Integrative transcriptomic and flavonoid metabolomic analysis reveals how bagging inhibits skin coloration in ‘Hongyang’ kiwifruit (Actinidia chinensis)

Bagging is an eco-friendly cultivation practice that improves fruit appearance; however, its effects on kiwifruit skin coloration and the associated mechanisms remain unclear. In this study, physiological, metabolomic, and transcriptomic analyses were conducted to reveal how bagging regulated color formation in ‘Hongyang’ kiwifruit. Bagging treatment lightened skin color primarily by reducing carotenoid accumulation, with a minor additional effect on anthocyanin content, which was relatively low even under control conditions (11 µg/g at 130 DAP). Metabolome profiling detected 33 differential metabolites (15 increased and 18 decreased), with the levels of all differential metabolites in the flavonoid biosynthesis pathway (map00941) significantly lower in bagged than in control fruit skin. Based on integrated physiological, metabolomic, and transcriptomic data, we found that the decrease in anthocyanin accumulation in bagged fruits was associated with an increase in one metabolite (neohesperidin) and decreases in four other differentially expressed metabolites (butin, afzelechin, eriodictyol, and gallocatechin), as well as the downregulation of several anthocyanin biosynthesis structural genes, including CHS , CYP73A , DFR , and F3H , and differential expression of MBW transcription factors. These correlative findings suggest a potential regulatory link between neohesperidin and anthocyanin reduction. Additionally, bagging treatment markedly altered the expression of two key carotenoid biosynthesis genes: crtZ was downregulated by 95%, whereas LCY-ε was upregulated by 2.16-fold. These changes may be associated with the observed reduction in total carotenoid content. These results identify candidate genes and metabolites potentially associated with bagging-induced fruit color lightening and provide a reference for optimizing bagging practices to improve the color and quality of kiwifruit.