autosomal recessive cystic kidney disease and a leading genetic cause of established renal failure (ERF in children and young adults. Early presenting symptoms in children with NPHP include polyuria, nocturia, or secondary enuresis, pointing to a urinary concentrating defect. Renal ultrasound typically shows normal kidney size with increased echogenicity and corticomedullary cysts. Importantly, NPHP is associated with extra renal manifestations in 10–15% of patients. The most frequent extrarenal association is retinal degeneration, leading to blindness. Increasingly, molecular genetic testing is being utilised to diagnose NPHP and avoid the need for a renal biopsy. In this paper, we discuss the latest understanding in the molecular and cellular pathogenesis of NPHP. We suggest an appropriate clinical management plan and screening programme for individuals with NPHP and their families.

  20. Genetic erosion of diversity in cereals

    Petrović Sofija; Dimitrijević Miodrag

    2012-01-01

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

  1. Genetic Diversity of Neisseria gonorrhoeae Housekeeping Genes

    Viscidi, Raphael P.; Demma, James C.

    2003-01-01

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

  2. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques.

    Onda, Yoshihiko; Mochida, Keiichi

    2016-08-01

    Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study. PMID:27499684

  3. Mining Online Store Client Assessment Classification Rules with Genetic Algorithms

    Galinina, A; Paršutins, S

    2011-01-01

    The paper presents the results of the research into algorithms that are not meant to mine classification rules, yet they contain all the necessary functions which allow us to use them for mining classification rules such as Genetic algorithm (GA). The main task of the research is associated with the application of GA to classification rule mining. A classic GA was modified to match the chosen classification task and was compared with other popular classification algorithms – JRip, J48 and Nai...

  4. Genetic Programming Approach for Predicting Surface Subsidence Induced by Mining

    2006-01-01

    The surface subsidence induced by mining is a complex problem, which is related with many complex and uncertain factors.Genetic programming (GP) has a good ability to deal with complex and nonlinear problems, therefore genetic programming approach is proposed to predict mining induced surface subsidence in this article.First genetic programming technique is introduced, second, surface subsidence genetic programming model is set up by selecting its main affective factors and training relating to practical engineering data, and finally, predictions are made by the testing of data, whose results show that the relative error is approximately less than 10%, which can meet the engineering needs, and therefore, this proposed approach is valid and applicable in predicting mining induced surface subsidence.The model offers a novel method to predict surface subsidence in mining.

  5. Managing genetic diversity and society needs

    Arthur da Silva Mariante

    2008-07-01

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

  6. A Survey of Association Rule Mining Using Genetic Algorithm

    Anubha Sharma

    2012-08-01

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

  7. Genetic Diversity of Koala Retroviral Envelopes

    Wenqin Xu

    2015-03-01

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

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

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

    2009-01-01

    Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using ...

  9. Genetic diversity between human metapneumovirus subgroups

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

  10. Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World's Agro-ecological Zones.

    Khazaei, Hamid; Caron, Carolyn T; Fedoruk, Michael; Diapari, Marwan; Vandenberg, Albert; Coyne, Clarice J; McGee, Rebecca; Bett, Kirstin E

    2016-01-01

    Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countries to estimate genetic diversity and genetic structure using 1194 polymorphic single nucleotide polymorphism (SNP) markers which span the lentil genome. Using principal coordinate analysis, population structure analysis and UPGMA cluster analysis, the accessions were categorized into three major groups that prominently reflected geographical origin (world's agro-ecological zones). The three clusters complemented the origins, pedigrees, and breeding histories of the germplasm. The three groups were (a) South Asia (sub-tropical savannah), (b) Mediterranean, and (c) northern temperate. Based on the results from this study, it is also clear that breeding programs still have considerable genetic diversity to mine within the cultivated lentil, as surveyed South Asian and Canadian germplasm revealed narrow genetic diversity. PMID:27507980

  11. Conservation of Genetic Diversity in Culture Plants

    MAXIM A.

    2010-08-01

    Full Text Available The most important international document relating to the conservation of biodiversity is one adopted by theUN in Rio de Janeiro (1992 that "Convention on Biodiversity". Based on this agreement, the EU has taken a series ofmeasures to reduce genetic erosion in agriculture, which grew with the expansion of industrialized agriculture.Throughout its existence, mankind has used some 10,000 growing plant species. According to FAO statistics, today,90% of food production is ensured by some 120 growing plant species. In addition to drastic reduction in specificdiversity, the advent of industrialized agriculture has generated a process of strong genetic erosion. Old varieties andlocal varieties of crops have mostly been affected, in favour of "modern" varieties. Landraces are characterized by highheterogenity. They have the advantage of being much better adapted to biotic and abiotic stress conditions (diseases,pests, drought, low in nutrients, etc. and have excellent taste qualities, which can justify a higher price recovery thancommercial varieties. Thanks to these features, these crops need small inputs, which correspond to the concept ofsustainable development. Landraces are an invaluable genetic potential for obtaining new varieties of plants and are bestsuited for crop cultivation in ecological systems, becoming more common. Also, for long term food security in thecontext of global warming, rich genetic diversity will be require. “In situ” and “ex situ” conservation are the two majorstrategies used in the conservation of plant genetic resources. There is a fundamental difference between these twostrategies: “ex situ” conservation involves sampling, transfer and storage of a particular species population away fromthe original location, while “in situ” conservation (in their natural habitat implies that the varieties of interest,management and monitoring their place of origin takes place in the community to which they belong. These

  12. Molecular diversity and genetic relationships in Secale

    E. SANTOS; M. MATOS; P. SILVA; A. M. FIGUEIRAS; C. BENITO; O. PINTO-CARNIDE

    2016-06-01

    The objective of this study was to quantify the molecular diversity and to determine the genetic relationships amongSecalespp. and among cultivars ofSecale cerealeusing RAPDs, ISSRs and sequence analysis of six exons ofScMATE1gene.Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR primers. A total of 435 markers (242 RAPDsand 193 ISSRs) were obtained, with 293 being polymorphic (146 RAPDs and 147 ISSRs). Two RAPD and nine ISSR primersgenerated more than 80% of polymorphism. The ISSR markers were more polymorphic and informative than RAPDs. Further,69% of the ISSR primers selected achieved at least 70% of DNA polymorphism. The study of six exons of theScMATE1gene also demonstrated a high genetic variability that subsists inSecalegenus. One difference observed in exon 1 sequencesfromS. vaviloviiseems to be correlated with Al sensitivity in this species. The genetic relationships obtained using RAPDs,ISSRs and exons ofScMATE1gene were similar.S. ancestrale ,S. kuprijanoviiandS. cerealewere grouped in the same clusterandS. segetalewas in another cluster.S. vaviloviishowed evidences of not being clearly an isolate species and having greatintraspecific difference

  13. A genetic programming based business process mining approach

    Turner, Christopher James

    2009-01-01

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

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

    Parvez Rahi

    2014-04-01

    Full Text Available In the advance age of technology, there is an increasing availability of digital documents in various languages in various fields. Data mining is gaining popularity in field of knowledge discovery. Data mining is the knowledge discovery process by which we can analyze the large amounts of data from various data repositories and summarizing it into information useful to us. Due to its importance of extracting information/ knowledge from the large data repositories, data mining has become an essential part of human life in various fields. Data mining has a very wide area of applications, and these applications have enriched the human life in various fields including scientific, medical, business, education etc. Here in this paper we will discuss the emphasis of Neural Network and Genetic Algorithm in the field of data mining.

  15. Comparative assessment of genetic diversity in cytoplasmic and nuclear genome of upland cotton.

    Egamberdiev, Sharof S; Saha, Sukumar; Salakhutdinov, Ilkhom; Jenkins, Johnie N; Deng, Dewayne; Y Abdurakhmonov, Ibrokhim

    2016-06-01

    The importance of the cytoplasmic genome for many economically important traits is well documented in several crop species, including cotton. There is no report on application of cotton chloroplast specific SSR markers as a diagnostic tool to study genetic diversity among improved Upland cotton lines. The complete plastome sequence information in GenBank provided us an opportunity to report on 17 chloroplast specific SSR markers using a cost-effective data mining strategy. Here we report the comparative analysis of genetic diversity among a set of 42 improved Upland cotton lines using SSR markers specific to chloroplast and nuclear genome, respectively. Our results revealed that low to moderate level of genetic diversity existed in both nuclear and cytoplasm genome among this set of cotton lines. However, the specific estimation suggested that genetic diversity is lower in cytoplasmic genome compared to the nuclear genome among this set of Upland cotton lines. In summary, this research is important from several perspectives. We detected a set of cytoplasm genome specific SSR primer pairs by using a cost-effective data mining strategy. We reported for the first time the genetic diversity in the cytoplasmic genome within a set of improved Upland cotton accessions. Results revealed that the genetic diversity in cytoplasmic genome is narrow, compared to the nuclear genome within this set of Upland cotton accessions. Our results suggested that most of these polymorphic chloroplast SSRs would be a valuable complementary tool in addition to the nuclear SSR in the study of evolution, gene flow and genetic diversity in Upland cotton. PMID:27155886

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

    Ana Daniela Lopes; Carlos Alberto Scapim; Maria de Fátima Pires da Silva Machado; Claudete Aparecida Mangolin; Tereza Aparecida Silva; Liriana Belizário Cantagali; Flávia França Teixeira; Freddy Mora

    2015-01-01

    Information on genetic diversity is essential to the characterization and utilization of germplasm. The genetic diversity of twenty-two sweet corn cultivars (seventeen open-pollinated varieties, OPV, and five hybrids, H) was investigated by applying simple sequence repeat markers. A total of 257 primers were tested, of which 160 were found to be usable in terms of high reproducibility for all the samples tested; 45 were polymorphic loci, of which 30 were used to assess the genetic diversity o...

  17. Genetic diversity increases insect herbivory on oak saplings.

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

    2012-01-01

    A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Quercus robur) half-sib families. We quantified genetic diversity at the plot level by genotyping all oak saplings and assessed overall damage caused by ectophagous and endophagous herbivores along a gradient of increasing genetic diversity. Damage due to ectophagous herbivores increased with the genetic diversity in oak sapling populations as a result of higher levels of damage in mixtures than in monocultures for all families (complementarity effect) rather than because of the presence of more susceptible oak genotypes in mixtures (selection effect). Assemblages of different oak genotypes would benefit polyphagous herbivores via improved host patch location, spill over among neighbouring saplings and diet mixing. By contrast, genetic diversity was a poor predictor of the abundance of endophagous herbivores, which increased with individual sapling apparency. Plant genetic diversity may not provide sufficient functional contrast to prevent tree sapling colonization by specialist herbivores while enhancing the foraging of generalist herbivores. Long term studies are nevertheless required to test whether the effect of genetic diversity on herbivory change with the ontogeny of trees and local adaptation of specialist herbivores. PMID:22937168

  18. Genetic diversity in the Yangtze finless porpoise by RAPD analysis

    He Shunping; Wang Ding; Wang Wei; Chen Daoquan; Zhao Qingzhong; Gong Weiming

    2005-01-01

    To estimate the genetic diversity in the Yangtze finless porpoise (Neophocaenaphocaenoides asiaeorientalis), the randomly amplified polymorphic DNA techniquewas applied to examine ten animals captured from the Yangtze River. Out of 20 arbitrary primers used in the experiment, seventeen produced clearly reproducible bged from 0.0986 to 0.5634. Compared with other cetacean populations, this genetic distance is quite low. Such a low genetic diversity suggests that this population may be suffering from reduced genetic variation, and be very fragile. More studiesare needed for understanding the basis for this apparent low genetic diversity and to help protect this endangered, unique population.

  19. Population genetic diversity and fitness in multiple environments

    McGreevy Thomas J

    2010-07-01

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

  20. Genetic Diversity of RAPD Mark for Natural Davidia involucrata Populations

    Congwen Song; Manzhu Bao

    2006-01-01

    The genetic diversity and genetic variation within and among populations of five natural Davidia involucrata populations were studied from 13 primers based on random amplified polymorphic DNA (RAPD) analysis.The results show that natural D.involucrata population has a rich genetic diversity,and the differences among populations are significant.Twenty-six percent of genetic variation exists among D.involucrata populations,which is similar to that of the endangered tree species Liriodendron chinense and Cathaya argyrophylla in China,but different from more widely distributed tree species.The analysis of the impacts of sampling method on genetic diversity parameters shows that the number of sampled individuals has little effect on the effective number of alleles and genetic diversity,but has a marked effect on the genetic differentiation among populations and gene flows.This study divides the provenances of D.involucrata into two parts,namely,a southeast and a northwest provenance.

  1. Impact of mining on tree diversity of the silica mining forest area at Shankargarh, Allahabad, India

    Kumud Dubey; K.P.Dubey

    2011-01-01

    The Shankargarh forest area is rich in silica,a major mineral used in glass industry.Extensive open cast silica mining has severely damaged the forest as well as productivity of the region.An understanding of the impact of mining on the environment partienlarly on vegetation characteristics is a prerequisite for further management of these mining sites,especially in the selection of species for reclamation works.The present paper deals with the study of the tree composition of silica mining area of Shgankargarh forest,at both disturbed and undisturbed sites.Tree vegetation study was conducted at undisturbed and disturbed sites of Shankargarh forests using standard quadrate method.Density,abundance and frequency values of tree species were calculated.Species were categorized into different classes according to their frequency.The importance value index (IVI) for each species was determined.Species diversity,Concentration of dominance,Species richness and Evenness index were calculated for the undisturbed and disturbed sites.The distribution pattern of the species was studied by using Whifford's index.Similarity index between tree composition of disturbed and undisturbed sites was determined by using Jaccard's and Sorenson's index of similarity.Tree species showed a drastic reduction in their numbers in disturbed sites compared to that of the undisturbed sites.The phytosociological indices also illustrated the impact of mining on the tree composition of the area.The present study led to the conclusion that resultant tree vegetation analysis can be used as important tool for predicting the suitability of particular species for revegetating the mined areas.

  2. Genetic diversity of human RNase 8

    Chan Calvin C

    2012-01-01

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

  3. Endemic insular and coastal Tunisian date palm genetic diversity.

    Zehdi-Azouzi, Salwa; Cherif, Emira; Guenni, Karim; Abdelkrim, Ahmed Ben; Bermil, Aymen; Rhouma, Soumaya; Salah, Mohamed Ben; Santoni, Sylvain; Pintaud, Jean Christophe; Aberlenc-Bertossi, Frédérique; Hannachi, Amel Salhi

    2016-04-01

    The breeding of crop species relies on the valorisation of ancestral or wild varieties to enrich the cultivated germplasm. The Tunisian date palm genetic patrimony is being threatened by diversity loss and global climate change. We have conducted a genetic study to evaluate the potential of spontaneous coastal resources to improve the currently exploited Tunisian date palm genetic pool. Eighteen microsatellite loci of Phoenix dactylifera L. were used to compare the genetic diversity of coastal accessions from Kerkennah, Djerba, Gabès and continental date palm accessions from Tozeur. A collection of 105 date palms from the four regions was analysed. This study has provided us with an extensive understanding of the local genetic diversity and its distribution. The coastal date palm genotypes exhibit a high and specific genetic diversity. These genotypes are certainly an untapped reservoir of agronomically important genes to improve cultivated germplasm in continental date palm. PMID:26895027

  4. Beauveria bassiana: quercetinase production and genetic diversity

    Eula Maria de M. B Costa

    2011-03-01

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

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

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

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

    Zhenzhen Liu; Xiuying Guo; Baoyu Li; Ming Wang; Xi Wang; Keliang Wu

    2010-01-01

    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...

  7. Predicting mining activity with parallel genetic algorithms

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

    2005-01-01

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

  8. Extreme genetic diversity in asexual grass thrips populations.

    Fontcuberta García-Cuenca, A; Dumas, Z; Schwander, T

    2016-05-01

    The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations. PMID:26864612

  9. High Performance Data mining by Genetic Neural Network

    Dadmehr Rahbari

    2013-10-01

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

  10. Genetic diversity increases insect herbivory on oak saplings.

    Bastien Castagneyrol

    Full Text Available A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Quercus robur half-sib families. We quantified genetic diversity at the plot level by genotyping all oak saplings and assessed overall damage caused by ectophagous and endophagous herbivores along a gradient of increasing genetic diversity. Damage due to ectophagous herbivores increased with the genetic diversity in oak sapling populations as a result of higher levels of damage in mixtures than in monocultures for all families (complementarity effect rather than because of the presence of more susceptible oak genotypes in mixtures (selection effect. Assemblages of different oak genotypes would benefit polyphagous herbivores via improved host patch location, spill over among neighbouring saplings and diet mixing. By contrast, genetic diversity was a poor predictor of the abundance of endophagous herbivores, which increased with individual sapling apparency. Plant genetic diversity may not provide sufficient functional contrast to prevent tree sapling colonization by specialist herbivores while enhancing the foraging of generalist herbivores. Long term studies are nevertheless required to test whether the effect of genetic diversity on herbivory change with the ontogeny of trees and local adaptation of specialist herbivores.

  11. The structural diversity of artificial genetic polymers

    Anosova, Irina; Kowal, Ewa A.; Dunn, Matthew R.; Chaput, John C.; Van Horn, Wade D.; Egli, Martin

    2015-01-01

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeg...

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

    Melissa D Conrad

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

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

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

    2015-07-01

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

  14. Keel A Data Mining Tool: Analysis With Genetic

    Ms. Pooja Mittal

    2012-06-01

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

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

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

    2014-01-01

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

  16. Inference of genetic diversity in popcorn S3 progenies.

    Pena, G F; do Amaral, A T; Ribeiro, R M; Ramos, H C C; Boechat, M S B; Santos, J S; Mafra, G S; Kamphorst, S H; de Lima, V J; Vivas, M; de Souza Filho, G A

    2016-01-01

    Molecular markers are a useful tool for identification of complementary heterotic groups in breeding programs aimed at the production of superior hybrids, particularly for crops such as popcorn in which heterotic groups are not well-defined. The objective of the present study was to analyze the genetic diversity of 47 genotypes of tropical popcorn to identify possible heterotic groups for the development of superior hybrids. Four genotypes of high genetic value were studied: hybrid IAC 125, strain P2, and varieties UENF 14 and BRS Angela. In addition, 43 endogamous S3 progenies obtained from variety UENF 14 were used. Twenty-five polymorphic SSR-EST markers were analyzed. A genetic distance matrix was obtained and the following molecular diversity parameters were estimated: number of alleles, number of effective alleles, polymorphism information content (PIC), observed and expected heterozygosities, Shannon diversity index, and coefficient of inbreeding. We found a moderate PIC and high diversity index, indicating that the studied population presents both good discriminatory ability and high informativeness for the utilized markers. The dendrogram built based on the dissimilarity matrix indicated six distinct groups. Our findings demonstrate the genetic diversity among the evaluated genotypes and provide evidence for heterotic groups in popcorn. Furthermore, the functional genetic diversity indicates that there are informative genetic markers for popcorn. PMID:27173336

  17. Understanding Genetic Diversity of Sorghum Using Quantitative Traits

    Sinha, Sweta; Kumaravadivel, N.

    2016-01-01

    Sorghum is the important cereal crop around the world and hence understanding and utilizing the genetic variation in sorghum accessions are essential for improving the crop. A good understanding of genetic variability among the accessions will enable precision breeding. So profiling the genetic diversity of sorghum is imminent. In the present investigation, forty sorghum accessions consisting of sweet sorghum, grain sorghum, forage sorghum, mutant lines, maintainer lines, and restorer lines were screened for genetic diversity using quantitative traits. Observations were recorded on 14 quantitative traits, out of which 9 diverse traits contributing to maximum variability were selected for genetic diversity analysis. The principle component analysis revealed that the panicle width, stem girth, and leaf breadth contributed maximum towards divergence. By using hierarchical cluster analysis, the 40 accessions were grouped under 6 clusters. Cluster I contained maximum number of accessions and cluster VI contained the minimum. The maximum intercluster distance was observed between cluster VI and cluster IV. Cluster III had the highest mean value for hundred-seed weight and yield. Hence the selection of parents must be based on the wider intercluster distance and superior mean performance for yield and yield components. Thus in the present investigation quantitative data were able to reveal the existence of a wide genetic diversity among the sorghum accessions used providing scope for further genetic improvement. PMID:27382499

  18. Maintenance of genetic diversity through plant-herbivore interactions

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

    2013-01-01

    Identifying the factors governing the maintenance of genetic variation is a central challenge in evolutionary biology. New genomic data, methods and conceptual advances provide increasing evidence that balancing selection, mediated by antagonistic species interactions, maintains functionally-important genetic variation within species and natural populations. Because diverse interactions between plants and herbivorous insects dominate terrestrial communities, they provide excellent systems to ...

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

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

  20. Impacts of genetic bottlenecks on soybean genome diversity

    Hyten, David L; Song, Qijian; Zhu, Youlin; Choi, Ik-Young; Nelson, Randall L.; Costa, Jose M.; Specht, James E; Shoemaker, Randy C.; Cregan, Perry B

    2006-01-01

    Soybean has undergone several genetic bottlenecks. These include domestication in Asia to produce numerous Asian landraces, introduction of relatively few landraces to North America, and then selective breeding over the past 75 years. It is presumed that these three human-mediated events have reduced genetic diversity. We sequenced 111 fragments from 102 genes in four soybean populations representing the populations before and after genetic bottlenecks. We show that soybean has lost many rare...

  1. Understanding Genetic Diversity of Sorghum Using Quantitative Traits

    Sinha, Sweta; Kumaravadivel, N.

    2016-01-01

    Sorghum is the important cereal crop around the world and hence understanding and utilizing the genetic variation in sorghum accessions are essential for improving the crop. A good understanding of genetic variability among the accessions will enable precision breeding. So profiling the genetic diversity of sorghum is imminent. In the present investigation, forty sorghum accessions consisting of sweet sorghum, grain sorghum, forage sorghum, mutant lines, maintainer lines, and restorer lines w...

  2. Genetic diversity in farm animals - A review

    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.

    2010-01-01

    Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, m

  3. The Host Genetic Diversity in Malaria Infection

    Vitor R. R. de Mendonça; Marilda Souza Goncalves; Manoel Barral-Netto

    2012-01-01

    Populations exposed to Plasmodium infection develop genetic mechanisms of protection against severe disease. The clinical manifestation of malaria results primarily from the lysis of infected erythrocytes and subsequent immune and inflammatory responses. Herein, we review the genetic alterations associated with erythrocytes or mediators of the immune system, which might influence malaria outcome. Moreover, polymorphisms in genes related to molecules involved in mechanisms of cytoadherence and...

  4. Hitchhiker's guide to genetic diversity in socially structured populations

    L.S.PREMO

    2012-01-01

    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].

  5. Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. Langbinanensis

    2002-01-01

    Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. Langbinanensis were examined by means of electrophoresis technique. Analysis of 9 enzyme systems including 16 loci showed that all the three natural populations of the pine were high in genetic diversity but low in inter -population genetic differentiation. The proportion of polymorphic loci is 0.667 , with eachlocus holding 2.13 alleles, averagely. The average expected and obse rved heterozygosity was 0.288 and 0.197, respectively. The gene differentiation among populations was 0.052, but the mean genetic distance was only 0.015.

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

    Afrooz Alimohamadi

    2012-11-01

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

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

    Afrooz Alimohamadi

    2012-12-01

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

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

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

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

    Kesinee Gatphayak

    2013-01-01

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

  10. The structural diversity of artificial genetic polymers.

    Anosova, Irina; Kowal, Ewa A; Dunn, Matthew R; Chaput, John C; Van Horn, Wade D; Egli, Martin

    2016-02-18

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space. PMID:26673703

  11. Optimization of Association Rule Mining through Genetic Algorithm

    RUPALI HALDULAKAR,

    2011-03-01

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

  12. Regional specificity of genetically diverse garlic varieties

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

  13. Great ape genetic diversity and population history

    Prado-Martinez, Javier; Sudmant, Peter H.; Kidd, Jeffrey M.;

    2013-01-01

    species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central...

  14. The Host Genetic Diversity in Malaria Infection

    Vitor R. R. de Mendonça

    2012-01-01

    Full Text Available Populations exposed to Plasmodium infection develop genetic mechanisms of protection against severe disease. The clinical manifestation of malaria results primarily from the lysis of infected erythrocytes and subsequent immune and inflammatory responses. Herein, we review the genetic alterations associated with erythrocytes or mediators of the immune system, which might influence malaria outcome. Moreover, polymorphisms in genes related to molecules involved in mechanisms of cytoadherence and their influence on malaria pathology are also discussed. The results of some studies have suggested that the combinatorial effects of a set of genetic factors in the erythrocyte-immunology pathway might be relevant to host resistance or susceptibility against Plasmodium infection. However, these results must be interpreted with caution because of the differences observed in the functionality and frequency of polymorphisms within different populations. With the recent advances in molecular biology techniques, more robust studies with reliable data have been reported, and the results of these studies have identified individual genetic factors for consideration in preventing severe disease and the individual response to treatment.

  15. Status, Distribution, and Diversity of Birds in Mining Environment of Kachchh, Gujarat

    Nikunj B. Gajera

    2013-01-01

    Full Text Available Opencast mining is one of the major reasons for the destruction of natural habitats for many wildlife including birds. The Kachchh region belongs to the arid part of India and is one of the rich areas of mineral resources in the country. In the recent time and after the 2001 earthquake, mining and other developmental activities are increased, and as a result, the natural habitats of birds are disturbed and fragmented. So, this study was conducted to assess the impact of mining and associated activities on the diversity and distribution of birds. Birds were studied by surveying 180 transects along 9 zones around three selected major mines, and each zone is made in every 2 km radius from the mine. Based on the record, it was found that the density and diversity of birds are highest in zone 5 and lowest in zone 1 and zone 2, respectively. The result indicates that the diversity and abundance of birds were less in zones which are located close to the mines in comparison to the zones far from the mines. In conclusion, mining and its associated activities have some impacts on the diversity and distribution of birds in Kachchh region in India.

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

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

    2012-01-01

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

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

    Ana Daniela Lopes

    2015-12-01

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

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

    Homar R. Gill-Langarica

    2011-01-01

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

  19. Conservation of Genetic Diversity in Culture Plants

    A. Maxim

    2010-01-01

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

  20. Genetic gain and gene diversity of seed orchard crops

    Kang, Kyu-Suk [Swedish Univ. of Agricultural Sciences, Umeaa (Sweden). Dept. of Forest Genetics and Plant Physiology

    2001-07-01

    Seed orchards are the major tool for deploying the improvement generated by breeding programs and assuring the consistent supply of genetically improved seed. Attainment of genetic gain and monitoring of gene diversity through selection and breeding were studied considering the factors: selection intensity; genetic value; coancestry; fertility variation; and pollen contamination. The optimum goal of a seed orchard is achieved when the orchard population is under an idealized situation, i.e., panmixis, equal gamete contributions from all parental genotypes, non-relatedness and no pollen contamination. In practice, however, due to relatedness among parents, variation in clonal fertility and ramet number, and gene migration from outside, the realized genetic gain and gene diversity deviate from the expectation. In the present study, the genetic value of seed orchard crops (genetic gain, G) could be increased by selective harvest, genetic thinning and/or both. Status number (N{sub S}) was used to monitor the loss of gene diversity in the process of forest tree domestication, and calculated to be reasonably high in most seed orchards. Fertility of parents was estimated based on the assessment of flowering or seed production, which was shown to be under strong genetic control. Variation in fertility among orchard parents was a general feature and reduced the predicted gene diversity of the orchard crop. Fertility variation among parents could be described by the sibling coefficient ({psi}). {psi} was estimated to be 2 (CV = 100% for fertility). In calculating {psi}, it was possible to consider, besides fertility variation, the phenotypic correlation between maternal and parental fertilities, and pollen contamination. Status number was increased by controlling parental fertility, e.g., equal seed harvest, mixing seed in equal proportions and balancing parental contribution. By equalizing female fertility among over-represented parents, it was possible to effect a

  1. Genetic Diversity Based on Allozyme Alleles of Chinese Cultivated Rice

    TANG Sheng-xiang; WEI Xing-hua; JIANG Yun-zhu; D S Brar; G S Khush

    2007-01-01

    Genetic diversity was analyzed with 6 632 core rice cultivars selected from 60 282 Chinese rice accessions on the basis of 12 allozyme loci, Pgil, Pgi2, Ampl, Amp2, Amp3, Amp4, Sdh1, Adh1, Est1, Est2, Est5 and Est9, by starch gel electrophoresis. Among the materials examined, 52 alleles at 12 polymorphic loci were identified, which occupied 96.3% of 54 alleles found in cultivated germplasm of O.sativa L. The number of alleles per locus ranged from 2 to 7 with an average of 4.33. The gene diversity (He) each locus varied considerably from 0.017 for Amp4 to 0.583 for Est2 with an average gene diversity (Ht) 0.271, and Shannon-Wiener index from 0.055 to 0.946 with an average of 0.468. The degree of polymorphism (DP) was in a range from 0.9 to 46.9% with an average of 21.4%. It was found that the genetic diversity in japonica (Keng) subspecies was lower in terms of allele's number, Ht and S-W index, being 91.8, 66.2 and 75.7% of indica (Hsien) one, respectively. Significant genetic differentiation between indica and japonica rice has been appeared in the loci Pgil, Amp2, Pgi2, and Est2, with higher average coefficient of genetic differentiation (Gst) 0.635, 0.626, 0.322 and 0.282, respectively. Except less allele number per locus (3.33) for modern cultivars, being 76.9% of landraces, the Ht and S-W index showed in similar between the modern cultivars and the landraces detected. In terms of allozyme, the rice cultivars in the Southwest Plateau and Central China have richer genetic diversity. The present study reveals again that Chinese cultivated rice germplasm has rich genetic diversity, showed by the allozyme allele variation.

  2. Genetic diversity among ancient Nordic populations.

    Linea Melchior

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

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

    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)

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

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

    2006-08-01

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

  5. Genetic diversity measures of the Croatian Spotted goat

    Pavić Vesna

    2011-01-01

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

  6. The genetic diversity of Plasmodium vivax: a review

    Wanessa Christina de Souza-Neiras

    2007-06-01

    Full Text Available The genetic diversity of Plasmodium vivax has been investigated in several malaria-endemic areas, including the Brazilian Amazon region, where this is currently the most prevalent species causing malaria in humans. This review summarizes current views on the use of molecular markers to examine P. vivax populations, with a focus on studies performed in Brazilian research laboratories. We emphasize the importance of phylogenetic studies on this parasite and discuss the perspectives created by our increasing understanding of genetic diversity and population structure of this parasite for the development of new control strategies, including vaccines, and more effective drugs for the treatment of P. vivax malaria.

  7. Assessment of genetic diversity in Brazilian barley using SSR markers

    Jéssica Rosset Ferreira

    2016-03-01

    Full Text Available Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC, with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs.

  8. Assessment of genetic diversity in Brazilian barley using SSR markers

    Ferreira, Jéssica Rosset; Pereira, Jorge Fernando; Turchetto, Caroline; Minella, Euclydes; Consoli, Luciano; Delatorre, Carla Andréa

    2016-01-01

    Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs. PMID:27007902

  9. Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger

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

    2012-01-01

    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...

  10. Genetic characteristics of diversity of apple resistance to apple scab

    Sikorskaitė-Gudžiūnienė, Sidona

    2014-01-01

    The aim of the research. To identify genes involved in V. inaequalis induced resistance response in Malus sp. and to develop apple hybrids with pyramidic resistance. Specific aims: 1. To characterize the genetic diversity and resistance to apple scab in the collection of apple genetic resources; 2. To develop apple hybrids of pyramidic resistance for apple breeding; 3. To characterize apple nuclear proteome and to perform a comparative genomic analysis of V. inaequalis induced Malus response;...

  11. Dynamic Change of Genetic Diversity in Conserved Populations with Different Initial Genetic Architectures

    LU Yun-feng; LI Hong-wei; WU Ke-liang; WU Chang-xin

    2013-01-01

    Maintenance and management of genetic diversity of farm animal genetic resources (AnGR) is very important for biological, socioeconomical and cultural significance. The core concern of conservation for farm AnGR is the retention of genetic diversity of conserved populations in a long-term perspective. However, numerous factors may affect evolution of genetic diversity of a conserved population. Among those factors, the genetic architecture of conserved populations is little considered in current conservation strategies. In this study, we investigated the dynamic changes of genetic diversity of conserved populations with two scenarios on initial genetic architectures by computer simulation in which thirty polymorphic microsatellite loci were chosen to represent genetic architecture of the populations with observed heterozygosity (Ho) and expected heterozygosity (He), observed and mean effective number of alleles (Ao and Ae), number of polymorphic loci (NP) and the percentage of polymorphic loci (PP), number of rare alleles (RA) and number of non-rich polymorphic loci (NRP) as the estimates of genetic diversity. The two scenarios on genetic architecture were taken into account, namely, one conserved population with same allele frequency (AS) and another one with actual allele frequency (AA). The results showed that the magnitude of loss of genetic diversity is associated with genetic architecture of initial conserved population, the amplitude of genetic diversity decline in the context AS was more narrow extent than those in context AA, the ranges of decline of Ho and Ao were about 4 and 2 times in AA compared with that in AS, respectively, the occurrence of first monomorphic locus and the time of change of measure NP in scenario AA is 20 generations and 23 generations earlier than that in scenario AS, respectively. Additionally, we found that NRP, a novel measure proposed by our research group, was a proper estimate for monitoring the evolution of genetic diversity

  12. GENETIC DIVERSITY OF THE WILD AND REARED PSEUDOSCIAENA CROCEA

    王军; 苏永全; 全成干; 丁少雄; 张纹

    2001-01-01

    The genetic diversity of both wild and reared Pseudosciaena crocea (Richardson) col-lected from Guan-Jing-Yang in Ningde, China in May 1999 was investigated by random amplified poly-morphic DNA (RAPD) in the present study. The polymorphism and mean difference of the wild popula-tion as revealed by RAPD were 18.9% and 0.0960 respectively, and those of the reared stocks were rel-atively lower, with 16.7% in polymorphism and 0.0747 in mean difference. The genetic distance be-tween the two stocks was 0.0041. From the comprehensive investigation, the main reasons for the loss of genetic diversity were probably overilshing, small number of parents as broodstocks and the debatable arti-ficial ranching. Results from this study also showed that the large yellow croaker populations distributed along Fujian coastal waters including Guan-Jing-Yang still potentially wide genetic variability. It is sug-gested that genetic management and prevention should be scientifically conducted in order to maintain and improve the genetic diversity of the P. crocea population.

  13. GENETIC DIVERSITY OF THE WILD AND REARED PSEUDOSCIAENA CROCEA

    2001-01-01

    The genetic diversity of both wild and reared Pseudosciaena crocea (Richardson) collected from Guan-Jing-Yang in Ningde, China in May 1999 was investigated by random amplified polymorphic DNA (RAPD) in the present study. The polymorphism and mean difference of the wild population as revealed by RAPD were 18.9% and 0.0960 respectively, and those of the reared stocks were relatively lower, with 16.7% in polymorphism and 0.0747 in mean difference. The genetic distance between the two stocks was 0.0041. From the comprehensive investigation, the main reasons for the loss of genetic diversity were probably overfishing, small number of parents as broodstocks and the debatable artificial ranching. Results from this study also showed that the large yellow croaker populations distributed along Fujian coastal waters including Guan-Jing-Yang still potentially wide genetic variability. It is suggested that genetic management and prevention should be scientifically conducted in order to maintain and improve the genetic diversity of the P. crocea population.

  14. Genetic diversity of noroviruses in Brazil

    Julia Monassa Fioretti

    2011-12-01

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

  15. Genetic Diversity among Ancient Nordic Populations

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R;

    2010-01-01

    locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the...... ancient Danes (average 13%) than among extant Danes and Scandinavians ( approximately 2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic...... samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for...

  16. Genetic diversity of natural Hepatacodium miconioides populations in Zhejiang Province

    LI Junmin; JIN Zexin

    2006-01-01

    Hepatacodium miconioides is the Class Ⅱ protected plant species in China.This paper studies the genetic diversity and differentiation of its nine natural populations in Zhejiang Province by using random amplified polymorphic DNA (RAPD) technique.Twelve random primers were selected in the amplification,and 164 repetitive loci were produced.The percentage of polymorphic loci in each H.miconioides population ranged from 14.60% to 27.44%,with an average of 20.73%.Among the test populations,Kuochangshan had the highest percentage of polymorphic loci,Simingshan took the second place,and Guanyinping had the lowest percentage.As estimated by Shannon index,the genetic diversity within H.miconioides populations accounted for 27.28% of the total genetic diversity,while that among H.miconioides populations accounted for 72.72%.The genetic differentiation among H.miconioides populations as estimated by Nei index was 0.715,7.This figure was generally consistent with that estimated by Shannon index,i.e.,the genetic differentiation among populations was relatively high,but that within populations was relatively low.The gene flow among H.miconioides populations was relatively low (0.198,7),and the genetic similarity ranged from 0.655,7 to 0.811,9,with an average of 0.730,6.The highest genetic distance among populations was 0.422,9,while the lowest was 0.208,3.All the results showed that there was a distinct genetic differentiation among H.miconioides populations.The genetic distance matrix of nine test populations was calculated using this method,and the clustering analysis was made using the unweighted pair group method with arithmetic mean (UPGMA).The cluster analysis suggested that the ninepopulations of H.miconioides in Zhejiang Province could be divided into two groups,the eastern Zhejiang group and the western Zhejiang group.

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

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

    2013-01-01

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

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

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand ...

  19. Genetic diversity of Ascaris in southwestern Uganda

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

    2012-01-01

    Despite the common occurrence of ascariasis in southwestern Uganda, helminth control in the region has been limited. To gain further insights into the genetic diversity of Ascaris in this area, a parasitological survey in mothers (n=41) and children (n=74) living in two villages, Habutobere and M...

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

    Hughes, William Owen Hamar; Boomsma, Jacobus Jan

    2006-01-01

    of host genetic diversity on parasite evolution by carrying out serial passages of a virulent fungal pathogen through leaf-cutting ant workers of known genotypes. Parasite virulence increased over the nine-generation span of the experiment while spore production decreased. The effect of host...

  1. Multi-objective Uniform-diversity Genetic Algorithm (MUGA)

    Jamali, Ali; Nariman-zadeh, Nader; Atashkari, Kazem

    2008-01-01

    A new multi-objective uniform-diversity genetic algorithm (MUGA) has been proposed and successfully used for some test functions and for thermodynamic cycle optimization of ideal turbojet engines. It has been shown that the performance of this algorithm is superior to that

  2. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    GULNAR SHIKHSEYIDOVA

    2015-06-01

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

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

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

    2014-01-01

    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...

  4. Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers*

    Ocelák M.

    2015-12-01

    Full Text Available The diversity and genetic relationships in 173 sacha inchi samples were analyzed using ISSR markers. Thirty ISSR primers were used, only 8 showed variability in tested samples. ISSR fragments ranged from 200 to 2500 bp. The mean number of bands per primer was 12 and the average number of polymorphic bands per primer was 11. The lowest percentages of polymorphic bands (27%, gene diversity (0.103, and Shannon’s information index (0.15 were exhibited by the Santa Lucia population, which was also geographically most distant. This fact may be attributed to a very small size of this group. In contrast, the Dos de Mayo population exhibited the highest percentage of polymorphic bands (78%, and the Santa Cruz population the highest Nei’s gene diversity index (0.238 and Shannon’s information index (0.357. The obtained level of genetic variability was 36% among tested populations and 64% within populations. Although the diversity indices were low, a cluster analysis revealed 8 clusters containing mainly samples belonging to individual populations. Principal coordinate analysis clearly distinguished Chumbaquihui, Pucallpa, Dos de Mayo, and Aguas de Oro populations, the others were intermixed. The obtained results indicated the level of genetic diversity present in this location of Peru, although it is influenced by anthropological aspects and independent on the geographical distances.

  5. Determination of genetic diversity among some almond accessions

    Pinar Hasan

    2015-01-01

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

  6. GENETIC RESOURCES AND DIVERSITY IN DAIRY BUFFALOES OF PAKISTAN

    M. SAJJAD KHAN, NAZIR AHMAD1 AND MUQARRAB ALI KHAN2

    2007-10-01

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

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

    Shao, Yafang; Bao, Jinsong

    2015-08-01

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

  8. Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest.

    Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

    2016-01-01

    A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community. PMID:26860815

  9. [Genetic diversity of eukaryotic picoplankton of eight lakes in Nanjing].

    Zhao, Bi-ying; Chen, Mei-jun; Sun, Ying; Chen, Fei-zhou; Yang, Jia-xin

    2010-05-01

    The method of terminal restriction fragment length polymorphism (T-RFLP) was used to study the genetic diversity of eukaryotic picoplankton (0.2-5.0 microm) in the pelagic and littoral zones in 8 lakes with different trophic status in Nanjing. The objectives of this study were to confirm the difference of the genetic diversity of eukaryotic picoplankton among lakes and the main factors affecting this difference. T-RFLP indicated that there were various fingerprints among lakes and zones. The average terminal restriction fragments (T-RFs) in the littoral and pelagic zones were 16.4 and 15.9, respectively. The littoral zone in Lake Nan and the pelagic zone in Lake Mochou had 30 T-RFs and 27 T-RFs, respectively. The T-RFs were the least abundant (10) in the pelagic zone in Lake Baijia with relatively low trophic status. The genetic diversity of eukaryotic picoplankton was higher in the littoral zone than that in the pelagic zone except Lake Pipa and Mochou. The cluster analysis indicated that the similarities of the littoral zones and the pelagic zones were very high except Lake Baijia, Qian and Nan. The canonical correspondence analysis between the genetic diversity of eukaryotic picoplankton and environmental factors revealed the concentration of chlorophyll a had the most important impact on the eukaryotic picoplankton communities (p = 0.004). The results indicated that the genetic diversity of eukaryotic picoplankton is affected by the trophic status and has the difference in the pelagic and littoral zones. PMID:20623867

  10. Genetic diversity and molecular genealogy of local silkworm varieties

    Zhouhe Du

    2013-03-01

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

  11. Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene.

    Martin, Simon H; Möst, Markus; Palmer, William J; Salazar, Camilo; McMillan, W Owen; Jiggins, Francis M; Jiggins, Chris D

    2016-05-01

    A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. PMID:27017626

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

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

    2014-06-01

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

  13. Allozymes Genetic Diversity of Quercus mongolica Fisch in China

    LI Wenying; GU Wanchun

    2006-01-01

    A gel electrophoresis method was used to study the genetic diversity of 8 Quercus mongolica populations throughout its range in China.Eleven of 21 loci from 13 enzymes assayed were polymorphic.Q.mongolica maintained low level of genetic variation compared with the average Quercus species.At the species level,: the mean number of alleles per locus (A) was 1.905, the percentage of polymorphic loci (P) was 52.38%, the observed heterozygosity (He) was 0.092 and the expected heterozygosity (He) was 0.099.At the population level, the estimates were A =1.421, P =28.976%, Ho= 0.088, He =0.085.Genetic differentiation (Gst was high among populations, it was 0.107.According to the UPGMA cluster analysis based on the genetic distance, 4 populations located in northeast and 2 populations in southwest of the geographical distribution are classified into 2 subgroups, but there was no clear relationship between genetic distance and geographic distance among populations.The low level of genetic diversity of Q.mongolica might be related to the long-term exploitation as economic tree species in history are comparatively seriously disturbed and damaged by human beings, and most of the existing stands are secondary forests.

  14. PLANT DIVERSITY OF THE ZHELTOKAMENSKIY OPEN CAST MINES

    Yarova T.A.

    2012-11-01

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

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

    Salama Al-Hamidhi

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

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

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

    2013-08-01

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

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

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

  18. Genetic diversity and construction of core collection in Chinese wheat genetic resources

    HAO ChenYang; DONG YuChen; WANG LanFen; YOU GuangXia; ZHANG HongNa; GE HongMei; JIA JiZeng; ZHANG XueYong

    2008-01-01

    Genetic diversity among 5029 accessions representing a proposed Chinese wheat core collection was analyzed using 78 pairs of fluorescent microsatellite (SSR) primers mapped to 21 chromosomes. A stepwise hierarchical sampling strategy with priority based on 4×105 SSR data-points was used to construct a core collection from the 23090 initial collections. The core collection consisted of 1160 accessions, including 762 landraces, 348 modern varieties and 50 introduced varieties. The core ac-counts for 23.1% of the 5029 candidate core accessions and 5% of the 23090 initial collections, but retains 94.9% of alleles from the candidate collections and captures 91.5% of the genetic variation in the initial collections. These data indicate that it is possible to maintain genetic diversity in a core col-lection while retaining fewer accessions than the accepted standard, i.e., 10% of the initial collections captured more than 70% of their genetic diversity. Estimated genetic representation of the core con-structed by preferred sampling (91.5%) is much higher than that by random sampling (79.8%). Both mean genetic richness and genetic diversity indices of the landraces were higher than those of the modern varieties in the core. Structure and principal coordinate analysis revealed that the landraces and the modern varieties were two relatively independent subpopulations. Strong genetic differentia-tion associated with ecological environments has occurred in the landraces, but was relatively weak in the modern cultivars. In addition, a mini-core collection was constructed, which consisted of 231 ac-cessions with an estimated 70% representation of the genetic variation from the initial collections. The mini-core has been distributed to various research and breeding institutes for detailed phenotyping and breeding of genetic introgression lines.

  19. Bacterial Diversity in a Mine Water Treatment Plant▿ †

    Heinzel, Elke; Hedrich, Sabrina; Janneck, Eberhard; Glombitza, Franz; Seifert, Jana; Schlömann, Michael

    2008-01-01

    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”.

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

    Guillermo Velo-Antón

    Full Text Available BACKGROUND: Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3% to 69% in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium. CONCLUSIONS/SIGNIFICANCE: Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants and heritability of anomalies would be useful to better understand the complex origin of anomalies in natural populations.

  1. Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers*

    Ocelák M.; Čepková P. Hlásná; Viehmannová I.; Dvořáková Z.; Huansi D.C.; Lojka B.

    2015-01-01

    The diversity and genetic relationships in 173 sacha inchi samples were analyzed using ISSR markers. Thirty ISSR primers were used, only 8 showed variability in tested samples. ISSR fragments ranged from 200 to 2500 bp. The mean number of bands per primer was 12 and the average number of polymorphic bands per primer was 11. The lowest percentages of polymorphic bands (27%), gene diversity (0.103), and Shannon’s information index (0.15) were exhibited by the Santa Lucia population, which was a...

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

    Ermis Yanes Paz

    2012-01-01

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

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

    Ackermann Alejandro A

    2012-12-01

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

  4. Genetic diversity and maternal origin of Bangladeshi chicken.

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

    2013-06-01

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

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

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

    2012-01-01

    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...

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

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

    2011-01-01

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

  7. Genetic Diversity Enhances Restoration Success by Augmenting Ecosystem Services

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

    2012-01-01

    Disturbance and habitat destruction due to human activities is a pervasive problem in near-shore marine ecosystems, and restoration is often used to mitigate losses. A common metric used to evaluate the success of restoration is the return of ecosystem services. Previous research has shown that biodiversity, including genetic diversity, is positively associated with the provision of ecosystem services. We conducted a restoration experiment using sources, techniques, and sites similar to actua...

  8. Genetic and biological diversity among isolates of Neospora caninum.

    Schock, A; Innes, E A; Yamane, I; Latham, S M; Wastling, J M

    2001-07-01

    Neospora caninum is a protozoan parasite that causes bovine abortion. The epidemiology of N. caninum is poorly understood and little is known about the genetic diversity of the parasite, or whether individual isolates differ in virulence. Such diversity may, among other factors, underlie the range of pathologies seen in cattle. In this study we analysed biological and genetic variation in 6 isolates of N. caninum originating from canine and bovine hosts by measurement of growth rate in vitro, Western blotting and random amplification of polymorphic DNA (RAPD). This comparative analysis of intra-species diversity demonstrated that heterogeneity exists within the species. The relative growth rate in vitro, as assessed by 3[H]uracil uptake, showed significant variation between isolates. However, no significant differences were detected between the antigenic profiles of each isolate by Western blotting. RAPD-PCR was performed on DNA from the 6 Neospora isolates; 3 strains of Toxoplasma gondii, Sarcocystis sp. and Cryptosporidium parvum were also analysed. Twenty-six RAPD primers gave rise to 434 markers of which 222 were conserved between all the Neospora isolates and distinguished them from the other Apicomplexa. An additional 54 markers were unique for Neospora but were polymorphic within the species and able to differentiate between the individual isolates. The RAPD data were subjected to pair-wise similarity and cluster analysis and showed that the Neospora isolates clustered together as a group, with T. gondii as their nearest neighbour. N. caninum isolates showed no clustering with respect either to host or geographical origin. The genetic similarity between Neospora isolates from cattle and dogs suggests that these hosts may be epidemiologically related, although further analysis of bovine and canine field samples are required. The genetic and biological diversity observed in this study may have important implications for our understanding of the pathology and

  9. Loss of Genetic Diversity of Jatropha curcas L. through Domestication: Implications for Its Genetic Improvement

    Sanou, Haby; Angel Angulo-Escalante, Miguel; Martinez-Herrera, Jorge; Kone, Souleymane; Nikiema, Albert; Kalinganire, Antoine; Hansen, Jon Kehlet; Kjaer, Erik Dahl; Graudal, Lars; Nielsen, Lene Rostgaard

    2015-01-01

    Jatropha curcas L. has been promoted as a “miracle” tree in many parts of the world, but recent studies have indicated very low levels of genetic diversity in various landraces. In this study, the genetic diversity of landrace collections of J. curcas was compared with the genetic diversity of the....... Mating system could not be estimated in the landraces from Mali and populations from Veracruz, Puebla, and Morelos (Mexico), as these were highly monomorphic. The observed low level of genetic diversity in some of the populations and landraces suggests that breeding programs should test for genetic...

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

    K. Poornamala; R. Lawrance

    2012-01-01

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

  11. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

    2011-01-01

    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....

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

    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...

  13. Characterisation of the genetic diversity of Brucella by multilocus sequencing

    MacMillan Alastair P

    2007-04-01

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

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

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

    2005-12-01

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

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

    Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

    2014-11-01

    In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

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

    Juan Miguel Cordero-Solórzano

    2015-06-01

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

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

    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)

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

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

    2013-01-01

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

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

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

    2013-09-01

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

  20. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

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

    Dong Hwan Lee

    2014-06-01

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

  2. Limited genetic diversity preceded extinction of the Tasmanian tiger.

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

    2012-01-01

    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

  3. Molecular assessment of genetic diversity in mung bean germplasm

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

    2008-04-01

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

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

    Tanweer Kumar

    2014-07-01

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

  5. Genetic diversity of coronaviruses in Miniopterus fuliginosus bats.

    Du, Jiang; Yang, Li; Ren, Xianwen; Zhang, Junpeng; Dong, Jie; Sun, Lilian; Zhu, Yafang; Yang, Fan; Zhang, Shuyi; Wu, Zhiqiang; Jin, Qi

    2016-06-01

    Coronaviruses, such as severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, pose significant public health threats. Bats have been suggested to act as natural reservoirs for both these viruses, and periodic monitoring of coronaviruses in bats may thus provide important clues about emergent infectious viruses. The Eastern bent-wing bat Miniopterus fuliginosus is distributed extensively throughout China. We therefore analyzed the genetic diversity of coronaviruses in samples of M. fuliginosus collected from nine Chinese provinces during 2011-2013. The only coronavirus genus found was Alphacoronavirus. We established six complete and five partial genomic sequences of alphacoronaviruses, which revealed that they could be divided into two distinct lineages, with close relationships to coronaviruses in Miniopterus magnater and Miniopterus pusillus. Recombination was confirmed by detecting putative breakpoints of Lineage 1 coronaviruses in M. fuliginosus and M. pusillus (Wu et al., 2015), which supported the results of topological and phylogenetic analyses. The established alphacoronavirus genome sequences showed high similarity to other alphacoronaviruses found in other Miniopterus species, suggesting that their transmission in different Miniopterus species may provide opportunities for recombination with different alphacoronaviruses. The genetic information for these novel alphacoronaviruses will improve our understanding of the evolution and genetic diversity of coronaviruses, with potentially important implications for the transmission of human diseases. PMID:27125516

  6. Sézary Syndrome: Translating Genetic Diversity into Personalized Medicine.

    Chevret, Edith; Merlio, Jean-Philippe

    2016-07-01

    Sézary syndrome is probably the most studied cutaneous T-cell lymphoma subtype. Beyond the consensus criteria for Sézary syndrome diagnosis, Sézary cells display heterogeneous phenotypes and differentiation profiles. In the face of SS diversity, the great hope is to develop targeted therapies based on next-generation sequencing to define the genetic landscape of Sézary syndrome. Prasad et al. report on the use of exome sequencing and RNA sequencing to study selected CD4(+) blood cells from 15 patients with erythroderma Sézary syndrome, 14 of whom fulfilled the conventional criteria for diagnosis. The most common genetic abnormality, TP53 gene deletion on chromosome arm 17p and/or mutation, was observed in 58% of patients. However, mutations affecting PLCG1, STAT5B, GLI3, and CARD11 each were detected in only one individual. Nevertheless, Prasad et al. report single point mutations or copy number alterations in several new genes and in new fusion genes, with predicted biological relevance. This information underscores the diversity of genetic alterations and of the mechanisms of alterations of single genes. At the individual level, Sézary cells may combine alterations of genes involved in T-cell signaling, NF-kB and JAK-signal transducer and activator of transcription pathways, apoptosis control, chromatin remodeling, and DNA damage response. The therapeutic relevance of these potential targets needs to be evaluated with tests of function. PMID:27342034

  7. Genetic diversity of Colombian sheep by microsatellite markers

    Ricardo Ocampo

    2016-03-01

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

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

    Jin Xie

    2014-06-01

    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.

  9. A Survey of Association Rule Mining Using Genetic Algorithm

    Anubha Sharma

    2012-01-01

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

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

    Parvez Rahi; Bhumika Gupta

    2014-01-01

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

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

    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

  12. Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages. PMID:24376692

  13. Diversity and Distribution of Arsenic-Related Genes Along a Pollution Gradient in a River Affected by Acid Mine Drainage.

    Desoeuvre, Angélique; Casiot, Corinne; Héry, Marina

    2016-04-01

    Some microorganisms have the capacity to interact with arsenic through resistance or metabolic processes. Their activities contribute to the fate of arsenic in contaminated ecosystems. To investigate the genetic potential involved in these interactions in a zone of confluence between a pristine river and an arsenic-rich acid mine drainage, we explored the diversity of marker genes for arsenic resistance (arsB, acr3.1, acr3.2), methylation (arsM), and respiration (arrA) in waters characterized by contrasted concentrations of metallic elements (including arsenic) and pH. While arsB-carrying bacteria were representative of pristine waters, Acr3 proteins may confer to generalist bacteria the capacity to cope with an increase of contamination. arsM showed an unexpected wide distribution, suggesting biomethylation may impact arsenic fate in contaminated aquatic ecosystems. arrA gene survey suggested that only specialist microorganisms (adapted to moderately or extremely contaminated environments) have the capacity to respire arsenate. Their distribution, modulated by water chemistry, attested the specialist nature of the arsenate respirers. This is the first report of the impact of an acid mine drainage on the diversity and distribution of arsenic (As)-related genes in river waters. The fate of arsenic in this ecosystem is probably under the influence of the abundance and activity of specific microbial populations involved in different As biotransformations. PMID:26603631

  14. Diversity Controlling Genetic Algorithm for Order Acceptance and Scheduling Problem

    Cheng Chen

    2014-01-01

    Full Text Available Selection and scheduling are an important topic in production systems. To tackle the order acceptance and scheduling problem on a single machine with release dates, tardiness penalty, and sequence-dependent setup times, in this paper a diversity controlling genetic algorithm (DCGA is proposed, in which a diversified population is maintained during the whole search process through survival selection considering both the fitness and the diversity of individuals. To measure the similarity between individuals, a modified Hamming distance without considering the unaccepted orders in the chromosome is adopted. The proposed DCGA was validated on 1500 benchmark instances with up to 100 orders. Compared with the state-of-the-art algorithms, the experimental results show that DCGA improves the solution quality obtained significantly, in terms of the deviation from upper bound.

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

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

    2014-01-01

    Numerous studies have examined the genetic diversity and genetic structure of invading species, with contrasting results concerning the relative roles of genetic diversity and phenotypic plasticity in the success of introduced populations. Increasing evidence shows that asexual lineages of aphids are able to occupy a wide geographical and ecological range of habitats despite low genetic diversity. The anholocyclic aphid Melanaphis sacchari is a pest of sugarcane and sorghum which originated i...

  16. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

    Carolyn A. Young

    2015-04-01

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

  17. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

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

    2015-01-01

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

  18. New insights into the genetic and metabolic diversity of thiocyanate-degrading microbial consortia.

    Watts, Mathew P; Moreau, John W

    2016-02-01

    Thiocyanate is a common contaminant of the gold mining and coal coking industries for which biological degradation generally represents the most viable approach to remediation. Recent studies of thiocyanate-degrading bioreactor systems have revealed new information on the structure and metabolic activity of thiocyanate-degrading microbial consortia. Previous knowledge was limited primarily to pure-culture or co-culture studies in which the effects of linked carbon, sulfur and nitrogen cycling could not be fully understood. High throughput sequencing, DNA fingerprinting and targeted gene amplification have now elucidated the genetic and metabolic diversity of these complex microbial consortia. Specifically, this has highlighted the roles of key consortium members involved in sulfur oxidation and nitrification. New insights into the biogeochemical cycling of sulfur and nitrogen in bioreactor systems allow tailoring of the microbial metabolism towards meeting effluent composition requirements. Here we review these rapidly advancing studies and synthesize a conceptual model to inform new biotechnologies for thiocyanate remediation. PMID:26596573

  19. Genetic diversity analysis of Brassica oleracea L.by SSR

    2007-01-01

    SSR analysis on genetic diversity of 30 samples was carried out. Five primers selected from 36 primers were used to amplify 30 samples in this experiment, PCR products were separated by 6% polyacrylamide gel electrophoresis, silver staining and photographed. The results of SSR were analyzed by UPGMA clustering. The results showed that a total of 21 gene alleles were detected by 5 SSR primers. The number of alleles ranged from 2 to 5 with an average of 4.2.PIC range was 0.257-0.921, with an average of 0.543. The average coefficient of genetic similarity of SSR markers among materials was 0.432. Some of cabbage cultivars in the experiment were divided into four groups except cultivars which come from Japan.

  20. Genetic Diversity of Indonesian Snake Fruits as Food Diversification Resources

    Tri Budiyanti

    2015-01-01

    Full Text Available Indonesia is one of the megabiodivesity, which is rich with germplasms including tropical fruit. Snake fruit (Salacca spp. is a native fruit of Indonesia with a scaly peel and sweet-tart taste. The genetic diversity of 17 accessions of Indonesian snake fruit was resolved using the Random Amplified Polymorphic DNA Polymerase Chain Reaction with 5 primers. The study demonstrated that the samples were grouped in six different clusters with coefficient of similarity ranged from 0.12 to 0.71. The value indicated the wide range of genetic variability among the tested plants. This variability was an important resources for the snake fruit breeding program in developing the consumer‘s preferred product which by the end supports the plant diversification program.

  1. Genetic Diversity of Eight Domestic Goat Populations Raised in Turkey

    Bulut, Zafer; Kurar, Ercan; Ozsensoy, Yusuf; Altunok, Vahdettin; Nizamlioglu, Mehmet

    2016-01-01

    The objective of this study was to determine the intra- and intergenetic diversities of eight different goat populations in Turkey including Hair, Angora, Kilis, Yayladag, Shami, Honamli, Saanen, and Alpine. A total of 244 DNA samples were genotyped using 11 microsatellites loci. The genetic differentiation between breeds was considerable as a result of the statistically significant (P 0.05). Heterozygosity values ranged between 0.62 and 0.73. According to the structure and assignment test, Angora and Yayladag goats were assigned to the breed they belong to, while other breeds were assigned to two or more different groups. Because this study for the first time presented genetic data on the Yayladag goat, results of structure analysis and assigned test suggest that further analyses are needed using additional and different molecular markers. PMID:27092309

  2. Mining diverse small RNA species in the deep transcriptome.

    Vickers, Kasey C; Roteta, Leslie A; Hucheson-Dilks, Holli; Han, Leng; Guo, Yan

    2015-01-01

    Transcriptomes of many species are proving to be exquisitely diverse, and many investigators are now using high-throughput sequencing to quantify non-protein-coding RNAs, namely small RNAs (sRNA). Unfortunately, most studies are focused solely on microRNA changes, and many investigators are not analyzing the full compendium of sRNA species present in their large datasets. We provide here a rationale to include all types of sRNAs in sRNA sequencing analyses, which will aid in the discovery of their biological functions and physiological relevance. PMID:25435401

  3. Analysis of Distributed and Adaptive Genetic Algorithm for Mining Interesting Classification Rules

    YI Yunfei; LIN Fang; QIN Jun

    2008-01-01

    Distributed genetic algorithm can be combined with the adaptive genetic algorithm for mining the interesting and comprehensible classification rules. The paper gives the method to encode for the rules, the fitness function, the selecting, crossover, mutation and migration operator for the DAGA at the same time are designed.

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

    Jordana Jordi

    2001-07-01

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

  5. Whole mitochondrial genome genetic diversity in an Estonian population sample.

    Stoljarova, Monika; King, Jonathan L; Takahashi, Maiko; Aaspõllu, Anu; Budowle, Bruce

    2016-01-01

    Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25% of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7% in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85%, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99% for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions. PMID:26289416

  6. Genetic diversity in the SIR model of pathogen evolution.

    Isabel Gordo

    Full Text Available We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR. We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts, where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0(1+s is higher than the fitness of the resident strain (R(0. We show that this invasion probability is given by the relative increment in R(0 of the new pathogen (s. By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  7. On the Biological and Genetic Diversity in Neospora caninum

    John T. Ellis

    2010-03-01

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

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

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

    2011-01-01

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

  9. Parallel responses of species and genetic diversity to El Nino Southern Oscillation-induced environmental destruction

    D.F.R. Cleary; C.Y. Fauvelot; J. Genner; S.B.J. Menken; A.O. Mooers

    2006-01-01

    Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to

  10. Genetic diversity among five T4-like bacteriophages

    Bertrand Claire

    2006-05-01

    Full Text Available Abstract Background Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Results Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Conclusion Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4

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

    Donato Matassino

    2014-01-01

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

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

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

    2015-01-01

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

  13. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Garrido-Sanz, Daniel; Meier-Kolthoff, Jan P; Göker, Markus; Martín, Marta; Rivilla, Rafael; Redondo-Nieto, Miguel

    2016-01-01

    The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR. PMID:26915094

  14. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Daniel Garrido-Sanz

    Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

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

    Jane E Stewart

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

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

    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

  17. Genetic diversity assessment in brassica germplasm based on morphological attributes

    Genetic diversity of 28 Brassica genotypes was studied using different morphological attributes. Data were recorded on days to maturity (DM), plant height (PH), primary branches plant (PBPP), pod length (PL), seed pod (SP), 1000 - seed weight (1000 - SW), yield plant (YPP) and oil (percentage). Three checks (Pakola, CM and TA), were used to check the performance of collected materials with already available brassica varieties. significant statistical differences were observed among the tested genotypes based on the studied morphological traits. Among the tested genotypes, genotype keelboat proved to be superior as compared to other studied genotypes due to maximum level of studied traits like pod length (7.03 cm), seed pod (32.33), 1000 - seed weight (5.38 g), seed yield plant (110.8 g) and oil content (52.9 percentage. The highest level of performance recorded by kalabat in terms of branches plant, pod length (cm), number of seed pod, seed yield plant (g), 1000 - seed weight (g) and oil content (percentage), indicates that this genotype is genetically different and superior than the other studied genotype. Therefore, genotype kalabat can be either used as variety after adaptability trials over a larger area or included in Brassica breeding programmes as a good source of genetic variation. (author)

  18. The Nuclear DNA Content and Genetic Diversity of Lampetra morii

    Yan, Xinyu; Meng, Wenbin; Wu, Fenfang; Xu, Anlong; Chen, Shangwu; Huang, Shengfeng

    2016-01-01

    We investigated the nuclear DNA content and genetic diversity of a river lamprey, the Korean lamprey Lampetra morii, which is distributed in the northeast of China. L. morii spends its whole life cycle in fresh water, and its adult size is relatively small (~160 mm long) compared with that of other lampreys. The haploid nuclear DNA content of L. morii is 1.618 pg (approximately 1.582 Gb) in germline cells, and there is ~15% germline DNA loss in somatic cells. These values are significantly smaller than those of Petromyzon marinus, a lamprey with a published draft genome. The chromosomes of L. morii are small and acrocentric, with a diploid modal number of 2n = 132, lower than some other lampreys. Sequence and AFLP analyses suggest that the allelic polymorphism rate (~0.14% based on examined nuclear and mitochondrial DNA sequences) of L. morii is much lower than that (~2%) of P. marinus. Phylogenetic analysis based on a mitochondrial DNA fragment confirms that L. morii belongs to the genus Lampetra, which, together with the genus Lethenteron, forms a sister group to P. marinus. These genetic background data are valuable for subsequent genetic and genomic research on L. morii. PMID:27388621

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

    Hoda Anila

    2012-01-01

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

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

    Flávio de Oliveira Francisco

    2013-01-01

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

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

    Nováková, Alena

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

  2. Influence of Engineering Bacteria Quantitative Inspection on Diversity of Anpeng Alkali Mine Resources Exploitation

    Yu Tao

    2016-01-01

    Cadmium (Cd) is a heavy metal pollutant seriously threatening creatures, and highly concentrated Cd in soil severely inhibits the activity of microbial populations. Soil in Anpeng Alkali Mine area in Nanyang city (Henan province) is seriously polluted by heavy metal. Both copper (Cu) and Cd content are found to be over standard, in which, Cu belongs to mild contamination while Cd is a serious contamination. To detect diversity of microbial communities in soil in the process of bioremediation,...

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

    Selkoe, Kim; Gaggiotti, Oscar Eduardo; Treml, Eric; Wren, Johanna; Donovan, Marie; Consortium, Hawaii Reef Connectivity; Toonen, Robert

    2016-01-01

    O.E.G. was supported by the Marine Alliance for Science and Technology for Scotland (MASTS). Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here we use seascape genetic analysis of a diversity metric, allelic richness, for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbor the greatest genetic diversity on average. We found ...

  4. Genetic Diversity Analysis of Lates calcarifer (Bloch 1790) in Captive and Wild Populations Using RAPD Markers

    Muthusamy RAJASEKAR; Muthusamy THANGARAJ; Thathiredypalli R. BARATHKUMAR; Jayachandran SUBBURAJ; Kaliyan MUTHAZHAGAN

    2012-01-01

    Lates calcarifer (Bloch 1790) is one of the major economically important cultivable fish species in India. In this study, three populations of L. calcarifer was selected to assess the genetic diversity. Of which, two wild (Mudaslodai, Muthupettai) and one captive (Mutukadu) population. The genetic diversity of three populations of this species was studied using Random Amplified Polymorphic DNA (RAPD) markers. Ten random primers were used for the assessment of their genetic diversity and const...

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

    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

    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 δ-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

  6. Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei (Primulaceae):implications for its conservation

    Yuan HUANG; Chang-Qin ZHANG; De-Zhu LI

    2009-01-01

    Omphalogramma souliei Franch. Is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. Souliei in NW Yunnan, China. The genetic diversity at the species level is low with P= 42.5% (percentage of polymorphic bands) and Hsp=0.1762 (total genetic diversity). However, a high level of genetic differentiation among populations was detected based on different measures (Nei's genetic diversity analysis: Gst=0.6038; AMOVA analysis: Fst=0.6797). Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenog-amy predominated and autogamy played an assistant role in O. Souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.

  7. Genetic diversity in cyanobacterial symbionts of thalloid bryophytes.

    Rikkinen, Jouko; Virtanen, Viivi

    2008-01-01

    Two species of thalloid liverworts, Blasia pusilla and Cavicularia densa, form stable symbioses with nitrogen-fixing cyanobacteria. Both bryophytes promote the persistence of their cyanobacterial associations by producing specialized gemmae, which facilitate the simultaneous dispersal of the host and its nitrogen-fixing symbionts. Here the genetic diversity of cyanobacterial symbionts of Blasia and Cavicularia is examined. The results indicate that the primary symbionts of both bryophytes are closely related and belong to a specific group of symbiotic Nostoc strains. Related strains have previously been reported from hornworts and cycads, and from many terricolous cyanolichens. The evolutionary origins of all these symbioses may trace back to pre-Permian times. While the laboratory strain Nostoc punctiforme PCC 73102 has been widely used in experimental studies of bryophyte-Nostoc associations, sequence-identical cyanobionts have not yet been identified from thalloid liverworts in the field. PMID:18325923

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

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

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

    Angela R. Piergiovanni

    2010-05-01

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

  10. Genetic diversity of rhizobia nodulating native Vicia spp. in Sweden.

    Ampomah, Osei Yaw; Huss-Danell, Kerstin

    2016-05-01

    Despite the recognition that Rhizobium leguminosarum sv. viciae is the most common symbiont of Vicia species worldwide, there is no available information on rhizobia nodulating native Vicia species in Sweden. We have therefore studied the genetic diversity and phylogeny of root nodule bacteria isolated from V. cracca, V. hirsuta, V. sepium, V. tetrasperma and V. sylvatica growing in different locations in Sweden as well as an isolate each from V. cracca in Tromsø, Norway, and V. multicaulis in Siberia, Russia. Out of 25 isolates sampled from the six Vicia species in 12 different locations, there were 14 different genotypes based on the atpD, recA and nodA gene phylogenies. All isolates were classified into Rhizobium leguminosarum sv. viciae group based on the concatenated atpD and recA phylogeny and the nodA phylogeny. PMID:26924220

  11. [Genetic Diversity of Vitis vinifera L. in Azerbaijan].

    Salayeva, S J; Ojaghi, J M; Pashayeva, A N; Izzatullayeva, V I; Akhundova, E M; Akperov, Z I

    2016-04-01

    To examine the genetic diversity of Vitis vinifera L., growing in the Republic of Azerbaijan in the region near the Caspian Sea, nuclear genomes of 31 cultivated and 34 wild grapevine accessions were studied at population and individual levels using five ISSR primers. In total, 51 fragments were amplified, of which 45 were found to be polymorphic. A high level of polymorphism was revealed (the mean PPF and PIC values constituted 87.69% and 0.94, respectively). High values of the EMR, MI, and RP indices showed the effectiveness of the application of ISSR primers and the possibility of their use in further investigations in this direction. Cluster analysis based on Nei's genetic distance values showed that all genotypes could be grouped into seven main clusters. Furthermore, no differences between the wild and cultivated grape wine accessions were revealed. For instance, there was no distinct distribution of the accessions according to their geographical localization. On the basis of the PIC values, the group of cultivars from Absheron Peninsula--was distinguished by the highest polymorphism level (PIC = 0.36). Natural populations from the Guba and Shabran regions were characterized by a relatively low polymorphism level (PIC = 0.31 and PIC = 0.28, respectively); and a wild population from Nabran demonstrated the lowest polymorphism level (PIC = 0.25). The data obtained confirmed paleontological and historical data of different periods, provide the supposition that Azerbaijan is the center of diversity of V. vinifera L. In addition, our data indicate that Azerbaijan grape landraces originated from local wild forms. PMID:27529978

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

    Zhaoxia Cui; Huan Zhang; Linsheng Song; Feng You

    2011-01-01

    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...

  13. Genetic diversity among sea otter isolates of Toxoplasma gondii

    Sundar, N.; Cole, R.A.; Thomas, N.J.; Majumdar, D.; Dubey, J.P.; Su, C.

    2008-01-01

    Sea otters (Enhydra lutris) have been reported to become infected with Toxoplasma gondii and at times succumb to clinical disease. Here, we determined genotypes of 39 T. gondii isolates from 37 sea otters in two geographically distant locations (25 from California and 12 from Washington). Six genotypes were identified using 10 PCR-RFLP genetic markers including SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico, and by DNA sequencing of loci SAG1 and GRA6 in 13 isolates. Of these 39 isolates, 13 (33%) were clonal Type II which can be further divided into two groups at the locus Apico. Two of the 39 isolates had Type II alleles at all loci except a Type I allele at locus L358. One isolate had Type II alleles at all loci except the Type I alleles at loci L358 and Apico. One isolate had Type III alleles at all loci except Type II alleles at SAG2 and Apico. Two sea otter isolates had a mixed infection. Twenty-one (54%) isolates had an unique allele at SAG1 locus. Further genotyping or DNA sequence analysis for 18 of these 21 isolates at loci SAG1 and GRA6 revealed that there were two different genotypes, including the previously identified Type X (four isolates) and a new genotype named Type A (14 isolates). The results from this study suggest that the sea otter isolates are genetically diverse.

  14. Population structure and genetic diversity of moose in Alaska.

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P moose in Alaska with population expansion from interior Alaska westward toward the coast. PMID:18836148

  15. SSRs transferability and genetic diversity of three allogamous ryegrass species.

    Guo, Zhi-Hui; Fu, Kai-Xin; Zhang, Xin-Quan; Zhang, Cheng-Lin; Sun, Ming; Huang, Ting; Peng, Yan; Huang, Lin-Kai; Yan, Yan-Hong; Ma, Xiao

    2016-02-01

    Simple sequence repeat (SSR) markers are widely applied in studies of plant molecular genetics due to their abundance in the genome, codominant nature, and high repeatability. However, microsatellites are not always available for the species to be studied and their isolation could be time- and cost-consuming. To investigate transferability in cross-species applications, 102 primer pairs previously developed in ryegrass and tall fescue were amplified across three allogamous ryegrass species including Lolium rigidum, Lolium perenne and Lolium multiflorum. Their highly transferability (100%) were evidenced. While, most of these markers were multiple loci, only 17 loci were selected for a robust, single-locus pattern, which may be due to the recentness of the genome duplication or duplicated genomic regions, as well as speciation. A total of 87 alleles were generated with an average of 5.1 per locus. The mean polymorphism information content (PIC) and observed heterozygosity (Ho) values at genus was 0.5532 and 0.5423, respectively. Besides, analysis of molecular variance (AMOVA) revealed that all three levels contributed significantly to the overall genetic variation, with the species level contributing the least (P<0.001). Also, the unweighted pair group method with arithmetic averaging dendrogram (UPGMA), Bayesian model-based STRUCTURE analysis and the principal coordinate analysis (PCoA) showed that accessions within species always tended to the same cluster firstly and then to related species. The results showed that these markers developed in related species are transferable efficiently across species, and likely to be useful in analyzing genetic diversity. PMID:26874459

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

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

    2015-08-01

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

  17. Genetic diversity and biogeography of red turpentine beetle Dendroctonus valens in its native and invasive regions

    Yan-Wen Cai; Xin-Yue Cheng; Ru-Mei Xu; Dong-Hong Duan; Lawrence R. Kirkendall

    2008-01-01

    Sequences of 479 bp region of the mitochondrial COI gene were applied to detect population genetic diversity and structure of Dendroctonus valens populations. By comparing the genetic diversity between native and invasive populations, it was shown that the genetic diversity of Chinese populations was obviously lower than that of native populations with both indices of haplotype diversity and Nei's genetic diversity, suggesting genetic bottleneck occurred in the invasive process of D. valens, and was then followed by a relatively quick population buildup. According to phylogenetic analyses of haplotypes, we suggested that the origin of the Chinese population was from California, USA. Phylogenetic and network analysis of native populations of D. valens revealed strong genetic structure at two distinct spatial and temporal scales in North America. The main cause resulting in current biogeographic pattern was supposedly due to recycled glacial events. Meanwhile, a cryptic species might exist in the Mexican and Guatemalan populations.

  18. Does population size affect genetic diversity? A test with sympatric lizard species.

    Hague, M T J; Routman, E J

    2016-01-01

    Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations. PMID:26306730

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

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

    2013-01-01

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

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

    Ming-Cheng Luo

    2013-03-01

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

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

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

    2014-01-01

    Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions

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

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

    2003-01-01

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

  3. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

    Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

    2016-01-01

    Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. PMID:26663614

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

    Engelsma, K.A.

    2012-01-01

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

  5. Cryptosporidium within-host genetic diversity: systematic bibliographical search and narrative overview.

    Grinberg, Alex; Widmer, Giovanni

    2016-07-01

    Knowledge of the within-host genetic diversity of a pathogen often has broad implications for disease management. Cryptosporidium protozoan parasites are among the most common causative agents of infectious diarrhoea. Current limitations of in vitro culture impose the use of uncultured isolates obtained directly from the hosts as operational units of Cryptosporidium genotyping. The validity of this practice is centred on the assumption of genetic homogeneity of the parasite within the host, and genetic studies often take little account of the within-host genetic diversity of Cryptosporidium. Yet, theory and experimental evidence contemplate genetic diversity of Cryptosporidium at the within-host scale, but this diversity is not easily identified by genotyping methods ill-suited for the resolution of DNA mixtures. We performed a systematic bibliographical search of the occurrence of within-host genetic diversity of Cryptosporidium parasites in epidemiological samples, between 2005 and 2015. Our results indicate that genetic diversity at the within-host scale, in the form of mixed species or intra-species diversity, has been identified in a large number (n=55) of epidemiological surveys of cryptosporidiosis in variable proportions, but has often been treated as a secondary finding and not analysed. As in malaria, there are indications that the scale of this diversity varies between geographical regions, perhaps depending on the prevailing transmission pathways. These results provide a significant knowledge base from which to draw alternative population genetic structure models, some of which are discussed in this paper. PMID:27021167

  6. Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains

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

    2006-07-06

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

  7. Recognition of Spontaneous Combustion in Coal Mines Based on Genetic Clustering

    2006-01-01

    Spontaneous combustion is one of the greatest disasters in coal mines. Early recognition is important because it may be a potential inducement for other coalmine accidents. However, early recognition is difficult because of the complexity of different coal mines. Fuzzy clustering has been proposed to incorporate the uncertainty of spontaneous combustion in coal mines and it can give a clear degree of classification of combustion. Because FCM clustering tends to become trapped in local minima, a new approach of fuzzy c-means clustering based on a genetic algorithm is therefore proposed. Genetic algorithm is capable of locating optimal or near optimal solutions to difficult problems. It can be applied in many fields without first obtaining detailed knowledge about correlation. It is helpful in improving the effectiveness of fuzzy clustering in detecting spontaneous combustion. The effectiveness of the method is demonstrated by means of an experiment.

  8. Pulsed Field Gel Electrophoresis and Genetic Diversity in Mycobacterium tuberculosis

    Mohammad Poyeede

    2013-07-01

    Full Text Available AbstractBackground and objective: Tuberculosis is a considerable public health problem due to its high risk of person-to-person transmission, morbidity, and mortality especially in developing countries. According to the World Health Organization there is the emergence of multi-drug resistant M. tuberculosis and the association of TB with HIV has led to TB being declared. Molecular genotyping methods are important in detecting the dominance of transmission or reinfection in a population. During one year study genotyping of 100 of M. tuberculosis (M.t. isolates from patients referred to Pasteur Institute of Iran were accomplished with PFGE method. Material and methods: After identification of M.t. isolates and performing of antibiotic susceptibility test using standard methods, Melted Incert agarose and lysozyme were mixed with bacterial suspension to prepare PFGE plaques. After lyses and washing process the plaques digested with XbaI restriction enzyme. Finally the digested DNA fragments on 1% agarose with PFGE method were stained with ethidium bromide and analyzed with GelcomparII software.Results: Dendrogram of genetic diversity among 100 M.t. isolates were obtained in comparison of molecular weight marker and revealed two common types. Pulsotype A with 71 isolates and just one MDR and pulsotype B included 29 isolates and 3 MDR cases. No correlation between antibiotypes and pulsotypes were observed.Conclusion: It is very important to know about the existence of any clonal expansion of special M.t. genotypes with resistant strains. Our research shows 3 MDR isolates into the low incidence pulsotype B which could be an alarm for more accurate MDR-TB surveillance program. Probably such observed limited polymorphism may be due to conservation of restriction sites of XbaI enzyme. In order to investigate the genetic relatedness of isolates using other restriction enzymes and different molecular typing methods simultaneously were recommended.

  9. Genetic diversity among isolates of stemphylium solani from cotton

    MEHTA Y.R.

    2001-01-01

    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.

  10. Genetic Diversity in A Core Subset of Wild Barley Germplasm

    Yong-Bi Fu

    2012-06-01

    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.

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

    Grünwald Niklaus J

    2011-02-01

    Full Text Available Abstract Background Phytophthora infestans (Mont. de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana and tree tomato (Solanum betaceum, all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, β-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.

  12. Genetic structure and diversity of Oryza sativa L.in Guizhou, China

    ZHANG DongLing; CAO YongSheng; WANG XiangKun; LI ZiChao; ZHANG HongLiang; WEI XingHua; QI YongWen; WANG MeiXing; SUN JunLi; DING Li; TANG ShengXiang; QIU Zong'En

    2007-01-01

    Preserving many kinds of rice resources and rich variations, Guizhou Province is one of the districts with the highest genetic diversity of cultivated rice (Oryza sativa L.) in China. In the current research, genetic diversity and structure of 537 accessions of cultivated rice from Guizhou were studied using 36 microsatellite markers and 39 phenotypic characters. The results showed that the model-based genetic structure was the same as genetic-distance-based one using SSRs but somewhat different from the documented classification (mainly based on phenotype) of two subspecies. The accessions being classified into indica by phenotype but japonica by genetic structure were much more than that being classified into japonica by phenotype but indica by genetic structure. Like Ding Ying's taxonomic system of cultivated rice, the subspecific differentiation was the most distinct differentiation within cultivated rice. But the differentiation within indica or japonica population was different: japonica presented clearer differentiation between soil-watery ecotypes than indica, and indica presented clearer differentiation between seasonal ecotypes than japonica. Cultivated rices in Guizhou revealed high genetic diversity at both DNA and phenotypic levels. Possessing the highest genetic diversity and all the necessary conditions as a center of genetic diversity, region Southwestern of Guizhou was suggested as the center of genetic diversity of O. sativa L. from Guizhou.

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

    VIVI YUSKIANTI

    2012-09-01

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

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

    Emmanuvel Rajan, K.

    2006-12-01

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

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

    K Sankar

    2011-05-01

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

  16. Investigation of Web Mining Optimization Using Microbial Genetic Algorithm

    Dipali Tungar

    2014-02-01

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

  17. New insights into the genetic diversity of zooxanthellae in Mediterranean anthozoans

    Casado-Amezúa, Pilar; Machordom, Annie; Bernardo, João; González-Wangüemert, Mercedes

    2014-01-01

    Symbiotic dinoflagellates of the genus Symbiodinium, also called zooxanthellae, are found in association with a wide diversity of shallow-water anthozoans. The Symbiodinium genus includes numerous lineages, also referred to as clades or phylotypes, as well as a wide diversity of genetic sub-clades and sub-phylotypes. There are few studies characterizing the genetic diversity of zooxanthellae in Mediterranean anthozoans. In this study, we included anthozoans from the We...

  18. Genetic diversity of bovine Neospora caninum determined by microsatellite markers.

    Salehi, N; Gottstein, B; Haddadzadeh, H R

    2015-10-01

    Neospora caninum is one of the most significant parasitic organisms causing bovine abortion worldwide. Despite the economic impact of this infection, relatively little is known about the genetic diversity of this parasite. In this study, using Nc5 and ITS1 nested PCR, N. caninum has been detected in 12 brain samples of aborted fetuses from 298 seropositive dairy cattle collected from four different regions in Tehran, Iran. These specimen (Nc-Iran) were genotyped in multilocus using 9 different microsatellite markers previously described (MS4, MS5, MS6A, MS6B, MS7, MS8, MS10, MS12 and MS21). Microsatellite amplification was completely feasible in 2 samples, semi-completely in 8 samples, and failed in 2 samples. Within the two completely performed allelic profiles of Nc-Iran strains, unique multilocus profiles were obtained for both and novel allelic patterns were found in the MS8 and MS10 microsatellite markers. The Jaccard's similarity index showed significant difference between these two strains and from other standard isolates derived from GenBank such as Nc-Liv, Nc-SweB1, Nc-GER1, KBA1, and KBA2. All samples originating from the same area showed identical allelic numbers and a correlation between the number of repeats and geographic districts was observed. PMID:25988829

  19. Exhaustive search for conservation networks of populations representing genetic diversity.

    Diniz-Filho, J A F; Diniz, J V B P L; Telles, M P C

    2016-01-01

    Conservation strategies routinely use optimization methods to identify the smallest number of units required to represent a set of features that need to be conserved, including biomes, species, and populations. In this study, we provide R scripts to facilitate exhaustive search for solutions that represent all of the alleles in networks with the smallest possible number of populations. The script also allows other variables to be added to describe the populations, thereby providing the basis for multi-objective optimization and the construction of Pareto curves by averaging the values in the solutions. We applied this algorithm to an empirical dataset that comprised 23 populations of Eugenia dysenterica, which is a tree species with a widespread distribution in the Cerrado biome. We observed that 15 populations would be necessary to represent all 249 alleles based on 11 microsatellite loci, and that the likelihood of representing all of the alleles with random networks is less than 0.0001. We selected the solution (from two with the smallest number of populations) obtained for the populations with a higher level of climatic stability as the best strategy for in situ conservation of genetic diversity of E. dysenterica. The scripts provided in this study are a simple and efficient alternative to more complex optimization methods, especially when the number of populations is relatively small (i.e., <25 populations). PMID:26909939

  20. Genetic Diversity in Gorkhas: an Autosomal STR Study.

    Preet, Kiran; Malhotra, Seema; Shrivastava, Pankaj; Jain, Toshi; Rawat, Shweta; Varte, L Robert; Singh, Sayar; Singh, Inderjeet; Sarkar, Soma

    2016-01-01

    Genotyping of highly polymorphic autosomal short tandem repeat (STR) markers is a potent tool for elucidating genetic diversity. In the present study, fifteen autosomal STR markers were analyzed in unrelated healthy male Gorkha individuals (n = 98) serving in the Indian Army by using AmpFlSTR Identifiler Plus PCR Amplification Kit. In total, 138 alleles were observed with corresponding allele frequencies ranging from 0.005 to 0.469. The studied loci were in Hardy-Weinberg Equilibrium (HWE). Heterozygosity ranged from 0.602 to 0.867. The most polymorphic locus was Fibrinogen Alpha (FGA) chain which was also the most discriminating locus as expected. Neighbor Joining (NJ) tree and principal component analysis (PCA) plot clustered the Gorkhas with those of Nepal and other Tibeto-Burman population while lowlander Indian population formed separate cluster substantiating the closeness of the Gorkhas with the Tibeto-Burman linguistic phyla. Furthermore, the dataset of STR markers obtained in the study presents a valuable information source of STR DNA profiles from personnel for usage in disaster victim identification in military exigencies and adds to the Indian database of military soldiers and military hospital repository. PMID:27580933

  1. Assessment of genetic diversity in germplasm of linseed

    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)

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

    M.J. Hasan

    2014-06-01

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

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

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

    2013-01-01

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

  4. Genetic Divergence, Implication of Diversity, and Conservation of Silkworm, Bombyx mori

    Bindroo, Bharat Bhusan; Manthira Moorthy, Shunmugam

    2014-01-01

    Genetic diversity is critical to success in any crop breeding and it provides information about the quantum of genetic divergence and serves a platform for specific breeding objectives. It is one of the three forms of biodiversity recognized by the World Conservation Union (IUCN) as deserving conservation. Silkworm Bombyx mori, an economically important insect, reported to be domesticated over 5000 years ago by human to meet his requirements. Genetic diversity is a particular concern because ...

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

    K. Anjani

    2010-03-01

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

  6. Intracolonial genetic diversity in honey bee (Apis mellifera) colonies increases pollen foraging efficiency

    Multiple mating by honey bee queens results in colonies of genotypically diverse workers. Recent studies have demonstrated that increased genetic diversity within a honey bee colony increases the variation in the frequency of tasks performed by workers. We show that genotypically diverse colonies, ...

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

    Groenen Martien AM

    2002-09-01

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

  8. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes

    Fontaine, Albin; Ar Gouilh, Meriadeg; Moltini-Conclois, Isabelle

    2016-01-01

    Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. PMID:27304978

  9. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes.

    Lequime, Sebastian; Fontaine, Albin; Ar Gouilh, Meriadeg; Moltini-Conclois, Isabelle; Lambrechts, Louis

    2016-06-01

    Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. PMID:27304978

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

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

    2013-01-01

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

  11. Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers

    CHEN Zhong; ZHAO Ru; GU Senchang; YAN Wen; CHENG Zhou; CHEN Muhong; LU Weifeng; WANG Shuhong; LU Baorong; LU Jun; ZHANG Fan; XIANG Rong; XIAO Shangbin; YAN Pin

    2006-01-01

    Genetic diversity is the basic and most important component of biodiversity. It is essential for the effective conservation and utilization of genetic resources to accurately estimate genetic diversity of the targeted species and populations. This paper reports analyses of genetic diversity of a wild soybean population using three molecular marker technologies (AFLP, ISSR and SSR), and computer simulation studies of randomly selected subsets with different sample size (5-90 individuals) drawn 50 times from a total of 100 wild soybean individuals. The variation patterns of genetic diversity indices, including expected heterozygosity (He), Shannon diversity index (/), and percentage of polymorphic loci (P), were analyzed to evaluate changes of genetic diversity associated with the increase of individuals in each subset. The results demonstrated that (1) values of genetic diversity indices of the same wild soybean population were considerably different when estimated by different molecular marker techniques; (2) genetic diversity indices obtained from subsets with different sample sizes also diverged considerably; (3) P values were relatively more reliable for comparing genetic diversity detected by different molecular marker techniques; and (4) different diversity indices reached 90% of the total genetic diversity of the soybean population quite differently in terms of the sample size (number of individuals) analyzed.When using the P value as a determinator, 30-40individuals could capture over 90% of the total genetic diversity of the wild soybean population. Results from this study provide a strong scientific basis for estimating genetic diversity and for strategic conservation of plant species.

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

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

    Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

  13. Sampling strategy for wild soybean (Glycine soja) populations based on their genetic diversity and fine-scale spatial genetic structure

    ZHU Weiyue; ZHOU Taoying; ZHONG Ming; LU Baorong

    2007-01-01

    A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated.Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples),in addition to investigating the fine-scale spatial genetic structure within the population.The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88,expected heterozygosity (He) 0.431,Shannon diversity index (/) 0.699,and percentage of polymorphic loci (P) 100%.Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation.The regression model of the four diversity indexes with the change of sample sizes was computed.As a result,27-52 individuals can reach 95% of total genetic variability of the population.Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m.The study provided a scientific basis for the sampling strategy of wild soybean populations.

  14. An adaptive genetic algorithm with diversity-guided mutation and its global convergence property

    李枚毅; 蔡自兴; 孙国荣

    2004-01-01

    An adaptive genetic algorithm with diversity-guided mutation, which combines adaptive probabilities of crossover and mutation was proposed. By means of homogeneous finite Markov chains, it is proved that adaptive genetic algorithm with diversity-guided mutation and genetic algorithm with diversity-guided mutation converge to the global optimum if they maintain the best solutions, and the convergence of adaptive genetic algorithms with adaptive probabilities of crossover and mutation was studied. The performances of the above algorithms in optimizing several unimodal and multimodal functions were compared. The results show that for multimodal functions the average convergence generation of the adaptive genetic algorithm with diversity-guided mutation is about 900 less than that of adaptive genetic algorithm with adaptive probabilities and genetic algorithm with diversity-guided mutation, and the adaptive genetic algorithm with diversity-guided mutation does not lead to premature convergence. It is also shown that the better balance between overcoming premature convergence and quickening convergence speed can be gotten.

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

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

    2013-01-01

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

  16. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation

    Pradeep Singh; Akshay Nag; Rajni Parmar; Sneha Ghosh; Brijmohan Singh Bhau; Ram Kumar Sharma

    2015-12-01

    The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (m : 3.37), low genetic differentiation (ST : 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  17. Characterization of bacterial diversity associated with calcareous deposits and drip-waters, and isolation of calcifying bacteria from two Colombian mines.

    García G, Mariandrea; Márquez G, Marco Antonio; Moreno H, Claudia Ximena

    2016-01-01

    Bacterial carbonate precipitation has implications in geological processes and important biotechnological applications. Bacteria capable of precipitating carbonates have been isolated from different calcium carbonate deposits (speleothems) in caves, soil, freshwater and seawater around the world. However, the diversity of bacteria from calcareous deposits in Colombia, and their ability to precipitate carbonates, remains unknown. In this study, conventional microbiological methods and molecular tools, such as temporal temperature gradient electrophoresis (TTGE), were used to assess the composition of bacterial communities associated with carbonate deposits and drip-waters from two Colombian mines. A genetic analysis of these bacterial communities revealed a similar level of diversity, based on the number of bands detected using TTGE. The dominant phylogenetic affiliations of the bacteria, determined using 16S rRNA gene sequencing, were grouped into two phyla: Proteobacteria and Firmicutes. Within these phyla, seven genera were capable of precipitating calcium carbonates: Lysinibacillus, Bacillus, Strenotophomonas, Brevibacillus, Methylobacterium, Aeromicrobium and Acinetobacter. FTIR and SEM/EDX were used to analyze calcium carbonate crystals produced by isolated Acinetobacter gyllenbergii. The results showed that rhombohedral and angular calcite crystals with sizes of 90μm were precipitated. This research provides information regarding the presence of complex bacterial communities in secondary carbonate deposits from mines and their ability to precipitate calcium carbonate from calcareous deposits of Colombian mines. PMID:26686610

  18. Mapping genetic and phylogenetic diversity of a temperate forest using remote sensing based upscaling methods

    Escriba, C. G.; Yamasaki, E.; Leiterer, R.; Tedder, A.; Shimizu, K.; Morsdorf, F.; Schaepman, M. E.

    2015-12-01

    Functioning and resilience of forest ecosystems under environmental pressures increases when biodiversity at genetic, species, canopy and ecosystem level is higher. Therefore mapping and monitoring diversity becomes a necessity to assess changes in ecosystems and understanding their consequences. Diversity can be assessed by using different metrics, such as diversity of functional traits or genetic diversity amongst others. In-situ approaches have provided useful, but usually spatially constrained information, often dependent on expert knowledge. We propose using remote sensing in combination with in-situ sampling at different spatial scales. We map phylogenetic and genetic diversity using airborne imaging spectroscopy in combination with terrestrial and airborne laser scanning, as well as exhaustive in-situ sampling schemes. To this end, we propose to link leaf optical properties using a taxonomic approach (spectranomics) to genetic and phylogenetic diversity. The test site is a managed mixed temperate forest on the south-facing slope of Laegern Mountain, Switzerland (47°28'42.0" N, 8°21'51.8" E, 682 m.a.s.l.). The intensive sampling area is roughly 300m x 300m and dominant species are European beech (Fagus sylvatica) and Ash (Fraxinus excelsior). We perform phylogenetic and intraspecific genetic variation analyses for the five most dominant tree species at the test site. For these species, information on functional biochemical and architectural plant traits diversity is retrieved from imaging spectroscopy and laser scanning data and validated with laboratory and in-situ measurements. To assess regional-scale genetic diversity, the phylogenetic and genetic signals are quantified using the remote sensing data, resulting in spatially distributed intra-specific genetic variation. We discuss the usefulness of combined remote sensing and in-situ sampling, to bridge diversity scales from genetic to canopy level.

  19. Genetic diversity of Swiss sheep breeds in the focus of conservation research.

    Glowatzki-Mullis, M-L; Muntwyler, J; Bäumle, E; Gaillard, C

    2009-04-01

    There is constant pressure to improve evaluation of animal genetic resources in order to prevent their erosion. Maintaining the integrity of livestock species as well as their genetic diversity is of paramount interest for long-term agricultural policies. One major use of DNA techniques in conservation is to reveal genetic diversity within and between populations. Forty-one microsatellites were analysed to assess genetic diversity in nine Swiss sheep breeds and to measure the loss of the overall diversity when one breed would become extinct. The expected heterozygosities varied from 0.65 to 0.74 and 10.8% of the total genetic diversity can be explained by the variation among breeds. Based on the proportion of shared alleles, each of the nine breeds were clearly defined in their own cluster in the neighbour-joining tree describing the relationships among the breeds. Bayesian clustering methods assign individuals to groups based on their genetic similarity and infer the number of populations. In STRUCTURE, this approach pooled the Valais Blacknose and the Valais Red. With BAPS method the two Valais sheep breeds could be separated. Caballero & Toro approach (2002) was used to calculate the loss or gain of genetic diversity when each of the breeds would be removed from the set. The changes in diversity based on between-breed variation ranged from -12.2% (Valais Blacknose) to 0% (Swiss Black Brown Mountain and Mirror Sheep); based on within-breed diversity the removal of a breed could also produce an increase in diversity (-0.6% to + 0.6%). Allelic richness ranged from 4.9 (Valais Red) to 6.7 (Brown Headed Meat sheep and Red Engadine Sheep). Breed conservation decisions cannot be limited to genetic diversity alone. In Switzerland, conservation goals are embedded in the desire to carry the cultural legacy over to future generations. PMID:19320774

  20. Gene Flow and Genetic Diversity of a Broadcast-Spawning Coral in Northern Peripheral Populations

    Yuichi Nakajima; Akira Nishikawa; Akira Iguchi; Kazuhiko Sakai

    2010-01-01

    Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadca...

  1. Population structure and genetic diversity of the perennial medicinal shrub Plumbago

    Panda, Sayantan; Naik, Dhiraj; Kamble, Avinash

    2015-01-01

    Knowledge of the natural genetic variation and structure in a species is important for developing appropriate conservation strategies. As genetic diversity analysis among and within populations of Plumbago zeylanica remains unknown, we aimed (i) to examine the patterns and levels of morphological and genetic variability within/among populations and ascertain whether these variations are dependent on geographical conditions; and (ii) to evaluate genetic differentiation and population structure...

  2. Chapter 10: Mining genome-wide genetic markers.

    Xiang Zhang

    Full Text Available Genome-wide association study (GWAS aims to discover genetic factors underlying phenotypic traits. The large number of genetic factors poses both computational and statistical challenges. Various computational approaches have been developed for large scale GWAS. In this chapter, we will discuss several widely used computational approaches in GWAS. The following topics will be covered: (1 An introduction to the background of GWAS. (2 The existing computational approaches that are widely used in GWAS. This will cover single-locus, epistasis detection, and machine learning methods that have been recently developed in biology, statistic, and computer science communities. This part will be the main focus of this chapter. (3 The limitations of current approaches and future directions.

  3. Levels of genetic diversity and taxonomic status of Epinephelus species in United Arab Emirates fish markets.

    Ketchum, Remi N; Dieng, Mame M; Vaughan, Grace O; Burt, John A; Idaghdour, Youssef

    2016-04-30

    Understanding the patterns of genetic diversity of fish species is essential for marine conservation and management. This is particularly important in the Arabian Gulf where marine life is subject to extreme environmental conditions that could impact genetic diversity. Here we assess genetic diversity of the most commercially important fish in the United Arab Emirates; groupers (Epinephelus spp.). Sequencing of 973 bp mitochondrial DNA from 140 tissue samples collected in four main fish markets revealed 58 haplotypes clustered within three groups. Data analysis revealed the presence of three distinct Epinephelus species being marketed as one species (hammour): Epinephelus coioides, Epinephelus areolatus and Epinephelus bleekeri. We report species-specific genetic markers and demonstrate that all three species exhibit relatively low levels of genetic variation, reflecting the effect of overfishing and environmental pressures. In light of the genetic evidence presented here, conservation and management of groupers in the UAE warrant the implementation of species-specific measures. PMID:26656801

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

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

    2013-01-01

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

  5. Genetic diversity in Chinese modern wheat varieties revealed by microsatellite markers

    HAO; Chenyang; WANG; Lanfen; ZHANG; Xueyong; YOU; Guangxia; DONG; Yushen; JIA; Jizeng; LIU; Xu; SHANG; Xunwu; LIU; Sancai; CAO; Yongsheng

    2006-01-01

    Genetic diversity of 1680 modern varieties in Chinese candidate core collections was analyzed at 78 SSR loci by fluorescence detection system. A total of 1336 alleles were detected, of which 1253 alleles could be annotated into 71 loci. For these 71 loci, the alleles ranged from 4 to 44 with an average of 17.6, and the PIC values changed from 0.19 to 0.89 with an average of 0.69. (1) In the three genomes of wheat, the average genetic richness was B>A>D, and the genetic diversity indexes were B>D>A. (2) Among the seven homoeologous groups, the average genetic richness was 2=7>3>4>6>5>1, and the genetic diversity indexes were 7>3>2>4>6>5>1. As a whole, group 7 possessed the highest genetic diversity, while groups 1 and 5 were the lowest. (3) In the 21 wheat chromosomes, 7A, 3B and 2D possessed much higher genetic diversity, while 2A, 1B, 4D, 5D and 1D were the lowest. (4) The highest average genetic diversity index existed in varieties bred in the 1950s, and then it declined continually. However, the change tendency of genetic diversity among decades was not greatly sharp. This was further illustrated by changes of the average genetic distance between varieties. In the 1950s it was the largest (0.731). Since the 1960s, it has decreased gradually (0.711, 0.706, 0.696, 0.695). The genetic base of modern varieties is becoming narrower and narrower. This should be given enough attention by breeders and policy makers.

  6. Genetic diversity and differentiation of Mongolian indigenous cattle populations

    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

  7. Hybrid origin of a cichlid population in Lake Malawi: implications for genetic variation and species diversity.

    Smith, Peter F; Konings, Ad; Kornfield, Irv

    2003-09-01

    The importance of species recognition to taxonomic diversity among Lake Malawi cichlids has been frequently discussed. Hybridization - the apparent breakdown of species recognition - has been observed sporadically among cichlids and has been viewed as both a constructive and a destructive force with respect to species diversity. Here we provide genetic evidence of a natural hybrid cichlid population with a unique colour phenotype and elevated levels of genetic variation. We discuss the potential evolutionary consequences of interspecific hybridization in Lake Malawi cichlids and propose that the role of hybridization in generating both genetic variability and species diversity of Lake Malawi cichlids warrants further consideration. PMID:12919487

  8. Genetic Diversity and Population Structure in a Legacy Collection of Spring Barley Landraces Adapted to a Wide Range of Climates

    Walther, Alexander; Özkan, Hakan; Graner, Andreas; Kilian, Benjamin

    2014-01-01

    Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type – and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches. PMID:25541702

  9. Genetic diversity and population structure in a legacy collection of spring barley landraces adapted to a wide range of climates.

    Raj K Pasam

    Full Text Available Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485 adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type - and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches.

  10. Reduction of Genetic Diversity of the Harpy Eagle in Brazilian Tropical Forests

    2016-01-01

    Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest. PMID:26871719