Moderate warming promotes growth and flavonoid biosynthesis in the altitudinal medicinal plant Gentiana lawrencei var. farreri

High-altitude endangered medicinal plants face increasing extinction risk, and ex situ conservation through low-altitude cultivation represents a key protective strategy. Low temperature is a defining feature of altitudinal habitats. However how moderate warming influences growth performance and secondary metabolite accumulation in cold-adapted medicinal plants remains poorly understood. We investigated the altitudinal medicinal plant Gentiana lawrencei var. farreri ( G. farreri ) under different day/night temperature regimes, integrating morphological, physiological, transcriptomic and metabolomic analyses. Moderate warming (25/15 °C) significantly increased leaf area, root length, and shoot and root dry biomass, while reducing soluble sugar and protein contents. Antioxidant enzyme activities, as well as proline and malondialdehyde levels, were decreased. Weighted gene co-expression network analysis identified a temperature-responsive module closely associated with multiple stress-related traits, in which the plant–pathogen interaction pathway was prominently enriched. Key regulatory nodes, including FLS2 and CDPK, showed temperature-dependent expression patterns. Levels of flavonoids, including p -coumaric acid, dihydromyricetin, delphinidin and cyanidin, were markedly increased under moderate warming. These results demonstrate that moderate warming alleviates temperature limitation on growth and promotes flavonoid accumulation in G . farreri . Our findings provide insight into the physiological and molecular acclimation of alpine medicinal plants to moderate warming and offer a scientific basis for optimizing low-altitude ex situ cultivation under climate warming.