Integrated Transcriptome–Metabolome Analysis of Differential Steroidal Saponin Accumulation and Candidate Biosynthetic Genes in Polygonatum cyrtonema

Polygonatum cyrtonema is a traditional medicinal and edible plant, and steroidal saponins are among its major bioactive constituents. However, the molecular basis of their tissue-specific accumulation remains unclear. In this study, integrated metabolomic and transcriptomic analyses were performed on multiple tissues of ‘LJ1’ from Jingning and rhizome germplasm resources of different provenance, including wild-derived materials and the cultivar ‘LJ1’, to characterize tissue-dependent steroidal saponin accumulation and the associated gene–metabolite relationships in P. cyrtonema. Metabolomic analysis showed that steroidal saponins were significantly enriched in underground organs, with relative abundances 3–10 times higher than those in aerial tissues, indicating a distinct tissue-dependent distribution pattern. Transcriptomic analysis revealed that some members of gene families putatively involved in steroidal saponin biosynthesis, including CYP72A, DXS, DXR, and F26G, showed higher expression in tissues with high saponin accumulation. Although F26G and CYP72A showed positive Mantel correlations with the overall steroidal saponin profile, none of the six gene-set-level Mantel tests remained statistically significant after Benjamini–Hochberg correction. These families were therefore retained as expression- and homology-based candidates for future functional validation rather than as statistically supported gene–metabolite associations. Based on these findings, this study outlines a multilayered biosynthetic framework associated with steroidal saponin accumulation in P. cyrtonema, involving precursor supply, skeleton formation, and structural modification. These results provide a multi-omics overview of tissue-dependent steroidal saponin accumulation and its associated gene expression patterns and offer candidate gene resources for future functional and metabolic engineering studies.