Integrated transcriptomic and metabolomic analysis reveals light-induced modulation of anthocyanin biosynthesis in Chinese bayberry (<i>Myrica rubra</i>)

Chinese bayberry (<italic>Myrica rubra</italic>) is a subtropical fruit rich in anthocyanins, which are significantly regulated by light during ripening. This study employed integrated transcriptomic and metabolomic analyses to investigate the effects of light exposure on fruit quality and anthocyanin synthesis using various light-transmitting bag treatments. A greenhouse experiment demonstrated that no-transmitting bags (HQ) treatment during early fruit development significantly reduced coloration and quality indicators, including sucrose (55.3%), glucose (59.5%), fructose (37.5%), malic acid (36.6), oxalic acid (46.5), total flavonoids (60.1%), vitamin C (93.0%), and total anthocyanins (90.8%), while increasing acidity as compared to transmitting bags (WQ) treatment. Transcriptomic analysis revealed that expression levels of flavonoid synthesis genes were significantly reduced under light conditions. The expression of <italic>LDOX</italic> (Leucoanthocyanidin dioxygenase) gene was notably higher in WQ treatment, potentially contributing to bayberry fruit coloration. Metabolomic analysis identified 44 differential metabolites related to anthocyanin synthesis, with proanthocyanidins, delphinidin-3-O-galactoside, pelargonidin glucoside, and paeonidin glucoside levels significantly higher in WQ treatment compared to HQ. Furthermore, the integration of transcriptomic and metabolomic data identified the transcription factor <italic>HY5</italic> as a key regulator in light-mediated anthocyanin accumulation. Overall, this study provides novel insights into the molecular mechanisms underlying light-regulated pigmentation in Chinese bayberry fruits. The findings contribute to understanding fruit quality development during ripening and offer a scientific basis for enhancing fruit quality and refining cultivation techniques in Chinese bayberry and similar fruit species.