Multi-omics dissection of light-quality-modulated regulatory mechanisms underlying steroidal alkaloid biosynthesis in Fritillaria cirrhosa

Fritillaria cirrhosa D. Don, a shade-preferring and light-sensitive medicinal plant endemic to the Qinghai-Tibet Plateau, is a valuable source of pharmacologically active steroidal alkaloids (SAs). However, the molecular mechanisms through which light quality regulates SAs biosynthesis in cultivated populations remain largely unknown. We utilized spectral filter films (blue, yellow, and green, with white films as controls) to investigate the effects of light quality on SAs accumulation and the underlying molecular regulation. The results showed that blue film (BF) treatment, which increased the proportion of blue light to 43.1 % of the relative spectral composition, significantly increased the levels of imperialine, peimine, and peimisine—by 68.9 %, 72.1 %, and 54.3 %, respectively ( P< 0.05). Through metabolomic profiling we identified 938 bulb metabolites, revealing BF-induced shifts in amino acid and carbohydrate metabolism that are critical for SAs precursor supply. Transcriptomic analysis revealed 3054 differentially expressed genes in BF vs. WF, including 1757 upregulated genes linked to SAs biosynthesis (e.g., SMT1 and HMGCS). Enrichment analysis highlighted the BF-specific activation of steroidal alkaloid biosynthesis, starch and sucrose metabolism, and MAPK signaling pathways, suggesting roles in carbon allocation and stress responses. Key transcription factor families (WRKY, MYB, and bHLH), notably FcWRKY4 and FcWRKY6, showed strong positive correlations with SAs biosynthetic genes. WGCNA further identified regulatory modules comprising light perception components (UVR8 and HY2), phytohormone signaling elements, and core metabolic genes (SMT1 and SUS2), outlining a hierarchical regulatory network responsive to blue light. Collectively, these findings demonstrate that blue light enrichment promotes the biosynthesis of SAs in F. cirrhosa through the coordinated modulation of primary metabolism, activation of biosynthetic enzymes, and transcriptional regulation by light-responsive factors. The results of this study provide mechanistic insights and practical implications for optimizing secondary metabolite production in F. cirrhosa and other shade-adapted medicinal plants under controlled light conditions. • Blue light enhances medicinal steroidal alkaloids in F. cirrhosa bulbs. • BF upregulates MAPK signaling and starch/sucrose metabolism genes. • MAPK links SA biosynthesis (SMT1/HMGCS) to WRKY4/6/8 TFs under blue light. • UVR8-WRKY4-SMT1 module enables scalable SA-enriched cultivation strategy.