Integrated multi-omics analysis reveals distinct molecular features of key stages in cotton fiber development in

Introduction: Cotton fiber development is a critical biological process underlying fiber quality, and its regulation involves multiple molecular layers, including transcription, translation, and metabolism. Methods: To systematically elucidate the molecular basis of fiber development in Results: As fiber development progressed, the numbers of differentially expressed genes, proteins, and accumulated metabolites increased in both cultivars, indicating extensive molecular reprogramming during the later stages of development. Cross-omics comparisons identified plant hormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, cutin, suberin and wax biosynthesis, and ABC transporters as core pathways commonly involved in fiber development. SM11 exhibited stronger enrichment of phenylpropanoid metabolism, cytochrome P450, and MAPK signaling, whereas YM5 showed more pronounced enrichment of ribosome-related processes, fatty acid elongation, and nitrogen metabolism. Proteomic and metabolomic analyses further confirmed substantial differences between the two cultivars in phenylpropanoid and flavonoid metabolism, sugar metabolism, and lipid metabolism. Integrated multi-omics analysis further demonstrated that phenylpropanoid and flavonoid biosynthesis constitute key coordinated modules across the three omics layers. Metabolites such as taxifolin, dihydromyricetin, and sinapaldehyde were closely associated with candidate genes and proteins, together forming an interconnected regulatory network. Discussion: These findings provide mechanistic insights into the molecular regulation of cotton fiber development and identify candidate molecular targets for fiber quality improvement in