Multi-omics integrated analysis reveals the key metabolic regulation mechanisms of petal color in Phalaenopsis aphrodite Rchb.f.

key messageMultimodal integrated analysis reveals the key metabolic regulatory mechanism of butterfly orchid petal color and identifies the core genes of the anthocyanin biosynthesis pathway. Phalaenopsis aphrodite Rchb. f. (Phalaenopsis) is a globally important ornamental plant in the floriculture industry. Flower color is a critical trait determining its commercial value. To reveal the molecular mechanism of flower color formation and the conserved functions of key genes in Phalaenopsis, we performed transcriptome and metabolome multi-omics analyses on three cultivars with distinct petal colors with Pa_1 (white), Pa_2 (rose red) and Pa_3 (dark red). Integrated omics analysis confirmed that flavonoids and their glycosides are the primary pigments governing floral color variation, with the phenylpropanoid and flavonoid biosynthesis pathways serving as the core conserved regulatory routes. Key pathway structural genes, including Chalcone synthase (CHS), Flavanone 3-hydroxylase (F3H), Dihydroflavonol 4-reductase (DFR), and Anthocyanidin synthase (ANS), were significantly upregulated in dark-colored petals and positively regulate flavonoid metabolites (such as naringenin, luteolin, hesperetin, taxifolin, and leucocyanidin) to promote the accumulation of anthocyanins and flavonoids. WGCNA identified the core hub gene Phalaenopsis Chalcone synthase-Red1 (PhaCHS-R1), which belongs to the chalcone synthase family and performs a conserved limiting catalytic function in flavonoid synthesis in the petals of Phalaenopsis flowers. Such a role for PhaCHS-R1 was further demonstrated via the VIGS approach, an RNA silencing-mediated strategy which significantly decreased anthocyanin and flavonoid contents in the petals of flowers of VIGS plant, to result in the treated flowers displaying a distinctly lighter color. This study clarified the conserved regulatory mode of the phenylpropanoid-flavonoid pathway and elucidated the conserved function of PhaCHS-R1, providing important conserved gene resources for molecular breeding of flower color in Phalaenopsis and ornamental plants.