Multi-omics analysis reveals improvement of tomato quality by grafting on goji rootstock

Abstract

Abstract Background Tomato quality is a complex trait influenced by multiple genes involved in various complicated metabolic pathways. Materials and Methods This study sought to improve tomato taste and quality by grafting on goji rootstock. We integrated physiological and biochemical indicators, as well as metabolic and transcriptomic analysis, to evaluate tomato quality. Results The grafted tomatoes showed significant increases in soluble solids (51.48%), vitamin C (16.86%), soluble protein (16.19%), titratable acid (11.73%), anthocyanin (11.43%), and polysaccharide (9.43%) content compared to those of the control. Metabolomics analysis identified 234 differentially accumulated metabolites and transcriptome analysis identified 4213 differentially expressed genes between grafted and control tomatoes at three ripening stages (mature green, turning, and fully red). A total of 93 phenolic compounds, including flavonoids and phenolic acids, showed differential accumulation patterns between grafted and control tomatoes at the fully red stage. These changes were attributed to the upregulation of key genes (F3ʹH, F3ʹ5ʹH, DFR, and ANS) associated with flavonoids and anthocyanin synthesis in the goji rootstock compared to those of the control. The expression of genes involved in sucrose hydrolysis and starch synthesis, including invertase (INV), sucrase synthase (SUS), and beta-amylase (BAM) genes, were suppressed by goji grafting, resulting in increased levels of sugars. In addition, the consistency between the transcriptomic and metabolomic data provided a robust validation of the observed quality changes. Conclusions Taken together, our results demonstrate that grafting onto goji rootstock improves tomato quality by modulating multiple genes involved in phenylpropanoid, sucrose, and starch pathways during fruit development, providing valuable insights for improving the quality and taste of tomato.