Integrated transcriptomic and metabolomic analysis of the functional component dynamics during rose bud opening

• Effects of drying method on functional components of rose were studied. • Microwave and oven drying increases the functional component content. • Flavonoids and key genes increase during early developmental stages in roses. • 4-Coumarate-CoA ligase plays a role in flavonoid biosynthesis in roses. Rose ( Rosa rugosa Thunb.) contains various bioactive components that possess antioxidant, anti-inflammatory, and antibacterial properties, including flavonoids, polysaccharides, and polyphenols. However, methods of processing rose flowers influence the functional component contents. Therefore, this study examined the effects of different drying methods on the functional components of five rose varieties at different developmental stages and further employed an integrated transcriptomic and metabolomic approach to elucidate the flavonoid biosynthetic pathway and its key genes in fresh rose samples. Zizhi, Pingyin, Kushui, Bulgarian, and Damascus rose varieties were processed using three drying methods (oven, microwave, and sun), and the bioactive compounds were analysed. Notably, in Zizhi rose, the flavonoid content peaked at the S4 stage (0.0036 mg/g) while the polysaccharide content continued to increase during bud opening and remained high at the fully open stage (S5 stage). Additionally, in Kushui rose, the polyphenol content peaked at the S4 stage (1.30 mg/g). Among the drying treatments, microwave and oven drying significantly increased the functional component content in the five rose varieties. A total of 11,426 differentially expressed genes and 2591 differentially expressed metabolites were detected in the Zizhi/Kushui and Kushui/Bulgarian comparison groups, respectively. Weighted gene co-expression network analysis indicated that 4-coumarate-CoA ligase plays a critical role in the phenylpropanoid and flavonoid biosynthesis pathways. Additionally, key enzyme genes in the flavonoid biosynthesis pathway were highly expressed during the early developmental stages of rose buds in all varieties. In conclusion, this study provides a theoretical foundation for the utilisation of functional components in roses and the breeding of rose varieties.