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

S. Ramadevi
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Patancheru, 502 324
Andhra Pradesh, India
Tel: 91 40 3296161
Fax: 91 40 3241329

* Corresponding author

Keywords: bioinformatics, genetic markers, repeat motifs, simple sequence repeats, SSR.

Present address: # IITA, c/o Lambourn and Co., Carolyn House, 26 Dingwall Road, Croydon, CR9 3EE, United Kingdom.

Among various DNA duplication events, micro-satellites also referred as simple sequence repeats (SSR) are stretches of DNA containing tandem repeating di-, tri-, or tetra-nucleotide units ubiquitously distributed throughout the eukaryotic genomes. They are found to be abundant in plant genomes and are thought to be the major source of genetic variation in quantitative traits. Simple sequence repeats (SSR) or micro-satellites are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding. De novo generation of micro-satellite markers through laboratory-based screening of SSR-enriched genomic libraries is highly time consuming and expensive. The development of micro-satellite markers through these laboratory-based screening of SSR-enriched genomic libraries is highly time consuming and expensive. An alternative in well-studied species where abundant sequence data is already available is to use bioinformatics to screen these databases for sequences that contain SSR. Beyond the cost savings, this also offers the possibility of identifying STMS markers with rare SSR motifs for which it would be uneconomical to enrich through laboratory-based protocols. Finally, even for lesser-studied crops, this approach offers some potential for low cost development for limited number of markers, through the screening of related and allied crop. Nevertheless, markers developed in this way present a valuable resource for subsequent comparison between the model species and the related species

The genomic sequences from the public databases of related model species where abundant sequence data is already available can be screened for the presence of repeat motifs and possible primers which may yield products of 200 bp or above. All the genomic sequences of Medicago from the public domain database were searched and analysed of di-, tri-, and tetra-nucleotide repeats. Of the total of about 156,000 sequences which were searched, 7325 sequences were found to contain repeat motif and may yield SSR, which will yield product sizes of around 200 bp. Of these the most abundantly found repeats were the tri-nucleotide (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.


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