Rootstock-Dependent Regulation of Tomato Yield and Fruit Quality Revealed by Widely Targeted Metabolomics

In tomato production, grafting enhances stress resistance, increases yield, and improves fruit quality. However, the selection of rootstock types limits its broader adoption. This study systematically evaluated the effects of grafting with 16 different rootstocks on tomato survival rate and yield. Fruits from four rootstocks, Gangshi 319 self-grafted (CK), Gangshi 319 seedlings (A), Torubam (T), and Fanzhen No. 1 (F), were further selected for fruit quality analysis and broad target metabolomics. The results showed that, except for Qiezhen No. 3 (QZ3), the graft survival rates of all rootstocks exceeded 95%. Grafting with rootstock F significantly increased yield per plant and soluble solids content, whereas rootstock T significantly reduced both traits. Broad target metabolomics analysis identified 18 major metabolite categories, including lipids, ketoaldehydes and esters, and terpenoids. KEGG pathway enrichment analysis revealed that differentially accumulated metabolites between the F and T treatments were primarily enriched in pathways such as the citric acid cycle, phenylpropanoid biosynthesis, glyoxylate and dicarboxylate metabolism, flavonoid biosynthesis, cysteine and methionine metabolism, and glycerophospholipid metabolism. These findings indicate that rootstock F effectively enhances tomato fruit yield and soluble solids accumulation by coordinating primary and secondary metabolism. This study provides important metabolic level insights for the selection and application of high quality and high yield tomato rootstocks in grafting.