To explore the mechanism by which γ-aminobutyric acid (GABA) regulates the response of different salt-sensitive tomato seedlings under salt stress conditions, we used the previously selected salt-sensitive tomato ‘M82’ and the salt-tolerant introgression line ‘IL-7-5-5’. The following three treatments were set up: (1) a normal nutrient solution concentration as the control, (2) a nutrient solution with 200 mmol·L⁻¹ NaCl, and (3) a nutrient solution with 200 mmol·L⁻¹ NaCl and 35 mmol·L⁻¹ GABA. The concentration of the reactive oxygen species metabolism-related compounds and antioxidant enzyme activity in the leaves of tomato seedlings subjected to the different treatments were measured, and transcriptome and metabolome analyses were conducted. After adding GABA, the SOD, POD, and APX activity in the leaves of the ‘M82’ seedlings significantly increased, while the GR activity significantly decreased. In the ‘IL-7-5-5’ seedlings, the CAT, APX, and GR activity significantly increased. The combined results from the transcriptome and metabolome analysis in leaves indicated that in ‘M82’ seedlings, 52 metabolic pathways were enriched, which included plant signal transduction pathways, phenylpropanoid biosynthesis pathways, and amino sugar and nucleotide sugar metabolism pathways. In the salt-tolerant ‘IL-7-5-5′ seedling leaves, 59 metabolic pathways were enriched, which included plant signal transduction pathways, amino acid biosynthesis pathways, and carbon metabolism pathways. A further analysis revealed that both varieties had a higher number of differentially enriched genes and differential metabolites belonging to the plant hormone signal transduction and amino acid biosynthesis pathways, indicating that GABA enhances the salt tolerance of tomato seedlings by regulating these two mechanisms.

The mitochondrial calcium uniporter (MCU) is a key channel controlling mitochondrial Ca²⁺ homeostasis, yet its role in plant stress responses remains unclear. Using the tomato pan-genome, this study identified 66 MCU genes across 12 tomato species and grouped them into two distinct evolutionary subfamilies. Phylogenetic, collinearity, and selection pressure analyses revealed that MCU genes are evolutionarily conserved and have undergone strong purifying selection. In addition, one MCU gene located on chromosome 6 appears to have originated before the divergence of monocots and dicots, indicating an ancient evolutionary trajectory. Gene structure and conserved motif analyses confirmed their structural conservation, while promoter cis-element analysis suggested that MCU genes are widely involved in light and hormone responsiveness. Expression profiling under salt stress showed that multiple MCU genes are differentially regulated in a time-dependent manner: SolycMCU1 and SolycMCU2 respond rapidly at early stages, whereas SolycMCU5 and SolycMCU6 are upregulated during middle and late phases. These results highlight the functional diversification of MCU genes in tomato under salt stress. This study provides the first comprehensive evolutionary and functional analysis of the tomato MCU gene family, offering insights into their stress-regulatory mechanisms and potential use in breeding salt-tolerant tomatoes.