The JA signaling pathway modulates fruit branch internode development in Gossypium hirsutum L.: Insights from multi-omics investigations

The morphology of upland cotton ( Gossypium hirsutum L . ) fruit branches critically determines the architecture and photosynthetic capacity of cotton plants, as well as the adaptability to planting patterns and mechanical harvesting. While key genes involved in nulliplex branching have been identified in cotton, the molecular mechanisms underlying the development of various fruit branch types in upland cotton remain largely uncharacterized. Based on phenotypic identification and cytological measurement, this study integrated hormone profiling and transcriptomic analyses of four upland cotton varieties exhibiting varying lengths of the first internode of fruit branches. The results revealed that the loose internode phenotype arises from enhanced longitudinal growth of epidermal and xylem cells. In the short fruit branch internode group, jasmonic acid (JA) and salicylic acid (SA) accumulated significantly. Among the 954 differentially expressed genes (DEGs) between varieties with long and short internode lengths, 53 genes related to shoot apical meristem (SAM) development, the JA signaling pathway, and flowering regulation were predominantly upregulated in the short-internode group, imply a possible synergistic mechanism underlying the negative regulation of fruiting branch internode elongation. DEGs were predominantly enriched in hormone-related signaling pathways, with a strong emphasis on jasmonate signaling. Notably, members of the JAZ ( TIFY family) gene showed a strong correlation with internode length and hormone content. Silencing a JAZ gene TIFY11B ( GH_A05G1405 ) in short-internode cotton resulted in elongated internodes. The exploration offers novel insights into the molecular mechanisms underlying the internodes development of cotton fruiting branch from the perspective of hormone signal transduction. • The key genes involved in the internode development of fruit branches were identified through multi-omics investigations. • The accumulation of salicylic acid and jasmonic acid was negatively correlated with internode length. • Silencing the TIFY gene leads to an increase in the internode length of fruit branches. • The jasmonic acid pathway may play a crucial role in regulating the development of internodes in cotton fruit branches.