Integrative Transcriptomic and Metabolomic Approaches to Deep Pink Flower Color in Prunus campanulata and Insights into Anthocyanin Biosynthesis

Flower pigmentation is a critical trait in plants, influencing ecological interactions and ornamental value. This study investigates the mechanisms underlying petal coloration in Prunus campanulata and its hybrids, Prunus ‘Okame’ and Prunus ‘Yoko’. Morphological analysis revealed consistent flower size across varieties, indicating that color variation is not linked to structural differences. Physiological and biochemical analyses identified stages III and IV as critical for pigmentation, characterized by the significant accumulation of flavonoids and anthocyanins. Metabolomic profiling highlighted flavonoids as the dominant metabolites, with key compounds including chalcones, flavones, and anthocyanins contributing to color formation. Weighted gene co-expression network analysis (WGCNA) further identified several hub genes, including RPL34, NUDT12, and CYP78A9, within modules strongly correlated with pigment accumulation, suggesting their potential non-canonical roles in the coloration process. Environmental factors such as temperature and pH were found to influence pigment stability. Overall, this study provides insights into the genetic and biochemical regulation of flower pigmentation in P. campanulata, emphasizing the central role of flavonoid and anthocyanin biosynthesis.