A genome‐wide atlas of small secreted peptides ( SSPs ) in cotton identifies GDRP as a novel peptide hormone‐enhancing drought tolerance via ABA and MAPK signaling

SUMMARY Upland cotton ( Gossypium hirsutum ) and sea‐island cotton ( Gossypium barbadense ) are the two most widely cultivated cotton species, differing in their fiber quality and environmental adaptability. Small secreted peptides (SSPs) are key signaling molecules that regulate plant development and stress responses, yet their genome‐wide diversity and functional roles in cotton remain largely uncharacterized. Here, leveraging high‐quality genome assemblies, we systematically identified 2629 and 2331 SSPs in G. hirsutum and G. barbadense , respectively. Transcriptomic analyses revealed distinct species SSP expression dynamics: Expressed SSPs number declined during fiber and ovule development in G. hirsutum , but increased in G. barbadense , implicating SSPs in the superior fiber traits of the latter. Under abiotic stress, G. hirsutum displayed a predominantly downregulated SSPs profile, whereas G. barbadense maintained a more balanced transcriptional response, suggesting divergent stress adaptation strategies. Among the differentially expressed SSPs, we identified and characterized GDRP ( Gossypium Drought and Salt Resistance Peptide), a novel peptide strongly induced by both drought and salt stress. Exogenous application of GDRP significantly enhanced stress tolerance by reducing oxidative damage, improving water‐use efficiency, and promoting stomatal closure. VIGS (Virus‐Induced Gene Silencing) experiments have demonstrated that GhGDRP6 acts as a positive regulatory factor for drought tolerance. Mechanistically, GDRP activated abscisic acid (ABA) signaling by upregulating GhPYL4 and GhNACs , and repressing GhPP2Cs and GhPIP2;7 , key negative regulators of ABA‐mediated drought responses. Furthermore, GDRP induced the phosphorylation of GhMPK3 and GhMPK6 , two central kinases in the MAPK signaling cascade. Virus‐induced gene silencing of GhMPK3 or GhMPK6 abolished GDRP‐mediated drought tolerance, confirming a MAPK3/6‐dependent mechanism. Collectively, this study provides the first genome‐wide SSP atlas in cotton and uncovers GDRP as a previously uncharacterized peptide that modulates ABA and MAPK signaling to enhance abiotic stress resilience. These findings lay the foundation for peptide‐based crop improvement strategies targeting stress tolerance and yield stability in cotton.