Genomic sequence derived simple sequence repeats markers. A case study with medicago spp.

Mahalakshmi, V and Aparna, P and Ramadevi, S and Ortiz, R (2002) Genomic sequence derived simple sequence repeats markers. A case study with medicago spp. Electronic Journal of Biotechnology, 5 (3). pp. 233-242. ISSN 0717-3458

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Abstract

Simple sequence repeats (SSR) or microsatellites are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding. De novo generation of microsatellite markers through laboratory-based screening of SSR-enriched genomic libraries is highly time consuming and expensive. An alternative is to screen the public databases of related model species where abundant sequence data is already available. All the genomic sequences of Medicago from the public domain database were searched and analysed for di, tri and tetra nucleotide repeats. Of the total 156 000 sequences which were searched, 7325 sequences contained repeat motif and may yield SSR which will yield product sizes of around 200 bp. Of these, the most abundantly found repeats were the trinucleotide (5210) group. Except for a very small proportion (436), these link to the gene annotation database at TIGR (http://www.tigr.org). To facilitate further exploration of this resource, a dynamic database with options to search and link to other resources is available at (http://www.icrisat.org/text/research/ grep/homepage/genomics/medssrs1.asp) and on CDs from V.Mahalakshmi@cgiar.org

Item Type:	Article
Divisions:	UNSPECIFIED
CRP:	UNSPECIFIED
Uncontrolled Keywords:	bioinformatics, genetic markers, repeat motifs, simple sequence repeats, SSR
Subjects:	Others > Genetics and Genomics
Depositing User:	Ms K Syamalamba
Date Deposited:	07 Dec 2012 08:27
Last Modified:	07 Feb 2014 05:39
URI:	http://oar.icrisat.org/id/eprint/6285
Official URL:	http://www.ejbiotechnology.info/content/vol5/issue...
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	UNSPECIFIED
Links:	Google Scholar

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