Genome-Wide Identification and In Silico Characterization of the Salt Overly Sensitive 3/Calcineurin B-like (GhSOS3) Gene Family in Upland Cotton (Gossypium hirsutum L.) and Expression Profiling of Two Members Under Drought, Salt and Heat Stress

Upland cotton (Gossypium hirsutum L.) is a global cash crop cultivated extensively for its high-quality fiber and oil-rich seeds. Several gene families are involved in the regulatory pathways that enable plants to acclimate to adverse abiotic stresses. One such gene family is the Calcineurin B-like (CBL)/Salt Overly Sensitive-3 (SOS3) family of calcium-sensor proteins associated with plant signaling. Although GhSOS3 has previously been associated with salt–alkali stress responses in cotton, a family level genomic characterization of SOS3-like genes in the allotetraploid G. hirsutum genome has not been reported. We performed in silico characterization of the GhSOS3 gene family, including gene architecture, phylogenetic relationships, protein characterization, selection pressure, promoter elements, collinearity, chromosomal position, and protein structure modeling. This analysis identified five putative GhSOS3 genes. The encoded proteins showed conserved EF-hand-related motifs, with differences in gene structure, predicted physicochemical properties, and motif composition. Putative abscisic acid-responsive (ABRE), salicylic acid-responsive (SARE), drought stress-responsive (DSRE) and gibberellin-responsive (GRE) elements predicted in the promoters suggest that the GhSOS3 genes may be transcriptionally responsive to abiotic stress-related signals; however, these predictions require experimental validation. Experimentally, qPCR analysis showed stress- and time-dependent changes in the transcript abundance of GhSOS3-2 and GhSOS3-3 under drought, salt, and heat treatments in three cotton genotypes, indicating differential transcriptional responses to these stress conditions. Collectively, these findings establish a genomic and expression framework for future functional studies of GhSOS3 candidates in calcium-mediated stress responses in cotton.