Integrated transcriptomic and metabolomic analysis prioritizes candidate quinolizidine alkaloid biosynthetic genes in Sophora moorcroftiana

Sophora moorcroftiana is a leguminous shrub endemic to the Qinghai-Xizang Plateau and an important medicinal plant. Its bioactive properties are largely attributed to quinolizidine alkaloids (QAs) but the genes and regulatory networks underlying QA biosynthesis remain poorly characterized. Here, we integrated transcriptomic and widely targeted metabolomic profiling across roots, stems, leaves, and seeds of S. moorcroftiana to characterize tissue-specific specialized metabolism and prioritize candidate genes associated with QA accumulation. Metabolomic profiling detected diverse secondary metabolites, including several QAs with distinct tissue-specific abundance patterns. Co-accumulation and co-expression network analyses identified metabolite and gene modules associated with QA abundance. Integrative transcript–metabolite analyses further prioritized candidate enzyme families, including CuAO , DHDPS , PMT and CYP genes, as well as candidate transcriptional regulators potentially associated with QA biosynthesis. Several CYP candidates were repeatedly recovered across correlation and multivariate analyses, while (-)-sparteine and lupinine shared co-accumulation patterns and overlapping candidate gene sets, suggesting partially shared regulatory or metabolic contexts. Our study provides transcriptomics and metabolomics resources for discovering QA candidate genes in S. moorcroftiana . The prioritized enzymes, metabolite modules and regulatory candidates establish a foundation for future biochemical and genetic validation of QA biosynthesis in this medicinal legume.