Abstract

Purple-fleshed sweet potato (PFSP) ( Ipomoea batatas ) is a rich source of anthocyanins, which serve as potent antioxidants and contribute to stress tolerance. However, the molecular mechanisms regulating anthocyanin biosynthesis in PFSP under phosphorus stress remain poorly understood. In this study, integrated transcriptomic and metabolomic analyses were conducted using the sweet potato cultivar (Xuzishu No. 8) grown under three phosphorus treatments: XP0 (0 g), XP1 (1.85 g), and XP2 (3.70 g). Although phosphorous did not significantly affect total anthocyanin content, however, marked changes were observed in the activities of key biosynthetic enzymes (CHl, DFR, OPC, PAL and UFGT). RNA-seq analysis identified 8,906 differentially expressed genes (DEGs) with 11,215 novel genes across the treatments. KEGG pathway enrichment analysis revealed that most DEGs were associated phenylpropanoid biosynthesis. Metabolomic profiling detected 110 differentially expressed metabolites (DEMs) among which six were common to all treatments and sixteen metabolites were shared between the treatment groups. Functional annotation of DEMs indicated an overall suppression of anthocyanin biosynthesis pathway, across the treatments, whereas, flavone and flavonol biosynthesis remained consistently active. Notably, Quercetin-3-O-glucoside appeared to play a key role in the restoring anthocyanin biosynthesis. Integrated transcriptome-metabolome analysis showed a strong coordinated regulation between DEGs and DEMs, particularly within anthocyanin and flavonoid biosynthetic pathways. Furthermore, Canonical correspondence analysis (CCA) and principal component analysis (PCA) biplot further revealed that anthocyanin accumulation is controlled by the combined action of multiple genes, with Tai6.6720 identified as a key regulatory gene closely linked with active metabolites (Pelargonidin-3-O- glucoside and cyanidin-3-O- glucoside). Overall, these findings highlight the significant impact of phosph