Long-Term Salinity-Responsive Transcriptome in Advanced Breeding Lines of Tomato

Soil salinity and the scarcity of freshwater resources are two of the most common environmental constraints that negatively affect plant growth and productivity worldwide. The tomato (Solanum lycopersicum Mill.) plant is moderately sensitive to salinity. The identification of salinity-responsive genes in tomato that control long-term salt tolerance could provide important guidelines for its breeding programs and genetic engineering. In this study, a holistic approach of RNA sequencing combined with measurements of physiological and agronomic traits were applied in two advanced tomato breeding lines (susceptible L46 and tolerant L56) under long-term salinity stress (9.6 dS m^-1). Genotype L56 showed the up-regulation of known and novel differentially expressed genes (DEGs) that aid in the salinity tolerance, which was supported by a high salt tolerance index (81%). Genotype L46 showed both similar and different gene families of DEGs. For example, 22 paralogs of CBL-interacting kinase genes were more up-regulated in L56 than in L45. In addition, L56 deployed more SALT OVERLY SENSITIVE paralogs than L45. However, both genotypes showed the up-regulation of ROS-detoxifying enzymes and ROS-scavenging proteins under salinity stress. Therefore, L56 was more effective in conveying the stress message downstream along all available regulatory pathways. The salt-tolerant genotype L56 is genetically robust, as it shows an enhanced expression of a complete network of salt-responsive genes in response to saline conditions. In contrast, the salt-susceptible genotype L46 shows some potential genetic background. Both genotypes have great potential in future breeding programs.