GhPMP3-2 positively regulates response to salt stress in upland cotton (Gossypium hirsutum L.)

Cotton is a globally important crop, but its production is critically impaired by salt stress. The PMP3 gene family serves as key regulators in plant adaptation to abiotic stresses. Here, a genome-wide characterization of PMP3 genes in Gossypium hirsutum was performed to dissect their evolutionary patterns and stress-responsive modules. Genome-wide screening detected 12 GhPMP3 genes, with unevenly dispersed across seven chromosomes. Evolutionary analysis clustered these genes into five subfamilies, with conserved exon-intron structures and domains reflecting functional constraints. The expansion of the GhPMP3 family was primarily driven by duplication events, particularly WGD and allotetraploidization, with purifying selection acting on these genes. cis-acting element analysis indicated that GhPMP3s were linked to abiotic stress adaptation. Dynamic expression profiling demonstrated that GhPMP3 genes were induced by multi-stress treatments. Co-expression analysis showed that GhPMP3–2 functioned as a hub node and co-expressed with numerous stress-related genes. Subcellular localization confirmed that GhPMP3–2 was located in the plasma membrane. VIGS experiments demonstrated that silencing GhPMP3–2 reduced cotton salt tolerance (via increased MDA and decreased proline). Taken together, this study comprehensively characterized the GhPMP3 gene family in cotton and identified GhPMP3–2 as a positive regulator of salt tolerance. These findings highlight GhPMP3–2 as a valuable target for breeding salinity-resilient cotton varieties, with practical implications for improving crop performance under salt stress.