Transcriptome–Metabolome Integration Reveals Mechanisms of Leaf Color Variation in Leafy Vegetable Sweet Potato

Leaf color, as a key ornamental and quality trait in leafy vegetable sweet potato, is controlled by the coordinated regulation of multiple pigment metabolic pathways. To dissect the mechanisms underlying leaf color variation, the integrated transcriptomic and metabolomic analyses were performed on three contrasting phenotypes: green (G), yellow (Y), and purple-red (R). The results showed that purplish-red leaves accumulated the highest levels of anthocyanins (16.36 mg·g−1) and total chlorophyll (2.54 mg·g−1), indicating that the synergistic accumulation of anthocyanins and chlorophyll contributes to their dark pigmentation. In contrast, yellow leaves contained the lowest carotenoid content yet displayed the highest carotenoid-to-chlorophyll ratio (6.44), suggesting that reduced chlorophyll levels coupled with a relatively higher carotenoid proportion underlie the yellow phenotype. Green leaves exhibited a more balanced pigment profile, with a total chlorophyll content of 1.94 mg·g−1. Transcriptomic profiling revealed elevated expression of anthocyanin biosynthetic genes CHS, CHI, F3H, and chlorophyll metabolism-related genes CHLG and CAO in purplish-red leaves, whereas carotenoid biosynthesis genes LCY and CYP97A3 showed specific regulation in yellow leaves. Collectively, these findings demonstrate that leaf color formation in leafy vegetable sweet potato is determined by the relative accumulation of chlorophylls, carotenoids, and anthocyanins, together with differential regulation of their biosynthetic pathways. This work provides novel insights into the molecular basis of leaf color variation and offers a theoretical foundation for genetic improvement of leafy vegetable sweet potato.