Unraveling the metabolic network and key bioactive compound accumulation during critical developmental stages of Gastrodia elata

Gastrodia elata Blume, a traditional medicinal plant, the dynamic metabolic changes and the mechanisms underlying the accumulation of medicinal components remain poorly understood during its key developmental stages (tubers before bolting, tubers after bolting, stems). This study utilized untargeted metabolomics to systematically analyze the metabolic composition and differences in tubers before bolting, tubers after bolting, and stems of G. elata f. elata, G. elata f. glauca, and dark red G. elata. We identified a total of 6209 metabolites, encompassing 17 major categories, and of these, 1624 differential metabolites (VIP > 1.5, P < 0.05) exhibited significant variations across developmental stages. Lipids, organic acids, and carbohydrates showed marked accumulation in tubers after bolting, while stems exhibited predominant enrichment of flavonoids, coumarins, and lignans. Lipids and flavonoids emerged as key differential metabolites governing the development of G. elata. Gastrodin and parishin C, two key bioactive constituents, were found to be significantly increased in both post-bolting tubers and stems (P < 0.05). Flavonoid biosynthesis, zeatin metabolism, and phytohormone signal transduction serve as the core metabolic pathways regulating the key developmental stages of Gastrodia elata. Meanwhile, amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, glycolysis/gluconeogenesis, and pentose and glucuronate interconversions form the central energy metabolic network underlying these critical developmental processes in G. elata. In addition, 22, 18, and 3 metabolites unique to G. elata f. elata, G. elata f. glauca, and dark red G. elata, respectively, were identified, which hold promise as potential markers for cultivar discrimination. This study reveals for the first time the molecular regulatory network of Gastrodia elata at key developmental stages from a metabolic perspective, providing important theoretical foundations for its growth regulation, quality improvement, and rational resource utilization.