Genome-wide transcriptome analysis and physiological variation modulates gene regulatory networks acclimating salinity tolerance in chickpea

•Up-regulation of HKTs, transmembrane transporters played important role in imparting tolerance under salt-stress.•Signal transduction under salt stress was prompt in response to upregulation of TF families, ERF, WRKY, NACs and MYB.•ICCV 10 and JG 11 engaged highly efficient machinery for signal transduction, transport and osmotic homeostasis.•Transcripts associated with metabolic pathways, hormone signalling and cell wall biogenesis were enriched under salt stress.Transcripts associated with crucial metabolic pathways, including hormone signaling, photosynthesis, lipid and carbohydrate metabolism, and cell wall biogenesis were enriched under salt stress.