Integrated metabolomics and transcriptomics analyses revealed the molecular mechanism of anthocyanin-mediated flower color transition in Brassica napus

The cultivation of colorful rapeseed ( Brassica napus L.) has become a unique focus in current breeding research. However, the mechanisms underlying flower color transition remain unclear. In this study, integrated metabolomic and transcriptomic analyses were performed on petal tissues from three B. napus genotypes (Bloodred, Rose, and Purple) at two developmental stages. A total of 79 anthocyanins and related metabolites were identified, of which 33 exhibited significant stage-dependent differences. Genotype-specific shifts in anthocyanin profiles directly determined changes in color saturation: Bloodred petals favored stable acylated cyanidins, Rose petals accumulated non‑acylated delphinidins, and Purple petals exhibited reduced petunidin content. Transcriptomic profiling revealed 52 differentially expressed structural genes involved in anthocyanin biosynthesis, most of which were downregulated at the later stage of flower development. Additionally, 45 transcription factors associated with anthocyanin regulation were identified. Among these, two R2R3-MYB TFs, BnaC03g11590D and BnaC04g51450D, were functionally characterized. Subcellular localization and transcriptional activity analyses showed that BnaC03g11590D acts as a transcriptional activator, while BnaC04g51450D functions as a transcriptional repressor. Yeast one-hybrid and dual-luciferase reporter assays further confirmed that BnaC04g51450D directly represses BnaPAL ( BnaA05g28470D ), thereby inhibiting anthocyanin biosynthesis in the Bloodred genotype. As a result, petal coloration becomes more dependent on the stability of previously accumulated pigments. Overall, these findings provide new insights into the regulatory mechanisms governing flower color transition from the early to the peak flowering stage in B. napus . • Integrated metabolomics and transcriptomics reveal petal color regulation in B. napus. • Anthocyanin biosynthesis drives flower color transition in colorful rapeseed. • Two R2R3-MYB transcription factors act as key color regulators in B. napus. • BnaC04g51450D represses anthocyanin synthesis via BnaPAL promoter interaction.