A Dual Perspective on Physio-molecular Insights Points Towards Ion Homeostasis as a Probable Pathway for Salt Tolerance in Pigeonpea [Cajanus Cajan (Millspaugh (L.)].

Salt stress is a major abiotic factor limiting crop productivity and sustainable agriculture globally. It disrupts ionic balance and induces oxidative stress through excessive Na⁺ and Cl⁻ accumulation, leading to programmed cell death. We describe here, a comparative physio-morphological and transcriptome analysis of two contrasting pigeonpea genotypes under salt stress conditions. The study assessed key physio-morphological parameters, including root and shoot length, K⁺ and Na⁺ concentrations, chlorophyll content, membrane stability index (MSI), and relative water content (RWC), revealing more pronounced effects in the salt-sensitive genotype. Transcriptome analysis generated a total of 29 billion raw paired-end reads and identified 11,722 differentially expressed genes, with 5,882 genes upregulated and 5,840 downregulated in the salt-tolerant genotype compared to the salt-sensitive. Among the DEGs, the expression of candidate genes, including calcium uniporter protein 2, ethylene response sensor 1, peroxidase 73, calmodulin-binding protein 60 B, chloride channel protein CLC-d, and K⁺ efflux antiporter 5 was studied using qRT-PCR in control and salt-treated shoot tissues of the salt-tolerant ICP14104 and salt-sensitive ICP12017. The upregulation of CLC-d in ICP14104 suggests its role in Cl⁻ exclusion and salinity tolerance. It may also enhance chlorophyll content under salt stress by reducing ion toxicity. This is further complemented by the strong expression of calcium uniporter protein 2, peroxidase 73, and ethylene response sensor 1, revealing their roles in salt stress regulation in ICP14104 via phytohormone signalling and antioxidant pathways. This regulation might have contributed to stabilizing physiological parameters such as RWC, and MSI in the tolerant genotype under salinity stress.