Full Text Available Abstract Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1 Unique Events Polymorphism (UEP (2 Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.
Full Text Available SciELO Brazil | Language: English Abstract in english In this paper we present a spatial stochastic model for genetic recombination, that answers if diversity is preserved in an infinite population of recombinat-ing individuals distributed spatially. We show that, for finite times, recombination may maintain all the various potential different types, b [...] ut when time grows infinitely, the diversity of individuals extinguishes off. So under the model premisses, recombination and spatial localization alone are not enough to explain diversity in a population. Further we discuss an application of the model to a controversy regarding the diversity of "Major Histocompatibility Complex" (MHC).
T. C., Coutinho; T.T.da, Silva; G.L., Toledo.
The range of genetic diversity within human populations is enormous. Genetic susceptibility to common chronic disease is a significant part of this genetic diversity, which also includes a variety of rare clear-cut inherited diseases. Modern DNA-based genomic analysis can now routinely lead to the identification of genes involved in disease susceptibility, provides the basis for genetic counselling in affected families, and more widely for a genetically targeted approach to disease prevention...
Bodmer, W. F.
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...
Sequeira, Tiago; Santos, Marcelo; Ferreira-lopes, Alexandra
With increasing availability and power of parallel computational resources, attention is drawn to the question of how best to apply those resources. Instead of simply finding the same answers more quickly, this thesis describes how parallel computational resources are used to explore disparate regions of a solution space by using diversity to steer the solution paths away from each other, thereby discouraging strictly greedy behavior. The formulation of models in a concept...
Fuzzy Modeling and Genetic Algorithms for Data Mining and Exploration is a handbook for analysts, engineers, and managers involved in developing data mining models in business and government. As you'll discover, fuzzy systems are extraordinarily valuable tools for representing and manipulating all kinds of data, and genetic algorithms and evolutionary programming techniques drawn from biology provide the most effective means for designing and tuning these systems.You don't need a background in fuzzy modeling or genetic algorithms to benefit, for this book provides it, along with detailed instruction in methods that you can immediately put to work in your own projects. The author provides many diverse examples and also an extended example in which evolutionary strategies are used to create a complex scheduling system.* Written to provide analysts, engineers, and managers with the background and specific instruction needed to develop and implement more effective data mining systems.* Helps you to understand the...
Genetic diversity of 62 genotypes of irrigated rice originating from BRRI, IRRI and China were studied through Mahalanobis D2statistic. The genotypes were grouped into five clusters. The cluster II and IV contained the highest number of genotypes (16) and the cluster I contained the lowest (7). The highest intra cluster distance was noticed for the cluster I and the lowest for cluster III. The highest inter cluster distance was observed between cluster I and cluster IV followed by ...
Islam, M. R.; Faruquei, M. A. B.; Bhuiyan, M. A. R.; Biswas, P. S.; Salam, M. A.
Machupo virus and Chapare virusare members of the Tacaribe serocomplex (virus family Arenaviridae) and etiological agents of hemorrhagic fever in humans in Bolivia. The nucleotide sequences of the complete Z genes, a large fragment of the RNA-dependent RNA polymerase genes, the complete glycoprotein precursor genes, and the complete nucleocapsid protein genes of 8 strains of Machupo virus were determined to increase our knowledge of the genetic diversity among the Bolivian arenaviruses. The r...
Cajimat, Maria N. B.; Milazzo, Mary Louise; Rollin, Pierre E.; Nichol, Stuart T.; Bowen, Michael D.; Ksiazek, Thomas G.; Fulhorst, Charles F.
The need to protect crop genetic resources has sparked a growing interest in the genetic diversity maintained in traditional farming systems worldwide. Although traditional seed management has been proposed as an important determinant of genetic diversity and structure in crops, no models exist that can adequately describe the genetic effects of seed management. We present a metapopulation model that accounts for several features unique to managed crop populations. Using traditional maize agr...
Heerwaarden, J.; Eeuwijk, F. A.; Ross-ibarra, J.
This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity. In recent years, there has been a significant increase in the application of molecular genetic methods for assessing the conservation and use of plant genetic resources. Molecular techniques have been applied in the analysis of specific genes, as well as to increase understanding of gene action, generate genetic maps and assist in the development of gene transfer technologi...
Linda Mondini; Arshiya Noorani; Pagnotta, Mario A.
Machupo virus and Chapare virus are members of the Tacaribe serocomplex (virus family Arenaviridae) and etiological agents of hemorrhagic fever in humans in Bolivia. The nucleotide sequences of the complete Z genes, a large fragment of the RNA-dependent RNA polymerase genes, the complete glycoprotein precursor genes, and the complete nucleocapsid protein genes of 8 strains of Machupo virus were determined to increase our knowledge of the genetic diversity among the Bolivian arenaviruses. The results of analyses of the predicted amino acid sequences of the glycoproteins of the Machupo virus strains and Chapare virus strain 200001071 indicated that immune plasma from hemorrhagic fever cases caused by Machupo virus may prove beneficial in the treatment of Bolivian hemorrhagic fever but not hemorrhagic fever caused by Chapare virus. PMID:19041349
Cajimat, Maria N B; Milazzo, Mary Louise; Rollin, Pierre E; Nichol, Stuart T; Bowen, Michael D; Ksiazek, Thomas G; Fulhorst, Charles F
Full Text Available Genetic diversity of 62 genotypes of irrigated rice originating from BRRI, IRRI and China were studied through Mahalanobis D2statistic. The genotypes were grouped into five clusters. The cluster II and IV contained the highest number of genotypes (16 and the cluster I contained the lowest (7. The highest intra cluster distance was noticed for the cluster I and the lowest for cluster III. The highest inter cluster distance was observed between cluster I and cluster IV followed by cluster I and cluster V, cluster I and cluster III, cluster III and cluster IV and lowest between cluster IV and cluster V. The highest cluster means for yield and other three yield contributing characters are obtained from cluster I, six highest and two second highest means for yield contributing characters are found in cluster III but the lowest cluster mean for yield. Therefore more emphasis should be given on cluster I for selecting genotypes as parents for crossing with the genotypes of cluster III, which may produce new recombinants with desired traits.
In general frequent itemsets are generated from large data sets by applying association rule mining algorithms like Apriori, Partition, Pincer-Search, Incremental, Border algorithm etc., which take too much computer time to compute all the frequent itemsets. By using Genetic Algorithm (GA) we can improve the scenario. The major advantage of using GA in the discovery of frequent itemsets is that they perform global search and its time complexity is less compared to other algorithms as the genetic algorithm is based on the greedy approach. The main aim of this paper is to find all the frequent itemsets from given data sets using genetic algorithm.
Ghosh, Soumadip; Sarkar, Debasree; Sarkar, Partha Pratim; 10.5121/ijaia.2010.1411
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...
Indira, K.; Kanmani, S.
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
Banks, Sam C; Cary, Geoffrey J; Smith, Annabel L; Davies, Ian D; Driscoll, Don A; Gill, A Malcolm; Lindenmayer, David B; Peakall, Rod
Theileria parasites infect a wide range of domestic and wild ruminants worldwide, causing diseases with varying degrees of severity. A broad classification, based on the parasite's ability to transform the leukocytes of host animals, divides Theileria into two groups, consisting of transforming and non-transforming species. The evolution of transforming Theileria has been accompanied by drastic changes in its genetic makeup, such as acquisition or expansion of gene families, which are thought to play critical roles in the transformation of host cells. Genetic variation among Theileria parasites is sometimes linked with host specificity and virulence in the parasites. Immunity against Theileria parasites primarily involves cell-mediated immune responses in the host. Immunodominance and major histocompatibility complex class I phenotype-specificity result in a host immunity that is tightly focused and strain-specific. Immune escape in Theileria is facilitated by genetic diversity in its antigenic determinants, which potentially results in a loss of T cell receptor recognition in its host. In the recent past, several reviews have focused on genetic diversity in the transforming species, Theileriaparva and Theileriaannulata. In contrast, genetic diversity in Theileriaorientalis, a benign non-transforming parasite, which occasionally causes disease outbreaks in cattle, has not been extensively examined. In this review, therefore, we provide an outline of the evolution of Theileria, which includes T. orientalis, and discuss the possible mechanisms generating genetic diversity among parasite populations. Additionally, we discuss the potential implications of a genetically diverse parasite population in the context of Theileria vaccine development. PMID:25102031
Sivakumar, Thillaiampalam; Hayashida, Kyoko; Sugimoto, Chihiro; Yokoyama, Naoaki
Assessing biodiversity in forests requires a reliable and sustainable monitoring concept, which must include all levels of diversity, the genetic, the species and the landscape level. Diversity studies should not be reduced to quantitative analysis, but qualitative interpretations are an important part for the understanding of the results. Also, the linkage of terrestrial data and remote sensing data as well the implementation of abiotic and biotic data collected on existing monitoring system...
Granke O; Kenter B; Wu, Kriebitzsch; Kohl M.; Olschofsky K; Kohler R
In general frequent itemsets are generated from large data sets by applying association rule mining algorithms like Apriori, Partition, Pincer-Search, Incremental, Border algorithm etc., which take too much computer time to compute all the frequent itemsets. By using Genetic Algorithm (GA) we can improve the scenario. The major advantage of using GA in the discovery of frequent itemsets is that they perform global search and its time complexity is less compared to other algo...
Soumadip Ghosh; Sushanta Biswas; Debasree Sarkar; Partha Pratim Sarkar
Full Text Available Assessing biodiversity in forests requires a reliable and sustainable monitoring concept, which must include all levels of diversity, the genetic, the species and the landscape level. Diversity studies should not be reduced to quantitative analysis, but qualitative interpretations are an important part for the understanding of the results. Also, the linkage of terrestrial data and remote sensing data as well the implementation of abiotic and biotic data collected on existing monitoring systems are useful sources to analyse cause-effect relationships and interactions between the different aspects of diversity.
Full Text Available At first, this study described the characteristics of truck transport in surface mine, then construct the model of truck dispatching and expound working principle and application of genetic algorithm. Finally, the typical experiment, by using the MATLAB genetic algorithm toolbox for calculation, showed that using genetic algorithm to optimize mine vehicle dispatching is feasible and effective.
Xin- Ming Lu
At first, this study described the characteristics of truck transport in surface mine, then construct the model of truck dispatching and expound working principle and application of genetic algorithm. Finally, the typical experiment, by using the MATLAB genetic algorithm toolbox for calculation, showed that using genetic algorithm to optimize mine vehicle dispatching is feasible and effective.
Xin- Ming Lu; Jiu- Chuan Wei; Ming- Xiang He; Bao-Xiang Huang
Two different uranium mine waste heaps near Ronneburg, Thuringia, Germany, which contain the remains of the activity of the former uranium-mining Soviet-East German company Wismut AG, were analyzed for the occurrence of lithotrophic and chemoorganotropic leach bacteria. A total of 162 ore samples were taken up to a depth of 5 m. Cell counts of ferrous iron-, sulfur-, sulfur compound-, ammonia-, and nitrite-oxidizing bacteria were determined quantitatively by the most-probable-number technique...
Schippers, A.; Hallmann, R.; Wentzien, S.; Sand, W.
This study tested whether increasing crop genetic diversity benefited farmland biodiversity in bread wheat (Triticum aestivum) fields, using an experimental approach in which arthropod and wild plant diversity were compared in a genetically homogeneous wheat variety vs. a variety mixture. The diversity of wild plant species was not affected by crop genetic diversity. However, we showed for the first time a positive impact of crop genetic diversity on below (collembola) and aboveground arthrop...
Chateil, Carole; Goldringer, Isabelle; Tarallo, Le?a; Kerbiriou, Christian; Le Viol, Isabelle; Ponge, Jean-franc?ois; Salmon, Sandrine; Gachet, Sophie; Porcher, Emmanuelle
Genetic diversity in reproductive abiotic stress tolerance has been investigated by cotton breeders throughout the public and private sectors. The primary focus of these studies has been the evaluation of abiotic stress responses during the development of the flower prior to anthesis. Sterility in...
Uncertainty surrounding the role of Dientamoeba fragilis in human disease could be due in part to the existence of pathogenic and nonpathogenic variants. Evidence for two genetically distinct forms was obtained using PCR-restriction fragment length polymorphism analysis of ribosomal genes. Future studies in humans will need to take D. fragilis diversity into account.
Johnson, Jeanette A.; Clark, C. Graham
Full Text Available SciELO Chile | Language: English Abstract in english Amplified fragmentlength polymorphism (AFLP) markers have been used to ascertain the intensity of inherent diversity and relatedness in cotton (Gossypium spp.) plants. The effectiveness of this method to distinguish inter and intra specific difference in cotton could be handy in cultivar recognition [...] and in marker assisted parental selection tool for plant breeders. Twenty cotton cultivars belonging to Gossypium hirsutum L., and G. arborium L. from the Pakistan and US origin were used for AFLP based genetic diversity estimates. The objective of this study was to assess the level of genetic variation among some cotton cultivars belonging to the old and new world species of cotton. Four EcoRI-MseI primer-pair combinations were used forthe AFLP analysis. The AFLP data assigned the genotypes into groups that corresponded with their origin and lineage relationships and showed a narrow genetic base among these cultivars.
Full Text Available This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity. In recent years, there has been a significant increase in the application of molecular genetic methods for assessing the conservation and use of plant genetic resources. Molecular techniques have been applied in the analysis of specific genes, as well as to increase understanding of gene action, generate genetic maps and assist in the development of gene transfer technologies. Molecular techniques have also had critical roles in studies of phylogeny and species evolution, and have been applied to increase our understanding of the distribution and extent of genetic variation within and between species. These techniques are well established and their advantages as well as limitations have been realized and described in this work. Recently, a new class of advanced techniques has emerged, primarily derived from a combination of earlier, more basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques, in order to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. Some of the advanced marker techniques utilize newer classes of DNA elements, such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. The most important and recent advances made in molecular marker techniques are discussed in this review, along with their applications, advantages and limitations applied to plant sciences.
The definition of molecular diversity and the development of measures for assessing the similarity or dissimilarity of molecules are central tasks for the design of novel biologically active compounds. Combinatorial chemistry allows the coupling of mathematical optimisation methods that do not require the a priori knowledge of structure-activity relationships with the synthesis of biologically active compounds. Genetic algorithms that computationally mimic Darwinian evolution have proven to be useful in solving multidimensional problems and are now being used successfully in various areas of combinatorial chemistry. Applications have been developed that help in the selection of diverse compound libraries and in the synthesis of biologically active molecules. PMID:9691070
Full Text Available Association rule (AR mining is a data mining task that attempts to discover interesting patterns or relationships between data in large databases. Genetic algorithm (GA based on evolution principles has found its strong base in mining ARs. This paper analyzes the performance of GA in Mining ARs effectively based on the variations and modification in GA parameters. The recent works in the past seven years for mining association rules using genetic algorithm is considered for the analysis. Genetic algorithm has proved to generate more accurate results when compared to other formal methods available. The fitness function, crossover rate, and mutation rate parameters are proven to be the primary parameters involved in implementation of genetic algorithm. Variations and modifications introduced in primary GA parameters are found to have greater impact in increasing the accuracy of the system moderately. The speedup of the system is found to increase when the selection and fitness function are altered.
The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen. PMID:25674097
Zhang, Chunxia; Vornam, Barbara; Volmer, Katharina; Prinz, Kathleen; Kleemann, Frauke; Köhler, Lars; Polle, Andrea; Finkeldey, Reiner
A diversion system has been designed to carry the flow from East Fork of Coal Creek around the area proposed for mining at Thunder Basin Coal Company's (TBCC) Coal Creek mine in Campbell County, Wyoming. This paper describes the field and analysis procedures necessary to prepare the diversion design and impact evaluation, and the innovative concepts developed for the diversion system design to minimize impacts on downstream channel stability. Under the proposed diversion system design, water from the East Basin of Coal Creek will be diverted at two locations. At one location, flow will be impounded by a small dam and decanted by a pump through a pipeline into East Fork at the location of the second diversion. At this location, a training dike will be placed across the stream channel to divert flows into a diversion channel. Gravity flow along the diversion channel will deliver water to a playa area which will be converted into a detention basin by placing a small dam across its southern end. Flows up to the magnitude of the 24-hour 2-year peak flow will be passed directly through the detention basin into Middle Fork with negligible attenuation of flow rates. For less frequent events, water will be stored in the detention basin in order to prevent velocities in Lower Middle Fork from exceeding the maximum permissible velocity above which scouring may occur. Evaporation and seepage losses from the diversion system were estimated to be small and should be more than offset by the addition of water from the playa drainage basin into the Coal Creek drainage. Velocities predicted for the Lower Middle Fork after the diversion is constructed are expected to be low enough that significant erosion of the channel is not expected to occur.
Bowles, D.S.; Grant, J.L.; Humphries, W.E.; O' Hayre, A.P.
Acetobacter diazotrophicus isolates that originated from different sugarcane cultivars growing in diverse geographic regions of Mexico and Brazil were shown to have limited genetic diversity. Measurements of polymorphism in the electrophoretic mobilities of metabolic enzymes revealed that the mean genetic diversity per enzyme locus (among the four electrophoretic types distinguished) was 0.064. The results of the genetic analysis indicate that the genetic structure of A. diazotrophicus is clo...
Caballero-mellado, Jesus; Martinez-romero, Esperanza
It is a commonly held view that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations. The underlying idea, known as the ‘monoculture effect,' is well documented in agricultural studies. Low genetic diversity in the wild can result from bottlenecks (that is, founder effects), biparental inbreeding or self-fertilization, any of which might increase the risk of epidemics. Host genetic diversity could buffer populations against epidemics ...
King, Kc; Lively, Cm
Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8?million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
Prado-Martinez, Javier; Sudmant, Peter H.
Web mining has become a vast area of Research in last few years. Web Mining Which deals with the extraction of interesting knowledge from logging information produced by web server. In this paper we present a survey generate clusters using a multi objective genetic algorithm. Genetic algorithm is also a very hot area of research. In this paper we will compare the error value between FCM(Fuzzy c-means) and FCM-MOGA(Fuzzy CMeans multi objective Genetic algorithm). Genetic algorithm follows some...
Ranu Singhal; NirupamaTiwari
Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detecte...
Costa, Eula Maria M. B.; Fabiana Cristina Pimenta; Christian Luz; Valéria de Oliveira; Marília Oliveira; Elda Bueno; Silvana Petrofeza
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.
Canine monocytic ehrlichiosis is a highly prevalent disease in Brazil, where the genetic diversity of Ehrlichia canis remains undefined. In this study, we used the TRP36 gene to examine the genetic diversity of E. canis strains from naturally infected dogs residing in five distinct geographic regions in Brazil. E. canis DNA was detected in 82/126 (65%) dogs by dsb-specific PCR and E. canis was isolated in cell culture from 13 dogs. Sequences obtained from dsb genes amplified from the isolates were identical to the US E. canis strain. An extended molecular characterization based on the TRP36 gene identified two major genogroups based on differences among eight isolates. Isolates with tandem repeat amino acid sequence (TEDSVSAPA) identical to the previously reported TRP36 sequence were found in the midwest, northeast and southeast regions of Brazil, and classified into the US genogroup. A novel Brazilian genotype with a different tandem repeat sequence (ASVVPEAE) was also identified in midwest, northern and southern regions. Similarity in the N-terminal sequence of a US genogroup member with the Brazilian genogroup suggested that genomic recombination between the two genogroups may have occurred. Other subtypes within the Brazilian genogroup were also identified using C-terminal amino acid divergence. We identified two distinct major Brazilian genogroups and several subtypes based on analysis of TRP36, and such information will be useful for further genotyping and possible associations with disease severity, understanding of the genetic and antigenic variability of E. canis, and for developing strain-specific vaccines and diagnostic methods based on TRP36. PMID:23490559
Aguiar, D M; Zhang, X; Melo, A L T; Pacheco, T A; Meneses, A M C; Zanutto, M S; Horta, M C; Santarém, V A; Camargo, L M A; McBride, J W; Labruna, M B
Full Text Available The most important international document relating to the conservation of biodiversity is one adopted by theUN in Rio de Janeiro (1992 that "Convention on Biodiversity". Based on this agreement, the EU has taken a series ofmeasures to reduce genetic erosion in agriculture, which grew with the expansion of industrialized agriculture.Throughout its existence, mankind has used some 10,000 growing plant species. According to FAO statistics, today,90% of food production is ensured by some 120 growing plant species. In addition to drastic reduction in specificdiversity, the advent of industrialized agriculture has generated a process of strong genetic erosion. Old varieties andlocal varieties of crops have mostly been affected, in favour of "modern" varieties. Landraces are characterized by highheterogenity. They have the advantage of being much better adapted to biotic and abiotic stress conditions (diseases,pests, drought, low in nutrients, etc. and have excellent taste qualities, which can justify a higher price recovery thancommercial varieties. Thanks to these features, these crops need small inputs, which correspond to the concept ofsustainable development. Landraces are an invaluable genetic potential for obtaining new varieties of plants and are bestsuited for crop cultivation in ecological systems, becoming more common. Also, for long term food security in thecontext of global warming, rich genetic diversity will be require. “In situ” and “ex situ” conservation are the two majorstrategies used in the conservation of plant genetic resources. There is a fundamental difference between these twostrategies: “ex situ” conservation involves sampling, transfer and storage of a particular species population away fromthe original location, while “in situ” conservation (in their natural habitat implies that the varieties of interest,management and monitoring their place of origin takes place in the community to which they belong. These twostrategies should not be viewed as alternatives or in opposition, but a complementary approach is required. Obviously,only the on farm preservation, with traditional technologies, allows a sustainable management of the varieties, becausethese, in their natural habitat, can continue their evolutionary processes under the pressures of the environment, man,and technology. Romania, with an agricultural area of 14,722 millions Ha, still has a very rich diversity of conservationvarieties in plants growing, but they risk losing if appropriate action is taken.
Full Text Available Web mining has become a vast area of Research in last few years. Web Mining Which deals with the extraction of interesting knowledge from logging information produced by web server. In this paper we present a survey generate clusters using a multi objective genetic algorithm. Genetic algorithm is also a very hot area of research. In this paper we will compare the error value between FCM(Fuzzy c-means and FCM-MOGA(Fuzzy CMeans multi objective Genetic algorithm. Genetic algorithm follows some steps and produce optimize solution. In using GA standard deviation and iteration value also affected. In this paper we have survey various paper based on Web log mining and FCM and GA.
Full Text Available Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater and stressful conditions (diluted seawater. The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation between AFLP diversity and population fitness overall; however, AFLP markers performed poorly at detecting modest but consequential losses of genetic diversity. High diversity lines in the stressful environment showed some evidence of relative improvement as the experiment progressed while the low diversity lines did not. Conclusions The combined effects of reduced average fitness and increased variability contributed to increased extinction rates for very low diversity populations. More modest losses of genetic diversity resulted in measurable decreases in population fitness; AFLP markers did not always detect these losses. However when AFLP markers indicated lost genetic diversity, these losses were associated with reduced population fitness.
McGreevy Thomas J
It is a commonly held view that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations. The underlying idea, known as the 'monoculture effect,' is well documented in agricultural studies. Low genetic diversity in the wild can result from bottlenecks (that is, founder effects), biparental inbreeding or self-fertilization, any of which might increase the risk of epidemics. Host genetic diversity could buffer populations against epidemics in nature, but it is not clear how much diversity is required to prevent disease spread. Recent theoretical and empirical studies, particularly in Daphnia populations, have helped to establish that genetic diversity can reduce parasite transmission. Here, we review the present theoretical work and empirical evidence, and we suggest a new focus on finding 'diversity thresholds.' PMID:22713998
King, K C; Lively, C M
Aknowledgment The area of Sveagruva have experienced several periods of coal mining. This study aim to evaluating changes in vegetation composition, species distributions and genetic structure using a combination of field and molecular analyses, to identify whether or not coal mining have effected plant life in Svea. Investigations on species and gene level were done on two Luzula species, L. confusa Lindeb. and L. nivalis (Laest.) Spreng. No direct correlation was found, and the soil pH ex...
Skottvoll, Bente Sved
The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers for each of the main livestock species, FAO has promoted the meta-analysis of local datasets, to achieve a global view of molecular genetic diversity. Analysis within the EU Globaldiv project of two ...
Ajmone Marsan, Paolo; Colli, Licia; Han, Jian Lin; Achilli, A.; Lancioni, H.; Joost, Ste?phane; Crepaldi, Paola; Pilla, Fabio; Stella, Alessandra; Taberlet, Pierre; Boettcher, Paul; Negrini, Riccardo; Lenstra, J. A.
Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely ...
Lv, J.; Qi, J.; Shi, Q.; Shen, D.; Zhang, S.; Shao, G.; Li, H.; Sun, Z.; Weng, Y.; Shang, Y.; Gu, X.; Li, X.; Zhu, X.; Zhang, J.; Treuren, R.
In this work, 22 Italian and 36 Spanish accessions from various germplasm repositories were studied at 16 microsatellite markers in order to study: (1) the genetic diversity in the Italian cultivars and (2) their genetic relationships with Spanish cultivated varieties. The analysis of SSR data showed a high level of genetic diversity among Italian cultivars. Several synonymies reported in literature were confirmed and new cases were identified. A dendrogram generated by UPGMA cluster analy...
Botta, Roberto; Boccacci, Paolo; Torello Marinoni, Daniela
Broussonetia papyrifera is an important native tree species with high economic value in southwest China. Its resources are drastically reduced because of over-harvesting and habitat fragmentation. In this study, 17 natural populations of B. papyrifera were analyzed using inter-simple sequence repeat (ISSR) markers to assess the genetic diversity and population structure. In total, 100 bands were obtained from 16 ISSR primers. The B. papyrifera populations showed relatively high genetic diversity at the species level [percentage of polymorphic bands (PPB): 96%; Nei's genetic diversity (HE): 0.3074; Shannon's information index (I): 0.4617], while the genetic diversity at the population level was relatively low (PPB: 53.2%; HE: 0.1826; I: 0.2735). Relatively high level of genetic differentiation among populations (41%) was disclosed by analysis of molecular variance, which agrees with the Nei's genetic diversity statistics (40.59%) and Shannon's information measure (40.76%). Gene flow among populations (NM) was only 0.7318. A significant correlation was observed between genetic and geographic distance among the studied populations (r=0.2948). We conjectured that the genetic diversity of B. papyrifera resulted from human disturbance, habitat fragmentation, small effective population size, and geographic barrier. Given the high genetic differentiation among populations, some utilization and conservation strategies were proposed. This study provides a reference for the sustainable use of the species in southwest China. PMID:25222255
Liao, S X; Deng, Z H; Cui, K; Cui, Y Z; Zhang, C H
Full Text Available Prunus davidiana, which is a wild species, can be used as rootstocks for cultivation of fruit trees, breeding germplasm for improving resistance to diseases and insects, pioneer trees for recovering vegetation in arid areas, decoration trees for parks and gardens, and a potential medicinal plant for human health. Despite the valuable characteristics of P. davidiana, the genetic variations of resources of P. davidiana remain unclear. In this study, we used seven natural populations (GE; GH; ST; SF; SJ; SY; NX short for Heshui, Gansu; Huating Gansu; Taibai, Shaanxi; Fuxian, Shaanxi; Jiaocheng, Shanxi; Yangquan, Shanxi; Xiji, Ningxia, respectively of P. davidiana collected at distribution center in China to generate a fingerprint using 15 SSR markers by multifluorophore fragment analysis to assess transportability of the markers, genetic diversity and genetic structure within and among populations. Our data show that a 92% transportability rate was found from closely related species of P. davidiana based on SSR markers developed, and DNA polymorphisms were also detected among accessions by the selected SSR markers. The SSR markers amplified 137 alleles in total for all accessions with an average value of 9.13 alleles, ranging from the highest value of 15 alleles for UDP96-013 to the lowest value of 3 alleles for CPPCT017. Rare alleles, present at less than or equal to 5% of all accessions by marker, showed the highest value in BPPCT 020. By analyzing all accessions, the majority of the 192 accessions from seven populations were found to cluster together according to the given populations, while the minority from the given populations was distributed within clusters. The SY population appeared to have the most diversity among populations, followed by the NX population according to comprehensive analysis of all indices. The seven populations analyzed by unweighted parsimony and principal coordinate analysis were divided into two groups: ST, SY and SF; NX, GE, SJ and GH. A stark difference was found in the genetic variation—with 16% among populations and 84% within populations. Our results from this study imply that most SSR markers developed from related species can be used for genetic analyses of P. davidiana; some markers have more relevant applications for genetic analyses such as UDP96-013 for diversity evaluation and BPPCT 020 for mining rare alleles in P. davidiana; SY and NX are preferred when considering conservation and agronomic utilization.
Full Text Available Abstract Background Ribonuclease 8 is a member of the RNase A family of secretory ribonucleases; orthologs of this gene have been found only in primate genomes. RNase 8 is a divergent paralog of RNase 7, which is lysine-enriched, highly conserved, has prominent antimicrobial activity, and is expressed in both normal and diseased skin; in contrast, the physiologic function of RNase 8 remains uncertain. Here, we examine the genetic diversity of human RNase 8, a subject of significant interest given the existence of functional pseudogenes (coding sequences that are otherwise intact but with mutations in elements crucial for ribonucleolytic activity in non-human primate genomes. Results RNase 8 expression was detected in adult human lung, spleen and testis tissue by quantitative reverse-transcription PCR. Only two single-nucleotide polymorphisms and four unique alleles were identified within the RNase 8 coding sequence; nucleotide sequence diversity (? = 0.00122 ± 0.00009 per site was unremarkable for a human nuclear gene. We isolated transcripts encoding RNase 8 via rapid amplification of cDNA ends (RACE and RT-PCR which included a distal potential translational start site followed by sequence encoding an additional 30 amino acids that are conserved in the genomes of several higher primates. The distal translational start site is functional and promotes RNase 8 synthesis in transfected COS-7 cells. Conclusions These results suggest that RNase 8 may diverge considerably from typical RNase A family ribonucleases and may likewise exhibit unique function. This finding prompts a reconsideration of what we have previously termed functional pseudogenes, as RNase 8 may be responding to constraints that promote significant functional divergence from the canonical structure and enzymatic activity characteristic of the RNase A family.
Chan Calvin C
Full Text Available Biodiversity is the variation of life at all levels of biological organization. One of the important components of biological diversity is the genetic diversity. Genetic diversity refers to the variation of genes or entire genome within and between populations of organisms. Keeping in view the significance of genetic diversity in wild plants, some research articles based on important wild plant genera and species of angiosperms including few rare, threatened, endemic, medicinal and economically important from different regions of the world are reviewed. The genetic diversity of plant species depends on different factors i.e. ecological, geographical, breeding system & anthropogenic effects. High genetic diversity is observed at species level even in small sized population by using AFLP, SSR, & ISSR genetic markers.
Muhammad Younas Khan Barozai, Sazia Saeed
Full Text Available Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min and isolate IP 11 (27.5 nmol/ml/min showed the best performances and IP 3a (9.5 nmol/mL/min presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detected by random amplified polymorphic DNA (RAPD analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase.
Eula Maria de M. B Costa
Full Text Available SciELO Brazil | Language: English Abstract in english Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 [...] (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detected by random amplified polymorphic DNA (RAPD) analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP) did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase.
Eula Maria de M. B, Costa; Fabiana Cristina, Pimenta; Christian, Luz; Valéria de, Oliveira; Marília, Oliveira; Elda, Bueno; Silvana, Petrofeza.
FASEB Breakthroughs in Bioscience article. "Knock-out" mice, in which specific genes have been inactivated, have been tremendously useful in helping researchers understand the genetic basis of disease. Moreover, "knock out" mice also serve as animal models for human diseases, allowing researchers to develop treatments and diagnostic tests for genetic diseases.
Cathryn M. Delude (The Writing Group)
Full Text Available The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variabilitywas maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode
Ana Paula Oliveira Nogueira
Dientamoeba fragilis is a common intestinal parasite of unsettled clinical significance. Differences in clinical outcome of parasitic infections may reflect parasite genetic diversity, and so tools to study intra-genetic diversity that could potentially reflect differences in clinical phenotypes are warranted. Here, we show that genetic analysis of three D. fragilis housekeeping genes enables clear distinction between the two known genotypes, but that integration of housekeeping genes in multi-locus sequencing tools for D. fragilis may have limited epidemiological and clinical value due to no further added genetic resolution. PMID:23681023
Stensvold, Christen Rune; Clark, C Graham; Röser, Dennis
Fragmentation of tropical forests has changed continuous tropical landscapes into a network of poorly connected fragments, reducing population sizes and potentially increasing genetic isolation. This study quantifies genetic diversity within and among the 7 extant populations of the endangered tropical tree Guaiacum sanctum in Costa Rica. We describe how genetic diversity differs between populations representing continuous and fragmented habitats. Allozyme analyses were conducted on adult samples from populations representing 2 geographic regions in northwestern Costa Rica. We found high levels of genetic diversity within the species (H(es) = 0.329) and significant but relatively small differences in allele frequencies among populations (G(ST) = 0.101) and between regions (G(ST) = 0.053). We found no differences in genetic diversity between fragmented and continuous populations. Evidence for significant isolation-by-distance (IBD) was seen only when all populations were analyzed. If populations within the 2 regions were analyzed separately, IBD ceased to be significant. Our results suggest that the patterns of genetic diversity observed for G. sanctum may be caused by the ancient separation of populations into 2 disjunct geographic regions with extensive historical rates of gene flow among populations within each region. Recent forest fragmentation has not yet affected patterns of genetic diversity in this species. PMID:20142457
Fuchs, Eric J; Hamrick, James L
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, Anostra...
Maccari, Marta; Amat, Francisco; Go?mez, A.
Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germ...
Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun
Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived ...
Ozge Karakas; Filiz Gurel; Ahu Altinkut Uncuoglu
Parasitic nematodes show levels of genetic diversity comparable to other taxa, but the functional consequences of this are not understood. Thus, a large body of theoretical work highlights the potential consequences of parasite genetic diversity for the epidemiology of parasite infections and its possible implications for the evolution of host and parasite populations. However, few relevant empirical data are available from parasites in general and none from parasitic nematodes in particular....
Paterson, S.; Viney, M. E.
Full Text Available AFLP and RAPD methods were used to investigate the genetic diversity of walnuts in western Sichuan plateau and Qinba mountainous regions. 35 samples were collected from 8 different regions, and 32 RAPD primers and 28 AFLP primer combinations were identified with polymorphism bands among the entire. 324 and 2155 fragments were respectively produced by RAPD and AFLP makers, and 86.1 % of RAPD bands and 57.2% of AFLP bands showed polymorphic with the size of 180~2000 bp and 50~1800 bp, respectively. The average amplified were 10.1 fragments per primer by RAPD and 76.9 fragments per pair primer by AFLP. The more polymorphic for genetic resource in Western Sichuan Plateau was observed by both RAPD and AFLP. The high number of alleles and the high expected genetic diversity detected with RAPD and AFLP markers indicate that western China has an important genetic diversity pool and abundant genetic variance of walnuts.
The extent of chromosomal-gene diversity among 261 isolates of Escherichia coli sharing single O, K, or H antigens and various combinations thereof was estimated by multilocus enzyme electrophoresis, which detects allelic variation in structural genes. The results of this study indicate that the genetic diversity among isolates sharing single antigenic determinants can approach or equal that observed among randomly chosen strains; that the magnitude of the diversity varies among antigens; and...
Caugant, D. A.; Levin, B. R.; Orskov, I.; Orskov, F.; Svanborg Eden, C.; Selander, R. K.
Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo-West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The Philippines are situated at the centre of the E. acoroides range, Yaeyama and Hainan are peripheral populations, and the Yaeyama population is at the northern limit of the species range. The powerful Kuroshio Current flows from the Philippines to Yaeyama. Genetic analyses using nine microsatellite markers indicated that reproduction of E. acoroides is mostly sexual. Clonal diversity does not decrease in northern populations, although genetic diversity does. However, the genetic diversity of the Yaeyama populations is greater than that of the Hainan populations. Significant genetic differentiation among most populations was evident; however, the Yaeyama and north-east Philippines populations were genetically similar, despite being separated by ~1100 km. An assignment test suggested that recruitment occurs from the north-east Philippines to Yaeyama. The strong current in this region is probably responsible for the extant genetic diversity and recruitment patterns. PMID:25384848
Nakajima, Yuichi; Matsuki, Yu; Lian, Chunlan; Fortes, Miguel D; Uy, Wilfredo H; Campos, Wilfredo L; Nakaoka, Masahiro; Nadaoka, Kazuo
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...
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.
During the last century, the selection for production traits of the main livestock species has led to a reduction in number of local populations with consequent loss of genetic variability. In Sardinia, the genetic improvement strategy has been based on selection for the local pure breed in sheep, whereas in the other species (cattle, swine and goat), an often unplanned crossbreeding with improved breeds has been applied. In this context, several studies on genetic diversity of th...
Carta, A.; Casu, S.; Usai, M. G.; Sechi, T.
Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity wa...
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.
We explore several different techniques in our quest to improve the overall model performance of a genetic algorithm calibrated probabilistic cellular automata. We use the Kappa statistic to measure correlation between ground truth data and data predicted by the model. Within the genetic algorithm, we introduce a new evaluation function sensitive to spatial correctness and we explore the idea of evolving different rule parameters for different subregions of the land. We reduce the time required to run a simulation from 6 hours to 10 minutes by parallelizing the code and employing a 10-node cluster. Our empirical results suggest that using the spatially sensitive evaluation function does indeed improve the performance of the model and our preliminary results also show that evolving different rule parameters for different regions tends to improve overall model performance. Copyright 2005 ACM.
Talaie, S.; Leigh, R.; Louis, S.J.; Raines, G.L.
Previously we have reported on the finding of genetic differences in the abiotic stress tolerance of cotton pollen. Genetic differences in sensitivity to humidity were observed impacting pollen survival in dry environments. The present study evaluated out-crossing rates in cotton lines whose polle...
Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied. PMID:25551388
Rodriguez-Bonilla, Lorraine; Cuevas, Hugo E; Montero-Rojas, Milly; Bird-Pico, Fernando; Luciano-Rosario, Dianiris; Siritunga, Dimuth
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)
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 f...
Ms. Pooja Mittal; Manju Narwal
Full Text Available This work is related to the KEEL (Knowledge Extraction basedon Evolutionary Learning tool, an open source software thatsupports data management and provides a platform for theanalysis of evolutionary learning for Data Mining problems ofdifferent kinds including as regression, classification,unsupervised learning. It includes a big collection of evolutionarylearning algorithms based on different approaches: Pittsburgh,Michigan. It empowers the user to perform complete analysis ofany genetic fuzzy system in comparison to existing ones, with astatistical test module for comparison.
Ms. Pooja Mittal
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.
Full Text Available Abstract Background The local connectivity and global position of a protein in a protein interaction network are known to correlate with some of its functional properties, including its essentiality or dispensability. It is therefore of interest to extend this observation and examine whether network properties of two proteins considered simultaneously can determine their joint dispensability, i.e., their propensity for synthetic sick/lethal interaction. Accordingly, we examine the predictive power of protein interaction networks for synthetic genetic interaction in Saccharomyces cerevisiae, an organism in which high confidence protein interaction networks are available and synthetic sick/lethal gene pairs have been extensively identified. Results We design a support vector machine system that uses graph-theoretic properties of two proteins in a protein interaction network as input features for prediction of synthetic sick/lethal interactions. The system is trained on interacting and non-interacting gene pairs culled from large scale genetic screens as well as literature-curated data. We find that the method is capable of predicting synthetic genetic interactions with sensitivity and specificity both exceeding 85%. We further find that the prediction performance is reasonably robust with respect to errors in the protein interaction network and with respect to changes in the features of test datasets. Using the prediction system, we carried out novel predictions of synthetic sick/lethal gene pairs at a genome-wide scale. These pairs appear to have functional properties that are similar to those that characterize the known synthetic lethal gene pairs. Conclusion Our analysis shows that protein interaction networks can be used to predict synthetic lethal interactions with accuracies on par with or exceeding that of other computational methods that use a variety of input features, including functional annotations. This indicates that protein interaction networks could plausibly be rich sources of information about epistatic effects among genes.
Genetic programming is a metaheuristic search method that uses a population of variable-length computer programs and a search strategy based on biological evolution. The idea of automatic programming has long been a goal of artificial intelligence, and genetic programming presents an intuitive method for automatically evolving programs. However, this method is not without some potential drawbacks. Search using procedural representations can be complex and inefficient. In addition, variable si...
Gustafson, Steven Matt
Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.
Homar R. Gill-Langarica
Full Text Available SciELO Brazil | Language: English Abstract in english A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collecti [...] on (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.
Homar R., Gill-Langarica; José S., Muruaga-Martínez; M.L. Patricia, Vargas-Vázquez; Rigoberto, Rosales-Serna; Netzahualcoyotl, Mayek-Pérez.
Full Text Available Abstract Background Understanding the population structure of Plasmodium species through genetic diversity studies can assist in the design of more effective malaria control strategies, particularly in vaccine development. Central America is an area where malaria is a public health problem, but little is known about the genetic diversity of the parasite’s circulating species. This study aimed to investigate the allelic frequency and molecular diversity of five surface antigens in field isolates from Honduras. Methods Five molecular markers were analysed to determine the genotypes of Plasmodium vivax and Plasmodium falciparum from endemic areas in Honduras. Genetic diversity of ama-1, msp-1 and csp was investigated for P. vivax, and msp-1 and msp-2 for P. falciparum. Allelic frequencies were calculated and sequence analysis performed. Results and conclusion A high genetic diversity was observed within Plasmodium isolates from Honduras. A different number of genotypes were elucidated: 41 (n?=?77 for pvama-1; 23 (n?=?84 for pvcsp; and 23 (n?=?35 for pfmsp-1. Pvcsp sequences showed VK210 as the only subtype present in Honduran isolates. Pvmsp-1 (F2 was the most polymorphic marker for P. vivax isolates while pvama-1 was least variable. All three allelic families described for pfmsp-1 (n?=?30 block 2 (K1, MAD20, and RO33, and both allelic families described for the central domain of pfmsp-2 (n?=?11 (3D7 and FC27 were detected. However, K1 and 3D7 allelic families were predominant. All markers were randomly distributed across the country and no geographic correlation was found. To date, this is the most complete report on molecular characterization of P. vivax and P. falciparum field isolates in Honduras with regards to genetic diversity. These results indicate that P. vivax and P. falciparum parasite populations are highly diverse in Honduras despite the low level of transmission.
Indigenous resources of the Asian pig population are less defined and only rarely compared with European breeds. In this study, five indigenous pig breeds from Viet Nam (Mong Cai, Muong Khuong, Co, Meo, Tap Na), two exotic breeds kept in Viet Nam (Large White, Landrace), three European commercial breeds (Pietrain, Landrace, Large White), and European Wild Boar were chosen for evaluation and comparison of genetic diversity. Samples and data from 317 animals were collected and ten polymorphic microsatellite loci were selected according to the recommendations of the FAO Domestic Animal Diversity Information System (DAD-IS; http://www.fao.org/dad-is/). Effective number of alleles, Polymorphism Information Content (PIC), within-breed diversity, estimated heterozygosities and tests for Hardy-Weinberg equilibrium were determined. Breed differentiation was evaluated using the fixation indices of Wright (1951). Genetic distances between breeds were estimated according to Nei (1972) and used for the construction of UPGMA dendrograms which were evaluated by bootstrapping. Heterozygosity was higher in indigenous Vietnamese breeds than in the other breeds. The Vietnamese indigenous breeds also showed higher genetic diversity than the European breeds and all genetic distances had a strong bootstrap support. The European commercial breeds, in contrast, were closely related and bootstrapping values for genetic distances among them were below 60%. European Wild Boar displayed closer r60%. European Wild Boar displayed closer relation with commercial breeds of European origin than with the native breeds from Viet Nam. This study is one of the first to contribute to a genetic characterization of autochthonous Vietnamese pig breeds and it clearly demonstrates that these breeds harbour a rich reservoir of genetic diversity. (author)
Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Devel...
McGreevy Thomas J; Kuhn Anne; Grear Jason S; Gutjahr-Gobell Ruth; Champlin Denise M; Markert Jeffrey A; Roth Annette; Bagley Mark J; Nacci Diane E
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.
Wanessa Christina de Souza-Neiras
Full Text Available Abstract Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies.
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.
Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies.
Kokotovic, Branko; Angen, Øystein
Full Text Available Genetic diversity of 25 accessions of Cymbopogon aromatic grasses including eight species, two hybrids and one mutant strain were analyzed using DNA markers generated by employing 20 primer pairs derived from cDNAs containing simple sequence repeat (SSR of rice genome. A total of 151 bands were produced ranging from 3 to 12 per primer pair. The polymorphic information content values varied from 0.143 to 0.916 with an average 0.715. Jaccard’s similarity coefficient ranged from 64 to 87% among the paired accessions. The level of diversity among different taxa/accessions observed during the present study was, however, low relative to the diversity level obtained due to RAPD markers in earlier studies. The pattern of genetic diversity neither matched with the known taxonomic classification, nor did it always match with the distribution of chemical constituents of the essential oils available in these accessions. Thus, present investigation though revealed poor correlation between the molecular and chemical diversity, indicating that chemical diversity in medicinal and aromatic species is not only result of genetic variability, but it also depends on a number of other factors. Thus this study may prove useful in several ways in Cymbopogon conservation and breeding programs and in the development of perfect markers though association mapping for genes involved in controlling agronomically important traits.
The development of landscaping and horticultural species of the genus Hydrangea is based on the exploitation of their phenotypic diversity, particularly associated with architectural forms and colours. The collection of genetic resources, located in Angers (France) is composed of 13 species which were introduced in Europe in the 18th century. The phytochemical analysis of inflorescences, for the first time studied on the whole genus, should allow to complete the genetic characterization of sp...
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 fragm...
Gill-langarica, Homar R.; Muruaga-marti?nez, Jose? S.; Patricia Vargas-va?zquez, M. L.; Rigoberto Rosales-Serna; Netzahualcoyotl Mayek-Pérez
The Asiatic wild dog or dhole was once very widely distributed across Asia but now has a very fragmented range. In this first genetic study of this little-known species, we obtained information on genetic diversity, phylogeography, and social structure using both mitochondrial control region sequencing and microsatellite genotyping of noninvasive faecal samples from wild populations, as well as from museum and captive samples. A pattern largely consistent with isolation by distance across the...
Iyengar, A.; Babu, Vn; Hedges, S.; Venkataraman, Ab; Maclean, N.; Morin, Pa
Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping. PMID:23708149
Ramu, P; Billot, C; Rami, J-F; Senthilvel, S; Upadhyaya, H D; Ananda Reddy, L; Hash, C T
Juglans regia L. belonging to the family Juglandaceae inhabits the northern parts of Pakistan. Biochemical analysis of the plant is not well documented in the country. Present research was the first documented attempt to study total seed storage proteins in 20 genotypes of Juglans regia collected from Swat, Dir and Chitral areas. A protocol was optimized for extraction and separation of seed storage protein from unprocessed seeds. Comparatively simple banding pattern (as compared to legumes and cereals) was observed in Juglans regia L. A total of 114 protein loci were detected in 20 genotypes giving an average of approximately 7 alleles per genotype. Genetic distances estimated during present study range from 0 to 60. Medium values of Genetic Distances (GDmax= 60%) was estimated among three comparisons. Twenty genotypes were grouped in three clusters based on dendrogram analysis. Genotypes collected from Chitral valley were predominantly grouped in one cluster. (author)
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...
Thirty-four soybean lines were assessed for twelve traits. The genetic distances were estimates using multivariate techniques, to identify parents to be included in breeding programs for hybridization. Grouping by the Tocher method, from generalized Mahalanobis distances, divided the 34 lines into four groups. The most important agronomic traits, weight of seeds per plot, plant height, height of first pod and days to maturity were considered when recommending for crossing. The following cross...
Valéria Carpentieri-Pípolo; Antônio Eduardo Pípolo; Flávio André Martins da Silva; Marcos Rafael Petek
Members of the genus Pleurotus, also commonly known as oyster mushroom, are well known for their socioeconomic and biotechnological potentials. Despite being one of the most important edible fungi, the scarce information about the genetic diversity of the species in natural populations has limited their sustainable utilization. A total of 71 isolates of Pleurotus species were collected from three natural populations: 25 isolates were obtained from Kakamega forest, 34 isolates from Arabuko Sokoke forest and 12 isolates from Mount Kenya forest. Thirteen isolates of locally grown Pleurotus species were obtained from laboratory samples for comparative data analysis. Amplified fragment length polymorphic markers and internal transcribed spacer sequences of the ribosomal DNA were used to estimate the genetic diversity and evaluate phylogenetic relationships respectively among and within populations. In total, five primer combinations were used to generate 293 polymorphic loci across the 84 isolates. The mean genetic diversity among the populations was 0.25 with the population from Arabuko Sokoke having higher (0.27) diversity estimates compared to Mount Kenya population (0.24). Diversity between the isolates from the natural population (0.25) and commercial cultivars (0.24) was not statistically significant. However diversity was greater within (89%; P > 0.001) populations than among populations. Homology search analysis against the GenBank database using 16 rDNA ITS sequences randomly selected from the two clades of AFLP dendrogram revealed three mushroom species: Pleurotus djamor, Pleurotus floridanus and Pleurotus sapidus. The three mushrooms formed part of the diversity of Pleurotus species in Kenya. The broad diversity within the Kenyan Pleurotus species suggests the possibility of obtaining native strains suitable for commercial cultivation. PMID:25344263
Otieno, Ojwang Daniel; Onguso, Justus Munguti; Matazyoh, Lexa Gomezgani; Onyango, Calvin; Wamalwa, Mark; Wanjala, Bramwel Waswa; Jagger, Harvey
Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid w...
Ming-Cheng Luo; Junhua Peng; Eviatar Nevo; Dongfa Sun; Yunliang Peng; Jirui Wang; You, Frank M.; Liang Chen; Daokun Sun; Jing Ren
Biological invasions are facilitated by the global transportation of species and climate change. Given that invasions may cause ecological and economic damage and pose a major threat to biodiversity, understanding the mechanisms behind invasion success is essential. Both the release of non-native populations from natural enemies, such as parasites, and the genetic diversity of these populations may play key roles in their invasion success. We investigated the roles of parasite communities, through enemy release and parasite acquisition, and genetic diversity in the invasion success of the non-native bumblebee, Bombus hypnorum, in the United Kingdom. The invasive B. hypnorum had higher parasite prevalence than most, or all native congeners for two high-impact parasites, probably due to higher susceptibility and parasite acquisition. Consequently parasites had a higher impact on B. hypnorum queens' survival and colony-founding success than on native species. Bombus hypnorum also had lower functional genetic diversity at the sex-determining locus than native species. Higher parasite prevalence and lower genetic diversity have not prevented the rapid invasion of the United Kingdom by B. hypnorum. These data may inform our understanding of similar invasions by commercial bumblebees around the world. This study suggests that concerns about parasite impacts on the small founding populations common to re-introduction and translocation programs may be less important than currently believed. PMID:24749545
Jones, Catherine M; Brown, Mark J F
Full Text Available Genetic variation at 20 microsatellite loci and genetic diversity were examined for Yangzhou Chicken. Observed and effective number of alleles across the microsatellite loci varied from 2-6 with an overall mean of 3.778 and 2.404, respectively. Observed and effective heterozygosity varied from 0.129-0.755 with an average of 0.422 and 0.517, respectively. Average polymorphism information content was 0.464. The genetic structure indicated that Yangzhou Chickens have substantial genetic variation. Population showed fairly high level of inbreeding (Fis = 0.184 and global heterozygote deficit. The allele frequency distribution is displayed an L shape, suggesting that no recent bottleneck affecting the genetic variability occurred. The information generated in this study will greatly aid in the establishment of effective breeding strategies for Yangzhou Chicken and may further be utilized for studying differentiation and relationships among different chicken breeds.
Biodiversity regulates ecosystem functions such as productivity, and experimental studies of species mixtures have revealed selection and complementarity effects driving these responses. However, the impacts of intraspecific genotypic diversity in these studies are unknown, despite it forming a substantial part of the biodiversity. In a glasshouse experiment we constructed plant communities with different levels of barley (Hordeum vulgare) genotype and weed species diversity and assessed their relative biodiversity effects through additive partitioning into selection and complementarity effects. Barley genotype diversity had weak positive effects on aboveground biomass through complementarity effects, whereas weed species diversity increased biomass predominantly through selection effects. When combined, increasing genotype diversity of barley tended to dilute the selection effect of weeds. We interpret these different effects of barley genotype and weed species diversity as the consequence of small vs large trait variation associated with intraspecific barley diversity and interspecific weed diversity, respectively. The different effects of intra- vs interspecific diversity highlight the underestimated and overlooked role of genetic diversity for ecosystem functioning. PMID:25250812
Schöb, Christian; Kerle, Sarah; Karley, Alison J; Morcillo, Luna; Pakeman, Robin J; Newton, Adrian C; Brooker, Rob W
Abstract Background Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow due to exchanges between herds. To quantify this relation, molecular data and analyses of the exchanges were combined for three endangered Belgian breeds. Methods For each breed, between 91 and 225 sheep were genotyped with 19 microsate...
Dumasy Jean-François; Daniaux Christel; Donnay Isabelle; Baret Philippe V
Full Text Available Buffalo is the main dairy animal in Pakistan. There are five known buffalo breeds in the country namely: Nili, Ravi, Nili-Ravi, Kundhi and Azi Kheli (or Azakhale. Population trend is available for Nili-Ravi and Kundhi breeds and is positive. Azi-Kheli breed was included in 2006 livestock census for the first time. General production system is low-input extensive system but high input intensive system prevails around most cities in the form of buffalo colonies for supplying fresh milk. Buffaloes are seasonal breeders. Vast diversity exits both at phenotypic and genetic level. Economic traits have a wide variation and genetic control is moderate for production traits but very low for reproduction traits. Inbreeding is inimical to genetic diversity and has been reported to deteriorate productivity. Efforts to improve productivity of the species are needed alongwith sustainable utilization of existing resources.
M. SAJJAD KHAN, NAZIR AHMAD1 AND MUQARRAB ALI KHAN2
Full Text Available Fennel (Foeniculum vulgare Mill. is an important medicinal plant with used for various purposes in different industries. In this study 25 different ecotypes of fennel from all over Iran were collected and their genetic diversity studied by seven ISSR primers. Seven ISSR primers generated 52 amplified fragments, of which 49 were polymorphic. The highest similarity coefficient among the ecotypes was between Chahestan and Haji abad whereas the minimum similarity coefficient observed between Fozveh and Moqan. In most cases, classifications were consistent with their geographical distribution for some ecotypes (like Givi and Khalkhal in close distance and although with similarity in climate (like Damavand and Alamot with same climate. This study revealed that ISSR marker could properly separate these ecotypes based on geographical distribution and similarity in climates and showed the wide genetic diversity among Iranian fennels. In term of conservation program, it is highly recommended at least one conservation program for several accessions with near genetical distance should be conducted.
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.
Mycobacterium avium, one of the species of the M. avium complex (MAC), includes 4 subspecies, i.e., M. avium subsp. hominissuis (MAH), M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS) and M. avium subsp. paratuberculosis (MAP), in turn classified into the S (sheep) and C (cattle) types. These subspecies, although closely related, represent distinct organisms, each endowed with specific pathogenetic and host range characteristics, ranging from environmental opportunistic bacteria that cause infections in swine and immunocompromised patients to pathogens of birds and ruminants. The present review summarizes the basic epidemiological and pathological features of the M. avium subspecies, describes the major genomic events responsible of M. avium subspecies diversity (insertion sequences, sequence variations in specific chromosome loci or genes, deletions, duplications and insertions of large genomic regions) and then reconstructs the phylogenetic relationships among the M. avium subspecies. PMID:24345519
Rindi, Laura; Garzelli, Carlo
Full Text Available SciELO Brazil | Language: English Abstract in portuguese Trinta e quatro linhagens de soja foram avaliadas para doze características. As distâncias genéticas foram estimadas utilizando técnicas multivariadas com objetivo de identificar parentais a serem incluidos em um programa de melhoramento envolvendo hibridação. O agrupamento pelo método de Tocher, a [...] partir das distâncias generalizadas de Mahalanobis, dividiu as 34 linhagens em 4 grupos. As caracterísiticas agronômicas mais importantes, peso de sementes por parcela, altura de planta, altura da primeira vagem e dias para maturação foram consideradas para a recomendação dos cruzamentos. Os seguintes cruzamentos foram recomendados baseado na divergência genética e nas características agronômicas chave: linhagens 23, 10, 2, 27 e 25 (grupo I) com genótipo 6 (grupoII) e com o genótipo 16 (grupo III). Portanto somente 10 cruzamentos poderiam ser realizados representando somente 2% do total de cruzamentos qu poderiam ser realizados em um dialelo parcial entre as 34 linhagens avaliadas as quais admitiriam até 561 combinações. Abstract in english Thirty-four soybean lines were assessed for twelve traits. The genetic distances were estimates using multivariate techniques, to identify parents to be included in breeding programs for hybridization. Grouping by the Tocher method, from generalized Mahalanobis distances, divided the 34 lines into f [...] our groups. The most important agronomic traits, weight of seeds per plot, plant height, height of first pod and days to maturity were considered when recommending for crossing. The following crosses were recommended based on the genetic divergence and the key agronomic traits: lines 23, 10, 2, 27 and 25 (group I) with genotype 6 (group II) and genotype 16 (group III). Thus only ten crosses would be made, representing only 2% of the total crosses which could be made in the partial diallel among the 34 lines assessed, which would allow up to 561 combinations.
Valéria, Carpentieri-Pípolo; Antônio Eduardo, Pípolo; Flávio André Martins da, Silva; Marcos Rafael, Petek.
Full Text Available Thirty-four soybean lines were assessed for twelve traits. The genetic distances were estimates using multivariate techniques, to identify parents to be included in breeding programs for hybridization. Grouping by the Tocher method, from generalized Mahalanobis distances, divided the 34 lines into four groups. The most important agronomic traits, weight of seeds per plot, plant height, height of first pod and days to maturity were considered when recommending for crossing. The following crosses were recommended based on the genetic divergence and the key agronomic traits: lines 23, 10, 2, 27 and 25 (group I with genotype 6 (group II and genotype 16 (group III. Thus only ten crosses would be made, representing only 2% of the total crosses which could be made in the partial diallel among the 34 lines assessed, which would allow up to 561 combinations.Trinta e quatro linhagens de soja foram avaliadas para doze características. As distâncias genéticas foram estimadas utilizando técnicas multivariadas com objetivo de identificar parentais a serem incluidos em um programa de melhoramento envolvendo hibridação. O agrupamento pelo método de Tocher, a partir das distâncias generalizadas de Mahalanobis, dividiu as 34 linhagens em 4 grupos. As caracterísiticas agronômicas mais importantes, peso de sementes por parcela, altura de planta, altura da primeira vagem e dias para maturação foram consideradas para a recomendação dos cruzamentos. Os seguintes cruzamentos foram recomendados baseado na divergência genética e nas características agronômicas chave: linhagens 23, 10, 2, 27 e 25 (grupo I com genótipo 6 (grupoII e com o genótipo 16 (grupo III. Portanto somente 10 cruzamentos poderiam ser realizados representando somente 2% do total de cruzamentos qu poderiam ser realizados em um dialelo parcial entre as 34 linhagens avaliadas as quais admitiriam até 561 combinações.
A century of heavy metal mining in the western United States has left a legacy of abandoned mines. While large operations have left a visible reminder, smaller one and two-man operations have been overgrown and largely forgotten. We revisited an area of northern Idaho that has not had active mining since at least 1932 and probably since 1910. At three sites along each of 10 mountain streams we sampled larval stream insects and correlated their community diversity to stream levels of arsenic, cadmium, lead, zinc, pH, temperature, oxygen content, and conductivity. Although the streams appear pristine, multivariate statistics indicated that cadmium and zinc levels were significantly correlated with fewer animals, fewer families, a smaller percentage of plecopterans (stoneflies), and lower Shannon H diversity values. After at least 75 years, abandoned mines appear to be still influencing stream communities. PMID:20680454
Lefcort, Hugh; Vancura, James; Lider, Edward L
Anthropogenic disturbances may leave imprints on patterns of intraspecific genetic diversity through their effects on population size, adaptation, migration, and mutation. We examined patterns of genetic diversity for a stream-dwelling minnow (the central stoneroller, Campostoma...
The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations. PMID:24373066
Pham, L D; Do, D N; Nam, L Q; Van Ba, N; Minh, L T A; Hoan, T X; Cuong, V C; Kadarmideen, H N
The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations.
Pham, L. D.; Do, Duy Ngoc
This study presents a fast and scalable multi-objective association rule mining technique using genetic algorithm from large database. The objective functions such as confidence factor, comprehensibility and interestingness can be thought of as different objectives of our association rule-mining problem and is treated as the basic input to the genetic algorithm. The outcomes of our algorithm are the set of non-dominated solutions. However, in data mining the quantity of data is growing rapidl...
Dehuri, S.; Jagadev, A. K.; Ghosh, A.; Mall, R.
Fifty-seven genotypes from eight population of Satureja bachtiarica was evaluated using fifteen ISSR and eleven RAPD markers. DNA profiling using RAPD primers amplified 84 loci, among which 81 were polymorphic with an average of 7.36 polymorphic fragments per locus. Also, using RAPD markers maximum and minimum polymorphic bands observed for Semyrom (77.38 %) and Farsan (40.48 %) populations, respectively. Semyrom population recorded the highest unbiased expected heterozygosity (0.259) and Shannon's Indices (0.38). While, the lowest values of unbiased expected heterozygosity (0.172) and Shannon's Index (0.245) were recorded for Eghlid and Farsan populations, respectively. On the other hand, ISSR primers produced 136 bands, from which 134 were polymorphic with an average of 9.06 polymorphic fragments per primer (98.52 %). The ISSR markers evaluation revealed that maximum and minimum polymorphic bands observed for Semyrom (66.18 %) and Farsan (31.62 %), respectively. Shahrekorud population recorded the highest unbiased expected heterozygosity (0.211) and Shannon's Indices (0.301). While, the lowest value of unbiased expected heterozygosity (0.175) observed for Farsan and Yazd populations and the lowest Shannon's Index (0.191) recorded by Farsan population. The overall results of the study revealed that both ISSR and RAPD markers were effective for evaluation of genetic variation of S. bachtiarica. PMID:24096911
Saidi, Mehdi; Movahedi, Khavar; Mehrabi, Ali Ashraf; Kahrizi, Danial
Full Text Available Eighty five different cultivars of Brassica rapa, B.juncea, B.napus, B. carinata, B. oleracea and hexaploid Brassica, collected from Bangladesh, Japan, China and Denmark, were analyzed for seed and leaf protein variations by SDS-PAGE to identify the polymorphic genetic markers for evaluation of genetic resources. Ten polymorphic markers were identified from seed protein and no identifiable polymorphic band was found from leaf protein. However, polymorphic markers clearly distinguished these Brassica species. Brassica rapa var. `yellow sarson` of Bangladesh origin showed uniquely identifiable four polymorphic bands for seed protein in contrast to the other B.rapa of brown-seeded type. The Bangladeshi and Japanese cultivars of B. rapa differed among protein quantity. Analytical results of SDS-PAGE for seed protein showed that hexaploid Brassica has the highest indices, such as % of polymorphic band, the degree of phenotypic diversity (Ho, diversity value for genetic marker (HEP and the sum of the effective number of alleles (SENA. The genetic diversity values of hexaploid Brassica were followed by amphidiploid (B. napus, B. juncea, B. carinata and diploid (B. oleracea, B. rapa species, respectively.
Rahman Md. Mukhlesur
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.
Wheat is one of the main sources of nutrition worldwide. Genetic improvement of the seed makes wheat a source of high quality flour for human consumption and for other industrial uses. With the help of molecular markers, the available germplasm of wheat can be assessed for future breeding programs. Therefore, the aim of the present work was to analyze the genetic diversity among 15 Pakistani wheat land races based on Random Amplified Polymorphism DNA (RAPD) markers. A total of 284 DNA fragments were amplified, ranging in size from 200bp to 1100bp by using six primers. The number of DNA fragments for each primer varied from 2 (OPC-6) to 9 (OPC-8) with an average of 6 fragments per primer. Out of 284 amplified products, 120 were monomorphic and 137 were polymorphic showing an average of 7.8% polymorphism per primer. One specific marker was detected both for OPC-1 and OPC-8, two for OPC-5, while no RAPD specific marker was detected for the remaining primers. The genetic similarity index values ranged from 0.36 to 0.93, with an average of 0.64. Maximum genetic similarity (91%) was observed between Sur bej and Khushkawa. On the contrary, minimum genetic similarity (32%) was observed in Khushkaba-1 and Khushkawa. The dendrogram resulting from the NTSYS cluster analysis showed that the studied genotypes are divided into two main clusters from the same node. The first cluster contained 13 land races, while the second cluster contained only 2 land races. The dendrogram cluster only 2 land races. The dendrogram clustered the genotypes into 5 groups and showed efficiency in identifying genetic variability. These results indicated the usefulness of RAPD technique in estimating the genetic diversity among wheat genetic resources. (author)
The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene f...
Ming Li; Zhong Zhao; Xingjun Miao; Jingjing Zhou
Full Text Available SciELO Chile | Language: English Abstract in english Background: The myrtle (Myrtus communis) is a common shrub widespread in the Mediterranean Basin. Its fruit and leaves exhibit antioxidant, antibacterial and antifungal properties, and are used for their content of essential oils and for their medicinal properties, but most commonly as an ingredient [...] in locally made liquor. The uncontrolled exploitation of natural stands has reduced both the species' geographical coverage and the size of individual populations. The selection of genotypes for controlled cultivation requires a characterization of the genetic diversity present both within and between populations. Results: Genotypic variation was evaluated using ISSR profiling and genetic diversity characterized using standard population genetics approaches. Two major clusters were identified: one capturing all the candidate cultivars selected from various Sardinian localities, and the other wild individuals collected from Asinara, Corsica and Surigheddu. A moderate level of gene flow between the Sardinian and Corsican populations was identified. Discriminant analysis of principal components revealed a level of separation among the wild populations, confirming the population structure identified by the clustering methods. Conclusions: The wild accessions were well differentiated from the candidate cultivars. The level of genetic variability was high. The genetic data were compatible with the notion that myrtle has a mixed pollination system, including both out-pollination by insects and self-pollination. The candidate cultivars are suggested to represent an appropriate basis for directed breeding.
Sara, Melito; Innocenza, Chessa; Patrizia, Erre; János, Podani; Maurizio, Mulas.
Full Text Available Aim of the study is the analysis of the genetic diversity among a set of Tunisian date palm varieties. We used different genetic markers generated from selected ISSR primers. Inter Simple Sequence Repeat (ISSR markers involve Polymerase Chain Reaction (PCR amplification of DNA using a single primer composed of a microsatellite sequence. ISSR technology rapidly reveals high polymorphic fingerprints and determines genetic diversity. Seven primers were used to cluster 10 date palm varieties and 82 polymorphic markers were sufficient to identify all of the studied varieties. These discrete molecular markers were used to estimate genetic distances among the 10 accessions and to examine their genetic relationships. Data analysis identified phenetic groups that were in agreement with those obtained according to agronomic traits and random amplified polymorphic DNA (RAPD markers. Among the 12 Simple Sequence Repeat (SSR motifs tested, the most abundant were AG. Present result provides evidence of divergence between Tunisian varieties that are organized in clusters. However, we are unable to identify all tested genotypes as mono varietal groups.
Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F(2) individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01. PMID:21637582
Karakas, Ozge; Gurel, Filiz; Uncuoglu, Ahu Altinkut
Full Text Available Abstract Transposable elements (TEs comprise a large fraction of mammalian genomes. A number of these elements are actively jumping in our genomes today. As a consequence, these insertions provide a source of genetic variation and, in rare cases, these events cause mutations that lead to disease. Yet, the extent to which these elements impact their host genomes is not completely understood. This review will summarize our current understanding of the mechanisms underlying transposon regulation and the contribution of TE insertions to genetic diversity in the germline and in somatic cells. Finally, traditional methods and emerging technologies for identifying transposon insertions will be considered.
O'Donnell Kathryn A
Full Text Available SciELO South Africa | Language: English Abstract in english Several studies have been conducted on the presence and diversity of airborne fungal spores in residential and occupational areas. This is the first investigation on this topic in the mining environment. The impact of fungi-especially as opportunistic pathogens-on their health and productivity needs [...] to be assessed, considering the compromised health of a large number of HIV-infected miners in South Africa. Accordingly, the aim of this study was to determine the abundance of fungal spores as well as the diversity of culturable airborne fungi in an active gold mine. The results indicate that three of the sampled sites in the mine contain abundant numbers of culturable airborne fungi. The first site was next to an auxiliary extraction fan, which could act as an accumulator for airborne fungal spores from the rest of the mine. The two other sites had high human activity, disturbances from which may contribute to an elevated fungal load in the air. The presence of timber supports at one site may serve as a growth substrate for several fungal genera. The diversity of filamentous fungal genera increased from outside the mine to deeper into the mine, whereas the diversity of yeast genera followed an opposite trend, with no yeasts detected deep in the mine. Although most of the isolates identified are not pathogens, they could still have a negative impact (either as opportunistic pathogens or allergens) on workers, especially immunocompromised persons if exposed to them for prolonged periods.
C.H., Pohl; W., Kriel; P., Venter; E., Van Heerden; J., Albertyn.
Full Text Available Plant genetic resources are essential components to meet future food security needs of world. Crop germplasm diversitycontributes to developing improved crop cultivars aimed at increasing crop productivity. The large size of germplasmcollections, coupled with unavailability of detailed data and information, has resulted in low use (<1% of germplasmleading to a narrow genetic base in many crops. The miniaturization of crop collections with almost full representation ofgenetic diversity in the form of mini core (~1% of the entire collection approach is an effective methodology to enrichand enhance crop improvement programs. The concept and process of developing mini core at The International CropsResearch Institute for the Semi-Arid Tropics (ICRISAT has been recognized worldwide as an “International PublicGood” (IPG. The mini core provides a means for accessing the larger collections for further exploration and also helps inproper assessment of genetic diversity and population structure and for association mapping and targeted gene mining.Use of mini core approach will lead to greater utilization of diverse germplasm for developing broad-based cultivars,especially in the context of climate change. Many national programs have shown immense interest in evaluating minicore as reflected by the supply of 114 sets of mini core of chickpea, groundnut, pigeonpea, sorghum, pearl millet, foxtailmillet and finger millet to researchers in 14 countries. Scientists have been able to identify new and diverse sources ofvariation for morpho-agronomic, quality, biotic, and abiotic stress resistance traits in various crops. The molecularcharacterization of the mini core will further enhance its use in plant breeding programs.
Hari D Upadhyaya*, Devvart Yadav, Naresh Dronavalli, CLL Gowda, and Sube Singh
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...
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...
Reynolds, Laura K.; Mcglathery, Karen J.; Waycott, Michelle
Bunias orientalis and Erigeron annuus are two alien herbal plant species invading native ecosystems in Lithuania. Both species have similar introduction and invasion history but differ in their life history traits and strategies of reproduction. We used random amplified polymorphic DNA (RAPD) data to compare the genetic diversity in invasive populations of these species. 42 RAPD bands were identified in B. orientalis and 70 RAPD bands in E. annuus. All six populations of B. orientalis were po...
Tunaitiene?, Virginija; Patamsyte?, Jolanta; C?e?sniene?, Tatjana; Kleizaite?, Violeta; Naugz?emys, Donatas; Ranc?elis, Vytautas; Z?vingila, Donatas
A collection of 51 Xanthomonas campestris strains from throughout the world was studied to detect and assess genetic diversity among pathogens of small grains. Isolates from barley, bread wheat, bromegrass, canary grass, cassava, maize, orchard grass, rice, rough-stalked meadow grass, rye, timothy, and triticale were analyzed by pathogenicity tests on bread wheat cv. Alondra and barley cv. Corona, indirect immunofluorescence, and restriction fragment length polymorphism (RFLP). Three probes w...
Bragard, C.; Verdier, V.; Maraite, H.
Green gram is also one of the important pulse crops. Conventional breeding methods are very much difficult to utilize in thedevelopment of new genotypes. Hence incorporation of the molecular approaches along with the conventional techniques ismost powerful method. Evaluation of the available wild accessions are more useful for selecting desirable gene sources.Genetic diversity analysis place an important role in this purpose. For this molecular analysis of selected 18 accessions ingreengram (...
M Pandiyan, N. Senthil
The genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal DNA restriction analysis (ARDRA), 16S rRNA sequence homology and phylogenetics analysis methods. Studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. A total of 28 ARDRA patterns were identified among the 299 siderophore-producing bacterial isolates. The 28 ARDRA patterns represented bacteria of 14 different genera belonging ...
Tian, Fang; Ding, Yanqin; Zhu, Hui; Yao, Liangtong; Du, Binghai
Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and for...
Rivarola, Maximo; Foster, Jeffrey T.; Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; Liu, Xinyue; Melake-berhan, Admasu; Huot Creasy, Heather; Puiu, Daniela; Rosovitz, M. J.; Khouri, Hoda M.; Beckstrom-sternberg, Stephen M.; Allan, Gerard J.; Keim, Paul; Ravel, Jacques
Biological invasions are facilitated by the global transportation of species and climate change. Given that invasions may cause ecological and economic damage and pose a major threat to biodiversity, understanding the mechanisms behind invasion success is essential.Both the release of non-native populations from natural enemies, such as parasites, and the genetic diversity of these populations may play key roles in their invasion success.We investigated the roles of parasite communities, thro...
Jones, Catherine M.; Brown, Mark J. F.; Ings, Thomas
With the help of 21 putative isoenzyme loci, the genetic diversity and variations of Viscum album ssp. album L. from 42 species, subspecies, varieties and hybrids of broadleaf trees, Viscum album ssp. austriacum (Wiesb.) Vollmann, from 4 populations of Scots pine (Pinus sylvestris L.) and Viscum album ssp. abietis (Wiesb.) Abromeit, from 8 populations of European silver fir (Abies alba Mill.) were analyzed. On the dendrog...
Full Text Available The aim of our work was to detect genetic variability in the set of 59 winter and spring triticale (x Triticosecale Witt. varieties using 5 wheat SSR markers. Totally, 35 alleles with an average number of 7 alleles per locus were detected. The highest number of alleles showed out Xbarc 004 (9. Based on the number and frequencies of alleles, the diversity index (DI, the probability of identity (PI and the polymorphic information content (PIC of SSR markers were calculated. The polymorphic information content (PIC ranged from 0.264 to 0.920 with an average of 0.654, which is generally considered sufficient for this purpose. For the assessment of genetic diversity the dendrogram, based on the hierarchical cluster analysis using UPGMA algorithm was prepared. Fifty nine triticale cultivars were grouped into three major clusters. The cultivar Terelland 22 (USA separated as unique one, second subcluster contained 3 cultivars and third one 55 cultivars. It was not possible to differentiate 15 genotypes between each other. For better differentiation it is necessary to use more polymorphic microsatellite markers. Results showed the utility of microsatellite markers for estimation of genetic diversity of triticale genotypes leading to genotype identification.
Full Text Available Sixty six genotypes of cowpea (Vigna unguiculata (L. Walp were investigated to understand the extent of genetic diversitythrough twelve quantitative traits. Mahalanobis’s D2 analysis established the presence of wide genetic diversity among thesegenotypes by the formation of 23 clusters. Cluster I had the maximum number of genotypes i.e 22 and cluster 23 had onlyone genotype. Intra cluster distance analysis revealed that the minimum intra cluster distance was observed in the cluster II.The inter-cluster distance (D was found to be the maximum between the clusters XXII and XXIII and the same wasminimum between clusters II and V. The results indicated that grain yield per plant contributed maximum to the totaldivergence followed by 100 seed weight and days to 50% flowering. Number of branches per plant had least contribution tothe total divergence followed by petiole length. The existence of wide genetic diversity among the types chosen from thesame geographical location was obviously seen. In the present study, the variety Vellayani local had the maximum value forplant height and pod length and thereby distinguished from other varieties and it is present singly in the cluster XXIII. Henceit is proved to be widely divergent, since its yield is high, it can be used for further crossing and yield improvement. Thecluster XVIII had the highest cluster mean values for number of clusters per plant and the cluster XIV has the highest meanvalue for grain yield per plant. These two clusters may be utilized in crossing programme which may yield in a widespectrum of variability and for selection for seed yield in the subsequent generations. The clustering pattern of the varietiesin the present study clearly indicated that there was no parallelism between genetic and geographic diversities. Based on themean performance and genetic divergence, the genotypes Vellayani local, NBC 7, Lola, CP 18, CP 150, ACM 05-07 can beused for crossing and further selection.
R.M.Nagalakshmi, R. Usha Kumari and M. B. Boranayaka
Production status, farming systems and genetic diversity of indigenous cattle in Sri Lanka were evaluated using six geographically distinct populations. The indigenous cattle population of the country is considered as a nondescript mixture of genotypes, and represents more than half of the total cattle population of 1.2 million heads. Five distinct indigenous populations were investigated for morphological analysis, and four were included in evaluating genetic differences. Farming systems were analysed using a pre-tested structured questionnaire. The genetic variation was assessed within and between populations using 15 autosomal and two Y-specific microsatellite markers, and compared with two indigenous populations from the African region. Farming system analysis revealed that indigenous cattle rearing was based on traditional mixed-crop integration practices and operates under limited or no input basis. The contribution of indigenous cattle to total tangible income ranged from zero to 90% reflecting the high variation in the purpose of keeping. Morphometric measurements explained specific phenotypic characteristics arising from geographical isolation and selective breeding. Though varying according to the region, the compact body, narrow face, small horns and humps with shades of brown and black coat colour described the indigenous cattle phenotype in general. Genetic analysis indicated that indigenous cattle in Sri Lanka have high diversity with average number of ave high diversity with average number of alleles per locus ranging from 7.9 to 8.5. Average heterozygosity of different regions varied within a narrow range (0.72 ± 0.04 to 0.76 ± 0.03). Genetic distances between regions were low (0.085 and 0.066) suggesting a similar mixture of genotypes across regions. Y-specific analysis indicated a possible introgression of Taurine cattle in one of the cattle populations. (author)
Glioblastoma (GBM) is a lethal malignancy whose clinical intransigence has been linked to extensive intraclonal genetic and phenotypic diversity and the common emergence of therapeutic resistance. This interpretation embodies the implicit assumption that cancer stem cells or tumor-propagating cells are themselves genetically and functionally diverse. To test this, we screened primary GBM tumors by SNP array to identify copy number alterations (a minimum of three) that could be visualized in single cells by multicolor fluorescence in situ hybridization. Interrogation of neurosphere-derived cells (from four patients) and cells derived from secondary transplants of these same cells in NOD-SCID mice allowed us to infer the clonal and phylogenetic architectures. Whole-exome sequencing and single-cell genetic analysis in one case revealed a more complex clonal structure. This proof-of-principle experiment revealed that subclones in each GBM had variable regenerative or stem cell activity, and highlighted genetic alterations associated with more competitive propagating activity in vivo. PMID:25533637
Piccirillo, Sara G M; Colman, Sue; Potter, Nicola E; van Delft, Frederik W; Lillis, Suzanne; Carnicer, Maria-Jose; Kearney, Lyndal; Watts, Colin; Greaves, Mel
Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358
Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C.; Kuhn, David N.; Glaz, Barry; Gilbert, Robert A.; Comstock, Jack C.; Wang, Jianping
Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358
Nayak, Spurthi N; Song, Jian; Villa, Andrea; Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C; Kuhn, David N; Glaz, Barry; Gilbert, Robert A; Comstock, Jack C; Wang, Jianping
Fluorescence PCR was applied to investigate the genetic diversities of 9 indigenous Chinese goat breeds and 1 exotic breed with 10 microsatellite DNA markers recommended by the Food and Agriculture Organization of the United Nations and the International Livestock Research Institute of Animal Genetics, which provide data for the preservation and utilization of indigenous goat breeds genetic resource. We found that the 7 breeds were high polymorphic while 3 breeds were moderate polymorphic. We also detected 119 alleles, and the effective allele number ranged from 1.4641 to 9.2911. The average heterozygosity of loci and breeds respectively varied from 0.2618 to 0.7672 and from 0.5196 to 0.7024. As well as SRCRSP23 site and Hexi cashmere goat had the highest average heterozygosity. Then we analyzed the phylogenetic trees (NJ and UPGMA), and found both of them were generally in accordance with their original breeding history and localities. PMID:20684301
Xu, Limei; Liu, Chousheng; Zhang, Liping; Wang, Zhigang; Han, Xu; Li, Xiaoxia; Chang, Shuang
Contaminant driven genetic erosion reported through the inspection of selectable traits can be underestimated using neutral markers. This divergence was previously reported in the aquatic system of an abandoned pyrite mine. The most sensitive genotypes of the microcrustacean cladoceran Daphnia longispina were found to be lacking in the impacted reservoir near the entrance of the metal rich acid mine drainage (AMD). Since that divergence could be, at least partially, accounted for by mutagenicity and genotoxicity of the AMD, the present study aimed at providing such a characterization. The Allium cepa chromosomal aberration assay, using root meristematic cells, was carried out, by exposing seeds to 100, 10, 1, and 0.1 % of the local AMD. Chromosomal aberrations, cell division phases and cell death were quantified after the AMD exposure and after 24 and 48 h recovery periods. The AMD revealed to be mutagenic and genotoxic, even after diluting it to 1 and 0.1 %. Dilutions within this range were previously found to be below the lethality threshold and to elicit sublethal effects on reproduction of locally collected D. longispina clonal lineages Significant mutagenic effects (micronuclei and chromosomal breaks) were also found at 0.1 % AMD, supporting that exposure may induce permanent genetic alterations. Recovery tests showed that AMD genotoxic effects persisted after the exposure. PMID:23686739
Sobral, Olímpia; Marin-Morales, Maria Aparecida; Ribeiro, Rui
Objective. To determine and evaluate the genetic diversity of six populations of red hybrid tilapia, with the purpose to assess the potential benefit of a future breeding program conducted at the Research Center for Aquaculture (Ceniacua), Colombia. Material and methods. A total of 300 individuals, representing a wide genetic variability, were genotyped using a fluorescent microsatellite marker set of 5 gene-based SSRs in 6 different farms belonging to 4 States of Colombia. Results. The resul...
Boris Briñez R.; Xenia Caraballo O.; Marcela Salazar V.
Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value. PMID:22369278
Diekmann, Onno E; Serrão, Ester A
Full Text Available Extracting of knowledge form large amount of data is an important issue in data mining systems. One of most important activities in data mining is association rule mining and the new head for data mining research area is privacy of mining. Today association rule mining has been a hot research topic in Data Mining and security area. A lot of research has done in this area but most of them focused on perturbation of original database heuristically. Therefore the final accuracy of released database falls down intensely. In addition to accuracy of database the main aspect of security in this area is privacy of database that is not warranted in most heuristic approaches, perfectly. In this paper we introduce new multi-objective method for hiding sensitive association rules based on the concept of genetic algorithms. The main purpose of this method is fully supporting security of database and keeping the utility and certainty of mined rules at highest level.
Mohammad Naderi Dehkordi
Full Text Available Abstract Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs. Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in diagnostic assay development can be identified.
MacMillan Alastair P
Genetic diversity is one of the key factors for the improvement of many crop plants including wheat. Many wheat scientistshave studied genetic diversity in wheat germplasm using different molecular markers which have provided a powerfulapproach to analyze genetic relationships among wheat germplasms. In this study, genetic diversity of CIMMYT(International maize and wheat improvement center) bread wheat lines collected from Russia was evaluated using 30sequence-related amplified polymorphism ...
Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (-/+ s.e.) allelic diversity was 5.9 (-/+ 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (-/+ s.e.) effective number of alleles (3.3 -/+ 1.27), observed heterozygosity (0.5306 -/+ 0.22), expected Levene's heterozygosity (0.6612 -/+ 0.15), expected Nei's heterozygosity (0.6535 -/+ 0.14), and polymorphism information content (0.6120 -/+ 0.03). Low values of Wright's fixation index, F(IS) (0.2433 -/+ 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal 'L' shaped distribution of mode-shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant M ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers. PMID:16385161
Gupta, A K; Chauhan, M; Tandon, S N
Does diversity beget diversity? Diversity includes a diversity of concepts because it is linked to variability in and of life and can be applied to multiple levels. The connections between multiple levels of diversity are poorly understood. Here, we investigated the relationships between genetic, bacterial, and chemical diversity of the endangered Atlanto-Mediterranean sponge Spongia lamella. These levels of diversity are intrinsically related to sponge evolution and c...
Noyer, Charlotte; Becerro, Mikel
Full Text Available SciELO Chile | Language: English Abstract in english Information about genetic dissimilarity is very important to corroborate genealogical relationships and to predict the most heterozygotic hybrid combinations. Eight popcorn S6 lines of diverse germplasm types were evaluated using simple sequence repeats (SSR) markers. Of a total of 51 evaluated poly [...] morphic primers, 15 were used for polymerase chain reaction (PCR) amplification. The genetic distance was estimated by Rogers’ modified distance. The different popcorn breeding programs in Brazil are possibly using highly similar base-populations. The genetic similarity of lines P1-3 and P8-1 was lowest, while P3-3 and P8-2 were genetically more similar. The cophenetic correlation showed that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) was reliable to discriminate the genotypes in five groups. The clusters were consistent with the estimates of genetic identity. There was a moderate coincidence degree between the groups and genealogy of lines. Higher levels of heterozygosity are expected from crosses between the group containing lines P3-3 and P7-3 with that of P1-3 and P7-4. Crosses between lines P1-3 and P8-1 are also promising.
Ana Paula, Ribeiro Trindade; Ronald José, Barth Pinto; Antonio Teixeira do, Amaral Júnior; Claudete Aparecida, Mangolin; Maria de Fátima Pires da, Silva Machado; Carlos Alberto, Scapim.
Full Text Available SciELO Brazil | Language: English Abstract in english Orchids are valuable pot plants and Cattleya intermedia is a promising species underused in breeding programs. Recently, breeding work with this species produced superior plants that are believed to be not the true species owing to the morphological differences from wild plants. The aim of this stud [...] y was to estimate the level of genetic diversity and interrelationships between wild and bred Cattleya intermedia collected at three different Brazilian states and from commercial breeders with RAPD markers. A total of 65 polymorphic bands were used to generate a genetic distance matrix. No specific groupings were revealed by the cluster analysis as bred materials were not different from wild plants. The genetic differentiation (F ST = 0.01626) was very low indicating a high gene flow in C. intermedia due to artificial crosses and a high differentiation between populations. The genetic variability available within this species is high enough to allow genetic progress in flower shape and size.
Nelson Barbosa, Machado Neto; Luiz Gonzaga Esteves, Vieira.
Full Text Available Goats are one of the most important livestock species in Albania. The aim of this study is evaluation of genetic diversity, genetic structure and genetic distances between six Albanian local goat breeds, using three set of markers: 31 microsatellite markers, AFLP markers based on three primer combinations, and 26 SNP markers. A total of 185 individuals representing six different Albanian goat breeds (Capore, Muzhake, Dukati, Liqenasi, Hasi and Mati were analyzed. All microsatellite markers were highly polymorphic. A total number of 331 alleles were observed at 30 microsatellite loci. The average observed heterozygosity was 0.673.The global heterozygosity deficit (FIT was estimated 0.11 and global breed differentiation evaluated by FST, was estimated 0.02. The AMOVA revealed that percentage of variation among populations was 2.04% and within populations was 97.96%. AFLP analysis using three primer combinations revealed 107 polymorphic markers. The FST value across all markers was 0.031, indicating that 3.1% of total genetic variation is due to breed differentiation. SNPs analysis indicated: Expected heterozygosity per locus ranged from 0.0059 to 0.526 with an average value for all loci, 0.316, while the values of observed heterozygosity (HO ranged from 0.0059 to 0.517, with an average value of 0.282. The results obtained here reflect gaot management in Albania. Based on the results of this study, we may conclude that Albanian goat breed are important reservoir of genetic diversity, have a low level of differentiation and high level of admixture.
Full Text Available Expressed sequence tag (EST markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum. In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29% contigs and 96 (10% singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs and metabolism and energy (singletons. EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725 being between Harmankaya99 and Sönmez2001, and the lowest (0.622 between Aytin98 and Izgi01.
Full Text Available SciELO Brazil | Language: English Abstract in english Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these [...] cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01.
Ozge, Karakas; Filiz, Gurel; Ahu Altinkut, Uncuoglu.
Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima's D and Fu and Li's F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949
Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun
The causal agent of witches' broom disease, Moniliophthora perniciosa is a hemibiotrophic and endemic fungus of the Amazon basin and the most important cocoa disease in Brazil. The purpose of this study was to analyze the genetic diversity of polysporic isolates of M. perniciosa to evaluate the adaptation of the pathogen from different Brazilian regions and its association with different hosts. Polysporic isolates obtained previously in potato dextrose agar cultures of M. perniciosa from different Brazilian states and different hosts (Theobroma cacao, Solanum cernuum, S. paniculatum, S. lycocarpum, Solanum sp, and others) were analyzed by somatic compatibility grouping where the mycelium interactions were distinguished after 4-8 weeks of confrontation between the different isolates of M. perniciosa based on the precipitation line in the transition zone and by protein electrophoresis through SDS-PAGE. The diversity of polysporic isolates of M. perniciosa was grouped according to geographic proximity and respective hosts. The great genetic diversity of M. perniciosa strains from different Brazilian states and hosts favored adaptation in unusual environments and dissemination at long distances generating new biotypes. PMID:22869076
Ferreira, L F R; Duarte, K M R; Gomes, L H; Carvalho, R S; Leal Junior, G A; Aguiar, M M; Armas, R D; Tavares, F C A
The Asiatic wild dog or dhole was once very widely distributed across Asia but now has a very fragmented range. In this first genetic study of this little-known species, we obtained information on genetic diversity, phylogeography, and social structure using both mitochondrial control region sequencing and microsatellite genotyping of noninvasive faecal samples from wild populations, as well as from museum and captive samples. A pattern largely consistent with isolation by distance across the Asian mainland was observed, with no clear subspecies distinctions. However, two major phylogeographical groupings were found across the mainland, one extending from South, Central, and North India (south of the Ganges) into Myanmar, and the other extending from India north of the Ganges into northeastern India, Myanmar, Thailand and the Malaysian Peninsula. We propose a scenario involving glaciation events that could explain this pattern. The origin of the dhole populations in Sumatra and Java is enigmatic and requires further study. Very low levels of genetic diversity were observed among wild dholes from Baluran National Park in Java, Indonesia, but in contrast, high levels were observed in Mudumalai Wildlife Sanctuary in South India. PMID:15969714
Iyengar, A; Babu, V N; Hedges, S; Venkataraman, A B; Maclean, N; Morin, P A
Articles selected by Faculty of 1000 Biology: genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ?-Proteobacteria diversity.
A selection of evaluations from Faculty of 1000 Biology covering genetically identical SNPs; detailed histone modification mapping; plant gene-expression diversity; photosynthesis gene evolution; ?-Proteobacteria diversity
Full Text Available The study was aimed at characterizing and analyzing the genetic diversity at the isozyme level of thirty coconut cultivars. Ten enzyme systems viz., Alcohol Dehydrogenase, Glutamate Oxaloacetate Transaminase, Glucose-6 Phosphate Dehydrogenase, Peroxidase, Esterase, ?-Amylase, Phosphorylase, Malate Dehydrogenase, Super Oxide Dismutase and Acid Phosphatase were studied using discontinuous polyacrylamide gel electrophoresis. Twenty loci and 40 alleles were observed, of which, 14 loci were polymorphic. Seven loci were heterozygous. Null alleles were observed for ACP, ADH and MDH. Greater heterozygosity was observed for Glucose-6 Phosphate Dehydrogenase and least for Super Oxide Dismutase. Among the cultivars, Nadora Tall and Calangute Tall showed maximum heterozygosity while Kulasekharam Green Dwarf showed least heterozygosity.
AFLP and RAPD methods were used to investigate the genetic diversity of walnuts in western Sichuan plateau and Qinba mountainous regions. 35 samples were collected from 8 different regions, and 32 RAPD primers and 28 AFLP primer combinations were identified with polymorphism bands among the entire. 324 and 2155 fragments were respectively produced by RAPD and AFLP makers, and 86.1 % of RAPD bands and 57.2% of AFLP bands showed polymorphic with the size of 180~2000 bp and 50~1800 bp, respec...
Zheng Xu; Tingxing Hu; Fan Zhang,
Many species persist as a metapopulation under a balance between the local extinction of subpopulations or demes and their recolonization through dispersal from occupied patches. Here we review the growing body of literature dealing with the genetic consequences of such population turnover. We focus our attention principally on theoretical studies of a classical metapopulation with a 'finite-island' model of population structure, rather than on 'continent-island' models or 'source-sink' models. In particular, we concern ourselves with the subset of geographically subdivided population models in which it is assumed that all demes are liable to extinction from time to time and that all demes receive immigrants. Early studies of the genetic effects of population turnover focused on population differentiation, such as measured by F(ST). A key advantage of F(ST) over absolute measures of diversity is its relative independence of the mutation process, so that different genes in the same species may be compared. Another advantage is that F(ST) will usually equilibrate more quickly following perturbations than will absolute levels of diversity. However, because F(ST) is a ratio of between-population differentiation to total diversity, the genetic effects of metapopulation processes may be difficult to interpret in terms of F(ST) on its own, so that the analysis of absolute measures of diversity in addition is likely to be informative. While population turnover may either increase or decrease F(ST), depending on the mode of colonization, recurrent extinction and recolonization is expected always to reduce levels of both within-population and species-wide diversity (piS and piT, respectively). One corollary of this is that piS cannot be used as an unbiased estimate of the scaled mutation rate, theta, as it can, with some assumptions about the migration process, in species whose demes do not fluctuate in size. The reduction of piT in response to population turnover reflects shortened mean coalescent times, although the distribution of coalescence times under extinction colonization equilibrium is not yet known. Finally, we review current understanding of the effect of metapopulation dynamics on the effective population size. PMID:11205346
Pannell, J R; Charlesworth, B
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
Vickers, Kasey C; Roteta, Leslie A; Hucheson-Dilks, Holli; Han, Leng; Guo, Yan
Full Text Available SciELO Brazil | Language: English Abstract in english Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained b [...] y analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.
Flávio de Oliveira, Francisco; Leandro Rodrigues, Santiago; Maria Cristina, Arias.
Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.
Flávio de Oliveira Francisco
Full Text Available DNA fingerprint was generated using jute specific SSR markers on 10 jute cultivars from two Corchorus species (C. olitorius and C. capsularis and the genetic relatedness among the cultivars was estimated. A total of 106 alleles were identified using 23 primer pairs among the 10 cultivars with an average of 4.61 ± 1.92 alleles per locus, and a mean genetic diversity of 0.68±0.16. Four C. olitorius cultivars could be easily distinguished with 6 markers using 5 primer pairs and six C. capsularis cultivars with 7 markers using 6 primer pairs. The UPGMA analysis enabled the grouping of the cultivars into two major clusters, which matched with the known information on jute. This experiment provides proof that in spite of low levels of genetic polymorphisms among jute cultivars, SSR markers can reliably distinguish among them. This finding reinforces the utility of SSR primers for providing unique genetic identities or fingerprints of various jute cultivars.
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.
Wheat is one most important cereal crops grown in Ethiopia. Yet, keeping in view insufficient information on exotic bread wheat genotypes is limiting the access to useful traits present among the genotypes in the Somali region of Ethiopia. The aim of the study was to assess the extent of genetic diversity among bread wheat genotypes. Twenty six bread wheat (Triticum aestivum L.) genotypes obtained from ICARDA-CIMMYT were tested at Gode and Kelafo research sites at three cropping seasons (2009/10, 2010/11 and 2011/12) under irrigation. The experiment was conducted in randomized complete block design with three replications. Ten agronomic traits were included in the study. The mean values, ranges and the coefficient of variation of the 10 characters indicated the existence of sufficient variability among genotypes. Multivariate techniques were used to classify 26 bread wheat genotypes. Principal component analysis showed that the first six principal components explained about 91.87% of the total variation. D2 analysis showed the 26 bread wheat genotypes grouped into six clusters. This made to become moderate diversity among the genotypes. The crosses between genotypes selected from cluster-III with cluster-VI and cluster V with cluster VI are expected to produce better genetic recombination and segregation in their progenies. Therefore, these bread wheat genotypes need to be crossed and selected to develop high yielding pure line variety. PMID:24511742
Degewione, A; Alamerew, S
Full Text Available Wheat is one most important cereal crops grown in Ethiopia. Yet, keeping in view insufficient information on exotic bread wheat genotypes is limiting the access to useful traits present among the genotypes in the Somali region of Ethiopia. The aim of the study was to assess the extent of genetic diversity among bread wheat genotypes. Twenty six bread wheat (Triticum aestivum L. genotypes obtained from ICARDA-CIMMYT were tested at Gode and Kelafo research sites at three cropping seasons (2009/10, 2010/11 and 2011/12 under irrigation. The experiment was conducted in randomized complete block design with three replications. Ten agronomic traits were included in the study. The mean values, ranges and the coefficient of variation of the 10 characters indicated the existence of sufficient variability among genotypes. Multivariate techniques were used to classify 26 bread wheat genotypes. Principal component analysis showed that the first six principal components explained about 91.87% of the total variation. D2 analysis showed the 26 bread wheat genotypes grouped into six clusters. This made to become moderate diversity among the genotypes. The crosses between genotypes selected from cluster-III with cluster-VI and cluster V with cluster VI are expected to produce better genetic recombination and segregation in their progenies. Therefore, these bread wheat genotypes need to be crossed and selected to develop high yielding pure line variety.
Full Text Available SciELO Brazil | Language: English Abstract in english Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their [...] rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.
Romina, Cuyeu; Beatriz, Rosso; Elba, Pagano; Gabriela, Soto; Romina, Fox; Nicolás Daniel, Ayub.
Full Text Available SciELO Chile | Language: English Abstract in english This study presents bacterial population analyses of microbial communities inhabiting three sites of acid mine drainage (AMD) in the Shen-bu copper mine, Gansu Province, China. These sites were located next to acid-leached chalcopyrite slagheaps that had been abandoned since 1995. The pH values of t [...] hese samples with high concentrations of metals ranged from 2.0 to 3.5. Amplified ribosomal DNA restriction analysis (ARDRA) was used to characterize the bacterial population by amplifying the 16S rRNA gene of microorganisms. A total of 39 operational taxonomic units (OTUs) were obtained from the three samples and sequenced from 384 clones. Sequence data and phylogenetic analyses showed that two dominant clones (JYC-1B, JYC-1D) in sample JYC-1 represented 69.5% of the total clones affiliated with Acidithiobacillus ferrooxidans (?-Proteobacteria), and the most dominant clones of JYC-2 and JYC-3 were affiliated with Caulobacter crescentus (?-Protebacteria). At the level of bacterial divisions, differences in the relative incidence of particular phylogenetic groups among the three samples and discrepancies in physicochemical characteristics suggested that the physico-chemical characteristics had an influence on phylogenetic diversity. Furthermore, the relationships between the discrepancies of physicochemical characteristics and the diversity of the bacteria communities in the three samples suggested that the biogeochemical properties, pH and concentration of soluble metal, could be key factors in controlling the structure of the bacterial population
Yu, Yang; Wuyang, Shi; Minxi, Wan; Yanfei, Zhang; Lihong, Zou; Jufang, Huang; Guanzhou, Qiu; Xueduan, Liu.
Sitobion avenae is a major agricultural pest of wheat in China. Using microsatellite markers, we studied the potential gene flow, genetic diversity, genetic differentiation, and genetic structure of seven S. avenae populations from different regions of China (Beijing, Hebei, Henan, Hubei, Jiangsu, Shandong, and Shanxi provinces). The populations from Henan, Shandong, and Jiangsu showed high levels of genic and genotypic diversity. By contrast, the genic diversity in the Beijing and Hebei popu...
Xin, Juan-juan; Shang, Qing-li; Desneux, Nicolas; Gao, Xi-wu
Hepatitis B virus (HBV) infection remains a major public health problem particularly in Asia and Pacific that belongs to hepatitis B endemic regions. With high genetic diversity of the entire genome, this DNA virus has been classified into eight genotypes, genotype A to H, and recently two new genotypes, I and J, has been found in Asia. Interestingly, distribution of HBV genetic diversity is geographically specific worldwide. Further, distribution of HBV genetic diversity in Indonesia is asso...
Thedja, M. D.
Garlic (Allium sativum L.) that is cultivated in Tunisia is heterogeneous and unclassified with no registered local cultivars. At present, the level of genetic diversity in Tunisian garlic is almost unknown. Inter Simple Sequence Repeats (ISSR) genetic markers were therefore used to assess the genetic diversity and its distribution in 31 Tunisian garlic accessions with 4 French classified clones used as control. It was the first time that ISSR markers were used to detect diversity...
Naouel Jabbes; Emmanuel Geoffriau; Valerie Le Clerc; Boutheina Dridi; Cherif Hannechi
Full Text Available Abstract Background Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Results Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Conclusion Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.
Full Text Available SciELO South Africa | Language: English Abstract in english Three indigenous Mozambican cattle breeds, namely the Angone, Landim and Bovino de Tete were characterized using six proteins, 13 autosomal microsatellite loci and one Y-specific microsatellite locus (INRA124). The Mashona breed from Zimbabwe was also studied to elucidate the origin of the Bovino de [...] Tete cattle. Expected mean heterozygosity ranged from 0.46 - 0.50 in the proteins and from 0.66 - 0.69 in the microsatellites. Population genetic variability was relatively high when compared to other African breeds. Only 4.5% of the total genetic variation could be attributed to the differences among the breeds. D A genetic distances and principal component analysis suggest that Mozambican breeds occupy an intermediate position between Indian Zebu and African taurine cattle. The genetic contribution from Indian Zebu, estimated by mR and average percentage of Zebu diagnostic alleles, was highest in the Angone breed and lowest in the Landim breed. The indicine Y-specific allele was fixed in the Angone breed (classified as Zebu), was found in 62% of the Bovino de Tete breed and was absent in the Landim breed (classified as Sanga). The hybrid nature of these breeds was also revealed by using an admixture model to infer population structure. Cluster analysis correctly assigned individuals to their rightful populations with probabilities ranging from 0.96 to 0.98, using prior population information. The results support the hypothesis of the Bovino de Tete cattle being a result of crossbreeding between Sanga and Zebu breeds. This study presents the first extensive information on the genetic diversity and relationships among Mozambican cattle breeds and with other breeds from different continents.
I., Bessa; I., Pinheiro; M., Matola; K., Dzama; A., Rocha; P., Alexandrino.
Full Text Available Domestic goat and sheep populations maintained for many generations with small numbers of male and female parents, or declining in total numbers, not only endure accumulated genetic drift but also a steady rise in inbreeding, which can be directly attributed to dispersive forces of evolutionary significance that influence gene frequency. Increasing effective population size shows theoretical promise in lessening the impact on erosion of biodiversity from genetic drift. For example, doubling the effective numbers of parents which increases effective population size reduces rate of inbreeding by nearly one-half in many of the scenarios in the present study. Similarly, equalizing the number of male and female parents can decrease the variance among progeny of each parent, which in turn increases effective population size. The recurring erosion of domestic goat and sheep diversity has contributed to decreased fecundity, reduced fitness and poor adaptability, all known to influence efficiency of production. The potential loss in performance of livestock and poultry following many generations of accumulated genetic drift, which often goes unnoticed, can be predicted for specific populations from precise estimates of their mean value, additive genetic variance and heritability along with their effective number of male and female parents. For example, when the effective population size decreases from 200 to 40, the potential reduction in mean performance for economically important traits of goat and sheep populations following 20 generations of accumulated genetic drift will nearly double. In contrast, increasing effective population size from 200 to 600 will have the potential reduction in mean performance. The accumulation of favourable mutations could imply an effective population size of 100 or more, which is equal to a rise in rate of inbreeding of 0.5% or less, may be acceptable in sustaining genetic response to artificial selection in commercial breeding populations. The application of quantitative genetic principles related to inbreeding and genetic drift make it possible to safeguard against erosion of genetic diversity in endangered breeds, populations and landraces while lessening the impact from potential loss in their performance. Conservation of domestic animal diversity can be achieved by managing the erosion of genetic variation based on breeding strategies which promote the mating of sires to all dams, in either ‘random bred’ or ‘balanced pedigreed’ breeding structure for populations of endangered domestic goats and sheep. Obviously, the in-situ and ex-situ conservation of live animals, along with cryogenic preservation of their gametes, stem cells, somatic cells, blood and gonads will be complementary to conservation breeding.
J. N. B. Shrestha
Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].
Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU
Avian paramyxoviruses (APMVs) belong to the genus Avulavirus in the family Paramyxoviridae and include at least nine serotypes, APMV-1 to -9, as well as two additional provisional serotypes. Newcastle disease virus (NDV), which comprises APMV-1, is the most extensively studied APMV because it is an important poultry pathogen. A moderate level of antigenic and genetic diversity is recognized for APMV-1 isolates, but our knowledge of the antigenic and genetic diversity of the other APMV serotypes is limited. APMV-4 is frequently isolated from waterfowl around the world. To date complete genome sequences of APMV-4 are available for only strains, which were isolated from ducks in Hong Kong, Korea and Belgium over a period of 37 years. We have carried out genome sequencing from the nucleocapsid (N) gene-end signal to the polymerase (L) gene-start signal of five APMV-4 strains recently isolated from Italy. Each of the eight APMV-4 strains has the same F protein cleavage site, DIQPR?F. They also share a high level of nucleotide and amino acid sequence identity: for example, the F and HN glycoproteins have greater than 97% sequence identity between the various strains. Thus, comparison of these eight strains of APMV-4 did not provide evidence of substantial diversity, in contrast to similar studies with APMV-2, -3, and -6, in which the F and HN glycoproteins exhibited up to 20-30% amino acid sequence variation within a subgroup. Reciprocal cross-HI assay using post infection chicken sera also failed to detect significant antigenic variation among the available APMV-4 strains. PMID:23178589
Nayak, Baibaswata; Nayak, Shreeraj; Paldurai, Anandan; Kumar, Sachin; De Nardi, Roberta; Terregino, Calogero; Collins, Peter L; Samal, Siba K
The conservation of genetic diversity has emerged as one of the central issues in conservation biology. Although researchers in the areas of evolutionary biology, population management, and conservation biology routinely investigate genetic variability in natural populations, onl...
Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were sele...
Galina Radeva; Anelia Kenarova; Velina Bachvarova; Katrin Flemming; Ivan Popov; Dimitar Vassilev; Sonja Selenska-Pobell
Full text: The production status, farming systems and genetic diversity of indigenous cattle in Sri Lanka were evaluated using six geographically distinct populations in Sri Lanka, which is a small island located below the southern tip of Indian subcontinent. The indigenous cattle population of the country is considered as a non-descript type mixture of genotypes, and represent more than the half of total cattle population of 1.2 million heads. Six distinct indigenous populations (NE, NC, So, No, TK and Th) were investigated for morphological and genetic differences. The respective farming systems were also evaluated to complete the requirement in developing conservation and utilization strategies. The sampling was carried out based on the non-existence of artificial insemination facilities to assure the target populations are indigenous. The six populations were assumed genetically isolated from each other in the absence of nomadic pattern of rearing and regular cattle migration. The farming systems were analyzed using a pre-tested structured questionnaire by single visits to each location. Single visits were practiced, as there is no variation in farming system according to the period of the year. Morphometric measurements were taken during the visit and the genetic variation was assessed within and between five populations using 15 autosomal and two Y-specific microsatellite markers. The farming system analysis revealed that indigenous cattle are reared as a traditt indigenous cattle are reared as a traditional practice in all the regions of the country under limited or no input situations. Since the low productivity masks its real contribution to the rural livelihood, the level of utilization was confounded within the attributes of respective farming systems. The contribution of indigenous cattle to total tangible income ranged from 0% to 90% in different regions reflecting the high variation in the purpose of keeping indigenous cattle. Integration with crop, especially with paddy was the common feature in systems across the regions. Morphometric measurements identified the specific phenotypic characteristics resulted by geographical isolation and selective breeding. Though vary according to the regional preferences, the compact body, narrow face, small horns and humps with shades of brown and black coat colour described the indigenous cattle phenotype in general. The diversity analysis based on microsatellite genotyping indicated that indigenous cattle in Sri Lanka has a high genetic diversity with average number of alleles per locus ranging from 7.9 to 8.5. Average heterozygosity of different regions varied within a narrow range (0.72 ± 0.04 to 0.76 ± 0.03). The genetic distances (DA) between regions were low (ranged between 0.085 and 0.066) suggesting a similar mixture of genotypes across regions despite the geographical isolation. However, two genetic clusters were visible though no relationship of those clusters with the geographical distribution of different regions could be observed. Introgression of taurine cattle was evidenced in one of the cattle populations (NC) as suggested by the Y-specific microsatellite analysis (author)
Full Text Available Abstract Background Plasmodium vivax, although causing a less serious disease than Plasmodium falciparum, is the most widespread of the four human malarial species. Further to the recent recrudescence of P. vivax cases in the Newly Independent States (NIS of central Asia, a survey on the genetic diversity and dissemination in Azerbaijan was undertaken. Azerbaijan is at the crossroads of Asia and, as such, could see a rise in the number of cases, although an effective malaria control programme has been established in the country. Methods Thirty-six P. vivax isolates from Central Azerbaijan were characterized by analysing the genetic polymorphism of the circumsporozoite protein (CSP and the merozoite surface protein 1 (MSP-1 genes, using PCR amplifications and amplicons sequencing. Results Analysis of CSP sequences showed that all the processed isolates belong to the VK 210 type, with variations in the alternation of alanine residue (A or aspartic acid residue (D in the repeat motif GDRA(A/DGQPA along the sequence. As far as MSP-1 genotyping is concerned, it was found that the majority of isolates analysed belong to Belem and Sal I types. Five recombinant isolates were also identified. Combined analysis with the two genetic markers allowed the identification of 19 plasmodial sub-types. Conclusion The results obtained in the present study indicate that there are several P. vivax clones circulating in Azerbaijan and, consequently, a careful malaria surveillance could be of paramount importance to identify, at early stage, the occurrence of possible P. vivax malaria outbreaks.
Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3?months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. PMID:24399611
Harbst, Katja; Lauss, Martin; Cirenajwis, Helena; Winter, Christof; Howlin, Jillian; Törngren, Therese; Kvist, Anders; Nodin, Björn; Olsson, Eleonor; Häkkinen, Jari; Jirström, Karin; Staaf, Johan; Lundgren, Lotta; Olsson, Håkan; Ingvar, Christian; Gruvberger-Saal, Sofia K; Saal, Lao H; Jönsson, Göran
To improve yield and quality of wheat, presence of genetic diversity is an important prerequisite. To estimate the extent of genetic variability, DNA markers including Randomly Amplified Polymorphic DNA (RAPD) have been widely used in various crops of agronomic importance. During present study, RAPDs were used to estimate genetic relationship among 10 Pakistani wheat varieties and to identify genetically diverse genotypes which can be used in future breeding programs. RAPD primers used during...
Aisha Naz; Zahoor Ahmed Swati; Khan, Imtiaz A.
Estimation of genetic diversity of Brassica germplasm provides the basis for rapeseed/mustard genetic improvement. Studies were undertaken to estimate the genetic diversity of 30 lines of Brassica napus using Randomly Amplified Polymorphic DNA (RAPD) primers. A total of 30 B. napus genotypes of local and exotic origin were characterized using molecular markers. Four RAPD primers were used to estimate the genetic distances among the genotypes in all the possible combinatio...
Mian Afaq Ahmad; Iqbal Munir; Waqar Ali; Zahoor Ahmad Swati; Muhammad Saeed Khattak; Quahir Sohail; Imran Khan
An analysis of genetic structure and differentiation in cultivated walnut (Juglans regia) using 15 microsatellite loci revealed a considerable amount of genetic variation with a mild genetic structure indicating five genetic groups corresponding to the centers of diversity within the home range of w...
There has been a renewed interest in the effects of genetic diversity on population-level and community-level processes. Many of these studies have found non-additive, positive effects of diversity, but these studies have rarely examined ecological mechanisms by which diverse populations increase productivity. We used the seed beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae) to study genetic diversity in insect host preference and fecundity and its effects on total productivity and resource use. We created genetically distinct lineages that varied in host preference and fecundity and then assembled groups consisting of one, three, five, or all ten lineages. We found that lineages with intermediate diversity had the highest productivity, though resource use did not change in diverse groups. In addition, lineages showed substantial plasticity in host preference when preference was assayed either individually or in groups, and productivity was much lower in groups than predicted by individual assays. These results highlight the interplay of genetic diversity, resource variation, and phenotypic plasticity in determining the ecological consequences of genetic diversity. In addition, when plasticity modifies a population's response to population density, this may create a complex interaction between genetic diversity and density, influencing selective pressures on the population and potentially maintaining genetic diversity across generations. PMID:24535057
Burls, K J; Shapiro, J; Forister, M L; Hoelzer, G A
Full Text Available Objective. To determine and evaluate the genetic diversity of six populations of red hybrid tilapia, with the purpose to assess the potential benefit of a future breeding program conducted at the Research Center for Aquaculture (Ceniacua, Colombia. Material and methods. A total of 300 individuals, representing a wide genetic variability, were genotyped using a fluorescent microsatellite marker set of 5 gene-based SSRs in 6 different farms belonging to 4 States of Colombia. Results. The result showed that the mean number of alleles per locus per population was 8.367. The population 5 had the highest mean number of alleles with 9.6 alleles, followed by population 4 with 9.4 alleles, population 2 with 9.2, population 3 with 8.0, population 1 with 7.2 and population 6 with 6.8 alleles. The analysis of the distribution of genetic variation was (17.32% among population, while among individuals within populations was (28.55% and within individuals was high (54.12%. The standard diversity indices showed that population 4 was the more variable (mean He=0.837 followed by population 1 (mean He=0.728, population 3 (mean He=0.721, population 5 (mean He=0.705, population 2 (mean He=0.690, population 6 (mean He=0.586. Highly significant deviations from Hardy–Weinberg, exhibited all of the populations, mostly due to deficits of heterozygotes. Genotype frequencies at loci UNH 106 of population 5 and loci UNH 172 of population 6 were Hardy-Weinberg equilibrium (HWE. Conclusions. The results of this study, contribute to the genetic breeding program of Tilapia, conduced by the Research Center for Aquaculture. The Fst distance showed that the samples are differentiated genetically and it is possible to use at the beginning of the genetic program. However, it is recommended to introduce others individuals to the crossbreeding program.
Boris Briñez R.
Full Text Available An experiment was conducted to analyze the genetic diversity among 38 maize germplasm accessions of the maizegermplasm bank of Department of Millets, TNAU, Coimbatore. Observations regarding 25 morphological traits wererecorded and the data matrix was used for estimation of Euclidian distance by Un-weighted Paired Group ArithmeticAverage (UPGMA method. Clustering was done by Sequential Agglomerative Hierarchical Non-overlapping (SAHNclustering. The genotypes were grouped in to four clusters. The grouping of the genotypes was not influenced by theirgeographical origin. Maximum dissimilarity was observed between the genotypes UMI 551 and UMI 696. Widely divergentclusters and genotypes were identified which could be further evaluated for their breeding value as parents and could beexploited in maize crop improvement.
A. Subramanian and N. Subbaraman
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)
Leishmaniasis caused by Leishmania (Leishmania) infantum is a zoonotic disease endemic in South Europe, from Portugal to the Middle East. The aim of the present study was to investigate the genetic diversity of L. infantum parasites in Iberian Peninsula. Twenty-four L. infantum strains isolated from immunocompetent patients with leishmaniasis from several localities of Portugal and Spain were studied. The use of kinetoplast DNA-PCR-restriction fragment length polymorphism as a molecular marker revealed intra-specific variation. No association was found between genotype and clinical form of the disease or patients age group. Two main clusters were identified with this marker: (i) zymodeme MON-1 strains and (ii) non-MON-1 strains. However, no association was found between strains variability and geographical distribution suggesting that parasite populations of different regions in the Iberian Peninsula are homogenous. PMID:21040506
Cortes, S; Chicharro, C; Cruz, I; Cristovão, J M; Cañavate, C; Campino, L
Amplified fragment length polymorphisms (AFLPs) were used to characterize the genotypic diversity of a total of 114 Gallibacterium anatis isolates originating from a reference collection representing 15 biovars from four countries and isolates obtained from tracheal and cloacal swab samples of chickens from an organic, egg-producing flock and a layer parent flock. A subset of strains was also characterized by pulsed-field gel electrophoresis and biotyping. The organic flock isolates were characterized by more than 94% genetic similarity, indicating that only a single clone was apparent in the flock. The layer parent flock isolates were grouped into two subclusters, each with similarity above 90%. One subcluster contained only tracheal isolates, while the other primarily included cloacal isolates. In conclusion, we show that AFLP analysis enables fingerprinting of G. anatis, which seems to have a clonal population structure within natural populations. There was further evidence of clonal lineages, which may have adapted to different sites within the same animal. PMID:12791918
Bojesen, Anders Miki; Torpdahl, Mia; Christensen, Henrik; Olsen, John Elmerdahl; Bisgaard, Magne
Amplified fragment length polymorphisms (AFLPs) were used to characterize the genotypic diversity of a total of 114 Gallibacterium anatis isolates originating from a reference collection representing 15 biovars from four countries and isolates obtained from tracheal and cloacal swab samples of chickens from an organic, egg-producing flock and a layer parent flock. A subset of strains was also characterized by pulsed-field gel electrophoresis and biotyping. The organic flock isolates were characterized by more than 94% genetic similarity, indicating that only a single clone was apparent in the flock. The layer parent flock isolates were grouped into two subclusters, each with similarity above 90%. One subcluster contained only tracheal isolates, while the other primarily included cloacal isolates. In conclusion, we show that AFLP analysis enables fingerprinting of G. anatis, which seems to have a clonal. population structure within natural populations. There was further evidence of clonal lineages, which may have adapted to different sites within the same animal.
Bojesen, A.M.; Torpdahl, Mia
Outbreaks of norovirus-associated gastroenteritis occur during all seasons and in various locations, and are recognized as one of the most common causes of nonbacterial food-borne infections. The molecular epidemiology of norovirus infections has not been well characterized in Belgium. To study the incidence of norovirus infections and the nature of the circulating genotypes, 3080 specimens were collected from patients with acute gastroenteritis between 2004 and 2014. Norovirus was detected with RT-PCR in 554 samples (18%). The circulating strains were genotyped based on the variability in the 5' end of the capsid gene (region C). The GII.4 genotype, which is detected predominantly worldwide, was also the most prevalent genotype in our study (87%). This study shows a high frequency and genetic diversity of norovirus in patients with acute gastroenteritis in health care facilities in Flanders, Belgium. PMID:25497349
Wollants, Elke; De Coster, Sarah; Van Ranst, Marc; Maes, Piet
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.
Angela R. Piergiovanni
The first data on mtDNA diversity in Besermyan, the Finno-Ugric ethnic group, related to Udmurts, are presented. An analysis of mtDNA polymorphism showed that Besermyan stood out from the other populations of Volga-Ural region due to the presence of a large proportion of the mongoloid component. The sample of Besermyan contained East Eurasian haplotypes not detected in ethnic populations of the Volga region and Cisurals, while they were detected in South Siberia, mostly among Turkic-speaking populations. An analysis of the genetic distances between Besermyan and the neighboring ethnic groups showed that Besermyan were distant from other populations of Volga-Ural region and close to Turkic-speaking populations of South Siberia. Thus, the data obtained favor the suggestion on the mixed Udmurto-Turkic origin of Besermyan. PMID:25508562
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. PMID:23538839
Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua
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.
Hydatid cyst caused by Echinococcus granulosus is one of the most important parasitic diseases around the world and many countries in Asia, including Iran, are involved with this infection. This disease can cause high mortality in humans as well as economic losses in livestock. To date, several molecular methods have been used to determine the genetic diversity of E. granulosus. So far, identification of E. granulosus using real-time PCR fluorescence-based quantitative assays has not been studied worldwide, also in Iran. Therefore, the aim of this study was to investigate the genetic diversity of E. granulosus from center of Iran using real-time PCR method. A total of 71 hydatid cysts were collected from infected sheep, goat, and cattle slaughtered in Isfahan, Iran during 2013. DNA was extracted from protoscolices and/or germinal layers from each individual cyst and used as template to amplify the mitochondrial cytochrome c oxidase subunit 1 gene (cox1) (420 bp). Five cattle isolates out of 71 isolates were sterile and excluded from further investigation. Overall, of 66 isolates, partial sequences of the cox1 gene of E. granulosus indicated the presence of genotypes G1 in 49 isolates (74.2%), G3 in 15 isolates (22.7%), and G6 in 2 isolates (3.0%) in infected intermediate hosts. Sixteen sequences of G1 genotype had microgenetic variants, and they were compared to the original sequence of cox1. However, isolates identified as G3 and G6 genotypes were completely consistent with original sequences. G1 genotype in livestock was the dominant genotype in Isfahan region, Iran. PMID:25246720
Pestechian, Nader; Hosseini Safa, Ahmad; Tajedini, Mohammadhasan; Rostami-Nejad, Mohammad; Mousavi, Mohammad; Yousofi, Hosseinali; Haghjooy Javanmard, Shaghayegh
Full Text Available Abstract Background Listeria monocytogenes can cause invasive diseases in humans and farm animals and is frequently isolated from dairy products and poultry. Listeriosis is uncommon in China but L. monocytogenes has been isolated from foods and food processing environments in China. However little is known of genetic diversity of Chinese L. monocytogenes isolates and their relationships with global isolates. Results Two hundred and twelve isolates of L. monocytogenes from food sources from 12 provinces/cities in China were analysed by serotyping, Pulsed Field Gel Electrophoresis (PFGE and Multi-locus Sequence Typing (MLST. The predominant serotypes are 1/2a, 1/2b and 1/2c accounting for 90.1% of the isolates. PFGE divided the isolates into 61 pulse types (PTs. Twenty nine PTs were represented by more than one isolates with PT GX6A16.0004 containing the most number of isolates. MLST differentiated the isolates into 36 STs, among which 15 were novel. The 3 most common STs were ST9 (29.1%, ST8 (10.7% and ST87 (9.2%, accounting for 49.0% of the isolates. Conclusions STs prevalent in other parts of the world are also prevalent in China including 7 STs (ST1-ST3, ST5, ST6, ST8, ST9 which caused maternal fetal infections or outbreaks, suggesting that these STs potentially can also cause severe human infections or outbreaks in China. Surveillance of these STs will provide important information for prevention of listeriosis. This study also enhances our understanding of genetic diversity of L. monocytogenes in China.
Taenia asiatica has made a remarkable journey through the scientific literature of the past 50 years, starting with the paradoxical observation of high prevalences of T. saginata-like tapeworms in non-beef consuming populations, to the full description of its mitochondrial genome. Experimental studies conducted in the 1980s and 1990s have made it clear that the life cycle of T. asiatica is comparable to that of T. saginata, except for pigs being the preferential intermediate host and liver the preferential location of the cysts. Whether or not T. asiatica can cause human cysticercosis, as is the case for Taenia solium, remains unclear. Given the specific conditions needed to complete its life cycle, in particular the consumption of raw or poorly cooked pig liver, the transmission of T. asiatica shows an important ethno-geographical association. So far, T. asiatica has been identified in Taiwan, South Korea, Indonesia, the Philippines, Thailand, south-central China, Vietnam, Japan and Nepal. Especially this last observation indicates that its distribution is not restricted to South-East-Asia, as was thought so far. Indeed, the molecular tools developed over the last 20 years have made it increasingly possible to differentiate T. asiatica from other taeniids. Such tools also indicated that T. asiatica is related more closely to T. saginata than to T. solium, feeding the debate on its taxonomic status as a separate species versus a subspecies of T. saginata. Furthermore, the genetic diversity within T. asiatica appears to be very minimal, indicating that this parasite may be on the verge of extinction. However, recent studies have identified potential hybrids between T. asiatica and T. saginata, reopening the debate on the genetic diversity of T. asiatica and its status as a separate species. PMID:24450957
Ale, Anita; Victor, Bjorn; Praet, Nicolas; Gabriël, Sarah; Speybroeck, Niko; Dorny, Pierre; Devleesschauwer, Brecht
Mating systems and population dynamics influence genetic diversity and structure. Species that experience inbreeding and limited gene flow are expected to evolve isolated, divergent genetic lineages. Metapopulation dynamics with frequent extinctions and colonizations may, on the other hand, deplete and homogenize genetic variation, if extinction rate is sufficiently high compared to the effect of drift in local demes. We investigated these theoretical predictions empirically in social spiders that are highly inbred. Social spiders show intranest mating, female-biased sex ratio, and frequent extinction and colonization events, factors that deplete genetic diversity within nests and populations and limit gene flow. We characterized population genetic structure in Stegodyphus sarasinorum, a social spider distributed across the Indian subcontinent. Species-wide genetic diversity was estimated over approximately 2800 km from Sri Lanka to Himalayas, by sequencing 16 protein-coding nuclear loci. We found 13 SNPs in 6592 bp (? = 0.00045) indicating low species-wide nucleotide diversity. Three genetic lineages were strongly differentiated; however, only one fixed difference among them suggests recent divergence. This is consistent with a scenario of metapopulation dynamics that homogenizes genetic diversity across the species' range. Ultimately, low standing genetic variation may hamper a species' ability to track environmental change and render social inbreeding spiders 'evolutionary dead-ends'. PMID:25348843
Settepani, V; Bechsgaard, J; Bilde, T
Quality production of the shrimp Penaeus monodon in hatchery operations depends heavily on the evaluation of genetic diversity and population structure of brood stocks. Mitochondrial DNA (mtDNA) sequences have been widely used to study genetic variability and relationships in many crustacean groups, and these same markers may be incorporated into evaluation studies of shrimp broods and populations. For this purpose we looked at variation in mitochondrial D-loop sequences as an indicator of genetic diversity in shrimp populations from a region of India that represents the main sources of new material for brood stocks. In our study of these populations the overall mean genetic diversity was 0.191. The highest level of genetic diversity (0.357) was observed in the Kakinada population, whereas the lowest diversity (0.0171) was observed in the Nellore population. The results also indicate that overall, the populations along the Andhra Pradesh coast are genetically diverse despite the fact that there is considerable gene flow between them. From the results, it is evident that east cost of India shows high genetic diversity among P. monodon broods and no evidence of loss of diversity due to excessive inbreeding. The fact that the genetic variability of these populations has been maintained, despite ten years of dependence on these broods, shows that at the present time there is no indication of over exploitation. PMID:24363984
Khedkar, Gulab Dattarao; Reddy, A Chandrashekar; Ron, Tetszuan Benny; Haymer, David
Biofortification of staple crops like potato via breeding is an attractive strategy to reduce human micronutrient deficiencies. A prerequisite is metabolic phenotyping of genetically diverse material which can be used as parents in breeding programs. Thus, the natural genetic diversity of thiamine a...
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.
Sundar, N.; Cole, R.A.; Thomas, N.J.; Majumdar, D.; Dubey, J.P.; Su, C.
Harvested yields of sour cherry (Prunus cerasus) cultivar ‘Stevnsbaer’ clones grown in Denmark have been highly variable over the years, yet some propagated derived trees selected from within the two widely grown clones of ‘Stevnsbaer’ clone ‘Birgitte’ and clone ‘Viki’ have consistently produced higher yields. A number of these selections were evaluated for yield and genomic differences to investigate variation between and within the ‘Birgitte’ and ‘Viki’ clones. Variation in yield was mainly found at the clonal level. The clone ‘Viki’ was found to be the highest yielding with an average of 20 kg/tree compared to only 7.0 kg/tree from clone ‘Birgitte’. The selected trees derived from within clone ‘Birgitte’ had a significantly higher, average yield over 7 years compared to the original ‘Birgitte’, indicating that such within-clone selection may be a possible approach for selection of improved breeding material. However, no differences in allele profile were found between or within the clones, calling into question the extent of the available genetic diversity and indicating that the observed variance in yield may have to be explained by other genetic mechanisms, including epigenetic change.
Clausen, Sabine Karin; Andersen, Sven Bode
Full Text Available Leishmania infantum (syn. Leishmania chagasi is the etiological agent of visceral leishmaniasis (VL in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular methods, multilocus microsatellite typing (MLMT, random amplification of polymorphic DNA (RAPD and simple sequence repeats-polymerase chain reaction (SSR-PCR, were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.
Full Text Available SciELO Brazil | Language: English Abstract in english Leishmania infantum (syn. Leishmania chagasi) is the etiological agent of visceral leishmaniasis (VL) in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular metho [...] ds, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.
Marcela, Segatto; Lucas Secchim, Ribeiro; Dorcas Lamounier, Costa; Carlos Henrique Nery, Costa; Márcia Rosa de, Oliveira; Sílvio Fernando Guimarães, Carvalho; Andréa Mara, Macedo; Helder Magno Silva, Valadares; Reynaldo, Dietze; Cristiana Ferreira Alves de, Brito; Elenice Moreira, Lemos.
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.
The geographic distribution of genetic diversity and the population structure of tetraploid wheat landraces in the Mediterranean basin has received relatively little attention. This is complicated by the lack of consensus concerning the taxonomy of tetraploid wheats and by unresolved questions regarding the domestication and spread of naked wheats. These knowledge gaps hinder crop diversity conservation efforts and plant breeding programmes. We investigated genetic diversity and population st...
Oliveira, Hugo R.; Campana, Michael G.; Jones, Huw; Hunt, Harriet V.; Leigh, Fiona; Redhouse, David I.; Lister, Diane L.; Jones, Martin K.
A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment l...
Juliana Morini Küpper Cardoso Perseguini; Alisson Fernando Chioratto; Maria Imaculada Zucchi; Carlos Augusto Colombo; Sérgio Augusto Moraes Carbonell; Jorge Mauricio Costa Mondego; Rodrigo Gazaffi; Antonio Augusto Franco Garcia; Tatiana de Campos; Anete Pereira de Souza; Luciana Benchimol Rubiano
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some ...
Zukurov, Jean P.; Nascimento-brito, Sieberth Do; Volpini, Angela C.; Oliveira, Guilherme; Janini, Luiz Mario R.; Antoneli, Fernando
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.
Molecular markers are effective tools to investigate genetic diversity for resistance to pathogens. NBS (nucleotide-binding site) profiling is a OCR (polymerase chain reaction)-based approach to studying genetic variability that specifically targets chromosome regions containing R-genes and R-gene analogues. We used NBS profiling to measure genetic diversity among 58 accessions of durum wheat. Mean polymorphism rates detected using MseI and AluI as restriction enzymes were 34% and 22%, respec...
Mantovani, P.; Linden, C. G.; Maccaferri, M.; Sanguineti, M. C.; Tuberosa, R.
Genealogical data have been used very widely to construct indices with which to examine the contribution of plant breeding programmes to the maintenance and enhancement of genetic resources. In this paper we use such indices to examine changes in the genetic diversity of the winter wheat crop in England and Wales between 1923 and 1995. We find that, except for one period characterized by the dominance of imported varieties, the genetic diversity of the winter wheat crop has been remarkably st...
Srinivasan, C. S.; Thirtle, Colin; Palladino, Paolo
The development of effective malaria vaccines may be hindered by extensive genetic diversity in the surface proteins being employed as vaccine antigens. Understanding of the extent and dynamics of genetic diversity in vaccine antigens is needed to guide rational vaccine design and to interpret the results of vaccine efficacy trials conducted in malaria endemic areas. Molecular epidemiological, population genetic, and structural approaches are being employed to try to identify immunologically ...
Takala, Shannon L.; Plowe, Christopher V.
Full Text Available Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.
The widespread use of Agent Orange (a mixture of phenoxyl herbicides) over Southern Vietnam by US Forces led to the decimation of mangrove forests in the Mekong Delta. Mangrove trees Avicennia alba were sampled across the Mekong Delta; their age was assessed using models based on internode growth and samples were genotyped for 6 microsatellite loci. The evolution of genetic diversity over time elapsed since local extinction was reconstructed and compared with the genetic diversity of an unaff...
Arnaud-haond, S.; Duarte, C. M.; Teixeira, S.; Massa, S. I.; Terrados, J.; Tri, N. H.; Hong, P. N.; Serra?o, Ester
Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and even death in humans and various other animal species. A collection of 174 C. botulinum strains were examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT A-G). Analysis of the16S rRNA sequences confirmed earlier reports of at least four distinct genomic backgrounds (Groups I-IV) each of which has independently acquired one or more BoNT serotypes through horizontal gene transfer. AFLP analysis provided higher resolution, and can be used to further subdivide the four groups into sub-groups. Sequencing of the BoNT genes from serotypes A, B and E in multiple strains confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes, and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven serotypes of BoNT were compared and show varying degrees of interrelatedness and recombination as has been previously noted for the NTNH gene which is linked to BoNT. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for treatment of botulism.
Hill, K K; Smith, T J; Helma, C H; Ticknor, L O; Foley, B T; Svennson, R T; Brown, J L; Johnson, E A; Smith, L A; Okinaka, R T; Jackson, P J; Marks, J D
The genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal DNA restriction analysis (ARDRA), 16S rRNA sequence homology and phylogenetics analysis methods. Studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. A total of 28 ARDRA patterns were identified among the 299 siderophore-producing bacterial isolates. The 28 ARDRA patterns represented bacteria of 14 different genera belonging to six bacterial divisions, namely ?-, ?-, ?-Proteobacteria, Sphingobacteria, Bacilli, and Actinobacteria. Especially, ?-Proteobacteria consisting of Pseudomonas, Enterobacter, Serratia, Pantoea, Erwinia and Stenotrophomonas genus encountered 18 different ARDRA groups. Results also showed a greater siderophore-producing bacterial diversity than previous researches. For example, Sphingobacterium (isolates G-2-21-1 and G-2-27-2), Pseudomonas poae (isolate G-2-1-1), Enterobacter endosymbiont (isolates G-2-10-2 and N-5-10), Delftia acidovorans (isolate G-1-15), and Achromobacter xylosoxidans (isolates N-46-11HH and N-5-20) were reported to be able to produce siderophores under low-iron conditions for the first time. Gram-negative isolates were more frequently encountered, with more than 95% total frequency. For Gram-positive bacteria, the Bacillus and Rhodococcus were the only two genera, with 1.7% total frequency. Furthermore, the Pseudomonas and Enterobacter were dominant in this environment, with 44.5% and 24.7% total frequency, respectively. It was also found that 75 percent of the isolates that had the high percentages of siderophore units (% between 40 and 60) belonged to Pseudomonas. Pseudomonas sp. G-229-21 screened out in this study may have potential to apply to low-iron soil to prevent plant soil-borne fungal pathogen diseases. PMID:24031358
Tian, Fang; Ding, Yanqin; Zhu, Hui; Yao, Liangtong; Du, Binghai
Full Text Available Abstract Background Plant genetic resources (PGR are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA, 117 in South and South East Asia (SSEA, and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53% than kabuli (46%, while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78% of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. Conclusion The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s, and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.
Gowda Cholenahalli LL
There is a general trend of biodiversity loss at global, regional, national and local levels. To monitor this trend, international policy processes have created a wealth of indicators over the last two decades. However, genetic diversity indicators are regrettably absent from comprehensive bio-monitoring schemes. Here, we provide a review and an assessment of the different attempts made to provide such indicators for tree genetic diversity from the global level down to the level of the management unit. So far, no generally accepted indicators have been provided as international standards, nor tested for their possible use in practice. We suggest that indicators for monitoring genetic diversity and dynamics should be based on ecological and demographic surrogates of adaptive diversity as well as genetic markers capable of identifying genetic erosion and gene flow. A comparison of past and present genecological distributions (patterns of genetic variation of key adaptive traits in the ecological space) of selected species is a realistic way of assessing the trend of intra-specific variation, and thus provides a state indicator of tree genetic diversity also able to reflect possible pressures threatening genetic diversity. Revealing benefits of genetic diversity related to ecosystem services is complex, but current trends in plantation performance offer the possibility of an indicator of benefit. Response indicators are generally much easier to define, because recognition and even quantification of, e.g., research, education, breeding, conservation, and regulation actions and programs are relatively straightforward. Only state indicators can reveal genetic patterns and processes, which are fundamental for maintaining genetic diversity. Indirect indicators of pressure, benefit, or response should therefore not be used independently of state indicators. A coherent set of indicators covering diversity-productivity-knowledge-management based on the genecological approach is proposed for application on appropriate groupsof tree species in the wild and in cultivation worldwide. These indicators realistically reflect the state, trends and potentials of the world's tree genetic resources to support sustainable growth. The state of the genetic diversity will be based on trends in population distributions and diversity patterns for selected species. The productivity of the genetic resource of trees in current use will reflect the possible potential of mobilizing the resource further. Trends in knowledge will underpin the potential capacity for development of the resource and current management of the genetic resource itself will reveal how well we are actually doing and where improvements are required.
Graudal, Lars; Aravanopoulos, Filippos
The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 - proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 +/- 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs. PMID:15644962
Bertin, P; Grégoire, D; Massart, S; de Froidmont, D
Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the 'mimosine story' in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability. PMID:22443591
John Wallace, R
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.
Full Text Available Abstract Background Phytophthora infestans (Mont. de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana and tree tomato (Solanum betaceum, all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, ?-tubulin and Avr3a and one mitochondrial (Cox1 region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. Results Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. Conclusions The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a.
Grünwald Niklaus J
In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in t...
Wouw, M. J.; Hintum, T. J. L.; Kik, C.; Treuren, R.; Visser, L.
Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.
Juliana Morini Küpper Cardoso Perseguini
Full Text Available SciELO Brazil | Language: English Abstract in english A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca be [...] an, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.
Juliana Morini Küpper Cardoso, Perseguini; Alisson Fernando, Chioratto; Maria Imaculada, Zucchi; Carlos Augusto, Colombo; Sérgio Augusto Moraes, Carbonell; Jorge Mauricio Costa, Mondego; Rodrigo, Gazaffi; Antonio Augusto Franco, Garcia; Tatiana de, Campos; Anete Pereira de, Souza; Luciana Benchimol, Rubiano.
Full Text Available Garlic (Allium sativum L. that is cultivated in Tunisia is heterogeneous and unclassified with no registered local cultivars. At present, the level of genetic diversity in Tunisian garlic is almost unknown. Inter Simple Sequence Repeats (ISSR genetic markers were therefore used to assess the genetic diversity and its distribution in 31 Tunisian garlic accessions with 4 French classified clones used as control. It was the first time that ISSR markers were used to detect diversity in garlic. Seventeen ISSR primers were screened; seven primers detected 73 polymorphic bands. A high level of polymorphic loci (p was found in Tunisian populations (54%. Nei’s total genetic diversity coefficient was 0.45 and 0.34 respectively for Tunisian and French garlic. Genetic distances observed between Tunisian accessions, ranged between 38.4 and 78.1%. Factor analysis of distances’ table (AFTD did not classify accessions on the base of geographical origin or morpho-physiological characters, particularly bolting ability, but confirmed the appurtenance of analyzed accessions to sativum botanical subspecies. There was sufficient diversity detected to start a national collection of garlic germplasm which is crucial for the conservation of genetic diversity and its valorization. Keywords: Allium sativum L., ISSR markers, genetic diversity, Tunisian garlic populations.
Since the completion of the human genome sequencing project, the discovery and characterization of human genetic variation is a principal focus for future research. Comparative studies across ethnically diverse human populations and across human and nonhuman primate species is important for reconstructing human evolutionary history and for understanding the genetic basis of human disease. In this review, we summarize data on patterns of human genetic diversity and the evolutionary forces (mutation, genetic drift, migration, and selection) that have shaped these patterns of variation across both human populations and the genome. African population samples typically have higher levels of genetic diversity, a complex population substructure, and low levels of linkage disequilibrium (LD) relative to non-African populations. We discuss these differences and their implications for mapping disease genes and for understanding how population and genomic diversity have been important in the evolution, differentiation, and adaptation of humans. PMID:14527305
Tishkoff, Sarah A; Verrelli, Brian C
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.
Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.
In an effort to increase the diversity of the membership of the National Society of Genetic Counselors (NSGC), the Membership Committee provided two $500 scholarships to genetic counseling students planning to attend the NSGC AEC meeting in Dallas, Texas in October 2010. Requirements for applicants of both scholarships included enrollment in the fall of 2010, good standing at an accredited genetic counseling training program, and NSGC membership or plans to join in 2011. Students who are from communities underrepresented in the NSGC, including, but not limited to, those of minority cultural/ethnic backgrounds and those with disabilities were eligible to apply for the "Diversity" scholarship. Students from all backgrounds who have an interest in diversity issues were eligible to apply for the "General" scholarship. Applicants wrote essays 1000 words or less answering the following questions: How has your identity as a member of a group underrepresented in the genetic counseling profession affected your pursuit of this career? What do you feel is lacking in genetic counseling to address the issues of underrepresented groups? What strategies do you recommend for addressing these issues and/or increasing diversity? Why do you think diversity is an important issue for the field of genetic counseling? What strategies do you recommend to attract and retain students, especially those from underrepresented populations, into the field of genetic counseling? How do you envision contributing to these strategies? The essays by the award recipients elucidated interesting perspectives and ideas for increasing diversity in the genetic counseling profession. PMID:21717287
Liu, Tina; Patek, Kyla; Schneider, Kami Wolfe
Full Text Available SciELO Brazil | Language: English Abstract in english This work investigated the genetic diversity and relationships among Capparis species growing in Syria using IRAP and ISSR techniques. Forty-seven samples of three Capparis species genotypes were collected from 21 different locations in Syria. The genotypes were morphologically identified based on t [...] he descriptions available in the literature. When IRAP technique was used, an average of 71.5% of the amplified fragments were polymorphic compared to 82.04% in ISSR. Morphological characterization along with the cluster and PCoA analyses of the data divided the studied genotypes into three groups. The groups included genotypes identified as Capparis spinosa L, C. sicula Duh., and C. aegyptia Lam. Based on the morphological description, molecular studies and statistical analyses of this study, C. aegyptia could be suggested as a separate species and not a varietal rank of C. spinosa (C. spinosa var. aegyptia (Lam.). Two samples (Alep1 and Idl) were not placed in any of the three distinctive groups, despite their closeness morphologically to C. spinosa. In PCoA analysis, sample Alep1 came between C. sicula and C. spinosa and Idl was placed between C. sicula and C. aegyptia. Although hybridization between Capparis species could occur, it was not clear from the present study if these two genotypes were hybrids.
Bassam, Al- Safadi; Hussam, Faouri; Rana, Elias.
We studied HIV genetic diversity in a cohort of 127 pregnant, HIV-infected women who received prenatal care at Sainte-Justine Hospital in Montreal, Canada, between 1999 and 2003. Clade assignments were derived by phylogenetic analysis of amplified pol sequences. Genotyping was successful in 103 of 127 women, 59 (57.3%) of whom were infected with clade B HIV-1, and 44 (42.7%) with nonclade B viruses, including subtypes A, C, D, F, G, and H. Four sequences remained unassigned. Forty-three of 44 women infected with non-clade B viruses were newcomers from sub-Saharan Africa, and subtype identity was consistent with those circulating in their countries of origin. These results highlight the epidemiologic importance of non-B HIV-1 in antenatal populations in a large North American urban center, underscore the influence of population movements on clade intermixing, and identify a group of patients who could be targeted for surveillance and drug therapy followup. PMID:16102312
Akouamba, Bertine S.; Viel, Janique; Charest, Hugues; Merindol, Natacha; Samson, Johanne; Lapointe, Normand; Brenner, Bluma G.; Lalonde, Richard; Harrigan, P. Richard; Boucher, Marc
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)
We use a genetic algorithm to calibrate a spatially and temporally resolved cellular automata to model mining activity on public land in Idaho and western Montana. The genetic algorithm searches through a space of transition rule parameters of a two dimensional cellular automata model to find rule parameters that fit observed mining activity data. Previous work by one of the authors in calibrating the cellular automaton took weeks - the genetic algorithm takes a day and produces rules leading to about the same (or better) fit to observed data. These preliminary results indicate that genetic algorithms are a viable tool in calibrating cellular automata for this application. Experience gained during the calibration of this cellular automata suggests that mineral resource information is a critical factor in the quality of the results. With automated calibration, further refinements of how the mineral-resource information is provided to the cellular automaton will probably improve our model.
Louis, S.J.; Raines, G.L.
A wide variety of microhabitats within the extremely acidic abandoned underground copper mine Zlaté Hory (Czech Republic) was investigated. SSU rDNA libraries were analyzed from 15 samples representing gossan, sulfide-leaching environments in the oxidation zone, and acidic water springs in the mine galleries. Microbial analyses were extended by analyses of chemical composition of water and solid phases and identification of arising secondary minerals. The microbial communities of the three main classes of microenvironments differed in almost every aspect. Among others, ecological partitioning of Acidithiobacillus ferrooxidans and the recently described A. ferrivorans was observed. Distinct types of communities inhabiting the water springs were detected. The more extreme springs (pH 2 mS/cm) were inhabited by "Ferrovum" spp. and A. ferrivorans, whereas Gallionella sp. dominated the less extreme ones. A new role for gossan in the extremely acidic ecosystem is proposed. This zone was inhabited by a large diversity of neutrophilic heterotrophs that appeared to be continuously washed out to the acidic environments localized downstream. Five species originating in gossan were found in several acidic habitats. Here they can survive and probably serve as scavengers of dead biomass, particularly from chemoautotrophic growths. No such process has been described from acidic mine environments so far. PMID:23065060
Falteisek, Lukáš; Cepi?ka, Ivan
We explored possible links between vector activity and genetic diversity in introduced populations of Limnoperna fortunei by characterizing the genetic structure in native and introduced ranges in Asia and South America. We surveyed 24 populations: ten in Asia and 14 in South America using the mitochondrial cytochrome c oxidase subunit I (COI) gene, as well as eight polymorphic microsatellite markers. We performed population genetics and phylogenetic analyses to investigate population genetic...
Ghabooli, Sara; Zhan, Aibin; Sardin?a, Paula; Paolucci, Esteban; Sylvester, Francisco; Perepelizin, Pablo V.; Briski, Elizabeta; Cristescu, Melania E.; Macisaac, Hugh J.
Full Text Available The use of fuzzy techniques has been considered to be one of the key components of data mining systems because of the affinity with human knowledge representation. A hybridization of fuzzy sets with genetic algorithms is described for Web mining in this paper. It is based on a hybrid technique that combines the strengths of rough set theory and genetic algorithm. The algorithm through the introduction of selection operators, crossover operators and mutation operators, improves the global convergence speed, and can effectively avoid prematurity. The role of fuzzy sets in handling the different types of uncertainties/impreciseness is highlighted. Experimental results indicate that this adaptive method significantly improves the performance in Web mining.
Livestock production plays an important role in Mongolian economy. Over the last decade it has contributed to around 80-90% of the gross domestic agricultural products and to 30% of the revenues generated from exportations. Cattle is one of the five traditional and most important livestock species of Mongolia together with horse, sheep, goat and camel. Out of a total of 1.57 millions Mongolian cattle, 1.55 millions supposedly belong to three indigenous Bos taurus cattle breeds, namely Mongol, Selenge and Khalkhun Golun, all herded under extensive pastoral systems. Indigenous Mongolian cattle are generally small but look sturdy and strong. They have a well-off coat of hair, solid forward looking shoulders and short stubby snouts, and they are used for meat, milk and transport. Beef production contributes to 30% of the total meat supply in Mongolia. The Mongol breed is by the far the commonest with 1.53 million animals and it is found almost throughout the country. The Selenge breed, found in Selenge province and numbering 9000 heads, was developed in middle of the 20th century by crossing the Kazakh Whiteheaded with the local Mongol cattle. The Khalkhun Golun breed was developed from local Mongol cattle and it is distributed in Eastern and Suhbaatar provinces with about 10,000 heads. Until now, to the best of our knowledge, only a single population of Mongolian cattle has been studied with microsatellite DNA markers and no information is available on the genetic relatirmation is available on the genetic relationship between the Mongolian indigenous cattle breeds. In this study, we collected samples from two populations of the Mongol cattle (sampled at Ikhtamir soum in North Hangay province and Tsogt soum in Govi Altay province) and one population of the Khalkhun Golun cattle (sampled at Tumentsogt soum in Suhbaatar province). Samples were characterised with nine microsatellite markers MGTG4B, ILSTS005, ILSTS006, ILSTS008, ILSTS023, ILSTS028, ILSTS036, ILSTS050 and ILSTS103. To assess the genetic diversity and relationship of Mongolian cattle populations with breeds from neighboring countries and exotic breeds, data from the ILRI cattle genotyping database were included. More particularly, we used previously obtained data from Asian taurine (Hanwoo, Yanbian and Japanese Black), two European taurine (Friesian and Charolais), two African taurine (Baoule and N'Dama) and two zebu breeds (Sahiwal and Ongole). For each breed, observed (Ho) and expected (He) heterozygosities as well as the mean number of alleles (MNA) across the nine loci were calculated between pairs of populations were also estimated and a UPGMA tree was constructed. The heterozygosities (Ho and He) in Mongolian cattle populations are similar to those obtained in Northeast Asian taurine breeds but the values are higher compared to the ones obtained for the European and African taurine breeds. The Mongol cattle in North Hangay has the highest corrected MNA value (all animals or 28 animals only). The UPGMA tree, built with the Reynolds' genetic distances, shows all six Northeast Asian cattle populations clustering into one group linked to the two European taurine breed. Interestingly, the two populations of the Mongol cattle are not closely related to each other. However, bootstrap values between the Northeast Asian taurine breeds, with the exception of the bootstrap value between Yanbian and Hanwoo, are relatively low, therefore the relationship between the Northeast Asian populations should be taken with caution. Fst values between the three Mongolian cattle populations are significant (P < 0.01), with the Govi Altay population being more differentiated from the North Hangay population than from the Khalkhun Golun breed (data not shown). Our data suggest that the traditional classification of Govi Altay and North Hangay populations as one breed, the Mongol cattle, should be revisited
Full Text Available Typha angustifolia has ecological characteristics of clonal growth similar to Phragmites australis. The plant spreads byclonal growth and seed dispersal. In this study, for the three stands which have different settlement age at the Baksiljiwetland in Korea, genetic diversity was estimated by random amplification of polymorphic DNA analysis to evaluate thechange in genetic diversity of T. angustifolia during stand development in the same population. Stand (ST 1 was the oldestand ST 4 was the youngest. ST 5 was in a small ditch out of the Baksilji. Although the ST 1, ST 2, and ST 3 did not differsignificantly in vegetational or physical environment, the genetic diversity estimated according to Nei’s gene diversity(h and the Shannon index (i increased in the order of ST 1 < ST 2 < ST 3 contrary to formative age. The genetic diversityof ST 4 was much higher than that of the other three stands. ST 4 has similar abiotic environmental conditions withslight T. angustifolia dominance, and seems to be in the early establishment stage. ST 5 differed from the other stands invegetational and soil environments, which can result in stressful cattail conditions. Even though the ST 5 stand was notyounger than the ST 4 stand, ST 5 showed the highest genetic diversity. Our results indicate that after early settlement ofthe T. angustifolia population, genetic diversity within the species decreased over time and that the decreasing pattern ofgenetic diversity within T. angustifolia stands is not likely to occur under stressful conditions.
Jae Geun Kim*
The genetic diversity of 45 bradyrhizobial isolates that nodulate several Lupinus and Ornithopus species in different geographic locations was investigated by 16S rDNA PCR-RFLP and sequence analysis, 16S-23S rDNA intergenic spacer (IGS) PCR-RFLP analysis, and ERIC-PCR genomic fingerprinting. Reference strains of Bradyrhizobium japonicum, B. liaoningense and B. elkanii and some Canarian isolates from endemic woody legumes in the tribe Genisteae were also included. The 16S rDNA-RFLP analysis resolved 9 genotypes of lupin isolates, a group of fourteen isolates presented restriction-genotypes identical or very similar to B. japonicum, while another two main groups of isolates (69%) presented genotypes that clearly separated them from the reference species of soybean. 16S rDNA sequencing of representative strains largely agreed with restriction analysis, except for a group of six isolates, and showed that all the lupin isolates are relatives of B. japonicum, but different lineages were observed. The 16S-23S IGS-RFLP analysis showed a high resolution level, resolving 19 distinct genotypes among 30 strains analysed, and so demonstrating the heterogeneity of the 16S-RFLP groups. ERIC-PCR fingerprint analysis showed an enormous genetic diversity producing a different pattern for each but two of the isolates. Phylogeny of nodC gene was independent from the 16S rRNA phylogeny, and showed a tight relationship in the symbiotic region of the lupin isolates with isolates from Canarian genistoid woody legumes, and in concordance, cross-nodulation was found. We conclude that Lupinus is a promiscuous host legume that is nodulated by rhizobia with very different chromosomal genotypes, which could even belong to several species of Bradyrhizobium. No correlation among genomic background, original host plant and geographic location was found, so, different chromosomal genotypes could be detected at a single site and in a same plant species, on the contrary, an identical genotype was detected in very different geographical locations and plants. PMID:14666990
Jarabo-Lorenzo, Adriana; Pérez-Galdona, Ricardo; Donate-Correa, Javier; Rivas, Raúl; Velázquez, Encarna; Hernández, Mariano; Temprano, Francisco; Martínez-Molina, Eustoquio; Ruiz-Argüeso, Tomás; León-Barrios, Milagros
To reveal the genetic diversity and genetic structure in Artemisia annua varieties (strains) populations, we detected the genetic polymorphism within and among eight varieties (strains) populations (192 individuals) by the approach of Start Codon Targeted Polymorphism (SCoT). The associated genetic parameters were calculated by POPGENE1.31 and the relationship was constructed based on UPGMA method. The results showed that, using 20 screened primers, a total of 145 bands were produced, of which 122 were polymorphic loci. At species level, there was a high level of genetic diversity among eight varieties (strains) populations (PPB = 84.1% ,H = 0.217 3 and H(sp) = 0.341 9). However, at the variety (strains) population level, genetic diversity was lower, the average of genetic parameters was PPB = 41.9%, H = 0.121 5, H(pop) = 0.186 8. The Nei's genetic differentiation coefficient was 0.441 0, indicate that most of the genetic variation in this species existed within the variety populations. The gene flow (N(m) = 0.633 9) was less among populations, indicating that the degree of genetic differentiation was higher. Genetic similarity coefficient were changed from 0.755 1 to 0.985 7. By clustering analysis, eight varieties (strains) were clustered into two major categories and it was also showed the same or similar genetic background varieties (strains) have a tendency to gather in the same group. Results suggest that, in variety breeding, breeders should strengthen the exchange of bred germplasm and increase mutual penetration of excellent genes, which would broaden the genetic base of A. annua. PMID:25522606
Chen, Da-xia; Cui, Guang-lin; Zhang, Xue; Li, Long-yun
Full Text Available Randomly amplified polymorphic DNA (RAPD markers were used in the present study to analyze genetic diversity and phylogenetic relationships among some race and hybrids of Romanian Bombyx mori. DNA from 8 hybrids and 1 race was amplified with 35 highly polymorphic RAPD primers, of which 21 markers generated polymorphic bands that were used to analyze genetic phylogeny and diversity. A total of 921 polymorphic bands were detected and UPGMA cluster analysis of Jaccard’s genetic distance grouped silkworm strains on the basis of their origin, obtaining a dendogram reflecting their genetic relationship.
Emilia Maria Furdui
Chicory is a crop with economically important roles and is cultivated worldwide. The genetic diversity and relationship of 80 accessions of chicories and endives were evaluated by sequence-related amplified polymorphism (SRAP) markers to provide a theoretical basis for future breeding programs in China. The polymorphic rate was 96.83%, and the average polymorphic information content was 0.323, suggesting the rich genetic diversity of chicory. The genetic diversity degree of chicory was higher (GS = 0.677) than that of endive (GS = 0.701). The accessions with the highest genetic diversity (effective number of alleles, NE = 1.609; Nei's genetic diversity, H = 0.372; Shannon information index, I = 0.556) were from Italy. The richest genetic diversity was revealed in a chicory line (NE = 1.478, H = 0.289, I = 0.443) among the 3 types (line, wild, and cultivar). The chicory genetic structure of 8 geographical groups showed that the genetic differentiation coefficient (GST) was 14.20% and the number of immigrants per generation (Nm) was 3.020. A GST of 6.80% and an Nm of 6.853 were obtained from different types. This observation suggests that these chicory lines, especially those from the Mediterranean region, have potential for providing rich genetic resources for further breeding programs, that the chicory genetic structure among different countries obviously differs with a certain amount of gene flow, and that SRAP markers could be applied to analyze genetic relationships and classifications of Cichorium intybus and C. endivia. PMID:25299087
Liang, X Y; Zhang, X Q; Bai, S Q; Huang, L K; Luo, X M; Ji, Y; Jiang, L F
Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat in warm and humid wheat-growing regions of the world. This fungus shows a high genetic diversity and morphological and physiologic variability. In this study, 19 polysporic and 57 monosporic isolates of B. sorokiniana were characterized using universal rice primers-URP-PCR. The results obtained when the dendrogram was constructed with all the data produced with the amplification products showed very distinct clusters. However, the similarity among the isolates was low where 37 and 26.3 % of the monosporic and polysporic isolates, respectively, showed similarity above 70 %. All primers amplified multiple DNA fragments of polysporic as well as the monosporic isolates. Isolates fingerprints were constructed based on binary characters revealed by the three primers. An amplified fragment of approximately 750 bp was observed among 40 % of the isolates, when primer URP-1F was used. When primers URP-4R and URP-2R were used, a fragment of 450 and 400 bp was present in 31.5 and 29 % of the isolates, respectively. It was expected a higher similarity among the isolates since the monosporic cultures were originated from the polysporic. The dendrogram did not enable the separation of B. sorokiniana isolates by their geographic origin. This low correlation suggests that gene transfer may have occurred by parasexual combination in this fungus population. However, in spite of the research efforts for that end, it has not been possible to establish patterns that characterize the profile of B. sorokiniana. PMID:25100225
Mann, Michele B; Minotto, Elisandra; Feltrin, Thaisa; Milagre, Luciana P; Spadari, Cristina; Van Der Sand, Sueli T
Rift Valley fever virus (RVFV), a member of the family Bunyaviridae, genus Phlebovirus, is the causative agent of Rift Valley fever (RVF), a mosquito-borne disease of ruminant animals and humans. The generation of a large sequence database has facilitated studies of the evolution and spread of the virus. Bayesian analyses indicate that currently circulating strains of RVFV are descended from an ancestral species that emerged from a natural reservoir in Africa when large-scale cattle and sheep farming were introduced during the 19th century. Viruses descended from multiple lineages persist in that region, through infection of reservoir animals and vertical transmission in mosquitoes, emerging in years of heavy rainfall to cause epizootics and epidemics. On a number of occasions, viruses from these lineages have been transported outside the enzootic region through the movement of infected animals or mosquitoes, triggering outbreaks in countries such as Egypt, Saudi Arabia, Mauritania and Madagascar, where RVF had not previously been seen. Such viruses could potentially become established in their new environments through infection of wild and domestic ruminants and other animals and vertical transmission in local mosquito species. Despite their extensive geographic dispersion, all strains of RVFV remain closely related at the nucleotide and amino acid level. The high degree of conservation of genes encoding the virion surface glycoproteins suggests that a single vaccine should protect against all currently circulating RVFV strains. Similarly, preservation of the sequence of the RNA-dependent RNA polymerase across viral lineages implies that antiviral drugs targeting the enzyme should be effective against all strains. Researchers should be encouraged to collect additional RVFV isolates and perform whole-genome sequencing and phylogenetic analysis, so as to enhance our understanding of the continuing evolution of this important virus. This review forms part of a series of invited papers in Antiviral Research on the genetic diversity of emerging viruses. PMID:22710362
Leptotrichia buccalis ATCC 14201 is a gram-negative, anaerobic rod-shaped bacterium resident in oral biofilm at the tooth surface. The sequenced genome of this organism reveals three contiguous genes at loci: Lebu_1525, Lebu_1526 and Lebu_1527. The translation products of these genes exhibit significant homology with phospho-?-glucosidase (Pagl), a regulatory protein (GntR) and a phosphoenol pyruvate-dependent sugar transport protein (EIICB), respectively. In non-oral bacterial species, these genes comprise the sim operon that facilitates sucrose isomer metabolism. Growth studies showed that L. buccalis fermented a wide variety of carbohydrates, including four of the five isomers of sucrose. Growth on the isomeric disaccharides elicited expression of a 50-kDa polypeptide comparable in size to that encoded by Lebu_1525. The latter gene was cloned, and the expressed protein was purified to homogeneity from Escherichia coli TOP10 cells. In the presence of two cofactors, NAD(+) and Mn(2+) ions, the enzyme readily hydrolyzed p-nitrophenyl-?-glucopyranoside 6-phosphate (pNP?G6P), a chromogenic analogue of the phosphorylated isomers of sucrose. By comparative sequence alignment, immunoreactivity and signature motifs, the enzyme can be assigned to the phospho-?-glucosidase (Pagl) clade of Family 4 of the glycosyl hydrolase super family. We suggest that the products of Lebu_1527 and Lebu_1525, catalyze the phosphorylative translocation and hydrolysis of sucrose isomers in L. buccalis, respectively. Four genetically diverse, but 16S rDNA-related, species of Leptotrichia have recently been described: L. goodfellowii, L. hofstadii, L. shahii and L. wadei. The phenotypic traits of these new species, with respect to carbohydrate utilization, have also been determined. PMID:22230464
Thompson, J; Pikis, A
Macaúba (Acrocomia aculeata) is a palm of economic importance, widely distributed in natural forests from Mexico to Uruguay. We analyzed the genetic diversity of populations of macaúba (A. aculeata) in the northern region of the State of Minas Gerais, Brazil. Young leaves from 10 macaúba individuals encompassing 49 genotypes of macaúba were collected from Montes Claros, Itacambira, Brasília de Minas, Mirabela, and Grão Mogol. After extraction and amplification of samples, the amplified fragments were separated by electrophoresis. We found high levels of genetic diversity within the populations. Genetic diversity indices were high, except in the Itacambira and Mirabela populations. Results show that Mirabela and Itacambira populations can require conservation strategies because they present lower values of genetic diversity. PMID:22535388
Oliveira, D A; Melo Júnior, A F; Brandão, M M; Rodrigues, L A; Menezes, E V; Ferreira, P R B
Fifteen expressed sequence tag (EST)-derived simple sequence repeats (EST-SSRs) were used to investigate genetic diversity in 139 plants obtained from seeds of 35 watermelon accessions collected from all the geographical provinces of Zimbabwe. In additi...
Claid Mujaju; Jasna Sehic; Hilde Nybom
In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as
O?zbek, O?zlem; Gidik, Betu?l Uc?ar 2013-01-01
O?zbek, O?zlem; Gidik, Betu?l Uc?ar
Full Text Available Abstract Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.
Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the...
Slobodan Katic; Dragan Milic; Ivana Seccareccia; Ksenija Taski-Ajdukovic; Goran Barac; Aleksandar Baburski; Nevena Nagl
North China Mountain Walnut (NCMW) is one of the ancestors of extant cultivated species, and a valuable gene resource for resistance breeding of walnut in China. Inter-Simple Sequence Repeat (ISSR) primers were designed to evaluate the level and pattern of genetic diversity in eight populations of NCMW. Nine ISSR primers yielded 91 amplification products with different sizes, of which 84 (92.31%) were polymorphic. A high species-level genetic diversity was detected with Nei’s (H = ...
Aiqing Ji; Yina Wang; Guoliang Wu; Wenjiang Wu; Hongyan Yang; Qihai Wang
Dalmatian or common sage (Salvia officinalis L.) is an outcrossing plant species native to East Adriatic coast. Random Amplified Polymorphic DNA markers (RAPD) were used to analyze genetic diversity and structure of ten natural populations from the East-Adriatic coastal region. The highest genetic diversity was found in populations from the central and south Dalmatia, while the highest frequency down-weighted marker values were found in the northernmost populations and the southern most inlan...
Zlatko Liber; Vesna Židovec; Sandro Bogdanovi?; Ivan Radosavljevi?; Monika Pruša; Maja Filipovi?; Ines Han Dovedan; Marija Jug-Dujakovi?; Zlatko Šatovi?
The genetic variation of seed protein was assayed by SDS-PAGE for ninety-two accessions of soybean (Glycine max). The germplasm represented five different origins/sources (Pakistan, USA, AVRDC, North Korea and Japan). To our knowledge, no studies have yet been made in Pakistan on the diversity of soybean germplasm based on protein electrophoresis. On the basis of SDS-PAGE, 26 reproducible bands were used for analysis and genetic diversity was estimated based on the number of different protein...
Faisal Anwar Malik, M.; Qureshi, Afsari S.; Muhammad Ashraf; Muhammad Rashid Khan; Asif Javed
Diversity was analyzed based on agronomic and morphologic traits and molecular data. The main objectives of this study were: 1. to estimate genetic diversity of wheat germplasm using agronomic and morphologic traits and molecular markers, 2. to investigate the existence of genetic erosion within tested wheat germplasm, 3. to explore potential utilization of combination of agronomic, morphologic and molecular markers in plant breeding. Forty winter bread wheat varieties were used originating f...
Sustaining and developing of genetic diversity in winter wheat germplasm is one of the main prerequisite for success in future winter wheat breeding programs. Selection of diverse parents is essential for creation of superior new varieties. Danger of genetic erosion specially exists in smaller breeding programs and selection for limited production area with similar growing conditions. Croatian winter wheat breeding has a long tradition but it is relatively small compared to countries with big...
Sonja Petrovi?; Sonja Mari?; Tihomir ?upi?; Georg Drezner; Ildikó Karsai
The Fusarium graminearum species complex (FGSC) is a group of mycotoxigenic fungi that are the primary cause of Fusarium head blight (FHB) of wheat worldwide. The distribution, frequency of occurrence, and genetic diversity of FGSC species in cereal crops in South America is not well understood compared to some regions of Asia, Europe and North America. Therefore, we examined the frequency and genetic diversity of a collection of 183 FGSC isolates recovered from wheat grown during multiple gr...
Giuseppina Mulè; Antonio Moretti; Virginia Fernandez Pinto; Stefania Somma; Cora Lilia Alvarez; Logrieco, Antonio F.; Gaetano Stea; Proctor, Robert H.
The present study was conducted to understand the genetic diversity of bread wheat's that grown in Iran, and to evaluate polymorphism information content (PIC) of some wheat SSR primers. Experiment was done in the genomics Laboratory in Islamic Azad University, Khorramabad branch, Iran in 2012. Ninety-two bread wheat varieties were assayed to study the genetic diversity and polymorphism based on forty whole-genome SSR markers. Eighty alleles were identified and 2 alleles per locus were det...
Reza Drikvand; Mohammad Reza Bihamta; Goodarz Najafian; Asa Ebrahimi
Jatropha curcas L. (jatropha) is an undomesticated plant that has recently received great attention for its utilization in biofuel production, rehabilitation of wasteland, and rural development. Knowledge of genetic diversity and marker-trait associations is urgently needed for the design of breeding strategies. The main goal of this study was to assess the genetic structure and diversity in jatropha germplasm with co-dominant markers (Simple Sequence Repeats (SSR) and Single Nucleotide Polym...
Montes, Juan M.; Frank Technow; Matthias Martin; Klaus Becker
The genetic diversity of 255 taro (Colocasia esculenta) accessions from Vietnam, Thailand, Malaysia, Indonesia, the Philippines, Papua New Guinea and Vanuatu was studied using AFLPs. Three AFLP primer combinations generated a total of 465 scorable amplification products. The 255 accessions were grouped according to their country of origin, to their ploidy level (diploid or triploid) and to their habitat—cultivated or wild. Gene diversity within these groups and the genetic distance between ...
Kreike, N.; Eck, H. J.; Lebot, V.
We investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybean Rj genotypes (non-Rj, Rj2Rj3, and Rj4). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer regi...
Shiro, Sokichi; Matsuura, Syota; Saiki, Rina; Sigua, Gilbert C.; Yamamoto, Akihiro; Umehara, Yosuke; Hayashi, Masaki; Saeki, Yuichi
Asra R, Syamsuardi, Mansyurdin, Witono JR. 2014. The study of genetic diversity of Daemonorops draco (Palmae) using ISSR markers. Biodiversitas 15: 109-114. The genetic diversity in five populations of Daemonorops draco(Willd.) Blume (Jernang: in Bahasa Indonesia) was analyzed using Inter Simple Sequence Repeat (ISSR) markers. The screening results from using 15 ISSR primers showed that only 5 of ISSR primers had clear and reproducible bands. Based on the data from the matrix binary analyzed ...
REVIS ASRA; SYAMSUARDI; MANSYURDIN; JOKO RIDHO WITONO
Full Text Available RAPD markers were used to investigate the genetic diversity of 31 Brazilian cassava clones. The results were compared with the genetic diversity revealed by botanical descriptors. Both sets of variates revealed identical relationships among the cultivars. Multivariate analysis of genetic similarities placed genotypes destinated for consumption "in nature" in one group, and cultivars useful for flour production in another. Brazil?s abundance of landraces presents a broad dispersion and is consequently an important resource of genetic variability. The botanical descriptors were not able to differentiate thirteen pairs of cultivars compared two-by-two, while only one was not differentiated by RAPD markers. These results showed the power of RAPD markers over botanical descriptors in studying genetic diversity, identifying duplicates, as well as validating, or improving a core collection. The latter is particularly important in this vegetatively propagated crop.
Full Text Available Calanthe tsoongiana is a rare terrestrial orchid endemic to China, and this species has experienced severe habitat loss and fragmentation. Inter-simple sequence repeat (ISSR markers were employed to assess the genetic diversity and differentiation of six populations of C. tsoongiana. Based on 124 discernible fragments yielded by eleven selected primers, high genetic diversity was revealed at the species level; however, genetic diversity at the population level was relatively low. High-level genetic differentiation among populations was detected based on analysis of molecular variance (AMOVA, indicating potential limited gene flow. No significant relationship was observed between genetic and geographic distances among the sampled populations. These results suggested that restricted gene flow might be due to habitat fragmentation and reduced population size as a result of human activities. Based on the findings, several conservation strategies were proposed for the preservation of this threatened species.
We present a multi-purpose genetic algorithm, designed and implemented with GPGPU/CUDA parallel computing technology. The model was derived from our CPU serial implementation, named GAME (Genetic Algorithm Model Experiment). It was successfully tested and validated on the detection of candidate Globular Clusters in deep, wide-field, single band HST images. The GPU version of GAME will be made available to the community by integrating it into the web application DAMEWARE (DAta Mining Web Application REsource, http://dame.dsf.unina.it/beta_info.html), a public data mining service specialized on massive astrophysical data. Since genetic algorithms are inherently parallel, the GPGPU computing paradigm leads to a speedup of a factor of 200× in the training phase with respect to the CPU based version.
Cavuoti, S.; Garofalo, M.; Brescia, M.; Paolillo, M.; Pescape', A.; Longo, G.; Ventre, G.
We present a multi-purpose genetic algorithm, designed and implemented with GPGPU / CUDA parallel computing technology. The model was derived from our CPU serial implementation, named GAME (Genetic Algorithm Model Experiment). It was successfully tested and validated on the detection of candidate Globular Clusters in deep, wide-field, single band HST images. The GPU version of GAME will be made available to the community by integrating it into the web application DAMEWARE (DAta Mining Web Application REsource (http://dame.dsf.unina.it/beta_info.html), a public data mining service specialized on massive astrophysical data. Since genetic algorithms are inherently parallel, the GPGPU computing paradigm leads to a speedup of a factor of 200x in the training phase with respect to the CPU based version.
Cavuoti, Stefano; Brescia, Massimo; Paolillo, Maurizio; Pescape', Antonio; Longo, Giuseppe; Ventre, Giorgio
The Main objective of this paper is to eliminate user uninterested rules and find the optimal patterns or association rules. Association rules are important basis of describing Web user’s behavior characteristic. Traditional algorithms of Web association rule mining, based on statistics, usually pays attention to the analysis on existing data, they can’t offer effective means and optimizing measure and cannot find out the latent and possible rules. In this paper we are proposing an effici...
Kolli Prabhakara Rao; Kalyana Chakravarthy, G.
Full Text Available Spatial data plays a key role in numerous applications such as network traffic, distributed security applications such as banking, retailing, etc., The spatial data is essential mine, useful for decision making and the knowledge discovery of interesting facts from large amounts of data. Many private institutions, organizations collect the number of congestion on the network while packets of data are sent, the flow of data and the mobility of the same. In addition other databases provide the additional information about the client who has sent the data, the server who has to receive the data, total number of clients on the network, etc. These data contain a mine of useful information for the network traffic risk analysis. Initially study was conducted to identify and predict the number of nodes in the system; the nodes can either be a client or a server. It used a decision tree that studies from the traffic risk in a network. However, this method is only based on tabular data and does not exploit geo routing location. Using the data, combined to trend data relating to the network, the traffic flow, demand, load, etc., this work aims at deducing relevant risk models to help in network traffic safety task. The existing work provided a pragmatic approach to multi-layer geo-data mining. The process behind was to prepare input data by joining each layer table using a given spatial criterion, then applying a standard method to build a decision tree. The existing work did not consider multi-relational data mining domain. The quality of a decision tree depends, on the quality of the initial data which are incomplete, incorrect or non relevant data inevitably leads to erroneous results. The proposed model develops an ant colony algorithm integrated with GA for the discovery of spatial trend patterns found in a network traffic risk analysis database. The proposed ant colony based spatial data mining algorithm applies the emergent intelligent behavior of ant colonies. The experimental results on a network traffic (trend layer spatial database show that our method has higher efficiency in performance of the discovery process compared to other existing approaches using non-intelligent decision tree heuristics.
Full Text Available North China Mountain Walnut (NCMW is one of the ancestors of extant cultivated species, and a valuable gene resource for resistance breeding of walnut in China. Inter-Simple Sequence Repeat (ISSR primers were designed to evaluate the level and pattern of genetic diversity in eight populations of NCMW. Nine ISSR primers yielded 91 amplification products with different sizes, of which 84 (92.31% were polymorphic. A high species-level genetic diversity was detected with Nei’s (H = 0.2592 and Shannon’s diversity (I = 0.4003. In contrast, the population-level genetic diversity was relatively lower (PPB = 43.27%, H = 0.1347, I = 0.1862. Coefficient of populations differentiation (GST was 0.5066, indicating that inter-population and intra-population variation contributed 50.66% and 49.34% respectively to the total genetic variability. This relative level of variation was further supported by AMOVA analysis. Limited gene flow (Nm = 0.5133., habitat fragmentation and geographical isolation might be responsible for the population structure of NCMW. UPGMA cluster analysis classified the eight populations into three groups which showed no significant relationship between the genetic similarity coefficient and geographic origin but showed remarkable association with morpho-physiological characters, particularly nut traits. The results of the study provide species-level and population-level genetic profiles for further exploitation and conservation of genetic diversity of NCMW.
Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)
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.
Asexual reproduction is commonly thought to be associated with low genetic diversity in animals. Echmepteryx hageni (Insecta: 'Psocoptera') is one of several psocopteran species that are primarily parthenogenetic, but also exists in small, isolated sexual populations. We used mitochondrial DNA sequences to investigate the population history and genealogical relationships between the sexual and asexual forms of this species. The asexual population of E. hageni exhibits extremely high mitochondrial haplotype diversity (H=0.98), whereas the sexual forms had significantly lower haplotypic diversity (H=0.25, after correcting for sample size). This diversity in asexuals represents one the greatest genetic diversities reported for asexual animals in the literature. Nucleotide diversities were also higher in asexual compared to sexual populations (?=0.0071 vs. 0.00027). Compared to other reported estimates of ? in insects, asexual nucleotide diversity is high, but not remarkably elevated. Three hypotheses might explain the elevated genetic diversity of asexual populations: (i) larger effective population size, (ii) greater mutation rate or (iii) possible recent origin of sexuals. In addition, phylogeographic analysis revealed little geographic structure among asexual E. hageni, although specimens from the upper Midwest form a single clade and are genetically differentiated. The mismatch distribution and neutrality tests indicate a historical population size increase, possibly associated with expansion from glacial refugia. PMID:21981306
Shreve, Scott M; Mockford, Edward L; Johnson, Kevin P
Full Text Available Estimation of genetic diversity of Brassica germplasm provides the basis for rapeseed/mustard genetic improvement. Studies were undertaken to estimate the genetic diversity of 30 lines of Brassica napus using Randomly Amplified Polymorphic DNA (RAPD primers. A total of 30 B. napus genotypes of local and exotic origin were characterized using molecular markers. Four RAPD primers were used to estimate the genetic distances among the genotypes in all the possible combinations. The genetic diversity study revealed different levels of genetic polymorphism for RAPD primers GLA05, GLA07, GLA09 and GLA10, resulting in amplification of 5.7, 3.5, 3.1 and 5.4 scorable bands (loci per genotype, respectively. Individual genetic distances observed among B. napus genotypes ranged from 6.5 to 51%. Bivariate data matrix was generated and genetic distances were calculated using Unweighted Pair Group of Arithmetic Mean (UPGMA procedure. The UPGMA cluster analyses revealed maximum genetic dissimilarity for 8966-1 and 8969-1 genotypes, closely followed by Ganyou-5, 89127-1, 89111-2 and Mlep-048. It is recommended that among the thirty B. napus genotypes, genetically distinct lines pointed out in the present study, should be used in future breeding programs for improvement of Brassica napus.
Mian Afaq Ahmad
Full Text Available Association Rule mining is very efficient technique for finding strong relation between correlated data. The correlation of data gives meaning full extraction process. For the mining of positive and negative rules, a variety of algorithms are used such as Apriori algorithm and tree based algorithm. A number of algorithms are wonder performance but produce large number of negative association rule and also suffered from multi-scan problem. The idea of this paper is to eliminate these problems and reduce large number of negative rules. Hence we proposed an improved approach to mine interesting positive and negative rules based on genetic and MLMS algorithm. In this method we used a multi-level multiple support of data table as 0 and 1. The divided process reduces the scanning time of database. The proposed algorithm is a combination of MLMS and genetic algorithm. This paper proposed a new algorithm (MIPNAR_GA for mining interesting positive and negative rule from frequent and infrequent pattern sets. The algorithm is accomplished in to three phases: a.Extract frequent and infrequent pattern sets by using apriori method b.Efficiently generate positive and negative rule. c.Prune redundant rule by applying interesting measures. The process of rule optimization is performed by genetic algorithm and for evaluation of algorithm conducted the real world dataset such as heart disease data and some standard data used from UCI machine learning repository.
Nikky Suryawanshi Rai
This article highlights advantages of entropy-based genetic diversity measures, at levels from gene expression to landscapes. Shannon’s entropy-based diversity is the standard for ecological communities. The exponentials of Shannon’s and the related “mutual information” excel in their ability to express diversity intuitively, and provide a generalised method of considering microscopic behaviour to make macroscopic predictions, under given conditions. The hierarchical nature of entropy...
Sherwin, William B.
Eggplant (Solanum melongena L.) is an important solanaceous crop with high phenotypic diversity and moderate genotypic diversity. Ninety-nine genotypes of eggplant germplasm (species (S. melongena, S. incanum, S. linnaeanum and S. gilo), landraces and heirloom cultivars) from 32 countries and five continents were evaluated for genetic diversity, population structure, fruit shape, and disease resistance to Phytophthora fruit rot. Fruits from each line were measured for fruit shape and evaluate...
Naegele, Rachel P.; Boyle, Samantha; Quesada-ocampo, Lina M.; Hausbeck, Mary K.
Durum wheat (Triticum durum Desf.) has been extensively cultivated in Algeria for many centuries. During this long period, the species encountered a large diversification implied by the great diversity of climates that led to great genetic diversity of the species. The purpose of this study is to improve the management of phytogenetic resources that can serve as potential breeders for the amelioration of wheat. The study aims at evaluating the diversity of 1019 accessions of durum wheat from ...
Boudour Leila; Gherroucha Hocine; Boukaboub Amar; Bouchtab Karima; Baka Mebarek; Samra Kheireddine
Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L.) genotypes was evaluated for intra- and inter-population diversity using a set of 768 genome-wide distributed single nucleotide polymorphism (SNP) markers, of which 657 obtained successful amplification and detected polymorphisms. Gene diversity and polymorphism information ...
Sukhjiwan Kaur; Cogan, Noel O. I.; Forster, John W.; Paull, Jeffrey G.
Rhizobia were isolated from root nodules of three tree legumes inoculated with dilution series of two tropical soils. The diversity of the isolates obtained from different soil dilutions was assessed by PCR-RFLP analysis of the internally transcribed spacer (ITS) region between the 16S and 23S rRNA genes. In both soils there was a strong effect of dilution on the genetic diversity of the populations with apparent diversity decreasing with increasing dilution.
Bala, A.; Murphy, P.; Giller, K. E.
The present research evaluated the diversity of a number of Iranian pomegranate cultivars using fruit morphological characteristics and AFLP markers. Thirty-one pomegranate cultivars were collected from Yazd Pomegranate Collection in Iran to study their diversity. Seven AFLP primer combinations were used to amplify a total of 112 polymorphic fragments (47.26%). By use of AFLPs, a low genetic diversity level was detected among cultivars. The relationship between fruit characteristics was analy...
Khayat, Mehdi; Nemati, Hossein; Farsi, Mohammad; Nemati, Zahra; Mirshamsi Kakhki, Amin; Tehranifar, Ali
In this work we evaluate a collection of 88 carrot cultivars and landraces for polymorphisms at SSR loci and use the obtained markers to assess the genetic diversity, and we show molecular evidence for divergence between Asiatic and Western carrot genetic pools. The use of primer pairs flanking repe...
Full Text Available SciELO South Africa | Language: English Abstract in english The genetic diversity of four protected indigenous chicken breeds was evaluated with 25 microsatellite markers. Polymorphism information content (PIC), heterozygosity with the estimator of genetic differentiation F ST and Nei's genetic distance were evaluated. The results showed that these four prot [...] ected local chicken populations showed high levels of diversity. The proportion of inter-population subdivision among the four protected local chicken populations was 16.0%. The average heterozygosity was 0.514, 0.581, 0.567 and 0.589 in Dongan, Xuefeng black-bone, Xianghuang and Taoyuan chickens, respectively, while the average PIC estimates were 0.455, 0.581, 0.557 and 0.576. A phylogenetic tree was constructed using genetic distance and the neighbour-joining method. Its topology reflects the general pattern of genetic differentiation among the four chicken breeds. The results also showed high genetic diversity and genetic variation among all the breeds. The information about the four local breeds estimated by microsatellite analysis may be useful as an initial guide for the effective conservation of chicken genetic diversity and developing conservation strategies.
Lin, Wei; Bin, Chen; Xiao-ying, Li; Sheng-gui, Liu; Jing-jing, Wang.
Abstract The aim of the present study was to investigate the genetic diversity of Gallibacterium isolates recovered from lesions in turkeys. Gallibacterium has been isolated from various bird species including turkeys, yet no larger investigations have been made to characterise Gallibacterium isolates from turkeys genetically. In the present investigation we genotyped 53 Gallibacterium isolates from turkeys, whereof 50 originated from 29 different flocks...
Bojesen, Anders Miki; Shivaprasad, H. L.
Full Text Available Parental selection is an important step in breeding programs, and genetic variability increases the chances of obtaining variance in progenies. The objectives of this study were to phenotype 29 wheat genotypes and determine the genetic variability among them, in order to identify potential parental lines for breeding programs at Embrapa Wheat. For phenotyping, traits such as plant height, cycle and grains characteristics were assessed and the data were analyzed by the Euclidean distance. The genetic distance was estimated using 97 microsatellite molecular markers and the data were analyzed by Nei72 coefficient. The average distance observed for phenotyping was 10.1, and the genetic distance was 31 %. SSR markers were efficient for selecting genetically diverse genotypes despite their phenotypic similarity, and lines PF 9027, PF 950351, PF 030132, PF 979002, PF 040488 and IWT 04019 can be used as parental for future crosses, since they have genetic diversity and suitable agronomic traits.
Full Text Available Annual medics are used for hey production, soil protection, biological fixation of N2 and green manure. In the present study, the inter and intra specific genetic diversity and relatedness of 4 diploid and two tetraploid (M. rugosa and M. scutellata annual medics were evaluated using microsatellite markers. PCR analysis was performed on genomic DNA from individual plant and PCR products were detected using standard polyacrylamide sequencing gel. Totally twenty five polymorphic alleles were observed in the studied species. Average intra-specific genetic diversity ranged from zero (0.0 in both M. rugosa and M. scutellata to 0.114 in M. minima species, and the level of genetic diversity was similar in both M. orbicularis and M. truncatula species. Analysis of molecular variance (AMOVA was used to partition the overall genetic diversity into within and among species, and between diploids and tetraploids. The results revealed significant (P<0.05 inter and intra-specific genetic variation. Pairwise comparisons based on Fst indicated significant differences among all of the species. Clustering analysis using UPGMA algorithm based on coancestary coefficient revealed a clear genetic relationship among species. The hypothesis on a common origin of two tetraploid species was supported by UPGMA clustering and phylogenetic analysis. The high level of Genetic diversity in spiny pod species respect to spineless pod species suggested the high importance of species with spiny pods in annual medics evolution. The findings support the usefulness of microsatellite markers for assessing inter and intra specific genetic diversity, differentiation and genetic relationships.
S. A. Mohammadi
1.Natural populations of Mediterranean commercial sponges have declined substantially over recent decades. The present study explored the distribution of genetic diversity of the endangered bath sponge Spongia lamella along the western Mediterranean and the Portuguese coast. Seven microsatellite markers were used to genotype 231 individuals scattered over nine populations. Basic genetic descriptors and population genetic analyses based on FST test, analyses of the molecular variance (AM...
Pe?rez-portela, R.; Noyer, Charlotte; Becerro, Mikel
Full Text Available The aim of this work was to study the genetic diversity among flue-cured tobacco cultivars. RAPD and AFLP analyses were used to assess the genetic similarity among selected accessions of flue-cured tobacco. Seventy eight RAPD and 154 AFLP polymorphic bands were obtained and used to assess the genetic diversity among 28 tobacco accessions. The cultivar relationships were estimated through the cluster analysis (UPGMA based on RAPD data and AFLP data. The accessions were grouped into three major clusters and these shared common ancestry clustered together.
Han Yao Zhang
To ascertain genetic diversity, population structure and linkage disequilibrium (LD) among a representative collection of Chinese winter wheat cultivars and lines, 90 winter wheat accessions were analyzed with 269 SSR markers distributed throughout the wheat genome. A total of 1,358 alleles were detected, with 2 to 10 alleles per locus and a mean genetic richness of 5.05. The average genetic diversity index was 0.60, with values ranging from 0.05 to 0.86. Of the three genomes of wheat, ANOVA ...
Chen, Xiaojie; Min, Donghong; Yasir, Tauqeer Ahmad; Hu, Yin-gang
Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies. PMID:25141177
Romiguier, J; Gayral, P; Ballenghien, M; Bernard, A; Cahais, V; Chenuil, A; Chiari, Y; Dernat, R; Duret, L; Faivre, N; Loire, E; Lourenco, J M; Nabholz, B; Roux, C; Tsagkogeorga, G; Weber, A A-T; Weinert, L A; Belkhir, K; Bierne, N; Glémin, S; Galtier, N
Full Text Available Despite substantial advances in genotyping techniques and massively accumulated data over the past half century, a uniform measurement of neutral genetic diversity derived by different molecular markers across a wide taxonomical range has not yet been formulated. We collected genetic diversity data on seed plants derived by AFLP, allozyme, ISSR, RAPD, SSR and nucleotide sequences, converted expected heterozygosity (He to nucleotide diversity (?, and reassessed the relationship between plant genetic diversity and life history traits or extinction risk. We successfully established a uniform ? criterion and developed a comprehensive plant genetic diversity database. The mean population-level and species-level ? values across seed plants were 0.00374 (966 taxa, 155 families, 47 orders and 0.00569 (728 taxa, 130 families, 46 orders, respectively. Significant differences were recovered for breeding system (p < 0.001 at the population level and geographic range (p = 0.023 at the species level. Selfing taxa had significantly lower ? values than outcrossing and mixed-mating taxa, whereas narrowly distributed taxa had significantly lower ? values than widely distributed taxa. Despite significant differences between the two extreme threat categories (critically endangered and least concern, the genetic diversity reduction on the way to extinction was difficult to detect in early stages.
Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple sequence repeat markers. A total of 539 alleles were detected. The allele number per locus ranged from 2 to 21, with a mean allele number of 9.2. The average genetic diversity index was 0.66, with values ranging from 0.01 to 0.89. Comparing the three genomes of wheat, the B genome had the highest genetic diversity (0.66) and the D genome the lowest diversity (0.61). A STRUCTURE analysis based on the Bayesian model-based cluster analysis followed by a graphical representation of the distances by non-parametric multidimensional scaling revealed a distinct partition of the Eritrean wheat accessions into two major groups. This is the first report of the genetic diversity and structure of Eritrean bread wheat. © 2013 NIAB.
Desta, Zeratsion Abera; Orabi, Jihad
Comprehensive studies on the genetic diversity and structure of endangered species are urgently needed to promote effective conservation and management activities. The big tree rhododendron, Rhododendron protistum var. giganteum, is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. Unfortunately, limited information is available regarding the population genetics of this species. Therefore, we conducted amplified fragment length polymorphism (AFLP) analysis to characterize the genetic diversity and variation of this species within and between remaining populations. Twelve primer combinations of AFLP produced 447 unambiguous and repetitious bands. Among these bands, 298 (66.67%) were polymorphic. We found high genetic diversity at the species level (PPL=66.67%, h=0.240, I=0.358) and low genetic differentiation (Gst=0.110) between the two populations. Gene flow between populations (Nm) was relatively high at 4.065. Analysis of molecular variance results revealed that 22% of the genetic variation was partitioned between populations, and 78% of the genetic variation was within populations. The presence of moderate-to-high genetic diversity and low genetic differentiation in the two populations can be explained by life history traits, pollen dispersal, and high gene flow (Nm=4.065). Bayesian structure and principal coordinate analysis revealed that 56 sampled trees were clustered into two groups. Our results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes. These results will assist with the design of conservation and management programs, such as in situ and ex situ conservation, seed collection for germplasm conservation, and reintroduction. PMID:25477251
Wu, Fu Qin; Shen, Shi Kang; Zhang, Xin Jun; Wang, Yue Hua; Sun, Wei Bang
Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese indigenous cattle populations, using microsatellite markers. A total of 410 individuals from six indigenous cattle populations and an exotic breed was characterized using 27 microsatellite markers A total of 362 alleles was detected and the number of alleles per locus ranged from 8 (INRA005 and ILSTS005) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean FIS=0.05) and genetic differentiation (mean FST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic diversity.
Pham, Lan Doan; Do, Duy Ngoc
Full Text Available When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking. A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration. Under conditions in which genetic and cultural variants are transmitted symmetrically, neutral genes may also hitchhike to higher frequencies on the coattails of adaptive cultural traits through a process called cultural hitchhiking. Cultural hitchhiking has been proposed to explain why some species of matrilineal whales display relatively low levels of mitochondrial DNA diversity, and it may be applicable to humans as well. This paper provides a critical review of recent models of both types of hitchhiking in socially structured populations. The models’ assumptions and predictions are compared and discussed in the hope that studies of reduced genetic diversity in humans might improve our understanding of reduced genetic diversity in other species, and vice versa [Current Zoology 58 (1: 287-297, 2012].
L. S. PREMO
Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers. PMID:24499432
Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A
Full Text Available Sixty three local land races of sorghum (Sorghum bicolor L. collected from different parts of Tamil Nadu were evaluated fortheir genetic diversity based on nine characters. The genotypes were grouped into 14 clusters indicating high genetic divergenceamong them. The study indicated no definite relationship between geographic and genetic diversity and geographic diversitycannot be used as an index of genetic diversity. Based on the inter cluster distance and cluster mean for various characters itcould be seen that the clusters VI, X, XII were the most divergent from the other clusters. The genotypes from these parentspossibly be utilized for hybridization programme. Days to flowering, plant height, ear head length and grain weight contributed
K. Ganesamurthy D. Punitha and M. Elangovan
Full Text Available RAPD molecular markers were used to analyze genetic diversity between 16 corn lines. Twenty-two primerswere used resulting in the amplification of 265 fragments, of which 237 (84.44% were polymorphic. Using the UPGMAmethod the genetic associations obtained showed 5 distinct heterotic groups. A principal coordinates analysis also showed anassociation of lines in 5 groups, in agreement with the results observed in the dendrogram. A bootstrap procedure wasapplied to verify whether the amount of markers used was sufficient to ensure reliability of the results, the procedure showeda coefficient of variation of 8.3%, suggesting that the markers were sufficient to assess genetic diversity between the analyzedlines. The high rate of polymorphism between lines revealed by RAPD markers indicated that the method is efficient to analyzegenetic diversity in corn lines and that the genetic divergence can be used to establish consistent heterotic groups between cornlines.
Daniela Cristina Bruel
Full Text Available Of the several hundred breeds of pigs in the world, many are in danger of extinction and others are threatened by inefficient use or loss due to cross breeding. Special efforts are required to conserve these genetic resources for food security and rural development but it is not possible to conserve all breeds. Microsatellites, which are short tandem nucleotide repeats found scattered throughout the genome of eukaryotes, have been used to evaluate genetic diversity present within livestock populations to assist in rationalising breed conservation programmes and ensure the greatest possible conservation of diversity. This review provides insights into the use of microsatellite markers to reveal origin, genetic structure and diversity within and across various domestic pig breeds around the world. However, in future, microsatellites may be replaced by panels of single nucleotide polymorphism (SNP markers for genome-wide population genetic analysis. Meanwhile, microsatellites are still widely employed and for some species may never be replaced by SNP.
Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ? type of geliadins. Conversely, the lowest number of bands were pertained to the ? type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to ? type while, the lowest one was belonged to ? type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.
The level of genetic diversity of aquatic species is a critical indicator of stream system condition for which few data exist. There is strong evidence suggesting that environmental stressors affect the genetic diversity of exposed populations. In order to study genetic diversi...
Carrot is one of the most economically important vegetables worldwide, however, genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to devel...
By using amplified fragment length polymorphism (AFLP) technique, an investigation was made on the genetic diversity and genetic differentiation of seven wild populations of Rhododendron concinnum in Qinling Mountains of Northwest China. A total of 182 amplification products were generated from three AFLP selective primer combinations, of which, 151 were polymorphic. The percentage of polymorphism was 83.1%. The change trends showed by the percentage of polymorphic loci (PPL), Nei's gene diversity (h), and Shannon's information index (I) were uniform, and the order of the populations was Meixian > Zhashui > Zhen' an > Huxian > Ningqiang > Nanzheng > Zhouzhi. The POPGENE analysis showed that the R. concinnum had higher genetic diversity at both species level (PPL = 91.22%, I = 0.7217, h = 0.5095) and population level (PPL = 77.56%, I = 0.6409, h = 0.4725). The coefficient of gene differentiation among the populations (Gst) was 0.0726, indicating that 92.74% of genetic variation occurred within the populations. The analysis of molecular variance (AMOVA) showed that 85.3% of the genetic variation was within the populations, and 14.7% of it was among the populations. The unweighted pair group method with arithmeticmean (UPGMA) indicated that there was no significant correlation between the genetic distance and the geographic distance among the R. concinnum populations. The conservation strategies for R. concinnum germplasm resources were put forward. PMID:23431779
Zhao, Bing; Xu, Man; Si, Guo-Chen; Li, Hou-Hua; Zhang, Yan-Long
The genetic diversity of 7 populations of Kandelia obovata in China was characterized using inter simple sequence repeats (ISSR) technique. A total of 50 primers were screened, of which 9 polymorphic and informative patterns were selected to determine genetic relationships. ISSR amplification was conducted on 140 individuals from 7 populations, and 88 polymorphic loci were detected from 106 total loci. The total percentage of polymorphic loci (PPL) was 83.02%. The percentage of PPL at the population level ranged from 32.08% to 47.17%, with an average of 39.89%. Nei's gene diversity (H) and Shannon's information index (I) of K. obovata at the species level were 0.3631 and 0.5203, respectively. The genetic differentiation coefficient (Gst) among populations was 0.5548. Among populations component accounted for 55.48% of the total variation, whereas the within populations component accounted for 44.52%, suggesting that genetic differentiation among K. obovata populations was relatively high. The gene flow among populations was 0.4012, indicating that gene flow was low among geographically diverse populations of K. obovata. The results of the genetic diversity and cluster analysis suggest that geographical isolation of K. obovata populations mainly results in low gene flow and random genetic drift, leading to genetic differentiation. (author)
The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups), broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (FST?=?0.117) between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (FST?=?0.116, Nm?=?1.89) than those in the eastern group (FST?=?0.049, Nm?=?4.91). Genetic distance between populations was positively and significantly correlated with geographic distance (r?=?0.56, P<0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs. PMID:24265688
Duan, Yun; Wu, Yu-qing; Luo, Li-zhi; Miao, Jin; Gong, Zhong-jun; Jiang, Yue-li; Li, Tong
Full Text Available This work was designed to ascertain the extent of genetic diversity in the pathogen population of Xanthomonas oryzae pv. oryzae (Xoo, the causal organism of bacterial blight of rice. The virulence of 52 strains of Xoo, collected from 12 rice growing states of India, were clip-inoculated on 16 rice genotypes possessing known genes for resistance. Based on the genetic distance, estimated by multivariate analysis isolates of Xoo could be classified into 13 clusters and five broad groups. The genetic variability of virulence in populations of Xoo was also measured by estimation of diversity indices viz. Shannon’s information function (H’, Levin’s diversity index (B, Hill’s generalized entropy (H2, trophic diversity index (D, dominance of virulence factors (?, the index of evenness or equitability (JH,, genetic richness index (d and normalized pathotypic diversity index (Hn. Wide genetic diversity in the pathogen populations from the country as well as from the eastern and southern regions was indicated by high estimates of H', B, H2, D, ?, d and low JH,. High estimates of Hn were attained for almost all populations of Xoo. With regard to the states, genotypic and pathotypic diversities were high in Andhra Pradesh and Orissa, while pathotypic diversity was high in the pathogen population from Gujarat, Punjab, Madhya Pradesh, Uttar Pradesh and Tamil Nadu. The existence of high diversities and the grouping of the pathogen isolates into clusters of similar in virulence facilitated a better understanding of the population structure of Xoo, to guide regional rice breeding programs and the deployment of resistance genes in disease control strategy.
Full Text Available Abstract Background Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L., which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. Results According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secondary centre of diversification. Conclusions A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the ‘Irano-Caucasian’ gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.
Full Text Available This article highlights advantages of entropy-based genetic diversity measures, at levels from gene expression to landscapes. Shannon’s entropy-based diversity is the standard for ecological communities. The exponentials of Shannon’s and the related “mutual information” excel in their ability to express diversity intuitively, and provide a generalised method of considering microscopic behaviour to make macroscopic predictions, under given conditions. The hierarchical nature of entropy and information allows integrated modeling of diversity along one DNA sequence, and between different sequences within and among populations, species, etc. The aim is to identify the formal connections between genetic diversity and the flow of information to and from the environment.
William B. Sherwin
By using Biolog technique, this paper studied the diversity of carbon source metabolism of microbial community in three farmland soils with different levels of arsenic (As) in an As mining area, and the relationships between the diversity of the carbon source metabolism and the main soil chemical properties. The total N (TN), total P (TP), total K (TK), organic matter (OM), total Cu, and total Zn contents in the three soils were in the order of medium level As > high level As > low level As. The average well color development (AWCD), Shannon index (H'), Simpson index (D), and McIntosh index (U) of soil microbes were significantly higher in the soils with medium and high levels As than in the soil with low level As. The principal component analysis and the fingerprints of the physiological carbon metabolism of the microbial community in the three soils demonstrated that the microbes in the soils with medium and high levels As had a significantly higher (Psource metabolism of soil microbial community. It was considered that soil nutrients could be the main factors affecting the community structure and functions of soil microbes in long-term contaminated soils. PMID:23705394
Hua, Jian-Feng; Lin, Xiang-Gui; Jiang, Qian; Zhang, Hua-Yong; Chen, Qian; Yin, Yun-Long
In this study, we describe the evolution of crop diversity in Flanders, using three indicators to measure diversity between crops and within crops: the Shannon index (H), the evenness index (E) - both used for diversity between and within crops - and genetic relatedness between varieties (CP). Despite the significant increase in the number of crops in Flanders, from 67 in 1950 to 101 in 2002, the results show a weak decrease in crop diversity between 1950 and 2002: H decreased from 2.52 to 2....
Meul, Marijke; Nevens, Frank; Reheul, Dirk
The Systems Genetics Resource (SGR) (http://systems.genetics.ucla.edu) is a new open-access web application and database that contains genotypes and clinical and intermediate phenotypes from both human and mouse studies. The mouse data include studies using crosses between specific inbred strains and studies using the Hybrid Mouse Diversity Panel. SGR is designed to assist researchers studying genes and pathways contributing to complex disease traits, including obesity, diabetes, atherosclero...
Nas, Atila; Pan, Calvin; Ingram-drake, Leslie A.; Ghazalpour, Anatole; Drake, Thomas A.; Sobel, Eric M.; Papp, Jeanette C.; Lusis, Aldons J.
Full Text Available To improve yield and quality of wheat, presence of genetic diversity is an important prerequisite. To estimate the extent of genetic variability, DNA markers including Randomly Amplified Polymorphic DNA (RAPD have been widely used in various crops of agronomic importance. During present study, RAPDs were used to estimate genetic relationship among 10 Pakistani wheat varieties and to identify genetically diverse genotypes which can be used in future breeding programs. RAPD primers used during present study produced an average of 1.9 alleles per primer. Size of scorable fragments ranged from 250-1000 bp. A high level of genetic dissimilarity (GD = up to 63% was estimated among the wheat varieties. Ten wheat varieties were grouped in 3 clusters using dendrogram analysis. Clusters A, B and C comprised land races, derivatives of Mexi-Pak and elite lines having alien gene, respectively.
Full Text Available The objective of the present study was to estimate the genetic relationship among the different Chrysanthemum cultivars with relation to their morphological and biochemical characteristics and geographical distribution. DNA fingerprinting using RAPD is very easy and inexpensive way to study the genetic diversity. Genetic distance between four mini Chrysanthemum cultivars was studied through RAPD analysis. Total of 40 primers have been screened from which four have been trailed for all the four genotypes. Similarity among the cultivars was very high showing low genetic diversity, which is quite expected. One of these primers can differentiate cultivars from each other. So RAPD can be used successfully to estimate the genetic distance and also for the species identification.
The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. Empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establi...
Milia, Nicola; Congiu, Alessandra; Anagnostou, Paolo; Montinaro, Francesco; Capocasa, Marco; Sanna, Emanuele; Bisol, Giovanni Destro
The snakehead fish Channa argus is an important food fish in China. We identified six microsatellite loci for C. argus. These six microsatellite loci and four other microsatellite markers were used to analyze genetic diversity in four cultured populations of C. argus (SD, JX, HN, and ZJ) and determine their relationships. A total of 154 alleles were detected at the 10 microsatellite loci. The average expected and observed heterozygosities varied from 0.70-0.84 and 0.69-0.83, respectively, and polymorphism information content ranged between 0.66 and 0.82 in the four populations, indicating high genetic diversity. Population JX deviated from mutation-drift equilibrium and may have experienced a recent bottleneck. Analysis of pairwise genetic differentiation revealed FST values that ranged from 0.028 to 0.100, which indicates a moderate level of genetic differentiation. The largest distances were observed between populations HN and SD, whereas the smallest distances were obtained between populations HN and JX. Genetic clustering analysis demonstrated that the ZJ and HN populations probably share the same origin. This information about the genetic diversity within each of the four populations, and their genetic relationships will be useful for future genetic improvement of C. argus through selective breeding. PMID:24615092
Zhu, S-R; Li, J-L; Xie, N; Zhu, L-M; Wang, Q; Yue, G-H
Full Text Available SciELO Brazil | Language: English Abstract in portuguese A abobrinha de inverno compõe um cultivo agrícola com valor econômico determinado exercendo, no entanto, um papel importante em zonas caracterizadas por um cultivo menos intensivo. Na Grécia, o cultivo da abobrinha se baseia, principalmente, em variedades locais conservadas a muitos anos por agricul [...] tores locais. Uma parte do cultivo nuclear da abobrinha, que é conservada pelo Banco Grego de Genes, foi melhorada utilizando-se dados morfológicos e moleculares, especialmente dezesseis cultivos de abobrinha classificados incompletamente, que foram diferenciados apenas com base em características morfológicas, em relação a uma avaliação à resistência contra o Fusarium Oxysporum, em dois isolamentos. Foi realizada uma análise molecular utilizando DNA Polimórficos Casual Amplificados índices (RAPDs), revelando um alto nível de polimorfismo. Para estudar a diversidade genética entre a coleção de abobrinhas, um procedimento de agrupamento foi realizado usando-se o algoritmo U.P.G.M.A. Dois dendrogramas independentes, um morfofisiológico e outro para dados moleculares, foram coletados, classificando as coleções em dois e três grupos básicos, respectivamente. Apesar do número diferente dos grupos, foram introduzidas muitas semelhanças entre os dois dendrogramas e um terceiro dendrograma foi produzido como resultado da combinação dos dois primeiros, baseado na distância de Gower e no algoritmo de agrupamento U.P.G.M.A. Para determinar o número ótimo dos grupos, a aproximação "upper tail" foi aplicada. O grupo mais aceitável das coleções foi conseguido usando-se índices RAPD, assim como a combinação dos dois grupos de dados diferentes, classificando as coleções em três grupos consideravelmente diferentes. Os grupos que correspondem às três espécies cultivadas diferentemente, que correspondem às três espécies cultivadas diferentemente por C.máxima Duch., C.moschata Duch. e C. pepo L. além disso, os mesmos resultados foram conseguidos usando-se a "Principal Component Analysis". Abstract in english In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium [...] oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.
Athanasios L., Tsivelikas; Olga, Koutita; Anastasia, Anastasiadou; George N., Skaracis; Ekaterini, Traka-Mavrona; Metaxia, Koutsika-Sotiriou.
Full Text Available Singh AK, Jamaluddin (2011 Status and diversity of arbuscular mycorrhizal fungi and its role in natural regeneration on limestone mined spoils. Biodiversitas 12: 107-111. Limestone mined spoils are devoid of adequate population of beneficial microbial flora. Arbuscular mycorrhizal fungi (AMF are very important constituent of plant- soil-microbe system. In mined spoils the population of AMF is greatly reduced and hence the spoils become very inhospitable for establishment of vegetation. In the present investigation, status of AMF population and its effect on natural regeneration process is studied. It is well known fact that the arbuscular mycorrhizal fungi play very important role in establishment of vegetation in degraded lands. Plantation of seedlings inoculated with arbuscular mycorrhizal fungi provide favorable soil conditions for naturally growing vegetation in the mined overburden spoils. Physico-chemical properties of soil are converted suitable for planted species and thus it allows other species to grow and also provide shade to protect the herbaceous vegetation. Introduction of plant species attracts immigration of other species and if they established, may result into a very distinctive floral cover on disturbed lands. Thus, invasion of native plant species along with planted species may play a significant role in increasing the plant diversity on mined
ANUJ KUMAR SINGH
Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic, which ranks 11th in the world and number one in organic cacao exports. In an effort to identify propagation mistakes, and estimate genetic diversity and population structure in cacao germplasm accessions a...
Full Text Available Abstract Background Febrile respiratory illness (FRI has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV and enteroviruses (HEV which are frequent causes of FRI. Resequencing Pathogen Microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking. Results Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV, which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen Microarray RPM-Flu v.30/31 (Tessarae RPM-Flu. The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level. Conclusion This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.
Blaney Kate M
Lichens associated with old forest are commonly assumed to be negatively affected by tree logging or natural disturbances. However, in this study performed in a spruce-dominated sylvopastoral landscape in the Swiss Jura Mountains, we found that genetic diversity of the epiphytic old-forest lichen Lobaria pulmonaria depends on the type of disturbance. We collected 923 thalli from 41 sampling plots of 1 ha corresponding to the categories stand-replacing disturbance (burnt), intensive logging (logged) and uneven-aged forestry (uneven-aged), and analysed the thalli at six mycobiont-specific microsatellite loci. We found evidence for multiple independent immigrations into demes located in burnt and logged areas. Using spatial autocorrelation methods, the spatial scale of the genetic structure caused by the clonal and recombinant component of genetic variation was determined. Spatial autocorrelation of genotype diversity was strong at short distances up to 50 m in logged demes, up to 100 m in uneven-aged demes, with the strongest autocorrelation up to 150 m for burnt demes. The spatial autocorrelation was predominantly attributed to clonal dispersal of vegetative propagules. After accounting for the clonal component, we did not find significant spatial autocorrelation in gene diversity. This pattern may indicate low dispersal ranges of clonal propagules, but random dispersal of sexual ascospores. Genetic diversity was highest in logged demes, and lowest in burnt demes. Our results suggest that genetic diversity of epiphytic lichen demes may not necessarily be impacted by stand-level disturbances for extended time periods. PMID:16599956
Werth, Silke; Wagner, Helene H; Holderegger, Rolf; Kalwij, Jesse M; Scheidegger, Christoph
Full Text Available Genetic diversity is one of the key factors for the improvement of many crop plants including wheat. Many wheat scientistshave studied genetic diversity in wheat germplasm using different molecular markers which have provided a powerfulapproach to analyze genetic relationships among wheat germplasms. In this study, genetic diversity of CIMMYT(International maize and wheat improvement center bread wheat lines collected from Russia was evaluated using 30sequence-related amplified polymorphism (SRAP primer combinations. 686 DNA band was obtained from the 23 primercombinations and approximately 90% of them were found to be polymorphic. Ratio of polymorphic loci, Shannon'sdiversity index and gene diversity were found 82.61%, 0.39 and 0.26 respectively. The three main clusters were found byusing UPGMA (Unweighted Pair Group Method with Arithmetic Mean cluster analysis method and the average rate ofgenetic similarity with 0.462. Two main clusters were shown in principal component analysis (PCA which is consistentwith the result of UPGMA. It can be concluded that SRAP markers can be used for wheat genetic diversity studies and havepotential linkage mapping, molecular characterizations and marker assisted selection (MAS breeding.
Full Text Available Assam of the northeastern region of India is unique in terms of its rich biodiversity and multiple ethnicity of its people. The impact of the resultant socio-religio-cultural diversity is also reflected in the diverse traditional ways of silkworm farming. We report the genetic diversity of Persea bombycina “Som” from different locations of Goalpara district of Assam, India, where random amplified polymorphic DNA (RAPD marker was used in this study. RAPD analyses of ten genotypes of “Som” from Goalpara district of Assam, India with B19 RAPD primer generated 86 bands, showing an average of 8.6 bands per sample and 30.2% (26 bands of these were polymorphic. The number of bands per accession ranged from 5 to 10 with a mean of 8.6 and the size range of the amplified bands was 250 - 6000 bp. In a UPGMA phenetic dendrogram based on Jaccard’s coefficient, the P. bombycina accessions showed a high level of genetic variation, as indicated by genetic similarity and revealed 10 “Som” genotypes in to three major clusters. This study may be useful in identifying diverse genetic stocks of P. bombycina, which may then be conserved on a priority basis. The RAPD primer used in this study was able to distinguish all the 10 genotypes of “Som” plants, which can be used to assess genetic diversity.
Sitobion avenae is a major agricultural pest of wheat in China. Using microsatellite markers, we studied the potential gene flow, genetic diversity, genetic differentiation, and genetic structure of seven S. avenae populations from different regions of China (Beijing, Hebei, Henan, Hubei, Jiangsu, Shandong, and Shanxi provinces). The populations from Henan, Shandong, and Jiangsu showed high levels of genic and genotypic diversity. By contrast, the genic diversity in the Beijing and Hebei populations was much lower. Despite this low genic diversity, the genotypic diversity of the Beijing population was higher than that of all of the other populations, except those from Jiangsu and Shandong. Overall, the genetic divergence among the seven S. avenae populations tested was high, though there was almost no differentiation between the Shandong and Henan populations. We observed significant negative correlation between the strength of gene flow and the geographic distances among populations. Based on genetic analysis, the seven S. avenae populations studied can be divided into four distinct clusters; (i) Hubei, (ii) Shanxi, (iii) Beijing and Hebei, and (iv) Shandong, Henan, and Jiangsu. The present results provide a basis for potentially optimizing integrated pest management (IPM) programs in China, through adapting control methods that target biological traits shared by various populations of the same genotype. PMID:25356548
Xin, Juan-Juan; Shang, Qing-Li; Desneux, Nicolas; Gao, Xi-Wu
Sitobion avenae is a major agricultural pest of wheat in China. Using microsatellite markers, we studied the potential gene flow, genetic diversity, genetic differentiation, and genetic structure of seven S. avenae populations from different regions of China (Beijing, Hebei, Henan, Hubei, Jiangsu, Shandong, and Shanxi provinces). The populations from Henan, Shandong, and Jiangsu showed high levels of genic and genotypic diversity. By contrast, the genic diversity in the Beijing and Hebei populations was much lower. Despite this low genic diversity, the genotypic diversity of the Beijing population was higher than that of all of the other populations, except those from Jiangsu and Shandong. Overall, the genetic divergence among the seven S. avenae populations tested was high, though there was almost no differentiation between the Shandong and Henan populations. We observed significant negative correlation between the strength of gene flow and the geographic distances among populations. Based on genetic analysis, the seven S. avenae populations studied can be divided into four distinct clusters; (i) Hubei, (ii) Shanxi, (iii) Beijing and Hebei, and (iv) Shandong, Henan, and Jiangsu. The present results provide a basis for potentially optimizing integrated pest management (IPM) programs in China, through adapting control methods that target biological traits shared by various populations of the same genotype. PMID:25356548
Xin, Juan-Juan; Shang, Qing-Li; Desneux, Nicolas; Gao, Xi-Wu
Full Text Available This paper analyzes the genetic diversity of 79 accessions of native potato varieties (Solanum spp. using 18 microsatellite markers. A random sample from Ayacucho, Cajamarca, Cusco, Huancavelica and Puno from "chacras" of farmers who collaborated with the "In situ conservation of native crops and wild relatives" were used. 17 markers amplified one single polymorphic locus, the mean number of alleles per locus was 8.79. The mean similarity was 0.62 and clustering indexes varied between 0.41 and 0.98. 19 loci showed a total of 166 alleles. Cuzco had the highest number of alleles (130 alleles. Of the 166 characterized alleles, 72 alleles (43.37% were common or shared with 5 sampling sites. Puno had the highest number of exclusive alleles (8 alleles. The 42 varieties of S. tuberosum subsp. andigena showed a mean diversity of 0.74 and 18 varieties of S. x chauchaan average diversity of 0.70. Polymorphism (PIC = 0.55 to 0.85 and genetic diversity indices show that microsatellites evaluated can identify high levels of genetic diversity, but also are not sufficient to discriminate differentiated by origin or species groups. Our analyzes indicate a high genetic diversity and are consistent with inventories and morphological characterizations performed in situ, we can also conclude that there would be a common pool of genes would be found widely distributed among the regions studied.
Full Text Available SciELO Chile | Language: English Abstract in english In Venezuela, pedigree analyses indicate that the rice varieties currently under cultivation are closely related. Effective breeding programs, based on knowledge of the genetic diversity of cultivars, are needed to broaden the genetic bases of rice germplasm in the country. In this study, we used a [...] set of 48 simple-sequence-repeat (SSR) markers to assess the genetic diversity of 11 Venezuelan rice cultivars, released by the National Rice Breeding Program between 1978 and 2007. A total of 203 alleles were detected, the number of alleles (NA) per marker ranged from 2 to 9, with an average of 4.23. The average genic diversity (H) over all SSR loci for the 18 genotypes was 0.524, ranging from 0.105 to 0.815. Positive correlations were found between H at each locus, NA, the allele size range and the maximum number of repeats. Venezuelan cultivars showed lower H (mean = 0.37) and NA (total = 124, mean = 2.58) than the whole sample. UPGMA-cluster-analysis based on genetic distance coefficients clearly separated all the genotypes, and showed that the Venezuelan rice varieties are closely related. Molecular identification of 7 Venezuelan cultivars could be done with 9 primers pairs which produced 10 genotype-specific-alleles. Although the genetic diversity was low, SSRs proved to be an efficient tool in assessing the genetic diversity of rice genotypes. Implications of the low genetic diversity detected and relatedness of Venezuelan cultivars are discussed.
Thaura, Ghneim Herrera; Duina, Posso Duque; Iris, Pérez Almeida; Gelis, Torrealba Núñez; Alejandro J, Pieters; César P, Martinez; Joe M, Tohme.
Full Text Available Abstract Background Despite the two-fold cost of sex, most of the higher animals reproduce sexually. The advantage of sex has been suggested to be its ability, through recombination, to generate greater genetic diversity than asexuality, thus enhancing adaptation in a changing environment. We studied the genetic diversity and the population structure of three closely related species of bag worm moths: two strictly sexual (Dahlica charlottae and Siederia rupicolella and one strictly asexual (D. fennicella. These species compete for the same resources and share the same parasitoids. Results Allelic richness was comparable between the sexual species but it was higher than in the asexual species. All species showed high heterozygote deficiency and a large variation was observed among FIS values across loci and populations. Large genetic differentiation was observed between populations confirming the poor dispersal ability of these species. The asexual species showed lower genotype diversity than the sexual species. Nevertheless, genotype diversity was high in all asexual populations. Conclusion The three different species show a similar population structure characterised by high genetic differentiation among populations and low dispersal. Most of the populations showed high heterozygote deficiency likely due to the presence of null alleles at most of the loci and/or to the Wahlund effect. Although the parthenogenetic D. fennicella shows reduced genetic diversity compared to the sexual species, it still shows surprisingly high genotype diversity. While we can not totally rule out the presence of cryptic sex, would explain this high genotype diversity, we never observed sex in the parthenogenetic D. fennicella, nor was there any other evidence of this. Alternatively, a non-clonal parthenogenetic reproduction, such as automictic thelytoky, could explain the high genotypic diversity observed in D. fennicella.
Full Text Available Ethiopia is one of the origins and centers of genetic diversity of sorghum. As sorghum ranks fifth in global cereal production, the study of its genetic diversity from its center of origin is important for its improvement. Therefore, the aim of the present study was to evaluate the within and among population genetic diversity of sorghum from Ethiopia using Inter Simple Sequence Repeat markers. Eight individuals from each of eleven sorghum populations of highland, intermediate and lowland ecological zones and one population of improved variety and stay-green cultivars were used for the study. DNA was extracted from young leaves and PCR was conducted using seven primers. A total of 55 clear and reproducible bands with 100% polymorphism were generated. The total genetic diversity (GD and Shannon’s diversity index (I were 0.205 and 0.296, respectively. North Gondar Intermediate altitude population showed the highest gene diversity (0.3 while the lowest diversity (0.1 was exhibited by North Shewa population. AMOVA showed that 44.45, 30.84 and 24.71% of the total variation was attributed to within populations, among populations and among groups, respectively. Group based UPGMA exhibited four distinct clusters whereas the population based UPGMA showed all populations clustered within its own ecological zone except North Gondar (I1 intermediate altitude population and improved varieties and stay-green (IM individuals that were clustered in the highland populations. Intermediate altitude populations exhibited higher genetic diversity than low and high altitude populations indicating these high and low altitude populations may have originated from the intermediates through ecological adaptations.
Full Text Available This study aimed to evaluate the genetic diversity by RAPD markers in 20 genotypes of ‘yellow’ passion fruit (Passiflora edulis Sims. The 16 primers generated 92 markers, 57 (62% of which were polymorphic. The genetic distance (gdij estimated by the complement of the Dice index (gdij = 0.19 and genotype grouping based on UPGMA algorithm showed low variability among genotypes. These results show a narrower genetic basis than reported for other Passiflora populations and the need to increase this variability by germplasm introduction. Divergent genotypes were also identified for the choice of parents for crosses for genetic gains in traits previously selected within the population studied.
Carlos Bernard Moreno Cerqueira-Silva
In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 +/- 0.07 to 0.87 +/- 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations. PMID:12530188
Moraes, N; Morgante, J S; Miyaki, C Y
Full Text Available In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 ± 0.07 to 0.87 ± 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations.
The Enterobacterial repetitive intergenic consensus (ERIC) marker was used to analyze the genetic variability of Mycosphaerella fijiensis, the causative agent of Black Sigatoka disease in banana plants. A total of 123 isolates were used, which were divided into populations based on their original hosts and collection sites in Brazil. A total of 9 loci were amplified, 77.8% of which were found to be polymorphic. The genetic diversity found in the population was 0.20. Analysis of molecular variance (AMOVA) demonstrated that the highest level of genetic variation is within populations. Cluster analysis revealed three main groups in Brazil, with no correlation between geographic and genetic distance. PMID:25299083
Silva, G F; Paixão, R D V; Queiroz, C B; Santana, M F; Souza, A; Sousa, N R; Hanada, R E; Gasparotto, L
Full Text Available During the last century, the selection for production traits of the main livestock species has led to a reduction in number of local populations with consequent loss of genetic variability. In Sardinia, the genetic improvement strategy has been based on selection for the local pure breed in sheep, whereas in the other species (cattle, swine and goat, an often unplanned crossbreeding with improved breeds has been applied.
Genetic variability of 15 sets of Plantago ovata Forsk. studied using 11 arbitrary oligonucleotide primers. Among the 90 DNAfragments produced 71 fragments were found to be polymorphic. The mean number of polymorphic bands per primer among 15Plantago ovata genotypes was 6.45 . The higher polymorphism (90.00 %) was exhibited by primer OPF-17, while the lowerpolymorphism (60.00 %) was detected by OPF-2. The genetic similarity matrix from RAPD data for 15 genotypes was calculatedbased on Jaccard...
Ashish G Vala, R. S. Fougat And G. C. Jadeja
Genetic variability is the clay of evolution, providing the base material on which adaptation and speciation depend. It is often assumed that most interspecific differences in variability are due primarily to population size effects, with bottlenecked populations carrying less variability than those of stable size. However, we show that population bottlenecks are unlikely to be the only factor, even in classic case studies such as the northern elephant seal and the cheetah, where genetic poly...
Amos, W.; Harwood, J.
Full Text Available SciELO Chile | Language: English Abstract in english Background Genetic diversity and genetic variation of 10 populations and subpopulations of Magnolia wufengensis, a new and endangered endemic species, were examined by inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) molecular markers. Compared with other endang [...] ered endemic Magnolia taxa, M. wufengensis holds a relatively high level of genetic variation. Result Total genetic diversity was found to be 87.7% for ISSR and 88.0% for SRAP markers. For polymorphic loci (P), the effective mean number of alleles (Ae) was 1.414 for ISSR markers and 1.458 for SRAP markers, while the mean expected heterozygosity (H) was 0.256 using ISSR and 0.291 for SRAP markers. Within-population variation was estimated for P as 74.9% using ISSR and 74.6% with SRAP markers; the number of alleles Ae was 1.379 with ISSR and 1.397 for SRAP and H 0.235 with ISSR and 0.247 for SRAP markers. Conclusion The analysis of molecular variation of both ISSR and SRAP marker systems indicated that most genetic variation is within populations, with values of 90.64% and 82.92% respectively. Mantel tests indicated a moderate association between the two marker systems and a low correlation between genetic and geographic distances. High levels of genetic diversity and low levels of population divergence suggest that genetic drift is not currently of great concern for this species. Severe habitat loss and fragmentation, predominantly ascribed to anthropogenic pressures, caused in-situ developing restriction of this species. Action for conserving this rare species for its long-term survival should be taken immediately.
Liyuan, Chen; Faju, Chen; Suichao, He; Luyi, Ma.
Eighteen populations of the endangered aromatic and medicinal plant Mentha cervina (Lamiaceae) were sampled across its natural range, in the western half of the Iberian Peninsula, and inter-simple sequence repeats (ISSRs) markers were used to assess genetic diversity and population structure. M. cervina populations exhibited a relatively low genetic diversity (percentage of polymorphic loci PPB ¼ 14.2–58.3%, Nei’s genetic diversity He ¼ 0.135–0.205, Shannon’s informat...
Rodrigues, Leandra; Berg, Ca?ssio Den; Po?voa, Orlanda; Monteiro, Ana
The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (F IT) in native chicken was 0.234±0.025. Over 30.7% of F IT was contributed by within-population deficiency (F IS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds. PMID:25178290
Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu
Full Text Available Dalmatian or common sage (Salvia officinalis L. is an outcrossing plant species native to East Adriatic coast. Random Amplified Polymorphic DNA markers (RAPD were used to analyze genetic diversity and structure of ten natural populations from the East-Adriatic coastal region. The highest genetic diversity was found in populations from the central and south Dalmatia, while the highest frequency down-weighted marker values were found in the northernmost populations and the southern most inland population. Although analysis of molecular variance (AMOVA revealed that most of the genetic diversity was attributable to differences among individuals within populations, highly significant ?ST values suggested the existence of genetic differentiation among populations. By assuming Hardy-Weinberg equilibrium within populations, the calculated FST value among population was moderate. Bayesian model-based clustering method revealed that at K = 2 all individuals belonging to two northern populations were assigned to a separate cluster from the individuals belonging to the rest of the population. At K = 3, the newly formed cluster grouped the majority of individuals belonging to populations from central Dalmatia. The high correlation between matrices of genetic and geographical distances showed that isolation by distance may play a considerable role in overall structuring of the genetic diversity.
Full Text Available SciELO Brazil | Language: English Abstract in english Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil) of Araucaria angustifolia in comparison with populations in the main [...] area of the species continuous natural distribution (southern Brazil), was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27), despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16), thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10%-15%). From Bayesian analysis, it is suggested that the nine populations tested form five "genetic clusters" (K = 5). Five of these populations, located in the northernmost limit of distribution of the species, represent three "genetic clusters". These results are in agreement with the pattern of geographic distribution of the studied populations.
Maria Isabel Ferreira de, Souza; Fabiano, Salgueiro; Mariana, Carnavale-Bottino; Durvalina Benedita, Félix; Marcio, Alves-Ferreira; Juliana Vitoria Messias, Bittencourt; Rogério, Margis.
Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91 %) than between populations (9 %). Results suggested moderate genetic differentiation among Napier grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation. PMID:23671788
Wanjala, Bramwel W; Obonyo, Meshack; Wachira, Francis N; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A; Proud, Janice; Hanson, Jean
Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide. PMID:25178197
da Cunha, Camila Pinto; Resende, Francisco Vilela; Zucchi, Maria Imaculada; Pinheiro, José Baldin
The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ?ST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.
Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.
Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an alternative, or even evolutionary stepping-stone, to switching between multiple systems. We hypothesized that mutations in gene regulation could lead to heritable control of chemotactic diversity. By simulating foraging and colonization of E. coli using a single-cell chemotaxis model, we found that different environments selected for different behaviors. The resulting trade-offs show that populations facing diverse environments would ideally diversify behaviors when time for navigation is limited. We show that advantageous diversity can arise from changes in the distribution of protein levels among individuals, which could occur through mutations in gene regulation. We propose experiments to test our prediction that chemotactic diversity in a clonal population could be a selectable trait that enables adaptation to environmental variability. DOI: http://dx.doi.org/10.7554/eLife.03526.001 PMID:25279698
Frankel, Nicholas W; Pontius, William; Dufour, Yann S; Long, Junjiajia; Hernandez-Nunez, Luis; Emonet, Thierry
Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He?=?0.0621), but higher at the species level (He?=?0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm?=?0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r?=?0.212, P?=?0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation. PMID:25333788
Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na
Full Text Available Abstract Background Castor bean (Ricinus communis is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale. We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs at 48 loci. Results Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74% followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ?PT values, p Conclusion Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.
Rabinowicz Pablo D
Full Text Available Due to the environmental changes and habitat destruction the mudskipper fish population is decreasing in recent years. To predict the fish population structure, frequent manual survey and molecular methods are widely used. Molecular markers such as RAPD, microsatellite, allozyme, D-loop haplotype are frequently adopted to assess the population structure of an organism. In this study ten- arbitrary primers were screened to estimate the genetic relationships and diversity of two mudskipper species (Boleophthalmus boddarti and B. dussumieri in Vellar estuary, Tamilnadu, India. By this RAPD marker study, the genetic diversity (H in B. boddarti was more (0.0116 ± 0.0066 than in B. dussumieri (0.0056 ± 0.0024 in Vellar estuary (India. The genetic distance between B. boddarti and B. dussumieri was 1.7943. By observing the species specific bands and the phylogenetic analysis it is revealed that these two species clearly deviated into separate clusters emphasizing the distinct species status.
Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.
Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie
The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow, and largely attributable to the cross-pollination and self-incompatibility reproductive system. A STRUCTURE (model-based program) analysis revealed that the 21 populations can be divided into two main groups, mainly based on geographic differences and genetic exchanges. The entire wild Siberia apricot population in China could be divided into two subgroups, including 107 accessions in subgroup (SG) 1 and 147 accessions in SG 2. A Mantel test revealed a significant positive correlation between genetic and geographic distance matrices, and there was a very significant positive correlation among three marker datasets. Overall, we recommend a combination of conservation measures, with ex situ and in situ conservation that includes the construction of a core germplasm repository and the implement of in situ conservation for populations HR, MY, and ZY. PMID:24384840
Li, Ming; Zhao, Zhong; Miao, Xingjun; Zhou, Jingjing
Full Text Available The aim of this study is to analyse genetic diversity, structure and differentiation of the giant frogs (Limnonectes blythii. One hundred and sixty four individuals from 4 populations in Mae Hong Son Province, Thailand were used for the analysis of genetic polymorphism at 7 microsatellite loci. The collection showed considerable polymorphism with observed number of alleles per locus ranging for seven different loci, with an average of 3.4 alleles per locus. Mean genetic diversity of the four populations with moderate level, but in populations with lower genetic diversity. Furthermore, the NJ tree approach clustering conWrmed the results of PAM is more differentiated than the others. The signiWcant levels of genetic structure among the sites were found in which could be resulting from isolation by distance rather than a position relative to habitat. The results of this study indicate that genetic structure could be useful for evaluation of neutral genetic variation particularly as the basis for inferring population and species capacity for species conservation and management decisions.
Knowledge of genetic diversity is important as it forms the basis for designing breeding programmes and making rational decisions on sustainable utilization of animal genetic resources. This study was designed to assess the efficiency of blood protein polymorphism as a rapid tool for assessing genetic diversity, using seven blood proteins (transferrin, albumin, haemoglobin, esterase A, esterase C, carbonic anhydrase and X-protein) and 457 indigenous fat-tailed (351) and fat-rumped (106) hair sheep in Kenya from 7 populations, with 40 Merino as controls. Transferrin was analysed using polyacrylamide gel electrophoresis and starch gel electrophoresis was used to analyse the other six loci. Of the seven loci analysed, two - carbonic anhydrase and X-protein - could not be interpreted. The five interpretable markers, however, showed low levels of polymorphism in allele numbers and heterozygosity. Multilocus mean FST values of 0.083 indicated a moderate genetic differentiation between the populations analysed. The Dm and Da genetic distance estimates showed the indigenous sheep populations in Kenya to be closely related genetically, with the dendrogram failing to resolve indigenous sheep into fat-tailed sheep and fat-rumped hair sheep. Due to its costs and modest equipment demands, blood protein polymorphism can be used as a rapid tool to assess genetic diversity and prioritize breeds to be analysed by microsatellite DNA markers. (author)markers. (author)
Full Text Available The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow, and largely attributable to the cross-pollination and self-incompatibility reproductive system. A STRUCTURE (model-based program analysis revealed that the 21 populations can be divided into two main groups, mainly based on geographic differences and genetic exchanges. The entire wild Siberia apricot population in China could be divided into two subgroups, including 107 accessions in subgroup (SG 1 and 147 accessions in SG 2. A Mantel test revealed a significant positive correlation between genetic and geographic distance matrices, and there was a very significant positive correlation among three marker datasets. Overall, we recommend a combination of conservation measures, with ex situ and in situ conservation that includes the construction of a core germplasm repository and the implement of in situ conservation for populations HR, MY, and ZY.
We explored possible links between vector activity and genetic diversity in introduced populations of Limnoperna fortunei by characterizing the genetic structure in native and introduced ranges in Asia and South America. We surveyed 24 populations: ten in Asia and 14 in South America using the mitochondrial cytochrome c oxidase subunit I (COI) gene, as well as eight polymorphic microsatellite markers. We performed population genetics and phylogenetic analyses to investigate population genetic structure across native and introduced regions. Introduced populations in Asia exhibit higher genetic diversity (H(E)?=?0.667-0.746) than those in South America (H(E)?=??0.519-0.575), suggesting higher introduction effort for the former populations. We observed pronounced geographical structuring in introduced regions, as indicated by both mitochondrial and nuclear markers based on multiple genetic analyses including pairwise ?(ST), F(ST), bayesian clustering method, and three-dimensional factorial correspondence analyses. Pairwise F(ST) values within both Asia (F(ST)?=?0.017-0.126, P?=?0.000-0.009) and South America (F(ST)?=0.004-0.107, P?=?0.000-0.721) were lower than those between continents (F(ST)?=?0.180-0.319, P?=?0.000). Fine-scale genetic structuring was also apparent among introduced populations in both Asia and South America, suggesting either multiple introductions of distinct propagules or strong post-introduction selection and demographic stochasticity. Higher genetic diversity in Asia as compared to South America is likely due to more frequent propagule transfers associated with higher shipping activities between source and donor regions within Asia. This study suggests that the intensity of human-mediated introduction vectors influences patterns of genetic diversity in non-indigenous species. PMID:23533614
Ghabooli, Sara; Zhan, Aibin; Sardiña, Paula; Paolucci, Esteban; Sylvester, Francisco; Perepelizin, Pablo V; Briski, Elizabeta; Cristescu, Melania E; MacIsaac, Hugh J
The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus. PMID:21735103
Hu, Jihong; Pan, Lei; Liu, Honggao; Wang, Shuzhen; Wu, Zhihua; Ke, Weidong; Ding, Yi
Genetic diversity and reproductive mode can control whether an introduced species becomes invasive. Here we use genetic tools to compare the non-native, invasive Phragmites australis to its native conspecific, P. australis subsp. americanus, in wetlands of Utah and southern Idaho. We found striking differences in genetic structuring, population diversity, and mode of reproduction between the two lineages. Non-native P. australis exhibited substantially more genetic homogeneity among populatio...
Kettenring, Karin M.; Mock, Karen E.
Full Text Available The present research evaluated the diversity of a number of Iranian pomegranate cultivars using fruit morphological characteristics and AFLP markers. Thirty-one pomegranate cultivars were collected from Yazd Pomegranate Collection in Iran to study their diversity. Seven AFLP primer combinations were used to amplify a total of 112 polymorphic fragments (47.26%. By use of AFLPs, a low genetic diversity level was detected among cultivars. The relationship between fruit characteristics was analyzed using the principal component analysis (PCA. The cluster analysis based on both fruit characteristics and AFLP data indicated that cultivars were not grouped according to their geographic origins. Moreover, the correlation between the diversity matrix based on fruit characteristics and Dice’s genetic similarity coefficient was insignificant (r=0.06. The results obtained from this study can improve the conservation and management of pomegranate germplasm resources and could be helpful in optimizing breeding programs.
Cellular signaling networks have evolved to enable swift and accurate responses, even in the face of genetic or environmental perturbation. Thus, genetic screens may not identify all the genes that regulate different biological processes. Moreover, although classical screening approaches have succeeded in providing parts lists of the essential components of signaling networks, they typically do not provide much insight into the hierarchical and functional relations that exist among these components. We describe a high-throughput screen in which we used RNA interference to systematically inhibit two genes simultaneously in 17,724 combinations to identify regulators of Drosophila JUN NH(2)-terminal kinase (JNK). Using both genetic and phosphoproteomics data, we then implemented an integrative network algorithm to construct a JNK phosphorylation network, which provides structural and mechanistic insights into the systems architecture of JNK signaling.
Bakal, Chris; Linding, Rune
Full Text Available Genetic variability of 15 sets of Plantago ovata Forsk. studied using 11 arbitrary oligonucleotide primers. Among the 90 DNAfragments produced 71 fragments were found to be polymorphic. The mean number of polymorphic bands per primer among 15Plantago ovata genotypes was 6.45 . The higher polymorphism (90.00 % was exhibited by primer OPF-17, while the lowerpolymorphism (60.00 % was detected by OPF-2. The genetic similarity matrix from RAPD data for 15 genotypes was calculatedbased on Jaccard’s coefficients of similarity ranged from 0.45 to 0.80. UPGMA cluster analysis reveals that the 15 genotypeswere clustered in to three clusters. Genetically distinct genotypes identified using RAPD markers could be potential sources ofgermplasm for Isabgol improvement.
Ashish G Vala1*, R.S.Fougat1 and G.C.Jadeja
Conventionally, crop improvement strategies rely not only on the availability of heritable genetic variations within utilisable genetic backgrounds but also on the transferability of the traits they control through hybridizations between the parental stocks. Procedures for producing hybrids of sexually reproducing plants are routine while for vegetatively propagated plants, hybridizations are usually impractical. The improvement of crops that lack botanical seeds necessitate therefore alternative strategies for generating and utilizing genetic variations. Induced mutagenesis generates allelic variants of genes that modulate the expression of traits. Some of the major drawbacks to the widespread use of induced mutations for vegetatively propagated plants include the difficulties of heterozygosity of the genetic backgrounds; the incidence of chimeras; and the confounding effects of linkage drags in putative mutants. In general, the inherent inefficiencies of the economies of time and space associated with induced mutagenesis are further exacerbated in vegetatively propagated crops mostly on account of the need for continual propagation. We highlight the mitigating roles on these drawbacks of the judicious integration of validated biotechnologies and other high throughput forward genetics assays in induced mutagenesis pipelines. Using cassava and banana as models, we demonstrate the use of cellular and tissue biology to achieve homozygosity, minimise or eliminate chimeraomozygosity, minimise or eliminate chimeras, and significantly shorten the duration of the generation of mutants. Additionally, the use of these biotechnologies to attain significantly reduced propagation footprints while evaluating putative mutants without compromising population size is also presented. We also posit that molecular biology approaches, especially reverse genetics and transcriptome assays, contributes significantly to enhancing the efficiency levels of the induced mutagenesis processes. The implications for crop improvement and functional genomics via the concerted application of biotechnologies in the generation, identification, and the tagging of mutation events in the genomes of vegetatively propagated crops are also discussed. (author)
Conventionally, crop improvement strategies rely not only on the availability of heritable genetic variations within utilizable genetic backgrounds, but also on the transferability of the traits they control through hybridizations between the parental stocks. Procedures for producing hybrids of sexually reproducing plants are routine, while for vegetatively propagated plants, hybridizations are usually impractical. Therefore, the improvement of crops that lack botanical seeds necessitates alternative strategies for generating and utilizing genetic variations. Induced mutagenesis generates allelic variants of genes that modulate the expression of traits. Some of the major drawbacks to the widespread use of induced mutations for vegetatively propagated plants include the difficulties of heterozygosity of the genetic backgrounds, the incidence of chimeras and the confounding effects of linkage drags in putative mutants. In general, the inherent inefficiencies of time and space economies associated with induced mutagenesis are further exacerbated in vegetatively propagated crops mostly on account of the need for continual propagation. We highlight the mitigating roles on these drawbacks of judicious integration of validated biotechnologies and other high throughput forward genetics assays in induced mutagenesis pipelines. Using cassava and banana as models, we demonstrate the use of cell and tissue biology to achieve homozygosity, minimize or eliminate chimeras, and signi minimize or eliminate chimeras, and significantly shorten the duration of the generation of mutants. Additionally, use of these biotechnologies to attain significantly reduced propagation footprints while evaluating putative mutants without compromising population size is also presented. We also posit that molecular biology approaches, especially reverse genetics and transcriptome assays, contribute significantly to enhancing the efficiency levels of the induced mutagenesis processes. The implications for crop improvement and functional genomics via the concerted application of biotechnologies in the generation, identification, and tagging of mutation events in the genomes of vegetatively propagated crops are also discussed. (author)
Two breeds - Ouled-Djellal and Hamra (85 animals) - were genotyped for 12 microsatellites using PCR and sequencing. Allele number and frequency were calculated, and 141 different alleles were found for these microsatellites, reflecting high genetic variability within these breeds. This study is being extended to other Algerian breeds to estimate variability and genetic distances between them. In parallel, blood samples from the various breeds are being collected to build up a DNA bank. The results should support establishment of a strategy to promote the use and development of locally adapted sheep resources. (author)
The life history traits of a clonal plant species, such as growth form and seedling recruitment pattern, influence the clonal diversity and structure within populations. Using Random Amplified Polymorphic DNA markers, we investigated the variation in clonal diversity and in spatial structure of clones in Vaccinium myrtillus populations from different habitats (mineral heath, peaty heath and beech grove). The partitioning of the genetic variability within and between populations was also studi...
Albert, T.; Raspe?, Olivier; Jacquemart, Anne-laure
Genetic divergence is an efficient tool for the selection of parents used in hybridization programme. In the present study,fifty three rice genotypes consisting of high yielding rice varieties/ cultures and IRRI germplasm lines were raised at RiceResearch Station, Tirur during Sornavari, 2009 to identify diverse genotypes. They were evaluated for eight yield and yieldattributing characters using D2 analysis, to study the diversity pattern among the genotypes. Based on the analysis, thegenotyp...
S Banumathy, R. Manimaran
Viral emergence can result from the adaptation of endemic pathogens to new or altered host environments, a process that is strongly influenced by the underlying sequence diversity. To determine the extent and structure of intrahost genetic diversity in a recently emerged single-stranded DNA virus, we analyzed viral population structures during natural infections of animals with canine parvovirus (CPV) or its ancestor, feline panleukopenia virus (FPV). We compared infections that occurred shor...
Hoelzer, Karin; Shackelton, Laura A.; Holmes, Edward C.; Parrish, Colin R.
The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles’ diversity represents an important criterion which could be later applied in planning for future forest management...
Garci?a Gil, Mari?a Rosario; Sestras, Radu E.; Floran, Valentina
The extent of knowledge regarding the diversity of globally distributed Ehrlichia canis strains has been limited to information gained from a few evolutionarily conserved genes. In this study, E. canis strains from the United States (strain Jake [US]), Brazil (strain São Paulo [BR]), and Israel (strain 611 [IS] and Ranana [IS-R]) were used to examine the antigenic and genetic diversities of four well-characterized major immunoreactive protein genes/proteins. gp36 and gp200 were the most dive...
Zhang, Xiaofeng; Luo, Tian; Keysary, Avi; Baneth, Gad; Miyashiro, Simone; Strenger, Carmela; Waner, Trevor; Mcbride, Jere W.
A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 lan...
Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh
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 suggest a novel macro-ecological pattern termed the species-genetic diversity correlation. We tested whether this prediction holds for areas affected by recent habitat disturbance using butterfly communities in east Kalimantan, Indonesia. Here, we show that both strong spatial and temporal correlations exist between species and allelic richness across rainforest habitats affected by El Niño Southern Oscillation-induced disturbance. Coupled with evidence that changes in species richness are a direct result of local extirpation and lower recruitment, these data suggest that forces governing variation at the two levels operate over parallel and short timescales, with implications for biodiversity recovery following disturbance. Remnant communities may be doubly affected, with reductions in species richness being associated with reductions in genetic diversity within remnant species. PMID:16958896
Cleary, Daniel F R; Fauvelot, Cécile; Genner, Martin J; Menken, Steph B J; Mooers, Arne Ø
Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by genetic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic behaviours (grooming and hygienic behaviour) of workers from genetically homogeneous and diverse colonies after exposure of their brood to the entomopathogenic fungus Metarhizium anisopliae. While workers from diverse colonies performed intensive allogrooming and quickly removed larvae covered with live fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest that reduced genetic diversity compromises the ability of Cardiocondyla colonies to quickly detect or react to the presence of pathogenic fungal spores before an infection is established, thereby affecting the dynamics of social immunity in the colony.
Ugelvig, Line V; Kronauer, Daniel Jan Christoph
In this essay we explore questions on how to increase the visibility and utility of genetic information for biodiversity managers and policy makers. This is discussed in the light of Aichi CBD Target 13, which for the first time impels signatories to minimise genetic erosion and safeguard genetic diversity. Drawing on qualitative results from a questionnaire sent to European conservation professionals by the ConGRESS Framework 7 Support Action (http://www.congressgenetics.eu), we summarise our preliminary findings on the attitudes and experiences of European conservation professionals in using genetics. We then discuss the implications of these findings for academics involved in conservation genetics and suggest that a much closer partnership between academic conservation geneticists and conservation practitioners is necessary if the full potential of genetic tools in conservation is to be realised. © 2013 Springer Science+Business Media Dordrecht.
Hoban, S.M.; Hauffe, H.C.
Full Text Available SciELO Brazil | Language: English Abstract in english Qualitative morphological and amplified fragment length polymorphism (AFLP) markers were compared for assessment of genetic diversity. Nine qualitative morphological traits were recorded to compare genetic relationships among 17 sorghum accessions with information derived from six AFLP primer combin [...] ations analysis. The mean morphological genetic similarity was lower in comparison to similarity computed using AFLP markers. Genetic similarity measured by AFLP markers was similar within the Ethiopian and South African material, as well as between South African and Ethiopian material. Morphological similarity was much higher in the Ethiopian material than in the South African material, indicating that the genotypes were related. The two techniques described genetic variability in different ways. Dendrogram generated from the morphological data matrix separated accession 216737 as being genetically distinct from the rest of the accessions. Accessions M101 and 97MW6127 were the most dissimilar accessions based on AFLP data.
Abe Shegro, Gerrano; Maryke Tine, Labuschagne; Angeline, van Biljon; Nemera Geleta, Shargie.
Many species exist as metapopulations in balance between local population extinction and recolonization, processes that may strongly affect the distribution of neutral genetic diversity within demes and in the metapopulation as a whole. In this paper we use both the infinite-alleles and the infinite-sites models to reframe Slatkin's propagule-pool and migrant-pool models in terms of mean within-deme and among-deme genetic diversity; the infinite-sites model is particularly relevant to DNA seq...
Pannell, Jr; Charlesworth, B.
Full Text Available The genetic diversity among seven Xanthomonas isolates representing four species was assessed using RAPD and ISSR PCR-based techniques. Both techniques revealed high degrees of polymorphisms among the studied isolates. A cluster dendrogram based on the combined data of RAPD and ISSR showed that genetic diversity exists in local isolates of Xanthomonas. In terms of percentage similarity values, the genomic variation was found to be in the range of 29.29% - 100% among the isolates. X. campestris (Mangifera indica remained unclustered in cluster dendrogram and revealed a unique genomic profile compared to other isolates used in this study.
Full Text Available SciELO Chile | Language: English Abstract in english This study was conducted to reveal genetic diversity among 100 Osmanthus fragrans cultivars using amplified fragment length polymorphism (AFLP) markers. Eight AFLP primer combinations produced a total of 443 polymorphic fragments with an average of 64 per primer combination. The percentage of polymo [...] rphic bands (86.81%), the resolving power (Rp) (32.71) and the PIC values (0.331) showed the efficiency of used primer combinations. The revealed AFLP makers were effective in distinguishing all the cultivars considered. Cluster analysis were performed to assess patterns of diversity among cultivars and showed the abundant genetic diversity. The overall distribution pattern of molecular variation suggested that 93.33% of the total genetic variance was within the identified groups and 6.67% of the genetic variation was among the identified groups. Our results showed that AFLP markers are useful for Osmanthus fragrans germplasm discrimination as well as for investigation of genetic diversity and variation. The information will facilitate germplasm identi?cation, conservation and new cultivar development.
Wang Jun, Yuan; Yuan Ji, Han; Mei Fang, Dong; Fu De, Shang.
Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security. PMID:25468001
Alam, M Amirul; Juraimi, Abdul Shukor; Rafii, Mohd Yusop; Hamid, Azizah Abdul; Arolu, Ibrahim Wasiu; Abdul Latif, M
Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki) that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations. PMID:24358194
Díez-del-Molino, David; Carmona-Catot, Gerard; Araguas, Rosa-Maria; Vidal, Oriol; Sanz, Nuria; García-Berthou, Emili; García-Marín, Jose-Luis
Landraces and close related species of hexaploid wheat (Triticum aestivum L.) offer a vast reservoir of genetic resources for wheat improvement to production on abiotic stressed soils. In order to utilize the wheat landrace and close relative gene pools, the evaluation of wheat landrace and close r...
Our knowledge of genetic variation at the nucleotide sequence level of Autographa californica multiple nucleopolyhedrovirus (AcMNPV; Baculoviridae: Alphabaculovirus) derives from complete genome sequences of the C6 clonal isolate of AcMNPV and the R1 and CL3 clonal isolates of AcMNPV variants Rachip...
Full Text Available Many viruses, including the clinically relevant RNA viruses HIV and HCV, exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different next-generation sequencing platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of next-generation sequencing to estimate viral diversity.
The pro-inflammatory cytokine tumour necrosis factor alpha (TNF-?) is associated with malaria virulence (disease severity) in both rodents and humans. We are interested in whether parasite genetic diversity influences TNF-mediated effects on malaria virulence. Here, primary infections with genetically distinct Plasmodium chabaudi chabaudi (P.c.c.) clones varied in the virulence and cytokine responses induced in female C57BL/6 mice. Even when parasitaemia was controlled for, a greater day 7 T...
Long, Gra?inne Helen; Chan, Brian; Allen, Judith; Read, Andrew F.; Graham, Andrea
Common bean (Phaseolus vulgaris L.) is an important export crop in Kyrgyzstan. The aim of this study was to assess the extent of genetic diversity, determine the population structure, and relate to the main gene pools grown in Kyrgyzstan. Twenty-eight common bean accessions (including five Kyrgyz cultivars, and main references from the Mesoamerica and South America) were evaluated with microsatellites. Nine polymorphic microsatellites were used to estimate genetic di...
Sergey Hegay; Mulatu Geleta; Tomas Bryngelsson; Larisa Gustavsson; Helena Persson Hovmalm; Rodomiro Ortiz
At the present study, the potential of micro satellite markers to assess the extent of genetic variability in Cuban traditional rice varieties was proved. The work was aimed at identifying alternative genetic diversity pools in this material in comparison to the most important commercial cultivars used in Cuban rice breeding program. For this, 52 traditional accessions, eleven cultivars representing the most planted Cuban material during the last decades and two parent cultivars were studied
The objective of this study was to characterize the genetic diversity within a Passiflora collection by PCR-RAPD markers. Genetic analysis was performed in 70 accessions, representing 11 species of the genus Passiflora. The use of only five primers produced 136 reproducible polymorphic bands. The hierarchical classification showed high levels of dissimilarities between and within the species studied. A clear separation was obtained among species and accessions of P. edulis and P. edulis f. fl...
Maria Lúcia Crochemore; Hugo Bruno Correa Molinari; Luiz Gonzaga Esteves Vieira
Quality production of the shrimp Penaeus monodon in hatchery operations depends heavily on the evaluation of genetic diversity and population structure of brood stocks. Mitochondrial DNA (mtDNA) sequences have been widely used to study genetic variability and relationships in many crustacean groups, and these same markers may be incorporated into evaluation studies of shrimp broods and populations. For this purpose we looked at variation in mitochondrial D-loop sequences as an indicator of ge...
Khedkar, Gulab Dattarao; Reddy, A. Chandrashekar; Ron, Tetszuan Benny; Haymer, David
Abstract Background The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae) is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate. Results We focused on this genetic...
Chen Charlotte; Hj, Barfuss Michael; Pröschold Thomas; Schagerl Michael
This work aimed to evaluate the symbiotic compatibility and nodulation efficiency of rhizobia isolated from Desmodium incanum, Lotus corniculatus, L. subbiflorus, L. uliginosus and L. glaber plants by cross-inoculation. Twelve reference strains and 21 native isolates of rhizobia were genetically analyzed by the BOX-PCR technique, which showed a high genetic diversity among the rhizobia studied. The isolates were also characterized based on their production of indolic compounds and siderophore...
Granada, Camille E.; Strochein, Marcos; Vargas, Luciano K.; Bruxel, Manuela; Sa?, Enilson Luiz Saccol; Passaglia, Luciane M. P.
Correlations between the genetic diversity of Leishmania infantum (syn. L. chagasi) isolates and their respective geographic origins support the theoretic assumption that visceral leishmaniasis probably originated in the Old World. Because dogs are widely considered to be the main reservoir of this disease, the present study aimed to investigate the degree of genetic divergence among 44 leishmanial canine isolates from two Brazilian cities, Jequié and Campo Grande, located approximately 2,02...
Da S Batista, Lui?s Fa?bio; Segatto, Marcela; Guedes, Carlos Eduardo S.; Sousa, Rosana S.; Rodrigues, Cleusa A. T.; Brazuna, Ju?lia Cristina M.; Silva, Joselli S.; Santos, Silvana O.; Larangeira, Daniela; Macedo, Andre?a Mara; Schriefer, Albert; Veras, Patri?cia S. T.
Among endosymbionts, Wolbachia pipientis is the most studied reproductive parasite. This parasite also induces the most diverse effects on its hosts. By manipulating host reproduction, Wolbachia is therefore expected to affect the host genetic structuration. Armadillidium vulgare (Isopod Crustacean) is known to host two feminizing Wolbachia strains (wVulC and wVulM), as well as another unidentified feminizing genetic factor (f). This work shows the discovery of a third Wolbachia strain that i...
Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated popu...
Navascue?s, M.; Emerson, B. C.
The genetic diversity of planktonic eukaryotic microorganisms (size range 3–40 µm) inhabiting 11 alpine lakes of the Central Pyrenees (Spain) was analysed by cloning and sequencing of the 18S rRNA gene. The selected lakes covered a wide range of environmental conditions representative of the regional landscape heterogeneity. Overall, we obtained 953 sequences (averaged length 750 bp) that were grouped in 343 representative OTUs (98% identity). The genetic richness was high, and the 18S rRN...
Triado?-margarit, Xavier; Casamayor, Emilio O.
Phytophthora colocasiae that causes taro leaf blight is one of the most devastating diseases of taro which is widely distributed in India. Inter and intra-specific genetic diversity among P. colocasiae isolates collected from same field was assessed using amplified fragment length polymorphism (AFLP) marker. Seven primer pairs produced 431 markers, of which 428 (99.2 %) were polymorphic. Considerable genetic variability was displayed by the isolates. The average value of the number of observ...
Nath, Vishnu Sukumari; Senthil, Muthukrishnan; Hegde, Vinayaka Mahabaleswar; Jeeva, Muthulekshmi Lajapathy; Misra, Raj Shekhar; Veena, Syamala Swayamvaran; Raj, Mithun
Studying genetic diversity is important because a decrease in genetic variability might result in a reduction of the plasticity of the crops to respond to changes in climate, pathogen populations, or agricultural practices. In this study, 72 Sardari wheat (Triticum aestivum L.) ecotypes were analyzed by AFLP markers and 17 phenotypic characters. Three pairs of EcoRI/MseI primer combinations produced 1582 polymorphic bands (with mean percentage of polymorphic 73.92%). Cluster analysis using Ja...
Siosemardeh, A.; Zh, Osamny
The genetic structure and temporal patterns of genetic diversity in a population of Burkholderia (Pseudomonas) cepacia, isolated from a southeastern blackwater stream, were investigated by multilocus enzyme electrophoresis. Allelic variation in seven structural gene loci was monitored at a single stream location at 0, 6, 12, and 24 h and at 2, 4, 8, 16, and 32 days. Over the length of the study, 217 isolates were collected, from which 65 unique electrophoretic types (ETs) were identified. Mos...
Wise, M. G.; Mcarthur, J. V.; Wheat, C.; Shimkets, L. J.
The extent and patterns of genetic diversity