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Development and characterization of genic SSR-markers in Medicago truncatula and its transferability in leguminous and non-leguminous species

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Title Development and characterization of genic SSR-markers in Medicago truncatula and its transferability in leguminous and non-leguminous species
 
Subject Medicago truncatula
unigene
EST-derived simple sequence repeats (eSSRs)
transferability
 
Description Expressed sequence tag (EST)-derived simple sequence repeat (eSSR) markers are important resources for gene discovery and comparative mapping aimed at crop improvement. In this study, we developed eSSR markers for Medicago truncatula and assessed their cross-species transferability. We detected 36,847 non-redundant sequences ("unigenes") from 198,642 M. truncatula EST sequences. Mining of microsatellites from the 36,847 unigene sequences (representing approximately 25.8 Mb) revealed 14,637 eSSRs in 11,750 SSR-containing ESTs, and primer pairs were successfully designed for 4,636 (39.5%). Of the 14 637 eSSRs, 82.6% were mononucleotide repeats and the rest (in descending order of abundance) were tri-, di-, penta-, and tetranucleotide repeats. When less stringent SSR detection criteria were used, the frequency of dinucleotide repeat motifs increased more than twofold, and the frequencies of di- (11%) and trinucleotide motifs (10.6%) were almost equal. This demonstrates that the eSSR frequency and distribution were related to the choice of search criteria. Forty-one randomly selected primer pairs were validated, and their transferability in three leguminous and three non-leguminous species was assessed. The markers showed a high level of transferability in the leguminous (53%-71%) and non-leguminous (33%-44%) species. The validation studies thus demonstrate the utility of the Medicago eSSRs in assessing genomic relationships in both leguminous and non-leguminous species.
We are grateful to the Director, National Institute of Plant
Genome Research (NIPGR) for providing facilities; to the
Council of Scientific and Industrial Research, Government
of India for providing a Senior Research Fellowship to Dr.Sarika Gupta; and to the Department of Biotechnology,
Government of India for providing financial support.
 
Date 2013-11-20T06:31:34Z
2013-11-20T06:31:34Z
2009
2 July 2009
 
Type Article
 
Identifier Genome, 52(9): 761-771
http://hdl.handle.net/123456789/112
 
Language en
 
Publisher NRC Res Press