Multi-omics Joint Analysis Reveals the Mechanism of Flower Color and Fragrance Variation in Lilium cernuum

Shaopeng Chen Zhiqun Chen Qianqian Zhuang ^* Hewen Chen

• Jilin Agricultural Science and Technology University, Jilin, China

Through comprehensive analysis of transcriptomics, metabolomics, and volatile metabolomics, this study reveals the molecular mechanisms underlying the variation in flower color and fragrance between L. cernuum var. album and L. cernuum. The results show that the content of flavonoids and anthocyanins in L. cernuum var. album is significantly lower than in L. cernuum, which is mainly due to the downregulation of key genes PAL, C4H, and 4CL in the Phenylpropanoid Pathway, leading to reduced synthesis of p-Coumaric acid and its downstream anthocyanins and volatile organic compounds Eugenol and Methyleugenol. Metabolomics analysis showed a significant decrease in the contents of metabolites such as Catechin, Chlorogenic acid, Epicatechin, Neohesperidin, and Prunin in the Flavonoid biosynthesis pathway in L. cernuum var. album, particularly Catechin and Epicatechin, which are intermediate products in the anthocyanin biosynthesis pathway. Their reduced content directly affects anthocyanin accumulation and color expression. Furthermore, gene expression data further supports this change, with 58 genes in the Flavonoid biosynthesis pathway in L. cernuum var. album being downregulated, covering the entire process of anthocyanin and flavonoid synthesis. The downregulation of these genes leads to a decrease in anthocyanin and flavonoid synthesis, which in turn affects flower color. In the Anthocyanin biosynthesis process, the contents of Cyanidin, Pelargonidin, and Peonidin in L. cernuum var. album were significantly reduced, directly leading to the change of flower color from purple-red to white. The downregulation of the UFGT gene, in particular, inhibited the glycosylation process of anthocyanin molecules, leading to anthocyanins being easily degraded or converted into other colorless compounds, preventing effective accumulation in the vacuoles of petal cells, thereby weakening or eliminating color expression. This study systematically elucidates the mechanisms of flower color and fragrance variation in L. cernuum var. album through multi-omics analysis, providing an important reference for further research on the regulation of plant color and fragrance.