Pathway Crosstalk and Metabolic Relay in the Phenylpropanoid–Carotenoid Axis Orchestrate Petal Coloration in Kalanchoe blossfeldiana

Background: Flower color is a primary determinant of ornamental value in flowering plants. Although the biosynthetic pathways of major petal pigments have been extensively documented, the systems-level mechanisms coordinating color diversification across multiple cultivars of Kalanchoe blossfeldiana remain less understood. This study aimed to establish a comparative metabolomic and transcriptomic framework to elucidate these mechanisms. Methods: Petal tissues were collected from five cultivars with white, yellow, orange, red, and purple–red flowers at the full-bloom stage. Metabolomics was performed for flavonoids and carotenoids using UPLC-MS/MS, and transcriptome sequencing was conducted via Illumina NovaSeq 6000. Integrative analysis of metabolome and transcriptome data, together with weighted gene co-expression network analysis, was employed to identify key metabolites, differentially expressed genes, and associated regulatory networks. Quantitative PCR was used to validate the expression patterns of key structural genes. Results: Petal color variation was shaped by coordinated flux partitioning between flavonoid and carotenoid networks rather than by isolated activation of single pathways. A metabolic relay pattern was observed in the phenylpropanoid–flavonoid axis, wherein shared upstream activation fed divergent downstream branches that directed accumulation toward distinct anthocyanin or flavonol profiles. Notably, yellow pigmentation relied more heavily on flavonoid flux than on carotenoid accumulation, and orange coloration arose from the synergistic co-accumulation of multiple pigment classes. Transcriptional module analysis identified gene networks associated with specific color phenotypes. Conclusions: These findings provide a systems-level understanding of pathway crosstalk in flower color formation and offer candidate targets for molecular breeding in K. blossfeldiana and related ornamental plants.