In silico development and validation of EST derived new SSR markers for drought tolerance in Cicer arietinum L.

Juhi Bhardwaj; Nilima Kumari; Rebecca Ford; Renu Yadav; Insoo Choi; Rajendra Kumar

Juhi Bhardwaj Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250 110;
Nilima Kumari Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250 110;
Rebecca Ford Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250 110;
Renu Yadav Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250 110;
Insoo Choi Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250 110;
Rajendra Kumar Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250 110;

Keywords: Chickpea, EST, microsatellites, drought tolerance

Abstract

Microsatellites have become a marker of choice in plant genetics and breeding research due to their unilocus, multiallelic and highly reproducible nature. In present study EST sequences isolated from chickpea root under water stress were assessed for the frequency, type and distribution of SSR motifs. Out of the 6400 ESTs (accession no. CDO 38847 to GR 394575), SSR sequences were identified in 348 singleton contigs and from these, 50 flanking primer pairs were designed. Out of these, 41 amplified a marker of the expected size range across nineteen diverse chickpea accessions. 11 of the primer pairs were size polymorphic with an average PIC value of 0.59 across the nineteen genotypes assessed.