Metabolomics-transcriptomics analysis reveals the mechanism by which Gentiana lawrencei var. farreri promotes flowering under different diurnal temperatures.

Gentiana lawrencei var. farreri (G. farreri) is an important endangered Tibetan medicinal plant. This study aimed to uncover temperature-mediated physiological and molecular mechanisms underlying growth and flowering of this endangered Tibetan medicinal herb, providing theoretical guidance for its standardized artificial cultivation. This study established three diurnal temperature treatments: 15/5 °C (S15), 20/10 °C (S20), and 25/15 °C (S25), and conducted integrated analyses of phenotypic, physiological, non-targeted metabolomic, and transcriptomic data. The results showed that S15 significantly promoted plant biomass accumulation and flowering, with a flowering rate of 45.83%, significantly higher than that of other treatments. S15 significantly reduced the levels of soluble sugar, soluble protein, fructose, and starch, while increasing CAT activity to enhance antioxidant capacity; endogenous hormones showed elevated gibberellin (GA) and decreased indole-3-acetic acid (IAA), establishing a hormonal balance favorable for flowering. Integrated metabolomic and transcriptomic analysis revealed that the flavonoid biosynthesis pathway (ko00941) is the core pathway responsive to temperature; S15 induces an increase in the contents of flavonoid metabolites including naringenin, delphinidin, petunidin, and peonidin, and simultaneously upregulates the expression of key genes including the PAL-encoding gene Cluster-62424.2, the 4CL-encoding gene Cluster-45063.0, and the CHS-encoding gene Cluster-44799.3 involved in flavonoid biosynthesis under this condition. S15 reduces the content of osmotic adjustment substances, increases GA content in plant branches, and enhances antioxidant capacity, which synergistically promotes the growth and flowering of G. farreri. Additionally, S15 mediates the accumulation of flavonoid compounds by regulating key genes involved in flavonoid biosynthesis, thereby elevating the accumulation of bioactive constituents isoorientin and isoscoparin-2″-O-β-D-glucopyranoside. This study can provide crucial theoretical support for the optimal temperature regulation and control in the artificial cultivation of G. farreri.