Alternaria solani infection reprograms potato leaf metabolism and highlights potential defence and metabolic markers

Potato ( Solanum tuberosum L.), the world’s fourth most cultivated crop, suffers yield losses of up to 40-50% from early blight caused by the necrotrophic fungal pathogen Alternaria solani . In this study we performed gas chromatography-mass spectrometry (GC-MS)-based untargeted metabolomics to characterize temporal alterations in metabolite composition, metabolic pathway regulation, and discriminatory biomarker metabolites in the susceptible Indian potato variety Kufri Jyoti , analyzing infected leaves, non-infected leaves, and lesion-associated necrotic tissues across four days post-inoculation (DPI).Metabolite annotation identified 58 compounds, including sugars, organic acids, amino acids, and secondary metabolites.. Multivariate analyses resolved distinct, largely non-overlapping metabolic clusters for control, infected leaves (1-4 DPI), and lesion tissue (Bs1-Bs3). A biphasic metabolic response was observed: early infection (1-2 DPI) was characterized by general suppression of primary metabolism, while late infection (3-4 DPI) showed pronounced upregulation of glycolysis, the TCA cycle, GS/GOGAT, and the shikimate pathway. Key discriminatory metabolites included asparagine, oxoproline, GABA, phenylalanine, and aromatic amino acids. Lesion tissues exhibited distinct metabolic fingerprints, with early disruption of amino acid recycling followed by a late rebound of defense-associated metabolites. Notably, defence-associated phenolics were detected exclusively within lesion tissue and were absent from whole-leaf profiles, demonstrating that spatially resolved lesion sampling captures defence chemistry that whole-leaf analysis alone would miss. The identified biomarker metabolites, particularly those linked to the shikimate and GS/GOGAT pathways, represent promising candidates for metabolite-assisted breeding and targeted crop protection strategies against early blight in potato.