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.

PDF Restricted to ICRISAT researchers only

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
Author Affiliation:	International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India
Subjects:	Crop Improvement > Genetics/Genomics Crop Improvement > Plant Breeding
Divisions:	General
Depositing User:	Mr B Krishnamurthy
Date Deposited:	08 Mar 2011 22:38
Last Modified:	08 Mar 2011 22:38
URI:	http://eprints.icrisat.ac.in/id/eprint/1611

Actions (login required)

View Item