Genome-Wide Identification and Abiotic Stress-Responsive Expression Analysis of the SOS1 Gene Family in Gossypium hirsutum L.

The Salt Overly Sensitive 1 (SOS1) gene family encodes plasma membrane Na+/H+ antiporters essential for ionic homeostasis and salt tolerance in plants. Here, we performed a comprehensive genome-wide characterization of SOS1 genes in allotetraploid cotton (Gossypium hirsutum L.). Fifteen GhSOS1 genes were identified and found unevenly distributed across the A and D subgenomes, indicating that segmental duplication, rather than tandem duplication, was the major driver of family expansion. Phylogenetic analysis resolved four well-supported clades, revealing deep conservation with dicot homologs from Arabidopsis thaliana, Solanum species, and Vigna trilobata, alongside cotton-specific diversification. Ka/Ks ratios indicated strong purifying selection with limited adaptive divergence. Conserved Na+/H+ exchanger domains and membrane-spanning architectures were maintained, whereas motif and promoter variation suggested functional specialization. Structural modeling confirmed typical multi-helical antiporter topology but revealed the absence of a cytoplasmic regulatory domain, implying alternative modes of regulation, possibly via oxidative stress–response components such as RCD1. Promoter analysis uncovered multiple stress- and hormone-responsive cis-elements, and expression profiling identified GhSOS1-5 and GhSOS1-11 as strongly induced by salt and drought stress. Collectively, these findings highlight the evolutionary retention, structural conservation, and regulatory diversification of GhSOS1 genes, establishing a foundation for improving abiotic stress resilience in cotton.