Integrated Physiological and Transcriptomic Analyses Reveal the Mechanism of Salt Acclimation-Induced Salinity Tolerance in Tomato Seedlings

Although salt acclimation is a recognized strategy for improving crop salt tolerance, its specific role in tomato (Solanum lycopersicum L.) remains unclear. This study investigated the effects of salt acclimation on enhancing salt tolerance in tomato seedlings through physiological and transcriptomic analyses. Here, we found that T3 acclimation treatment (irrigation with 14 mL of 7.5 g L−1 NaCl solution per plant) effectively conferred enhanced salt tolerance in tomato seedlings, with plant height, stem diameter, leaf area, chlorophyll content, net photosynthetic rate, and soluble protein content increasing by 4.52, 5.13, 3.16, 10.78, 11.85, and 25.96%, respectively, compared with the control. T3 treatment also reduced oxidative damage and ionic stress, as evidenced by reduced electrolyte leakage, lower malondialdehyde content, and a decreased root Na+/K+ ratio, while simultaneously boosting antioxidant enzyme activities. Membership function analysis confirmed T3 as the optimal treatment, with a 9 d duration consistently benefiting multiple cultivars. Transcriptomic analysis revealed that salt acclimation upregulated genes associated with phenylpropanoid biosynthesis, lignin catabolic process, and peroxidase activity, suggesting that these pathways might mediate acclimation-induced salt tolerance through promoting lignin biosynthesis to reduce Na+/K+ ratio and enhancing reactive oxygen species’ scavenging capacity to maintain cellular homeostasis. Our results indicate that tomato seedlings acclimated with 14 mL of 7.5 g L−1 NaCl solution per plant for 9 d significantly improves salt tolerance through coordinated physiological adjustments and transcriptional reprogramming.