Integrated metabolome and transcriptome landscape of four rapeseed petal colors provides a candidate gene-metabolite roadmap for flower color breeding

Rapeseed ( Brassica napus L.) petals exhibit diverse colors with specific phenotypes and excellent ornamental value. However, the mechanisms underlying their coloration remain poorly understood. Here we performed an integrative metabolomic and transcriptomic of white, yellow, dark purple, and dark red rapeseed petals to systematically dissect the color-specific pigments and their associated regulatory networks. Yellow petals predominantly accumulated tamarixetin-3-O-glucoside-7-O-rhamnoside and 4′-hydroxy-2,4,6-trimethoxydihydrochalcone, coinciding with high expression of chalcone synthase ( CHS ). In dark-purple petals, the acylated anthocyanins cyanidin-3-O-(6′-O-caffeoyl)sophoroside-7-O-glucoside and cyanidin-3-O-feruloylglucoside-5-O-glucoside were identified as the main pigments, and their accumulation was attributed to the coordinated activity of ANS1, CCoAAT2 , and CCoAOMT . Dark-red coloration was associated with the glycosylated anthocyanin peonidin-3-O-glucoside, whose abundance was regulated by ANS1, UGT79B2, MT1 , and MT2 . Weighted gene co-expression network analysis defined five flavonoid-specific modules and pinpointed MYB12, MYB114, MYB122, bHLH21 and bHLH96 as candidate transcription factors. Collectively, this gene-to-pigment framework established color-specific metabolic and regulatory linkages across four contrasting petal phenotypes, providing breeders with candidate molecular markers and prospective CRISPR targets for accelerating the development of ornamental rapeseed cultivars.