Integrated metabolomics and transcriptomics reveals difference involved in flavonoid and indole alkaloids biosynthesis in potato tuber flesh

Colored potatoes have garnered attention due to their higher nutrients compared to regular potatoes. This study describes a combined transcriptomic and metabolomic analysis of potato tubers originating from a single sexual cross between two parents with differing tuber skin and flesh colors. Through the use of RNA-seq, and UPLC-MS/ MS metabolomics, this study aimed to elucidate the genetic and metabolic variations involved in the trans-mission of traits from tetraploid potato parents to hybrid F1 offspring. Our analysis revealed unique genes and metabolites associated with flavonoids and alkaloids within each group of offspring. Phenolic acids, flavonoids, and alkaloids are highlighted as key contributors to the positive heterosis observed in the tubers of potato hy-brids, as assessed by calculating mid-parent heterosis for metabolites in three potato hybrids. At the overall metabolites level, hybrid SB (red-skinned and red-fleshed) exhibited a higher mid-parent heterosis than hybrid SA (purple-skinned and purple-fleshed) and SC (yellow-skinned and yellow-fleshed). Within hybrid SB tuber, specific accumulations of luteolin, salicin, isovitexin, and esculeoside B-5 were identified. Moreover, co-expression networks and correlation analysis pinpoint genes related to flavonoid and alkaloid biosynthesis. Notably, StDFR (dihydroflavonol reductase), a gene involved in flavonoid synthesis in potato tuber flesh, exhibits heightened expression in colored potato flesh. Additionally, we identified StYUCCA (indole-3-pyruvate mono-oxygenase), a gene regulating indole alkaloids synthesis, with elevated expression in yellow potato flesh. These findings provide insights into the utilization of heterosis breeding and the regulation of genes-metabolites in colored potato tuber flesh.