The TONNEAU1 Recruited Motif (TRM) gene family is integral to the growth and development of various plants, playing a particularly critical role in regulating the shape of plant organs. While the functions of the TRM gene family in other plant species have been documented, knowledge regarding the members of the tomato (Solanum lycopersicum). SlTRM gene family remains limited, and their specific roles are not yet well understood. In this study, we identified and analyzed 28 members of the SlTRM gene family in tomato using bioinformatics approaches based on the latest whole genome data. Our analysis included the examination of protein structures, physicochemical properties, collinearity analysis, gene structures, conserved motifs, and promoter cis-acting elements of the SlTRM gene family members. The phylogenetic analysis indicated that both tomato and Arabidopsis thaliana are categorized into five distinct subfamilies. Furthermore, we conducted a three-dimensional structure prediction of 28 SlTRM genes for the first time, utilizing AlphaFold3, a deep learning architecture developed by DeepMind. Subsequently, we analyzed public transcriptome data to assess the tissue specificity of these 28 genes. Additionally, we examined the expression of SlTRM genes using RNA-seq and qRT-PCR techniques. Our analysis revealed that SlTRM25 was significantly differentially expressed, leading us to hypothesize that it may be involved in the development of lateral branches in tomatoes. Finally, we predicted the regulatory interaction network of SlTRM25 and identified that it interacts with genes such as SlFAF3/4b, SlCSR-like1, SlCSR-like2, and SlTRM19. This study serves as a reference for the investigation of the tomato TRM gene family members and introduces a novel perspective on the role of this gene family in the formation of lateral branches in tomatoes, offering both theoretical and practical significance.

Leaves are the main site of photosynthesis in plants, and leaf color plays a major role in crop quality, yield, resistance, as well as other aspects. Although the genes related to photosynthesis have been well characterized in plants in general, yellow-green leaf mutants have not yet been fully studied in tomatoes. In the present study, a dark green leaf (GL) mutant was isolated from yellow-leaf tomato (wild-type). The dark GL displays a distinct yellow-green phenotype, and has a greater chlorophyll content and higher photosynthetic rate. Furthermore, the lamellae were clear, and the stroma and grana were orderly, with more stacking and larger starch grains according to the ultrastructure analysis of chloroplasts in GL leaves. Comparative transcriptome analysis of GL and wild-type plants was performed to identify the pathways and genes related to photosynthesis. In this work, a total of 292 differentially expressed genes (DEGs) between GL plants and WT plants were identified, of which 131 genes were upregulated and 161 genes were downregulated. The diterpenoid biosynthesis and photosynthesis antenna proteins were the two most significantly enriched in the first 20 pathways according to KEGG analysis. Most of the DEGs involved in diterpenoid biosynthesis and photosynthesis were antenna proteins. The photosynthesis antenna protein Solyc02g071030 (LHCB1) and the diterpenoid biosynthesis-related genes, Solyc08g005710 and Solyc09g059240, were significantly upregulated in GL leaves compared with WT leaves. The expression patterns of the DEGs were similar to those determined by qRT-PCR. Overall, our research not only revealed the diterpenoid biosynthesis and photosynthesis pathways involving in leaf color variation, but also identified the putative target genes for genetic manipulation in the future.

To clarify the regulatory mechanism of NLA on tomato plant architecture and fruit quality, wild-type (WT), nla mutant (narrow leaf angle), and NLA overexpression lines (OE1, OE2) were used as materials, and the study was carried out through genetic analysis, phenotypic and quality determination, and gene expression analysis. The results showed that the tomato leaf angle is controlled by a single gene with semi-dominant inheritance. The nla mutant forms a compact plant architecture due to reduced cell volume at the leaf angle. During vegetative growth, it exhibited significantly increased plant height and decreased stem diameter and crown width. During reproductive growth, it showed significantly higher height of the first inflorescence node and a significantly higher number of the first flowering node. The nla mutant maintained a higher SPAD value during the whole growth period. Mutation of NLA had no significant effect on soluble solids content, but significantly increased flavonoid and titratable acid contents. Meanwhile, the compact architecture optimizes plant spatial distribution, and higher flavonoid content improves antioxidant capacity. Molecular mechanism analysis combined with GA quantification showed that the nla mutant exhibited significantly higher contents of bioactive GA₁ and GA₄, which were closely associated with up-regulated expression of GA biosynthetic genes SlGA20ox1 and SlGA20ox2, as well as down-regulated expression of GA catabolic genes SlGA2ox4 and SlGID1.This study provides a theoretical basis for high-photosynthetic-efficiency breeding and high-quality cultivation of tomato.