Analysis of changes and biosynthesis mechanism of flavonoids in Peel of Coffea Arabica L. during ripening based on metabolome and transcriptome

Coffee peel, a major by-product of coffee processing, holds considerable economic potential. Presently, the majority of scientific research is concentrated on coffee beans, while studies focusing on the coffee peel remain insufficiently explored. In this study, the dynamic changes in flavonoids and associated regulatory genes in the coffee peel were systematically analyzed at four distinct maturity stages using transcriptomic and metabolomic approaches, complemented by the assessment of physical and chemical indicators. A total of 234 flavonoid metabolites were identified in this study, of which 83 exhibited significant differential expression. The key flavonoid metabolites identified during the maturation of coffee peel included morin, prunetin, naringenin, pinobanksin, and phlorizin. Correlation analysis revealed that the genes encoding CHS, CYP73A, and CYP75B1 were significantly positively correlated with most flavonoid metabolites. The study revealed a significant accumulation of flavonoids in coffee peel during the maturation process. Enzymes encoded by genes such as CHS, CYP73A, and CYP75B1 exerted significant positive regulatory effects on most flavonoids in the pathway and could serve as key candidate genes for studying the regulation of flavonoid metabolism during coffee peel development. These findings contribute to enhancing the utilization of coffee by-products in the industry and provide a foundation for future molecular breeding efforts focused on coffee varieties enriched with flavonoids.