Multi-Omics Analysis Reveals Adaptive Strategies of Meconopsis horridula to UV-B Radiation in the Qinghai-Tibet Plateau.

Meconopsis horridula, an endemic medicinal and alpine horticultural species of the Qinghai-Tibet Plateau, exhibits remarkable adaptation to high-altitude UV-B radiation. Despite its ecological and medicinal significance, the mechanisms underlying its UV-B adaptation remain poorly understood. Here, we used a PacBio full-length transcriptome as a reference, integrating RNA-seq and metabolomic data from altitudinal populations, with field-based transcriptomic and microbiome profiling under shade-controlled UV-B gradients, to elucidate UV-B adaptive regulatory networks. KEGG enrichment and environmental correlation analyses highlighted flavonoid biosynthesis as a central pathway in UV-B adaptation at high altitudes. Controlled UV-B gradient experiments identified 10 conserved flavonoid biosynthesis genes, including chalcone synthase (CHS). Overexpression of CHS in Arabidopsis thaliana increased flavonoid content by approximately 1.2-fold. Co-expression analysis further revealed that CHS-associated regulatory factors mediate coordinated responses, including reduced light signalling, enhanced antioxidant capacity and suppression of defence genes and anthocyanin biosynthesis inhibitors. CHS, in coordination with immune regulation, modulates high-centrality microbes, contributing to differential network regulation and microbiome stability. Enriched key microbes may mitigate the growth-defence trade-off under UV-B stress through antimicrobial, growth-promoting and antioxidant activities. Collectively, our findings reveal a flavonoid-centred adaptation framework that deepens our understanding of UV-B resilience in alpine plants and offers potential resources for crop improvement.