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

In this study, we sought to improve tomato taste and quality by grafting on goji rootstock. 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 %) contents 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 (F3'H, F3’5’H, DFR, ANS) associated with flavonoids and anthocyanin synthesis in the goji rootstock compared to the control. The expression of genes involved in sucrose hydrolysis and starch synthesis, including the 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. Altogether, 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.