Integrated Metabolic and Transcriptomic Profiles Furnish Insights to Flavonoid Variation in Dendrobium officinale From Different Areas in China

Dendrobium officinale ( D. officinale ), a plant of significant nutritional and medicinal value, has gained substantial attention in recent years. However, comprehensive studies focusing on the quality evaluation and comparative analysis of flavonoids in D. officinale across diverse geographical regions, along with investigations into the biological regulatory pathways linked to these compounds, remain scarce. This study employed RNA‐sequencing (RNA‐Seq) and metabolomics to systematically investigate flavonoid metabolites and gene expression profiles in D. officinale samples collected from eastern, central, and western China. Results revealed that samples from Zhejiang Province exhibited the highest total flavonoid (0.347%) and total polyphenol (0.679%) contents. UPLC‐MS/MS identified 111 differentially accumulated flavonoids (DAFs), with hesperetin, apigenin, and others being more abundant in Zhejiang samples. RNA‐Seq revealed 14,890 differentially expressed genes (DEGs). Key genes were identified, namely 4CL2 , 4CLL7 , CYP75B1 , CYP81E1 , BAHD1 , and BIBSY212 . 4CL, HCT, F3′M, and CHS were found to play crucial roles in flavonoid biosynthesis. This implies that gene expression differences across geographically distinct D. officinale populations lead to varied metabolic profiles. Elucidating the intricate molecular mechanisms underlying flavonoid accumulation in D. officinale not only provides novel insights into secondary metabolism but also offers support for quality control and optimizing functional compound profiles.