Integrative metabolomic and transcriptomic profiling deciphers flavonoid biosynthesis of bulbs in Lilium brownii var. Viridulum

Abstract Lilium brownii var. viridulum is rich in flavonoids, which offer antioxidant, anti-inflammatory, antitumor, and immunomodulatory effects. Recently, a novel, more resistant variant called L. brownii var. viridulum (Xuefeng, xf) was identified through individual plant selection. However, the metabolic and transcriptional profiles of xf, particularly concerning flavonoid metabolism, have not yet been compared to those of the traditional variant (Longya, ly). To address this gap, we performed an integrated metabolomic and transcriptomic analysis to systematically compare flavonoid metabolism between ly and xf. Our metabolomic analysis identified 85 flavonoids that are significantly enriched in the xf variety. In the transcriptomic analysis, we identified 59 differentially expressed enzyme genes, with expression levels in xf being significantly higher than those in ly, consistent with the metabolite profile. By combining transcriptome and metabolome, we identified one MYB transcription factor (Cluster-6560.0) and four bHLH transcription factors (Cluster-22934.6, Cluster-22934.10, Cluster-24120.2, and Cluster-24120.13) linked to anthocyanin synthesis. The co-expression of these identified genes supports the enrichment of flavonoids in xf, and this coordinated expression pattern of key enzymes was further confirmed via real-time quantitative PCR (qRT-PCR). In conclusion, this study enhances our understanding of the molecular mechanisms underlying flavonoid biosynthesis and provides a strong foundation for the genetic breeding of lilies.