Integrated Transcriptome and Metabolome Analysis Reveals the Molecular Basis Underlying Anthocyanin Biosynthesis Associated with Different Flower Colors in Vicia faba L.

Abstract Faba bean (Vicia faba L.) exhibits significant variation in flower color. To elucidate the underlying regulatory mechanisms, transcriptomic and metabolomic analyses were conducted on pink, gray, and white flower germplasms. Anthocyanin content was higher in pigmented flowers (162.29 μg/g) than in white flowers (36.28 μg/g). Compared to white flowers, gray flowers showed upregulation of four key metabolites related to petunidin, cyanidin, and delphinidin. Pink flowers encompassed 15 derivatives derived from cyanidin, delphinidin, peonidin, petunidin, and malvidin. Across the three flower colors, 70 structural genes involved in anthocyanin biosynthesis were differentially expressed. Integrated omics and weighted gene coexpression network analysis (WGCNA) identified 15 candidate regulators: ten structural genes (VfCHI4, four CHSs, four UFGTs, VfGST18) and five transcription factors (two MYBs, two bHLHs, one WRKY), all of which showed significant positive correlations with anthocyanin components. These results provide a valuable reference for understanding the molecular mechanisms underlying flower color variation.