Integrated Metabolomic and Transcriptomic Analyses Reveal the Differential Molecular Mechanisms Underlying Heat Stress Responses in Two Pinellia ternata Germplasms

Background:Pinellia ternata is a major medicinal herb widely utilized in traditional medicine, but is sensitive to high temperature, which often triggers a severe “sprout tumble” phenomenon. Methods: To elucidate the molecular mechanisms of heat tolerance in P. ternata, we screened two contrasting germplasms: the heat-tolerant JBX1 and the heat-sensitive XBX4. In the present study, a combined analysis of physiology, transcriptome, and metabolome was performed on JBX1 and XBX4 under heat stress at 40 °C. Results: JBX1 exhibited significantly greater leaf thickness, higher basal chlorophyll content, more stable antioxidant enzyme activities, and lower oxidative damage than XBX4 under heat stress. Transcriptomically, JBX1 maintained elevated basal expression of genes encoding key enzymes in carbon fixation, amino acid metabolism, and phenylpropanoid biosynthesis, as well as those encoding heat shock transcription factors (HSFs), heat shock proteins (HSPs), and the thermosensor Thermo-With ABA-Response 1 (TWA1). Metabolomically, JBX1 accumulated higher levels of key primary metabolites, antioxidants, and protective phenylpropanoids under both control and heat conditions. Notably, a “polarity reversal” emerged in nitrogen metabolism, where core amino acids accumulated in JBX1 but were depleted in XBX4. Integrated analysis revealed a more coordinated gene–metabolite network in JBX1 involving the phenylpropanoid, ATP-binding cassette (ABC) transporter, and glutathione pathways. Conclusions: Our findings demonstrate that JBX1 possessed stronger basal thermotolerance, which is derived from coordinated establishment of higher constitutive metabolic reserves and efficient dynamic metabolic reprogramming. This study provides insights into the molecular mechanisms of heat stress in P. ternata.