Multi-Omics Integrated Analysis Reveals the Key Metabolic Regulation Mechanisms of Petal Color in Phalaenopsis aphrodite

As an important ornamental plant worldwide, flower color is a key commercial trait in Phalaenopsis. In this study, petals from three Phalaenopsis cultivars with distinct colors (white, rose-red, and dark-red) were analyzed using integrated transcriptomics and metabolomics to systematically dissect the regulatory network underlying flower color development. Analyses revealed the flavonoid biosynthesis pathway as critical for coloration. Weighted gene co-expression network analysis (WGCNA) identified PhCHS-R1 as a central hub, correlating with leucocyanidin and luteolin levels. Functional validation in Arabidopsis PhCHS-R1 mutants showed significantly lighter seed coat color and reduced accumulation of color-related metabolites, including leucocyanidin and luteolin. These results confirm that PhCHS-R1 modulates pale flower color by regulating flavonoid biosynthesis. This study highlights the core role of flavonoid synthesis in Phalaenopsis coloration and identifies PhCHS-R1 as a key regulatory gene, offering theoretical insights and a potential target for genetic improvement of flower color.