AcMYB96 promotes anthocyanin accumulation in onion (Allium cepa L) without forming the MBW complex

Anthocyanins are major flavonoid compounds with established health benefits. Although the molecular mechanisms of MYB transcription factors (TFs) within the MYB–basic helix-loop-helix (bHLH)–WD-repeat protein (MBW) complex in anthocyanin biosynthesis have been revealed, the functions of other MYB TFs that are unable to form the MBW complex in this process remain unclear. In this study, we uncovered and extensively characterized an R2R3-MYB TF in onion (Allium cepa L.), named AcMYB96, which was identified as a potential anthocyanin activator. AcMYB96 was classified into subgroup 1 of the R2R3-MYB TF family and lacked the conserved sequences required for interactions with bHLH IIIf TFs. Consistently, yeast two-hybrid assays showed that AcMYB96 did not interact with any bHLH IIIf TFs examined, including AcB2 and AtTT8. The transcription pattern of AcMYB96 correlated with the level of anthocyanin accumulation, and its role in activating anthocyanin biosynthesis was confirmed through overexpression in the epithelial cells of onion bulbs and Arabidopsis. Yeast one-hybrid, electrophoretic mobility shift, and promoter transactivation assays further demonstrated that AcMYB96 promoted anthocyanin biosynthesis by binding to the promoters of the chalcone synthase (AcCHS1), anthocyanidin synthase (AcANS), and UDP-glucose-flavonoid 3-O-glucosyltransferase (AcUFGT) genes, thereby activating their expression independent of bHLH IIIf TFs. These results demonstrate that AcMYB96 activates anthocyanin biosynthesis without forming the MBW complex, providing a theoretical foundation to further enrich the gene resources for promoting anthocyanin accumulation and breeding red onions with high anthocyanin content.