Mining for heat stress responsive genes by RNA-Seq based comprehensive gene expression analyses in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.), an important legume crop, is adversely affected by abiotic stresses such as heat, drought and salinity. Amongst these stresses, heat stress is the main abiotic stress that has an adverse impact on almost all aspects of plant development, growth, reproduction and yield. Development of genomic resources is a pre-requisite to develop heat-tolerant chickpea varieties. In this context, RNA-Seqbased 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 ~514 million reads were generated and alignment of these reads against the available chickpea genome assembly resulted in mapping of 469 (92.9%) million reads. Furthermore, gene expression analysis resulted in identification of 7,670 significantly differentially expressed genes, including 874 novel genes between contrasting genotypes. A set of 56 stress responsive genes belonging to APETALA2/Ethylene Responsive Factor (AP2/ERF), Heat Shock Protein (HSP) and 90 families are selected for further validation using quantitative real time PCR. Moreover >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