Comparative transcriptome and metabolome profiling uncovers tissue-specific mechanisms in potato flesh and skin

Potato (Solanum tuberosum L.), a globally cultivated tuber crop, is crucial for food security. The metabolic specialization between tuber skin and flesh directly influences tuber stress resistance and quality. Transcriptome-metabolome analysis of two cultivars (IAW30 and IAY31) revealed tissue-specific metabolic profiles and molecular mechanisms. Flesh accumulates primary metabolites such as saccharides, amino acids and derivatives, and vitamins, whereas skin is enriched in secondary metabolites including glycoalkaloids and flavonoids. Marker metabolite analysis identified four flesh-specific and nine skin-specific compounds. Pathway enrichment indicated flesh metabolism directed toward nutrient storage, with significant enrichment in starch and sucrose metabolism and amino-acid biosynthesis. In contrast, skin metabolism is defense-oriented, showing pronounced enrichment in phenylpropanoid, solanine, flavonoid and suberin biosynthesis. Nine candidate genes from these key pathways provide molecular targets for developing new potato germplasm with high nutritional value and low toxicity. This integrative insight advances molecular insights for breeding strategies to optimize tuber composition.