Genome-Wide Identification and Characterization of the PP2C Gene Family in Gossypium barbadense Reveals Potential Candidates for Breeding Improved Stress Resistance, Fiber Character, and Early Maturing Cotton Varieties

The protein phosphatase 2C (PP2C) gene family plays vital roles in plant growth and stress responses, yet remains inadequately characterized in cotton, particularly in <i>Gossypium barbadense</i> renowned for its superior fiber quality. Here, we identified 152 GbPP2Cs in <i>Gossypium barbadense</i> through genome-wide analysis and comparative genomics with three related cotton species (<i>G. arboreum</i>, <i>G. raimondii</i>, and <i>G. hirsutum</i>), identifying 105, 105, and 204 GbPP2Cs, respectively. GbPP2Cs show uneven chromosomal distribution with notable clustering on A05, evolutionary conservation in gene structure and motif composition, and predominant nuclear/chloroplast localization. Phylogenetic analysis classified them into 15 subfamilies showing conserved evolution. Protein enrichment revealed 15 GbPP2Cs involved in mitogen-activated protein kinase (MAPK) and hormone signaling pathways. Expression profiling revealed distinct members responsive to biotic/abiotic stresses, fiber development stages, and maturity. Notably, we discovered potential pleiotropic regulators including two genes (<i>Gbar_D13G012000</i> and <i>Gbar_A13G012360</i>) co-regulating lint percentage and disease resistance, <i>GbAIP1</i> coordinating fiber length-strength trade-off, and <i>GbPP2C59</i> as a maturity negative candidate. These findings provide valuable genetic resources for cotton improvement.