Allelic Diversity and Association Analysis for Candidate Abiotiic Stress Responsive Genes with Drought Tolerance in Chickpea

Chickpea is an important food legume crop, particularly, for the semi-arid regions including Indian subcontinent. Its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes that are associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, eleven abiotic stress responsive candidate genes were selected on the basis of prior knowledge acquired from mutational, biochemical and linkage analysis of the traits. These 11 genes were subjected to allele specific sequencing across chickpea reference set comprising of 300 genotypes including 211 mini-core collection genotypes. In total, 1.3Mbp sequence data was generated. Multiple sequence alignment revealed 79 SNPs and 41 indels in ten candidate genes while, CAP2 gene was found to be conserved across all genotypes. Among ten candidate genes, maximum number of SNPs (34) were observed in ASR gene, amongst which 22 transitions, 13 transversions and one  tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029, while PIC values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Preliminary association analysis using SNPs identified in these candidate genes and extensive phenotype data identified 6 SNPs in ASR, 3 SNPs in Dehydrin and 3 SNPs in DREB associated with different traits like 100-seed weight, delta carbon, plant height, root surface area, root dry weight, pods per plant and yield. Identified marker trait association after further validation may be useful for enhancing drought tolerance in chickpea through molecular breeding.