Multi-omics, network pharmacology, and molecular docking provide insights into the genetic basis, bioactive, and potential antioxidant mechanisms in potato (Solanum tuberosum L.) flesh

• Lutein, pelargonidin-3-O-rutinoside, and delphinidin-3-O-rutinoside underlie yellow, red, and purple potato flesh pigmentation. • Flavonoids and phenolic acids are key contributors to antioxidant activity in red and purple potato fleshes. • F3H, F3′5′ H , and DFR regulate anthocyanin biosynthesis, while BCH1 and BCH2 promote carotenoid accumulation in yellow fleshes. • Transcription factors AN1, TT8, ASIL2, and WRKY6 regulate anthocyanin and carotenoid biosynthesis. • Pinobanksin and rhamnocitrin are identified as potential antioxidant targets. Potato ( Solanum tuberosum L.) is a major food crop with notable antioxidant potential. Among its various types, coloured-flesh potatoes have attracted widespread attention because of their strong antioxidant capacity and potential pharmacological effects, including blood pressure reduction and lipid-lowering properties. However, the differences in bioactivity and potential antioxidant mechanisms of different coloured potato flesh remain unclear. We employed a multi-omics approach, network pharmacology, and molecular docking, to investigate the genetic basis, bioactive compounds, and antioxidant mechanisms of four types of potato flesh. Metabolomic analysis revealed that anthocyanins were absent in bright-fleshed (white- and yellow-fleshed) potatoes, whereas lutein, pelargonidin-3-O-rutinoside, and delphinidin-3-O-rutinoside accumulated in association with yellow, red, and purple pigmentation, respectively. Random forest modelling revealed that flavonoids are the major contributors to antioxidant activity in coloured-flesh (red- and purple-fleshed) potatoes, followed by phenolic acids. Transcriptomic profiling indicated that the high expression of F3H, F3 ' 5′ H, and DFR promoted anthocyanin biosynthesis in coloured-flesh potatoes, while BCH1 and BCH2 enhanced carotenoid accumulation in yellow-fleshed potatoes. Further analysis of gene co-expression networks and promoter cis-elements revealed that TFs AN1, TT8, ASIL2 , and WRKY6 played regulatory roles in the biosynthesis of anthocyanins and carotenoids. Network pharmacology and molecular docking identified pinobanksin and rhamnocitrin as key antioxidant compounds that potentially target proteins, including AKT1, PTGS2, ESR1, PPARG, and SRC. These findings provide comprehensive insights into the molecular and metabolic regulation of pigmentation and antioxidant activity in potatoes and provide promising targets for improving the nutritional quality and functional traits of potato germplasm.