Candidate gene based SSRs associated with ABA mediated drought response in pigeon pea (Cajanus cajan (L.) Millsp.)

Despite being a drought tolerant crop, pigeonpea undergoes substantial yield losses due to drought stress in rainfed semi-arid zones of India. Since abscisic acid (ABA) plays a major role during drought, understanding the drought responsive mechanisms associated with ABA is important to combat the water scarcity. Many simple sequence repeats (SSRs) available on public databases are not specifically targeted towards ABA mediated drought response of pigeon pea. Hence the current study was undertaken based on the comprehensive literature survey and in silico analysis. We selected twelve candidate gene families associated with ABA mediated drought response in pigeon pea. Using pigeon pea draft genome information, we identified 37 genes from 12 gene families and developed a set of 110 new genic SSR markers associated with ABA mediated drought response. Of these, preliminary testing was carried out using 12 primer pairs, each representing one gene family on 40 diverse genotypes. As the crop maturity is an important trait potentially linked to drought and ABA response, we selected the genotypes based on the variation in crop maturity duration. Out of the 12 primer pairs screened 9 showed polymorphism. The early duration genotypes showed lesser nucleotide variation (NV) compared to medium and late for all the 9 SSR markers associated with their corresponding candidate genes. The current study utilized information from databases like KEGG and NCBI to develop ABA responsive candidate gene based genic SSR markers in pigeon pea. These markers were useful in revealing the polymorphism among the 40 selected pigeon pea genotypes. Further extension of current study is needed using a larger number of genotypes and developed genic SSRs for more comprehensive analysis.