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Molecules 2015, 20(7), 12469-12480; doi:10.3390/molecules200712469

Development and Characterization of Novel EST-SSRs from Larix gmelinii and Their Cross-Species Transferability

1
Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Key Laboratory of Urban Agriculture (North), Ministry of Agriculture, Beijing 10097, China
2
College of Horticulture Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600, China
3
State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin 150000, China
4
Beijing Key Laboratory of Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing 10081, China
*
Author to whom correspondence should be addressed.
Academic Editor: Derek J. McPhee
Received: 27 March 2015 / Revised: 12 June 2015 / Accepted: 29 June 2015 / Published: 9 July 2015
(This article belongs to the Section Molecular Diversity)
View Full-Text   |   Download PDF [1458 KB, uploaded 9 July 2015]   |  

Abstract

A set of 899 L. gmelinii expression sequence tags (ESTs), available at the National Center of Biotechnology Information (NCBI), was employed to address the feasibility on development of simple sequence repeat (SSR) markers for Larch species. Totally, 634 non-redundant unigenes including 145 contigs and 489 singletons were finally identified and mainly involved in biosynthetic, metabolic processes and response to stress according to BLASTX results, gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) maps. Approximately 11.7% (74) unigenes contained 90 candidate SSRs, which were mainly trinucleotides (29, 32.2%) and dinucleotides (26, 28.9%). A relatively high frequency of SSRs was respectively found in the Open Reading Frame (ORF, about 54.4%) and 5′-untranslated region (5′-UTR, 31.2%), while a low frequency was observed in the 3′-untranslated region (3′-UTR, about 14.4%). Of the 45 novel EST-SSRs markers, nine were found to be polymorphic at two L. gmelinii populations. The number of alleles per locus (Na) ranged from two to four, and the observed (Ho) and expected (He) heterozygosity values were 0.200–0.733 and 0.408–0.604, respectively. The inbreeding coefficients (FIS) for all loci were more than zero except Lg41. Most of these 9EST-SSR markers were transferable to its related species L. kaempferi, L. principis-rupprechtii and L. olgensis. These novel EST-SSRs will be useful for further research on comparative genomics, genetic resources conservation and molecular breeding in larch trees. View Full-Text
Keywords: Larix gmelinii; EST-SSRs; genetic diversity; cross-species transferability Larix gmelinii; EST-SSRs; genetic diversity; cross-species transferability
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Zhang, G.; Sun, Z.; Zhou, D.; Xiong, M.; Wang, X.; Yang, J.; Wei, Z. Development and Characterization of Novel EST-SSRs from Larix gmelinii and Their Cross-Species Transferability. Molecules 2015, 20, 12469-12480.

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