Unveiling Integrative Computational Analysis and Functional Profiling of GhSOS1 gene family in response to dual stresses Drought and Salinity in Gossypium hirsutum L.

Background The global production of upland cotton ( Gossypium hirsutum ) has declined in recent years due to increasing drought and salinity stress. SOS1 gene family plays a key role in maintaining ion homeostasis and enhancing stress resilience. Methods A genome-wide study was conducted to identify SOS1 genes, including analyses of gene structure, motifs, chromosomal distribution, phylogenetic relationships, Ka/Ks ratios, cis-regulatory elements, protein–protein interactions, 3D structures, and phosphorylation sites. Fifteen paralogs of G. hirsutum were identified and functionally characterized. For the validation of in-silico findings, expression of 15 genes was profiled during salt and drought stress by RNA-seq data that was available publicly and finally it led to selection of five highly responsive species. After exposing cotton seedlings to 400mM NaCl and 20% PEG, quantitative Realtime PCR was performed with different time intervals (0h, 3h, 6h, and 12 h). Results The presence of cis-regulatory elements, including ABRE, DRE/CRT, MYB sites, and other transcription factor motifs, further confirmed their stress response role. Ka/Ks analysis indicated strong conservation among gene paralogs, with most under purifying selection. Protein–protein interaction analysis revealed SOS1 association with antiporters, facilitating Na⁺ efflux across the plasma membrane to reduce drought and salinity effects. Prominent transcriptional changes induced by stress was confirmed by qPCR results. The results showed consistency with in-silico predictions by up-regulation of GhSOS1-5 and GhSOS1-11 . Conclusions Collectively, this is a comprehensive study of the SOS1 family in G. hirsutism which highlights its roles in conferring abiotic stress tolerance. These findings will serve as a valuable resource for molecular breeding.