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Abstract
The rising demand for organic food reflects growing consumer awareness of sustainable and health-conscious dietary choices. However, the current understanding of chemical diversity and related quality and nutritional value of organic crops is limited, with studies primarily focusing on a small subset of compounds, such as phenolics. This study aims to bridge this knowledge gap by comprehensively investigating the chemical composition of organic tomatoes compared to their conventional counterparts using pathway-based metabolomics approach. Two tomato cultivars 'Estiva' and 'Tomimaru Muchoo,’ were collected from three distinct farming systems: organic field, conventional field, and organic high-tunnel greenhouse. Marker compounds were first selected from differentially expressed metabolites from the relevant literature, followed by pathway-based metabolomics to identify candidate pathways potentially rewiring in organic tomatoes. Metabolomic analysis employed advanced analytical techniques, including Liquid Chromatography-Mass Spectrometry (LC-MS), High Performance Liquid Chromatography-Refractive Index Detector (HPLC-RID), and Gas Chromatography-Mass Spectrometry (GC-MS), to analyze non-volatiles, sugars, and volatile compounds, respectively, within the selected pathways. Differentially expressed metabolites between groups (e.g., organic field vs. conventional field) were identified and metabolic mechanisms through the pathways involved in organic tomato production were elucidated. This knowledge can be applied across diverse agricultural contexts, from crop breeding to optimizing cultivation practices for enhanced nutritional quality and consumer appeal.