Combined Metabolome and Transcriptome Analyses Reveals Anthocyanin Biosynthesis Profiles Between Purple and White Potatoes

Colored potatoes with red and purple skin or flesh possess significant nutritional value and health benefits due to their rich anthocyanin content. To investigate the genetic mechanisms underlying color formation, the high-anthocyanin-content purple-skinned and purple-fleshed potato line 15-12-16, and the white-skinned and white-fleshed Xiazhai 65 variety were used for ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, which was conducted to identify and quantify anthocyanins. RNA sequencing was performed to analyze the transcriptome. The results indicated a significant upregulation of genes within the anthocyanidin biosynthesis pathway in the purple potato, while these genes were either downregulated or absent in the white potato. The bHLH, MYB, and WRKY gene families exhibited a greater number of regulatory members, suggesting their pivotal role in color formation. Integrated analysis of the transcriptional and metabolic revealed that 12 differentially expressed genes (DEGs) related to the anthocyanidin biosynthetic had a significant correlation with 18 anthocyanin metabolites. Notably, the key gene St5GT in the anthocyanidin biosynthesis pathway was markedly upregulated in the purple skin and flesh. Furthermore, the overexpression of St5GT (PGSC0003DMG400004573) in tobacco contributed to anthocyanin accumulation. The expression of 10 DEGs was validated through quantitative real-time PCR. In conclusion, these findings provide new insights into anthocyanin biosynthesis and accumulation in purple potatoes, offering valuable candidate genes for the future breeding of colored potatoes.