Integrative transcriptomic and metabolomic analysis revealed the molecular mechanisms of fiber length difference between the micropylar end and chalazal end of ovule in interspecific hybrid cotton ( Gossypium hirsutum x Gossypium barbadense)

Cotton fiber is an indispensable raw material in the textile industry. Fiber length is an important fiber quality index, and the research on fiber length is also quite abundant. However, on the same ovule, there are only a few studies on the difference in fiber length development between the micropylar end and the chalazal end of the ovule. We elucidate the mechanism of fiber length differences at both ends of the ovule through the phenomics, transcriptome, and metabolome. The results show that 20, 25, and 30 days post anthesis (DPA) are the pivotal stages to causing the difference in fiber length at two ends of the ovules. Through the KEGG annotation of differentially expressed genes (DEGs), it was found that flavonoid biosynthesis, plant hormone signal transduction, and phenylpropanoid biosynthesis are enriched in DEGs, and similar conclusions were drawn in the analysis of differential abundant metabolites (DAMs). The results of in vitro culture of ovules showed that chlorogenic acid in the flavonoid pathway and scopolin downstream of the phenylpropanoid pathway have significant effects on fiber growth. Our research provide insights into the mechanism of cotton fiber elongation.