Differential metabolic reprogramming of two potato (Solanum tuberosum L.) cultivars under Alternaria alternata infection and tenuazonic acid exposure using GC–MS and FTIR analyses

Potato ( Solanum tuberosum L.) is highly susceptible to Alternaria alternata and its phytotoxin tenuazonic acid (TeA), which disrupt host metabolism and induce oxidative stress. However, differences between toxin- and pathogen-driven metabolic reprogramming and their cultivar-specific responses remain unclear. This study integrates biochemical assays, FTIR spectroscopy, GC–MS-based metabolomics, and multivariate analyses to characterize stress responses in Kufri Bahar (KB) and Kufri Himalini (KH). Both TeA exposure and pathogen infection triggered strong biochemical reprogramming, with significant increases in total phenolics and flavonoids accompanied by enhanced antioxidant capacity (lower IC 50 in DPPH and ABTS assays). Pathogen infection consistently induced greater responses than TeA alone. FTIR analysis revealed treatment-specific biochemical signatures, including intensified hydroxyl and phenolic bands, enhanced protein-associated amide signals, and increased carbohydrate-linked absorptions, indicating coordinated macromolecular remodeling. GC–MS profiling identified 54 putatively annotated volatile and semi-volatile metabolites, predominantly including fatty acids, phenolics, aldehydes, hydrocarbons, and nitrogen-containing compounds, with pathogen-treated samples showing the greatest metabolic reprogramming. Multivariate analysis confirmed distinct metabolic states: PCA explained 68.1% of total variance and separated treatments, while PLS-DA achieved robust discrimination (R 2 = 0.97, Q 2 = 0.93; p < 0.01). VIP analysis highlighted lipid-derived and nitrogenous metabolites as the primary contributors to class separation. Notably, KH exhibited stronger accumulation of defense-related metabolites and tighter clustering under stress, indicating superior metabolic coordination compared to KB. Alternaria alternata induces more extensive metabolic reprogramming than TeA alone. The integration of biochemical assays, FTIR, metabolomics, and chemometrics provides a robust framework for stress discrimination. The identified metabolomic signatures and chemometric models provide a promising framework for disease monitoring and resistance screening in potato.