Tomato (Solanum lycopersicum) is one of the most important vegetable crops in the world and abiotic stresses often cause serious problems in tomato production. It is thus important to identify new regulators in stress response and to devise new approaches to promote stress tolerance in tomato. Previous studies have shown that small secreted peptides (SSPs) are important signal molecules regulating plant growth and stress response by mediating intercellular communication. However, little is known about tomato SSPs, especially their roles in responding to abiotic stresses. Here we report the identification of 1,050 putative SSPs in the tomato genome, 557 of which were classified into 38 known SSP families based on their conserved domains. GO and transcriptome analyses revealed that a large proportion of SlSSPs might be involved in abiotic stress response. Further analysis indicated that stress response related cis-elements were present on the SlCEP promotors and a number of SlCEPs were significantly upregulated by drought treatments. Among the drought-inducible SlCEPs, SlCEP10 and SlCEP11b were selected for further analysis via exogenous application of synthetic peptides. The results showed that treatments with both SlCEP10 and SlCEP11b peptides enhanced tomato drought stress tolerance, indicating the potential roles of SlSSPs in abiotic stress response. Graphical Abstract

The transfer of genetic material between stocks and scions of grafted plants has been extensively studied; however, the nature and frequency of the transferred material remain elusive. Here, we report a grafting system involving woody goji as the stock and herbaceous tomato as the scion, which was developed using in vitro and in vivo approaches; the results confirmed horizontal transfer of multiple nuclear DNA fragments from donor goji cells to recipient tomato cells. Tomato tissues containing goji donor DNA fragments at or near the grafting junctions had a perennial-biased anatomical structure, from which roots or shoots were regenerated. Most of the fragments were plasmid-like extrachromosomal circular DNAs (eccDNAs) present in the regenerants derived from the cells and in their asexual offspring. Plants with transferred eccDNAs in regenerated roots or shoots (designated “Go-tomato”) were grown perennially and showed excellent agronomic performance. The present study provides new insights into the replication, expression, and potential function of eccDNAs in the pleiotropic traits of Go-tomato. Mobile eccDNAs offer evidence of stock-to-scion horizontal DNA transfer beyond chromosomes and organelles, thereby contributing to the molecular understanding of graft-induced genetic variation, evolution, and breeding.

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.