The transcriptomic and metabolomic mechanisms responsible for high medicinal quality in Dendrobium huoshanense under different cultivation techniques

BACKGROUND: Dendrobium huoshanense, a Traditional Chinese Medicine (TCM), is natively found in the wild near Huoshan in the Dabie Mountains of Anhui Province, China. However, overexploitation and habitat loss have led to its scarcity. Cultivation techniques have been adopted to meet the demand, but these methods are known to alter the medicinal qualities of D. huoshanense, although the underlying molecular mechanisms remain unclear. RESULTS: To elucidate the mechanisms behind these alterations, we conducted a study on D. huoshanense cultivated in three different environments: a facility, under forest conditions, and in a simulated habitat. Using transcriptomic and metabolomic analyses, we identified 5324 differentially expressed genes (DEGs) and 359 differentially accumulated metabolites (DAMs). The identified DEGs were primarily associated with the synthesis of isoquinoline alkaloids, flavones, flavonols, flavonoids, and phenylpropanoids, as well as the metabolism of various sugars. Among these, several key DEGs involved in polysaccharide biosynthesis (e.g., scrK, sacA, uxe, and GMPP), flavonoid biosynthesis (e.g., 4CL and F5H), and alkaloid biosynthesis (e.g., TYDC and TR1) were identified. Notably, D. huoshanense cultivated in the simulated habitat exhibited the highest concentrations of various bioactive compounds. Furthermore, we evaluated the expression of these key genes under abiotic stress conditions such as high temperature, low temperature, drought, and UV irradiation and found that each gene responded to a specific combination of these stresses. CONCLUSIONS: This study provides the first comprehensive evaluation of the effects of cultivation techniques on gene expression and metabolite accumulation in D. huoshanense using both metabolomic and transcriptomic approaches. The results identify key genes and metabolites involved in the biosynthesis of important medicinal compounds and their regulation under different cultivation conditions and stress responses. These findings lay a crucial foundation for future research on improving the medicinal quality of D. huoshanense, as well as its sustainable development and utilization.