| Summary: | The petals of <i>Paeonia lactiflora</i> ‘Coral Sunset’ change color from coral pink to pale yellow after flower opening. Pigment-targeted metabolomic analysis showed that the carotenoid and anthocyanin contents rapidly decreased after petal fading. SMART-sequencing and next-generation-sequencing analyses were performed to identify differentially expressed transcripts to characterize the candidate genes involved in petal fading. The expression of certain genes associated with anthocyanin and carotenoid synthesis and degradation was correlated with the petal-fading phenotype. The anthocyanin synthesis (AS) structural genes, <i>CHS</i>, <i>F3H</i>, <i>F3′H</i>, <i>DFR</i>, and <i>ANS</i>, and the carotenoid synthesis genes, <i>LCYB</i> and <i>LCYE</i>, were strongly expressed before fading, but their expression significantly declined after fading. In contrast, the expression of certain genes associated with oxidase activity and light signaling significantly increased after fading. Therefore, inhibition of pigment synthesis and accelerated pigment degradation may be crucial for petal fading. A R2R3-MYB family member of subgroup 4 (<i>MYBs-SG4</i>) showed the same expression pattern as the AS structural genes and functioned in the positive regulation of anthocyanin synthesis by forming the MBW protein complex. This is the first report of a SG4 member with a positive regulatory function. This study provides a foundation for elucidation of the mechanisms of pigment synthesis and metabolism, and a theoretical basis for flower-color-directed breeding.
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