Comprehensive Heat Transcriptome Analyses Towards Identification of Heat Stress Responsive Genes in Chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.), an important legume crop is adversely affected by abiotic stresses like heat, drought, salinity etc. Of these, heat/high temperature during reproduction is a major limiting factor for chickpea yield. Development of genomic resources is a pre-requisite to develop heat tolerant chickpea varieties. In this context, RNA-Seq based transcriptome analysis 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 alignment against the available comprehensive chickpea transcriptome assembly (CaTA v2) resulted in 44,185 out of 46,369 transcript assembly contigs. 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, >22,456 single nucleotide polymorphisms (SNPs)/INDELs were identified between parental genotypes of two mapping populations (ICC15614 × ICC 4567 and ICC 1356 × ICC 4567). Novel differentially expressed genes along with the marker resources identified in this study should help breeders in developing heat tolerant chickpea varieties in efficient manner.