Genetic architecture of the tomato fruit lipidome

The lipid composition of tomato (Solanum lycopersicum L.) fruit plays a crucial role in determining fruit quality, nutritional value, and the biosynthesis of key volatile organic compounds. Despite this importance, the metabolic diversity and genetic regulation of lipid composition in tomato fruit remain poorly understood. Here, we performed a genome-wide association study and QTL mapping for fruit lipid content from 550 tomato accessions and 107 backcross inbred lines in two consecutive seasons. Over 130 lipid compounds were identified in the population, allowing for the identification of over 600 metabolic QTL. We further described and validated candidate genes associated with lipid content. Among them is a lipase-like protein (TomLLP) whose function was validated in vivo using overexpression lines in tomato and knockout mutants in Arabidopsis. We also identified functions for three enzymes: a class III lipase (Sl-LIP8), a cyclopropane-fatty-acyl-phospholipid synthase (CFAPS1), and lipoxygenase C (TomLoxC). By utilizing knockout lines for CFAPS1 and CRISPR-Cas9 loss-of-function lines for Sl-LIP8 and TomLoxC, we demonstrated the functional importance of these enzymes in fruit lipid metabolism. Our study provides a comprehensive analysis of the tomato fruit lipidome and insights into key genes that shape natural variation in lipid content, establishing a framework for exploring how lipid dynamics may influence traits such as flavor and volatile formation.