Red apple varieties such as ‘Fuji’ and ‘Fortune’ can synthesize high numbers of anthocyanins and are preferred by more consumers. In recent years, red apple have attracted the attention of consumers due to their attractive appearance and their reported nutritional value. These results provide an important data for dissecting candidate genes and molecular basis governing green apple color formation in response to visible light and UV-B light. A series of metabolites and candidate genes were revealed through combined analysis of metabolome and transcriptome. The composition and contents of anthocyanins in green apple in UV-B-treatment very greatly. Expression profiles of several transcription factors of the families MYB, bHLH, NAC were highly correlated with the content of the anthocyanin. Furthermore, we performed qRT-PCR analysis of anthocyanin biosynthesis genes and predicted the gene of MD00G1134400 (a UDP glucose-flavonoid 3–0-glucosyltransferase) may be a candidate gene for anthocyanins accumulation and highly expressed in UV-B-treatment fruit. The flavonoid metabolic flux in the UV-B treatment increased the accumulation of cyanidin 3-glucoside and cyanidin 3, 5-diglucoside compared to under the light-treatment. Quantitative reverse transcription PCR (qRT-PCR) results confirmed changes in the expression levels of genes encoding metabolites involved in the flavonoid synthesis pathways. The metabolic analysis revealed that there were 152 and 178 significantly changed metabolites in the visible light and UV-B-treated green apple, respectively, compared to the control, and flavone, flavonol, and anthocyanin were the most significantly increased and transcriptomic analysis showed that 37,110 and 37,709 differentially expressed genes, including 382 and 475 transcription factors (TFs) were detected in light and UV-B-treatment fruit, respectively. Here, we explored the difference of metabolites and genes expression level in green apple by transcriptomic and metabolic. But there are few reports on the biosynthesis difference of anthocyanins in green apple by visible light and UV-B-treatment. Notably, in this study, the green skin color apple variety ‘white winter pearmain’ treated with ultraviolet-B (UV-B) exhibited red skins and marked anthocyanin accumulation, while visible light could not. In nature, green apple are associated with the accumulation of chlorophyll, while red apple varieties are associated with anthocyanins accumulation.
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