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      Development and Characterization of Polymorphic Genic-SSR Markers in Larix kaempferi

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          Abstract

          New simple sequence repeat (SSR) markers were developed in the Japanese larch ( Larix kaempferi) using unigene sequences for further genetic diversity studies and the genetic improvement of breeding programs. One thousand two handred and thirty five (1235) primer pairs were tested and 165 successfully identified in L. kaempferi. Out of the amplified candidate markers, 145 (90.6%) exhibited polymorphism among 24 individuals of L. kaempferi, with the number of alleles per locus (N a), observed heterozygosity (H o), expected heterozygosity (H e) and polymorphic information content (PIC) averaging at 4.510, 0.487, 0.518 and 0.459, respectively. Cross-species amplification of randomly selection of 30 genic-SSRs among the 145 polymorphic ones showed that 80.0% of the SSRs could be amplified in Larix olgensis, 86.7% could be amplified in Larix principi-rupprechtii and 83.0% could be amplified in Larix gmelinii. High rates of cross-species amplification were observed. The genic-SSRs developed herein would be a valuable resource for genetic analysis of Larix kaempferi and related species, and also have the potential to facilitate the genetic improvement and breeding of larch.

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          Genic microsatellite markers in plants: features and applications.

          Rajeev Varshney, Andreas Graner, Mark E. Sorrells (2005)
          Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.
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            microsatellite analyser(MSA): a platform independent analysis tool for large microsatellite data sets

            Daniel Dieringer, Christian Schlötterer (2003)
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              EST-SSRs as a resource for population genetic analyses.

              Richard Ellis, David J. Burke (2007)
              Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional 'anonymous' SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.
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                Author and article information

                Contributors
                Derek J. McPhee: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Molecules
                Journal ID (iso-abbrev): Molecules
                Journal ID (publisher-id): molecules
                Title: Molecules
                Publisher: MDPI
                ISSN (Electronic): 1420-3049
                Publication date (Electronic): 08 April 2015
                Publication date Collection: April 2015
                Volume: 20
                Issue: 4
                Pages: 6060-6067
                Affiliations
                [1 ]State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Rd., Beijing 100091, China
                [2 ]Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan Rd., Beijing 100091, China; E-Mails: xingbinsd@ 123456163.com (X.-B.C.); xieyunhui33@ 123456163.com (Y.-H.X.)
                Author notes
                [* ] Author to whom correspondence should be addressed; E-Mail: xmsun@ 123456caf.ac.cn ; Tel.: +86-10-6288-9685; Fax: +86-10-6287-2015.
                Article
                Publisher ID: molecules-20-06060
                DOI: 10.3390/molecules20046060
                PMC ID: 6272221
                PubMed ID: 25856058
                SO-VID: 6777d61c-abd0-4544-89d4-11aa47652ec1
                Copyright © © 2015 by the authors.
                License:

                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/).

                History
                Date received : 14 February 2015
                Date accepted : 26 March 2015
                Categories
                Subject: Article

                Keywords: larix kaempferi,unigene sequences,simple sequence repeat (ssr),polymorphism,cross-species amplification
                Data availability:
                Keywords: larix kaempferi, unigene sequences, simple sequence repeat (ssr), polymorphism, cross-species amplification

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