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      Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China

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          Abstract

          Start codon targeted polymorphism (SCoT) analysis was employed to distinguish 37 whipgrass ( Hemarthria compressa L.) clones and assess the genetic diversity and population structure among these genotypes. The informativeness of markers was also estimated using various parameters. Using 25 highly reproducible primer sets, 368 discernible fragments were generated. Of these, 282 (77.21%) were polymorphic. The number of alleles per locus ranged from five to 21, and the genetic variation indices varied. The polymorphism information content (PIC) was 0.358, the Shannon diversity index (H) was 0.534, the marker index (MI) was 4.040, the resolving power (RP) was 6.108, and the genotype index (GI) was 0.782. Genetic similarity coefficients (GS) between the accessions ranged from 0.563 to 0.872, with a mean of 0.685. Their patterns observed in a dendrogram constructed using the unweighted pair group method with arithmetic mean analysis (UPGMA) based on GS largely confirmed the results of principal coordinate analysis (PCoA). PCoA was further confirmed by Bayesian model-based STRUCTURE analysis, which revealed no direct association between genetic relationship and geographical origins as validated by Mantel’s test ( r = 0.2268, p = 0.9999). In addition, high-level genetic variation within geographical groups was significantly greater than that between groups, as determined by Shannon diversity analysis, analysis of molecular variance (AMOVA) and Bayesian analysis. Overall, SCoT analysis is a simple, effective and reliable technique for characterizing and maintaining germplasm collections of whipgrass and related species.

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          Most cited references34

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          Gene flow and the geographic structure of natural populations.

          M Slatkin (1987)
          There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.
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            Isolation of plant DNA from fesh tissue

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              Functional markers in plants.

              Different approaches (including association studies) have recently been adopted for the functional characterization of allelic variation in plants and to identify sequence motifs affecting phenotypic variation. We propose the term 'functional markers' for DNA markers derived from such functionally characterized sequence motifs. Functional markers are superior to random DNA markers such as RFLPs, SSRs and AFLPs owing to complete linkage with trait locus alleles. We outline the definition, development, application and prospects of functional markers.
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                Author and article information

                Contributors
                Role: External Editor
                Journal
                Molecules
                Molecules
                molecules
                Molecules
                MDPI
                1420-3049
                22 December 2014
                December 2014
                : 19
                : 12
                : 21541-21559
                Affiliations
                [1 ]Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: guozhihui-2008@ 123456163.com (Z.-H.G.); linzhuyan@ 123456126.com (K.-X.F.); zhangxq@ 123456sicau.edu.cn (X.-Q.Z.); baishiqie@ 123456yeah.net (S.-Q.B.); pengyanlee@ 123456163.com (Y.P.); huanglinkai@ 123456sicau.edu.cn (L.-K.H.); yanyanhong3588284@ 123456126.com (Y.-H.Y.); lwgrass@ 123456126.com (W.L.)
                [2 ]Sichuan Academy of Grassland Science, Chengdu 611731, China
                [3 ]Chongqing Municipal Institute of Animal Husbandry, Chongqing 400039, China; E-Mail: cq_fy001@ 123456163.com
                Author notes
                [* ]Author to whom correspondence should be addressed; E-Mail: maroar@ 123456126.com ; Tel.: +86-835-288-5369; Fax: +86-835-288-6080.
                Article
                molecules-19-21541
                10.3390/molecules191221541
                6271808
                25532848
                caffb7e6-6d8e-40d6-b657-cb5f5647890c
                © 2014 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/4.0/).

                Categories
                Article

                hemarthria compressa l.,start codon targeted polymorphism (scot),genetic diversity,geographic groups,genetic differentiation

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