Integrated multi-omics analysis identified three novel transcription factors that promote anthocyanin accumulation in blood-fleshed peaches (Prunus persica).

Blood-fleshed peach is an important and distinctive peach species widely distributed in southwestern China. Here, we compared the main fruit intrinsic quality indicators and antioxidant capacity of five blood-fleshed peach varieties from Sichuan Province and one white-fleshed peach cultivar, and clarified cyanidin-3-O-glucoside, pelargonidin-3-O-glucoside, and total anthocyanin are the three most critical intrinsic indicators influencing the total antioxidant capacity of blood-fleshed peaches. Combined metabolomic and transcriptomic analysis as well as transient transformation experiments in peach flesh revealed that two novel MYB transcription factors (PpMYB121, PpMYB158) and one bHLH transcription factor (PpbHLH59) play crucial roles in anthocyanin accumulation in blood-fleshed peach. Additionally, we constructed a molecular regulatory network for anthocyanin accumulation in blood-fleshed peach, including 17 structural genes, three transcription factors, and nine major anthocyanin components, which provides an important theoretical basis for refining the mechanism of anthocyanin accumulation in blood-fleshed peaches. In summary, this study improves our understanding of the nutritional value of blood-fleshed peach and provide targets for the improvement of peach varieties with high anthocyanin content.