Integrated Transcriptomic and Metabolomic Analyses Reveal Terpenoid and Flavonoid Biosynthesis in High‐Altitude Response of Incarvillea younghusbandii

Incarvillea younghusbandii Sprague is distributed in the sandy meadow and gravelly habitats on the Qinghai-Tibet Plateau (QTP). It is commonly used as a Tibetan herbal medicine to treat weakness, anemia, and other conditions. To date, there are no prior reports on how I. younghusbandii adapts to extreme high-altitude environments or on the differences in the medicinal active ingredients between its various tissues. This study collected leaf and root samples of I. younghusbandii from three altitudes (4100, 4600, and 5200 m) on the QTP, and performed integrated transcriptomic and metabolomic analyses to elucidate the basis for its adaptation to high-altitude extreme environments. A total of 67,375 unigenes and 849 metabolites were identified, including 90 terpenoids and 16 flavonoids. Altitude-associated reprogramming of secondary metabolism was evident, particularly in the terpenoid, flavonoid, and phenylpropanoid biosynthetic pathways. Key biosynthetic genes (such as CHS, F3H, ANS, TPS) were significantly upregulated at higher elevations, correlating with the accumulation of stress-mitigating metabolites such as scutellarein derivatives, diosmetin, luteoloside, α-curcumene, and (S)-oleuropeic acid. These compounds are likely involved in enhancing UV protection, antioxidant capacity and osmotic adjustment. Tissue-specific responses revealed stronger transcriptional and metabolomic shifts in leaves than in roots, reflecting greater exposure of leaves to environmental stressors. Beyond secondary metabolism, altitude-induced modulation was observed in protein processing in the endoplasmic reticulum (RAD23), plant hormone signal transduction (AUX/IAA), and MAPK signaling pathway (WRKY29), indicating a coordinated multi-pathway response. This study reveals a complex regulatory network underlying high-altitude adaptation in I. younghusbandii, provides new insights into alpine plant resilience, and lays a foundation for the conservation and sustainable pharmacological development of Tibetan medicinal resources.