Omics-based analysis of Pathogenesis-related 1 (PR-1) gene family in Gossypium spp.

Cotton is a crucial cash crop and a significant pillar of the fiber industry; however, its yield is significantly impacted by various abiotic and biotic stresses, which are further exacerbated by climate change. Therefore, the development of climate-resilient cotton genotypes is essential for sustainable cotton production under changing environmental conditions. This study deals with the PR-1 gene family, whose role in plant defense is to prevent pathogens from entering the plant and contributing to signaling mechanisms. In this comparative analysis, we identified 50 PR-1 genes in the tetraploid cotton species Gossypium hirsutum and Gossypium barbadense , and 32 PR-1 genes in their diploid ancestors, Gossypium arboreum and Gossypium raimondii. This indicates that polyploidization has influenced the evolution of PR-1 genes in cotton. By gene structure, conserved motif, and domain analysis, most PR-1 genes are characterized by a single intron and belong to the conserved CAP superfamily, indicating structural conservation during evolution. Synteny analysis revealed that the D-subgenome has more orthologous gene pairs than the A-subgenome, reflecting asymmetric gene retention. Promoter region analysis identified a high abundance of regulatory, hormone-responsive, and defense-related cis-elements, highlighting the PR-1 gene family's role in mediating responses to biotic and abiotic stresses. Physicochemical and subcellular localization analyses revealed that most PR-1 proteins are present in the extracellular region, and a few are localized in the plasma membrane. Protein-protein interaction (PPI) network analysis identified F4JBK4_ARATH as a dominant hub, suggesting an important role in plant immune signaling. Orthologous analysis indicates both evolutionary conservation and species-specific diversification, underscoring their significant roles in plant defense signaling. Several GhPR1 genes were rapidly induced under NaCl stress, with significantly higher expression levels in salt-tolerant cotton compared to sensitive genotypes. This suggests that tolerant plants activate defense responses more swiftly and effectively, whereas sensitive plants exhibit a delayed stress response.