Apple scar skin viroid disease induced physicochemical and metabolic alterations in Apples

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Abstract Apple scar skin disease (ASSD), caused by Apple scar skin viroid (ASSVd), is characterized by peel scarring, cracking, dappling, and fruit deformation, resulting in reduced fruit quality and marketability. Despite its economic importance, the physicochemical and metabolic alterations underlying disease progression remain poorly understood. To address this knowledge gap, apple fruits representing four stages of ASSD (healthy, lightly infected, moderately infected, and highly infected) were comprehensively characterized. ASSVd infection was confirmed by RT-PCR, amplicon sequencing, and phylogenetic analysis. Fruit morphology and quality attributes, including firmness, total soluble solids (TSS), pH, titratable acidity (TA), and total phenolic content (TPC), were evaluated. ASSVd infection significantly reduced fruit weight and firmness and altered TSS and TA, indicating progressive deterioration of fruit quality. To investigate the underlying metabolic changes, peel and pulp tissues were analysed separately using gas chromatography-mass spectrometry (GC-MS), while major soluble sugars were quantified by 1 H nuclear magnetic resonance ( 1 H NMR) spectroscopy. Integrated metabolomic analyses revealed distinct tissue-specific metabolic reprogramming during disease progression. Major soluble sugars declined significantly during early infection, followed by tissue-dependent recovery at later stages, whereas organic acids, amino acids, phenolics, lipids, polyols, and pentacyclic triterpenoids exhibited dynamic stage-dependent changes. Notably, lupeol accumulated progressively, whereas ursolic acid and oleanolic acid declined, indicating disease-associated alterations in host triterpenoid metabolism. Multivariate analyses demonstrated clear metabolic separation among disease stages. Lupeol, ursolic acid, and chlorogenic acid were identified as candidate discriminatory metabolites in the peel, whereas myo-inositol, chlorogenic acid, and aspartic acid were identified in the pulp. Collectively, these findings demonstrate that ASSD induces coordinated, tissue-specific physicochemical and metabolic reprogramming that compromises postharvest fruit quality and reshapes defence-associated metabolism. This study provides the first integrated metabolomic characterization of ASSD progression and identifies potential metabolic biomarkers for disease diagnosis and severity assessment. Graphical Abstract

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