Cotton Metabolism Regulatory Network: unraveling key genes and pathways in fiber development and growth regulation

Cotton (Gossypium hirsutum L.) is one of the world's most important commercial crops. However, the dynamics of metabolite abundance and the potential regulatory networks throughout its life cycle remain poorly understood. In this study, we developed a comprehensive Cotton Metabolism Regulatory Network (CMRN) encompassing various developmental stages, involving 2,138 metabolites and 90,309 genes expressed in upland cotton. By integrating high-resolution spatiotemporal metabolome and transcriptome data, we identified 1,958 differentially accumulated metabolites and 13,597 co-expressed differentially expressed genes between the dwarf mutant pagoda 1 (pag1) and its wild-type counterpart Zhongmiansuo 24 (ZM24). These metabolites and genes were classified into seven clusters based on tissue-specific accumulation patterns and gene expression at different developmental stages. KEGG enrichment analysis revealed significant differential genes and metabolites enrichment in the fatty acid elongation pathway, particularly in fibers. The differential involvement of genes and metabolites in the VLCFA synthesis pathway led to the identification of GhKCS1b_Dt as a key gene. Overexpression of GhKCS1b_Dt significantly promoted fiber elongation, while its silencing dramatically inhibited cotton fiber growth, underscoring its positive regulatory role in fiber elongation. This dataset provides a valuable resource for further research on metabolic pathways and gene regulatory networks, offering new insights for developing future cotton breeding strategies.