Development of highly polymorphic SSR markers for chickpea (Cicer arietinum L.) and their use in parental polymorphism

Simple sequence repeat (SSR) or microsatellite marker is currently the most preferred molecular marker system owing to their highly desirable properties viz., abundance, hyper-variability, and suitability for high-throughput analysis. Development of SSR markers using molecular methods is time consuming, laborious, and expensive. Use of computational approaches to mine ever-increasing sequences such as expressed sequence tags (ESTs) and genomic DNA sequences available in public databases permits rapid and economical discovery of SSRs. Because the number of SSR markers currently available in chickpea is very limited, the aim of this study was to develop and characterize more SSR markers. Twenty one hundred DNA sequences of chickpea were searched for SSRs and analyzed for the design of PCR primers amplifying the SSR reach regions. Di-nucleotide repeats were found to be the most abundant followed by tri-or mono-nucleotide repeats. The motifs AIT, GA/AG/CT/AC/TC/CA/TA, and CAA/TCT/AGA/CAG/TTG/ATT were the predominant mono-, di-, and tri-nucleotide SSRs, respectively. A subset of 64 primer pairs flanking SSR loci was used for screening polymorphism between two chickpea cultivars BG 256 and WR 315, which are parents of a Fusarium wilt mapping populations. Of them, 45 SSR markers (70.3%) were polymorphic between these two parents.