Integration of Metabolomic and Transcriptomic Analyses Reveals the Molecular Mechanisms of Flower Color Formation in .

Flower color is an important trait that affects the economic value of , a famous ornamental plant in the Rosaceae family. with purple-red flowers is uniquely charming and highly favored in landscape applications. However, little is known about its flower coloring mechanism, which stands as a critical obstacle on the path to innovative breeding for flower color. In this study, transcriptomic and targeted metabolomic analyses of purple-red and white were performed to elucidate the mechanism of flower color formation. In addition, the expression patterns of key genes were analyzed using an RT-qPCR experiment. The results showed that the differential metabolites were significantly enriched in the flavonoid synthesis pathway. A total of 14 anthocyanins emerged as the pivotal metabolites responsible for the differences in flower color between the two cultivars, comprising seven cyanidin derivatives, five pelargonium derivatives, and two paeoniflorin derivatives. Moreover, the results clarified that the metabolic pathway determining flower color in purple-red encompasses two distinct branches: cyanidin and pelargonidin, excluding the delphinidin branch. Additionally, through the integrated analysis of transcriptomic and metabolomic data, we identified 18 key genes responsible for anthocyanin regulation, thereby constructing the gene regulatory network for anthocyanin synthesis. Among them, ten genes (, , , , , , , , , and ) related to anthocyanin synthesis were significantly positively correlated with anthocyanin contents, indicating that they may be the key contributors to anthocyanin accumulation. Our investigation contributes a novel perspective to understanding the mechanisms responsible for flower color formation in . The findings of this study introduce novel strategies for molecular design breeding aimed at manipulating flower color in .