Comprehensive Transcriptome Analysis to Identify Heat Stress Responsive Genes in Chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.), an important legume crop is seriously challenged by abiotic stresses like heat, drought, salinity etc. Of these, heat/high temperature during reproduction is a major factor limiting the yield of chickpea. Development of genomic resources is a pre-requisite to facilitate chickpea breeding with enhanced heat tolerance. In this context, RNA-Seq was performed on vegetative (leaves and roots) and reproductive (leaves, roots and flowers) tissues of six contrasting heat responsive (tolerant - ICCV 92944, ICC 1356, ICC 15614 and sensitive - ICC 5912, ICC 4567, ICC 10685) genotypes. A total of ~504 million reads were generated and aligned against the available comprehensive chickpea transcriptome assembly (CaTA v2). As a result, 44,185 out of 46,369 transcript assembly contigs were covered. A total of 5,649 genes were significantly differentially expressed with ≥2 fold between tolerant and sensitive genotypes. In addition 1,172 novel genes were also found to be differentially expressed. A set of 56 genes belonging to APETALA2/Ethylene Responsive Factor (AP2/ERF) and Heat Shock Protein (HSP) 90 families were found to be differentially expressed and are selected for further validation using quantitative real time PCR. Furthermore, single nucleotide polymorphisms (SNPs)/INDELs were identified by aligning the reads to the reference kabuli (CDC Frontier) genome and >22,456 SNPs/INDELs were identified across the parental genotypes of two mapping populations (ICC15614 × ICC 4567 and ICC 1356 × ICC 4567). In summary, the known and novel differentially expressed genes along with the marker resources identified in this study open new avenues for heat tolerance breeding program in chickpea.