Transcriptomic analyses reveal the potential regulators of the storage root skin color in sweet potato

Background Sweet potato ( Ipomoea batatas (L.) Lam.) is an important storage root crop exhibiting diverse storage root skin and flesh colors across varieties. The storage root skin color (SRSC) is a vital commercial trait which significantly influences the marketability and consumer preference of sweet potato. Methods To clarify the regulatory mechanism of SRSC, the sweet potato storage root of two clones derived from a common origin, designed as M1-125 (red skin and yellow flesh) and M1-125T (yellow skin and yellow flesh), were sampled and transcriptomic sequenced in this study. Results Comparative analysis revealed that differentially expressed genes (DEGs) in the root skin were predominantly enriched in flavonoid and anthocyanin biosynthesis pathways. Key structural genes, including chalcone synthase ( CHS ), chalcone-favanone isomerase ( CHI ), favanone 3-hydroxylase ( F3H ) and dihydroflavonol 4-reductase ( DFR ), exhibited higher expression levels in the root skin of M1-125. Notably, a subset of myeloblastosis (MYB) transcription factors showed significant expression changes between two genotypes. Based on the protein-protein interaction (PPI) network, phylogenetic analysis and expression pattern, IbMYB75 , IbMYB3 , IbMYB6 and IbMYB4 were thought to be the cooperative regulators of root skin color. These findings provide valuable insights and foundation for further elucidating the molecular mechanisms governing skin color of sweet potato storage root.