Dual regulation of anthocyanins and proanthocyanidins by PpBL and its linkage to acidity in peach

Abstract Red-fleshed peach exhibits attractive anthocyanin (AN) pigmentation but is often accompanied by undesirable proanthocyanidin (PA)-derived astringency and high fruit acidity (FA), limiting its commercial value. The genetic mechanisms underlying this co-occurrence remain unclear. Using an F 1 population derived from ‘wen30’ and ‘wen48’, we identified co-localized QTLs for AN, PA, and FA within a 0.32–4.74 Mb region on chromosome 5. Integrating transcriptomics with Y1H, EMSA, and dual-luciferase assays, we demonstrated that PpBL functions as a key regulator of both AN and PA accumulation. PpBL directly activates PpUGT73C3 , independently of PpMYB10.1 , to promote AN biosynthesis, and enhances PA accumulation by directly upregulating PpLAR and PpANR ; PpUGT73C3 also contributes to PA accumulation via an unclear mechanism. In contrast, FA is not directly regulated by PpBL but is associated with a high-acidity PpTST1 allele tightly linked to a blood-TE insertion in the PpBL promoter. The haplotype carrying both the insertion and PpUGT73C3 coding variants confers elevated AN and PA but also increased FA due to linkage drag. These findings reveal pleiotropic control of color and astringency and a linkage-based association with acidity, providing insights for peach breeding.