Transcriptomic and metabolomic analyses reveal CmMYB308 as a key regulator in the pink flower color variation of ‘Dante Purple’ chrysanthemum

Abstract Flower color variation is a widespread natural occurrence that plays a significant role in floral breeding.We discovered a variation in the flower of the chrysanthemum cultivar ‘Dante Purple’ (abbreviated as ‘DP’), where the flower color shifted from purple to pink. Through tissue culture, we successfully propagated these pink flowers and designated them as DPM. By conducting transcriptome and metabolome analysis, we identified a reduction in the expression of key genes involved in anthocyanin biosynthesis—CmPAL, CmC4H, and Cm4CL—in the DPM. This downregulation led to an accumulation of phenylalanine and cinnamic acid within the general phenylpropanoid pathway (GPP), which prevented their conversion into cyanidin and cyanidin 3-glucoside. As a result, the flowers turned pink. Additional transformation and biochemical experiments confirmed that the upregulation of CmMYB308 gene expression in the DPM directly suppressed CmPAL-1 and CmC4H genes, which indirectly affected Cm4CL-3 expression and ultimately inhibited anthocyanin biosynthesis in the DPM. This study offers a preliminary insight into the molecular mechanism underlying chrysanthemum flower color mutation, paving the way for genetic improvements in chrysanthemum flower color breeding.