Multi-omics analysis reveals that anthocyanin metabolic flux determines the flower color of Dendrobium nobile

The flower color variation in Dendrobium nobile is an important model for studying orchid pigmentation, but the mechanism is unclear. In this study, two types of D. nobile deep purple petals (S) and light purple petals (Q) were used as experimental materials. Morphological observation, pigment content quantification, metabolomics and transcriptomics were comprehensively integrated to explore the mechanism of color difference. The results revealed no significant structural differences between the two types. However, the anthocyanin in S group (0.38 mg/g) was higher than that in Q group (0.16 mg/g), while the total flavonoid in Q group increased by 57% relative to the S group, which indicated that reduced anthocyanin accumulation is the direct cause of the light purple. Metabolomics identified 34 differential metabolites such as cyanidin‑3‑(6‑O‑p‑coumaroyl)‑glucoside, delphinidin‑3‑O‑glucoside, and naringenin‑7‑O‑glucoside were upregulated in S petals and contribute to the purple color. RNA-Seq revealed 15,460 DEGs, enriched in secondary and flavonoid metabolism. Integrated analysis showed that G8H is a candidate key regulator of flavonoid flux partitioning. In S group, high G8H expression directs naringenin toward anthocyanin biosynthesis, upregulates DnUGT‑like X1 and KFK09_007985 (GST) , meanwhile promotes anthocyanin glycosylation, transport, and vacuolar storage, leading to deep‑purple petals. The expression of G8H in Q group is downregulated, anthocyanin biosynthesis is blocked, metabolic flow shifts to the flavonol synthesis pathway. The upregulated rhamnosyltransferase gene significantly promoted a large accumulation of flavonols and ultimately forming light purple. This study elucidated the mechanism of differential regulation of flower color variation in D. nobile by flavonoid pathway branches, providing reference for molecular breeding of D. nobile and research on pigment metabolism in orchids.