Integrative transcriptomic and metabolomic analysis reveals molecular mechanisms in skin color variation in sweetpotato.

The skin color of the sweetpotato is an important indicator of consumer preference and varietal differentiation and it plays a significant role in the development of the sweetpotato industry. In this study, Pushu 32 (PsR: red skin and orange flesh) and its natural mutant (PsW: yellow skin and orange flesh) were used as experimental materials to investigate the molecular mechanisms underlying skin color variation through transcriptomics and metabolomics. Integrated transcriptomics and metabolomics analyses identified 308 differentially accumulated metabolites (DAMs) and 1631 differentially expressed genes (DEGs), which mainly enriched in anthocyanin and flavonoid biosynthesis pathways. And the primary metabolic basis for the skin color transition from red to yellow was a decrease in the accumulation of red pigments such as Cyanidin-3-O-Galactoside accompanied by an increase in the accumulation of yellow compounds such as Astragalin. The qRT-PCR analysis showed higher expression levels of flavonoid biosynthetic genes (4CL, CHS, CHI, F3H, F3'H, DFR, ANS, and GST) in PsR. Whereas, the FLS and HCT, which regulate the redirection of metabolic intermediate products to Chlorogenic acids, Quercetin and Kaempferol pathways, showed significantly higher expression in PsW. Correspondingly, the content of derivative compounds such as Chlorogenic acids, Quercetin, and Kaempferol were significantly higher in PsW. Moreover, two MYB transcription factors (g17105 and g2322) were proposed as candidate regulators potentially involved in the anthocyanin biosynthesis in sweetpotato skin. Collectively, these findings provide new insights into the molecular mechanisms of skin color formation in sweetpotato and offer a valuable foundation for future functional genomic studies.