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      Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie ( Boehmeria nivea L. Gaudich.), a premium textile fiber producing species

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          Abstract

          Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie ( Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (G ST = 0.27) and moderate gene flow (N m = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement.

          Highlights

          • Genetic diversity and population structure of ramie ( Boehmeria nivea) were assessed by SCoT markers.

          • SCoT markers revealed high polymorphism and resolving ability in Boehmeria nivea.

          • The wild ramie showed moderate heterozygosity and gene flow with high genetic variation, suggesting unidirectional gene flow.

          • The domesticated population exhibited highest heterozygosity and close association with introduced population.

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          Most cited references32

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          Rapid isolation of high molecular weight plant DNA.

          A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.
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            Ecological consequences of genetic diversity.

            Understanding the ecological consequences of biodiversity is a fundamental challenge. Research on a key component of biodiversity, genetic diversity, has traditionally focused on its importance in evolutionary processes, but classical studies in evolutionary biology, agronomy and conservation biology indicate that genetic diversity might also have important ecological effects. Our review of the literature reveals significant effects of genetic diversity on ecological processes such as primary productivity, population recovery from disturbance, interspecific competition, community structure, and fluxes of energy and nutrients. Thus, genetic diversity can have important ecological consequences at the population, community and ecosystem levels, and in some cases the effects are comparable in magnitude to the effects of species diversity. However, it is not clear how widely these results apply in nature, as studies to date have been biased towards manipulations of plant clonal diversity, and little is known about the relative importance of genetic diversity vs. other factors that influence ecological processes of interest. Future studies should focus not only on documenting the presence of genetic diversity effects but also on identifying underlying mechanisms and predicting when such effects are likely to occur in nature.
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              The population genetics of clonal and partially clonal diploids.

              The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).
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                Author and article information

                Contributors
                Journal
                Meta Gene
                Meta Gene
                Meta Gene
                Elsevier
                2214-5400
                20 February 2015
                February 2015
                20 February 2015
                : 3
                : 62-70
                Affiliations
                [a ]ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
                [b ]ICAR-National Institute of Research on Jute and Allied Fibre Technology, Kolkata 700040, India
                Author notes
                [* ]Corresponding author. pscrijaf@ 123456gmail.com
                Article
                S2214-5400(15)00004-3
                10.1016/j.mgene.2015.01.003
                4349193
                7219b37f-f942-4b81-b40d-2e98c2bf7589
                © 2015 The Authors. Published by Elsevier B.V.

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 20 September 2014
                : 6 January 2015
                : 9 January 2015
                Categories
                Article

                boehmeria nivea,ramie,scot,genetic diversity,amova,population structure,india

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