Decoding the Genetic Basis of Salinity Tolerance in Tomatoes through Ion Transport and Stress Regulation

Salinity remains a major obstacle to tomato production; yet, the interplay between ion accumulation and gene expression in conferring salinity tolerance is not fully understood. In this study, the cultivars ‘Sanibel’ and ‘Tasti-Lee’ were subjected to four salinity treatments [1.5 (T0), 4 (T1), 8 (T2), and 12 (T3) dS m–1] to examine morphological, ionic, and molecular responses. Elevated salinity led to significant declines in shoot and root dry weight, plant height, root length, and leaf number, with the steepest reduction observed at 12 dS m–1 (T3). Ion profiling revealed increasing Na and Cl concentrations in roots and shoots. However, ‘Tasti-Lee’ appeared to reach its highest Na and Cl accumulation in leaves at 8 dS m–1. Both cultivars also showed diminished K in leaves and stems; yet root K unexpectedly rebounded at the highest salinity. Gene expression analysis revealed that SOS1, SOS2, and NHX1─key mediators of Na+ extrusion and sequestration─were upregulated in the roots of both cultivars, while HKT1 was downregulated, suggesting decreased Na+ retrieval under severe stress. In leaves, genes such as SAL1, CLCg, NPF2.4, and NPF2.5 were downregulated, likely limiting the additional ion influx into photosynthetically active tissues. Variety-specific regulation also emerged. In ‘Sanibel’, NHX2 and CCC were upregulated in roots, indicating reliance on vacuolar Na+ compartmentalization and enhanced Cl– regulation, while ‘Tasti-Lee’ downregulated NPF2.4, suggesting a different route for restricting Cl– movement. In leaves, AKT1 and HSP90.7 were induced under T3 in ‘Tasti-Lee’ but not in ‘Sanibel’, whereas CCC and CLCc were upregulated in ‘Sanibel’ only. These different mechanisms of controlling Na+ and Cl– underscore both shared and cultivar-specific salinity-tolerance strategies, providing crucial insights for developing salt-tolerant tomato lines.