Development and assessment of EST-SSR marker for the genetic diversity among tobaccos (Nicotiana tabacum L.)

Development and assessment of EST-SSR marker for the genetic diversity among tobaccos (Nicotiana... Because of the advantages of EST-SSR markers, it has been employed as powerful markers for genetic diversity analysis, comparative mapping and phylogenetic studies. In this study, a total of 429,869 tobacco (Nicotiana tabacum L.) ESTs were downloaded from the public databases, which offers an opportunity to identify SSRs in ESTs by data mining, and 38,165 SSRs were identified from 379,967 uni-ESTs with the frequency of one SSR per 5.52 kb. Mono- and tri-nucleotide repeat motifs were the dominant repeat types, accounting for 40.53 and 34.51% of all SSRs, respectively. After eliminating mononucleotide-containing sequences, 86 pairs of primers were designed to amplify in four tobacco accessions. Only 15 primers (17.44%) showed polymorphism, and then they were further used to assess genetic diversity of 20 tobacco accessions. Unweighted pair-group method with arithmetic average dendrograms (UPGMA) and principal coordinates analysis plots (PCA) revealed genetic differentiation between N. rustica and N. tabacum, and between oriental tobacco and other accessions of N. tabacum. The present study reported the development of EST-SSR markers in tobacco by exploiting EST databases, and confirmed the effective way to develop markers. These EST-SSRs can serve in studies on cultivar identification, genetic diversity analysis, and genetics in tobacco. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Russian Journal of Genetics Springer Journals

Development and assessment of EST-SSR marker for the genetic diversity among tobaccos (Nicotiana tabacum L.)

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Publisher
Pleiades Publishing
Copyright
Copyright © 2015 by Pleiades Publishing, Inc.
Subject
Biomedicine; Human Genetics; Animal Genetics and Genomics; Microbial Genetics and Genomics
ISSN
1022-7954
eISSN
1608-3369
D.O.I.
10.1134/S1022795415020064
Publisher site
See Article on Publisher Site

Abstract

Because of the advantages of EST-SSR markers, it has been employed as powerful markers for genetic diversity analysis, comparative mapping and phylogenetic studies. In this study, a total of 429,869 tobacco (Nicotiana tabacum L.) ESTs were downloaded from the public databases, which offers an opportunity to identify SSRs in ESTs by data mining, and 38,165 SSRs were identified from 379,967 uni-ESTs with the frequency of one SSR per 5.52 kb. Mono- and tri-nucleotide repeat motifs were the dominant repeat types, accounting for 40.53 and 34.51% of all SSRs, respectively. After eliminating mononucleotide-containing sequences, 86 pairs of primers were designed to amplify in four tobacco accessions. Only 15 primers (17.44%) showed polymorphism, and then they were further used to assess genetic diversity of 20 tobacco accessions. Unweighted pair-group method with arithmetic average dendrograms (UPGMA) and principal coordinates analysis plots (PCA) revealed genetic differentiation between N. rustica and N. tabacum, and between oriental tobacco and other accessions of N. tabacum. The present study reported the development of EST-SSR markers in tobacco by exploiting EST databases, and confirmed the effective way to develop markers. These EST-SSRs can serve in studies on cultivar identification, genetic diversity analysis, and genetics in tobacco.

Journal

Russian Journal of GeneticsSpringer Journals

Published: Jul 7, 2015

References

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