Molecular insights into the role of plant transporters in salt stress response

The homeostasis of ions and reactive oxygen species in root and shoot play crucial roles in the tolerance of alfalfa to salt alkali stress

High pH saline-alkali stress, mainly NaHCO3, limited the development of animal husbandry in Songnen Plain. Ion imbalance and reactive oxygen species (ROS) metabolism disorder caused by saline-alkali stress inhibited plant growth. In this study, we compared the differences in ion absorption, transport and ROS metabolism between saline-tolerant alfalfa (ZD) and saline-sensitive alfalfa (ZM) under NaHCO3 stress using physiology and transcripomics techniques. WGCNA analysis identified key genes associated with NaHCO3 stress-induced changes. NaHCO3 stress inhibited the absorption of K+ and Mg2+, but activated Ca2+ signal. Furthermore, ZD maintained higher K+, Mg2+ and Ca2+ contents and the K+/Na+ ratio than ZM, this is mainly related to the higher expression of proteins or channel-encoding genes involved in ion absorption and transport in ZD. Antioxidant enzyme systems can be activated in response to NaHCO3 stress. Peroxidase (EC 1.11.1.6), catalase (EC 1.11.1.7) and glutathione transferase (EC 2.5.1.18) activities were higher in ZD than ZM, and most genes encoding the relevant enzymes also demonstrated a stronger up-regulation trend in ZD. Although NaHCO3 stress inhibited Trx-Prx pathway, ZD related enzymes and their genes were also inhibited less than ZM. WGCNA results identified many genes involved in ion absorption, transport and antioxidant systems that play an important role in NaHCO3 stress adaptation. Collectively, ZD has the stronger ion homeostasis regulation and ROS scavenging ability, so it's more resistant to NaHCO3. The results provide theoretical guidance for further understanding of the molecular mechanism of NaHCO3 resistance and provide potential genes for research to improve saline-alkali tolerance in alfalfa.

Plant membrane transporters function under abiotic stresses: a review

MAIN CONCLUSION

In the present review, we discussed the detailed signaling cascades via membrane transporters that confer plant tolerance to abiotic stresses and possible significant use in plant development for climate-resilient crops. Plant transporters play significant roles in nutrient uptake, cellular balance, and stress responses. They facilitate the exchange of chemicals and signals across the plant's membrane by signal transduction, osmotic adjustment, and ion homeostasis. Therefore, research into plant transporters is crucial for understanding the mechanics of plant stress tolerance. Transporters have potential applications in crop breeding for increased stress resistance. We discuss new results about various transporter families (ABC, MATE, NRAMP, NRT, PHT, ZIP), including their functions in abiotic stress tolerance and plant development. Furthermore, we emphasize the importance of transporters in plant responses to abiotic stresses such as drought, cold, salt, and heavy metal toxicity, low light, flooding, and nutrient deficiencies. We discuss the transporter pathways and processes involved in diverse plant stress responses. This review discusses recent advances in the role of membrane transporters in abiotic stress tolerance in Arabidopsis and other crops. The review contains the genes discovered in recent years and associated molecular mechanisms that improve plants' ability to survive abiotic stress and their possible future applications by integrating membrane transporters with other technologies.

Mechanisms by Which Exogenous Substances Enhance Plant Salt Tolerance through the Modulation of Ion Membrane Transport and Reactive Oxygen Species Metabolism

Soil salinization is one of the major abiotic stresses affecting plant growth and development. Plant salt tolerance is controlled by complex metabolic pathways. Exploring effective methods and mechanisms to improve crop salt tolerance has been a key aspect of research on the utilization of saline soil. Exogenous substances, such as plant hormones and signal transduction substances, can regulate ion transmembrane transport and eliminate reactive oxygen species (ROS) to reduce salt stress damage by activating various metabolic processes. In this review, we summarize the mechanisms by which exogenous substances regulate ion transmembrane transport and ROS metabolism to improve plant salt tolerance. The molecular and physiological relationships among exogenous substances in maintaining the ion balance and enhancing ROS clearance are examined, and trends and research directions for the application of exogenous substances for improving plant salt tolerance are proposed.

Combined transcriptomics and metabolomics analysis reveals salinity stress specific signaling and tolerance responses in the seagrass Zostera japonica

KEY MESSAGE

Multiple regulatory pathways of Zostera japonica to salt stress were identified through growth, physiological, transcriptomic and metabolomic analyses. Seagrasses are marine higher submerged plants that evolved from terrestrial monocotyledons and have fully adapted to the high saline seawater environment during the long evolutionary process. As one of the seagrasses growing in the intertidal zone, Zostera japonica not only has the ability to quickly adapt to short-term salt stress but can also survive at salinities ranging from the lower salinity of the Yellow River estuary to the higher salinity of the bay, making it a good natural model for studying the mechanism underlying the adaptation of plants to salt stress. In this work, we screened the growth, physiological, metabolomic, and transcriptomic changes of Z. japonica after a 5-day exposure to different salinities. We found that high salinity treatment impeded the growth of Z. japonica, hindered its photosynthesis, and elicited oxidative damage, while Z. japonica increased antioxidant enzyme activity. At the transcriptomic level, hypersaline stress greatly reduced the expression levels of photosynthesis-related genes while increasing the expression of genes associated with flavonoid biosynthesis. Meanwhile, the expression of candidate genes involved in ion transport and cell wall remodeling was dramatically changed under hypersaline stress. Moreover, transcription factors signaling pathways such as mitogen-activated protein kinase (MAPK) were also significantly influenced by salt stress. At the metabolomic level, Z. japonica displayed an accumulation of osmolytes and TCA mediators under hypersaline stress. In conclusion, our results revealed a complex regulatory mechanism in Z. japonica under salt stress, and the findings will provide important guidance for improving salt resistance in crops.

Multi-Omics Analysis of the Effects of Soil Amendment on Rapeseed (Brassica napus L.) Photosynthesis under Drip Irrigation with Brackish Water

Drip irrigation with brackish water increases the risk of soil salinization while alleviating water shortage in arid areas. In order to alleviate soil salinity stress on crops, polymer soil amendments are increasingly used. But the regulation mechanism of a polymer soil amendment composed of polyacrylamide polyvinyl alcohol, and manganese sulfate (PPM) on rapeseed photosynthesis under drip irrigation with different types of brackish water is still unclear. In this field study, PPM was applied to study the responses of the rapeseed (Brassica napus L.) phenotype, photosynthetic physiology, transcriptomics, and metabolomics at the peak flowering stage under drip irrigation with water containing 6 g·L-1 NaCl (S) and Na2CO3 (A). The results showed that the inhibitory effect of the A treatment on rapeseed photosynthesis was greater than that of the S treatment, which was reflected in the higher Na+ content (73.30%) and lower photosynthetic-fluorescence parameters (6.30-61.54%) and antioxidant enzyme activity (53.13-77.10%) of the A-treated plants. The application of PPM increased the biomass (63.03-75.91%), photosynthetic parameters (10.55-34.06%), chlorophyll fluorescence parameters (33.83-62.52%), leaf pigment content (10.30-187.73%), and antioxidant enzyme activity (28.37-198.57%) under S and A treatments. However, the difference is that under the S treatment, PPM regulated the sulfur metabolism, carbon fixation and carbon metabolism pathways in rapeseed leaves. And it also regulated the photosynthesis-, oxidative phosphorylation-, and TCA cycle-related metabolic pathways in rapeseed leaves under A treatment. This study will provide new insights for the application of polymer materials to tackle the salinity stress on crops caused by drip irrigation with brackish water, and solve the difficulty in brackish water utilization.

Genome-wide identification of the cation/proton antiporter (CPA) gene family and functional characterization of the key member BnaA05.NHX2 in allotetraploid rapeseed

Rapeseed (Brassica napus L.) is susceptible to nutrient stresses during growth and development; however, the CPA (cation proton antiporter) family genes have not been identified in B. napus and their biological functions remain unclear. This study was aimed to identify the molecular characteristics of rapeseed CPAs and their transcriptional responses to multiple nutrient stresses. Through bioinformatics analysis, 117 BnaCPAs, consisting of three subfamilies: Na+/H+ antiporter (NHX), K+ efflux antiporter (KEA), and cation/H+ antiporter (CHX), were identified in the rapeseed genome. Transcriptomic profiling showed that BnaCPAs, particularly BnaNHXs, were transcriptionally responsive to diverse nutrient stresses, including Cd toxicity, K starvation, salt stress, NH4+ toxicity, and low Pi. We found that the salt tolerance of the transgenic rapeseed lines overexpressing BnaA05.NHX2 was significantly higher than that of wild type. Subcellular localization showed that BnaA05.NHX2 was localized on the tonoplast, and TEM combined with X-ray energy spectrum analysis revealed that the vacuolar Na+ concentrations of the BnaA05.NHX2-overexpressing rapeseed plants were significantly higher than those of wild type. The findings of this study will provide insights into the complexity of the BnaCPA family and a valuable resource to explore the in-depth functions of CPAs in B. napus.

Genome-Wide Analysis of Cation/Proton Antiporter Family in Soybean (Glycine max) and Functional Analysis of GmCHX20a on Salt Response

Monovalent cation proton antiporters (CPAs) play crucial roles in ion and pH homeostasis, which is essential for plant development and environmental adaptation, including salt tolerance. Here, 68 CPA genes were identified in soybean, phylogenetically dividing into 11 Na+/H+ exchangers (NHXs), 12 K+ efflux antiporters (KEAs), and 45 cation/H+ exchangers (CHXs). The GmCPA genes are unevenly distributed across the 20 chromosomes and might expand largely due to segmental duplication in soybean. The GmCPA family underwent purifying selection rather than neutral or positive selections. The cis-element analysis and the publicly available transcriptome data indicated that GmCPAs are involved in development and various environmental adaptations, especially for salt tolerance. Based on the RNA-seq data, twelve of the chosen GmCPA genes were confirmed for their differentially expression under salt or osmotic stresses using qRT-PCR. Among them, GmCHX20a was selected due to its high induction under salt stress for the exploration of its biological function on salt responses by ectopic expressing in Arabidopsis. The results suggest that the overexpression of GmCHX20a increases the sensitivity to salt stress by altering the redox system. Overall, this study provides comprehensive insights into the CPA family in soybean and has the potential to supply new candidate genes to develop salt-tolerant soybean varieties.

Transcriptomic analysis reveals that methyl jasmonate confers salt tolerance in alfalfa by regulating antioxidant activity and ion homeostasis

Introduction

Alfalfa, a globally cultivated forage crop, faces significant challenges due to its vulnerability to salt stress. Jasmonates (JAs) play a pivotal role in modulating both plant growth and response to stressors.

Methods

In this study, alfalfa plants were subjected to 150 mM NaCl with or without methyl jasmonate (MeJA). The physiological parameters were detected and a transcriptomic analysis was performed to elucidate the mechanisms underlying MeJA-mediated salt tolerance in alfalfa.

Results

Results showed that exogenous MeJA regulated alfalfa seed germination and primary root growth in a dose-dependent manner, with 5µM MeJA exerting the most efficient in enhancing salt tolerance. MeJA at this concentration elavated the salt tolerance of young alfalfa seedlings by refining plant growth, enhancing antioxidant capacity and ameliorating Na+ overaccumulation. Subsequent transcriptomic analysis identified genes differentially regulated by MeJA+NaCl treatment and NaCl alone. PageMan analysis revealed several significantly enriched categories altered by MeJA+NaCl treatment, compared with NaCl treatment alone, including genes involved in secondary metabolism, glutathione-based redox regulation, cell cycle, transcription factors (TFs), and other signal transductions (such as calcium and ROS). Further weighted gene co-expression network analysis (WGCNA) uncovered that turquoise and yellow gene modules were tightly linked to antioxidant enzymes activity and ion content, respectively. Pyruvate decar-boxylase (PDC) and RNA demethylase (ALKBH10B) were identified as the most central hub genes in these two modules. Also, some TFs-hub genes were identified by WGCNA in these two modules highly positive-related to antioxidant enzymes activity and ion content.

Discussion

MeJA triggered a large-scale transcriptomic remodeling, which might be mediated by transcriptional regulation through TFs or post-transcriptional regulation through demethylation. Our findings contributed new perspectives for understanding the underneath mechanisms by which JA-mediated salt tolerance in alfalfa.

Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat

Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.

Jasmonate signaling controls negative and positive effectors of salt stress tolerance in rice

Plant responses to salt exposure involve large reconfigurations of hormonal pathways that orchestrate physiological changes towards tolerance. Jasmonate (JA) hormones are essential to withstand biotic and abiotic assaults, but their roles in salt tolerance remain unclear. Here we describe the dynamics of JA metabolism and signaling in root and leaf tissue of rice, a plant species that is highly exposed and sensitive to salt. Roots activate the JA pathway in an early pulse, while the second leaf displays a biphasic JA response with peaks at 1 h and 3 d post-exposure. Based on higher salt tolerance of a rice JA-deficient mutant (aoc), we examined, through kinetic transcriptome and physiological analysis, the salt-triggered processes that are under JA control. Profound genotype-differential features emerged that could underlie the observed phenotypes. Abscisic acid (ABA) content and ABA-dependent water deprivation responses were impaired in aoc shoots. Moreover, aoc accumulated more Na+ in roots, and less in leaves, with reduced ion translocation correlating with root derepression of the HAK4 Na+ transporter gene. Distinct reactive oxygen species scavengers were also stronger in aoc leaves, along with reduced senescence and chlorophyll catabolism markers. Collectively, our results identify contrasted contributions of JA signaling to different sectors of the salt stress response in rice.

Phylogenetic, structural, functional characterisation and effect of exogenous spermidine on rice (Oryza sativa) HAK transporters under salt stress

The HAK (High-affinity K+ ) family members mediate K+ transport that confers normal plant growth and resistance against unfavourable environmental conditions. Rice (Oryza sativa L.) HAK transporters have been extensively investigated for phylogenetic analyses with other plants species with very few of them functionally characterised. But very little information is known about their evolutionary aspects, overall structural, functional characterisation, and global expression pattern of the complete HAK family members in response to salt stress. In this study, 27 rice transporters were phylogenetically clustered with different dicot and monocot family members. Subsequently, the exon-intron structural patterns, conserved motif analyses, evolutionary divergence based different substitution matrix, orthologous-paralogous relationships were studied elaborately. Structural characterisations included a comparative study of secondary and tertiary structure, post-translational modifications, correspondence analyses, normal mode analyses, K+ /Na+ binding affinities of each of the OsHAK gene members. Global expression profile under salt stress showed clade-specific expression pattern of the proteins. Additionally, five OsHAK genes were chosen for further expression analyses in root and shoot tissues of two rice varieties during short-term salinity in the presence and absence of exogenous spermidine. All the information can be used as first-hand data for dissecting the administrative role of rice HAK transporters under various abiotic stresses.

Physiology and Gene Expression Analysis of Potato (Solanum tuberosum L.) in Salt Stress

The production of potato (Solanum tuberosum L.) faces a severe challenge due to the salinization of arable land worldwide. The cultivation of salt-tolerant potatoes is of great significance to ensure food security. In this study, two cultivars of 'Longshu 5' and 'Qingshu 9' were compared for physiological responses to salt stress, and then the salt tolerance of the two cultivars were assessed via principal component analysis. Furthermore, the Na⁺, K⁺, and Ca²⁺ flux of the cultivars under salt stress was recorded. Finally, the expression levels of ion transport-related genes and transcription factors in salt-tolerant cultivars were explored under NaCl stress. The results showed that the seven physiological indicators of salt tolerance were differed between the cultivars. Interestingly, soluble protein and sugar were early responsive to salt stress than proline in the salt-tolerance cultivar. Peroxidase and superoxide dismutase activity were significantly different in 'Longshu 5' under NaCl stress and without being significantly different in 'Qingshu9'. In addition, the salt tolerance of 'Longshu 5' was more tolerant than 'Qingshu 9' based on principal component evaluation. Meanwhile, the strong efflux of Na⁺, the stability of K⁺, and the high absorption of Ca²⁺ in 'Longshu 5' indicated salt adaption mechanisms in the salt-tolerant potato. In addition, we found that ion transport-related genes and transcription factors, such as StSOS1, StNHX4, StAKT1, StNAC24, and StCYP707A, played a role in the salt tolerance of 'Longshu 5'. In conclusion, the salt-tolerant potato can regulate physiological substances to adapt to salt stress, and ion transport related genes and transcription factors play a role in improving salt tolerance.

Ion transporters and their regulatory signal transduction mechanisms for salinity tolerance in plants

Soil salinity is one of the most serious threats to plant growth and productivity. Due to global climate change, burgeoning population and shrinking arable land, there is an urgent need to develop crops with minimum reduction in yield when cultivated in salt-affected areas. Salinity stress imposes osmotic stress as well as ion toxicity, which impairs major plant processes such as photosynthesis, cellular metabolism, and plant nutrition. One of the major effects of salinity stress in plants includes the disturbance of ion homeostasis in various tissues. In the present study, we aimed to review the regulation of uptake, transport, storage, efflux, influx, and accumulation of various ions in plants under salinity stress. We have summarized major research advancements towards understanding the ion homeostasis at both cellular and whole-plant level under salinity stress. We have also discussed various factors regulating the function of ion transporters and channels in maintaining ion homeostasis and ionic interactions under salt stress, including plant antioxidative defense, osmo-protection, and osmoregulation. We further elaborated on stress perception at extracellular and intracellular levels, which triggers downstream intracellular-signaling cascade, including secondary messenger molecules generation. Various signaling and signal transduction mechanisms under salinity stress and their role in improving ion homeostasis in plants are also discussed. Taken together, the present review focuses on recent advancements in understanding the regulation and function of different ion channels and transporters under salt stress, which may pave the way for crop improvement.

Alleviation of Oxidative Damage Induced by CaCl2 Priming Is Related to Osmotic and Ion Stress Reduction Rather Than Enhanced Antioxidant Capacity During Germination Under Salt Stress in Sorghum

Seed germination is the sensitive period to salt stress. Calcium chloride (CaCl2) has been proved as an effective priming agent which can promote the sorghum germination under salt stress. However, there are few reports on CaCl2 priming to improve the salt tolerance during seed germination. The present study investigated the effects of CaCl2 priming on sorghum germination, antioxidant metabolism, osmotic regulation and ion balance under salt stress (150 mM NaCl). The results revealed that the salt stress inhibited the elongation of mesocotyl and root and reduced the germination rate of sorghum. While CaCl2 priming significantly promoted the elongation of mesocotyl and root, and increased the germination rate of sorghum under salt stress. CaCl2 priming notably increased the content of osmotic substances in mesocotyl and root of sorghum under salt stress, and increased the relative water content in these tissues. CaCl2 priming decreased Na+ content and increased K+, Ca2+ contents and the K+/ Na+ in mesocotyl and root, such effects might be induced by up-regulating the expression of NHX2, NHX4, SOS1, AKT1, AKT2, HKT1, HAK1, and KUP. CaCl2 priming reduced the antioxidant enzymes activities and related gene expression compared with untreated sorghum seeds under salt stress. In short, CaCl2 priming improved sorghum germination by enhancing osmotic regulation and ion balance instead of antioxidant enzyme activity. However, the molecular mechanisms of Ca2+ signaling induced by CaCl2 priming in association with the enhanced germination in primed sorghum seeds under salt stress need to be addressed in future studies.

Root Na+ Content Negatively Correlated to Salt Tolerance Determines the Salt Tolerance of Brassica napus L. Inbred Seedlings

Soil salinization is a major environmental stressor that reduces the growth and yield of crops. Maintaining the balance of ions under salinity is vital for plant salt tolerance; however, little is known about the correlation between the salt tolerance of crops and the ion contents of their roots and shoots. Here, we investigated the poorly understood salt-tolerance mechanisms, particularly regarding ion contents (particularly Na+), in Brassica napus subsp. napus L., an agriculturally important species. Twenty B. napus inbred lines were randomly chosen from five salt-tolerance categories and treated with increasing concentrations of NaCl (0–200 mmol) for this work. We found that the root Na+ content is the most correlated limiting factor for the salt tolerance of B. napus; the higher the salt tolerance, the lower the root Na+ content. Correspondingly, the Ca2+/Na+ and K+/Na+ ratios of the roots were highly correlated with B. napus salt tolerance, indicating that the selective absorption ability of these ions by the roots and their translocation to the shoots play a pivotal role in this trait. These data provide a foundation for the further study of the molecular mechanisms underlying salt tolerance and for breeding salt-tolerant B. napus cultivars.

Plant Salinity Sensors: Current Understanding and Future Directions

Salt stress is a major limiting factor for plant growth and crop yield. High salinity causes osmotic stress followed by ionic stress, both of which disturb plant growth and metabolism. Understanding how plants perceive salt stress will help efforts to improve salt tolerance and ameliorate the effect of salt stress on crop growth. Various sensors and receptors in plants recognize osmotic and ionic stresses and initiate signal transduction and adaptation responses. In the past decade, much progress has been made in identifying the sensors involved in salt stress. Here, we review current knowledge of osmotic sensors and Na⁺ sensors and their signal transduction pathways, focusing on plant roots under salt stress. Based on bioinformatic analyses, we also discuss possible structures and mechanisms of the candidate sensors. With the rapid decline of arable land, studies on salt-stress sensors and receptors in plants are critical for the future of sustainable agriculture in saline soils. These studies also broadly inform our overall understanding of stress signaling in plants.

Ammonium and nitrate affect sexually different responses to salt stress in Populus cathayana

Nitrogen (N) fertilization is a promising approach to improve salt tolerance. However, it is poorly known how plant sex and inorganic N alter salt stress-induced Na⁺ uptake, distribution and tolerance. This study employed Populus cathayana Rehder females and males to examine sex-related mechanisms of salt tolerance under nitrate (NO₃ ^- ) and ammonium (NH₄ ⁺ ) nutrition. Males had a higher root Na⁺ efflux, lower root-to-shoot translocation of Na⁺ , and higher K⁺ /Na⁺ , which enhanced salt tolerance under both N forms compared to females. On the other hand, decreased root Na⁺ efflux and K⁺ retention, and an increased ratio of Na⁺ in leaves relative to shoots in females caused greater salt sensitivity. Females receiving NH₄ ⁺ rather than NO₃ ^- had greater net root Na⁺ uptake, K⁺ efflux, and translocation to the shoots, especially in leaves. In contrast, males receiving NO₃ ^- rather than NH₄ ⁺ had increased Na⁺ translocation to the shoots, especially in the bark, which may narrow the difference in leaf damage by salt stress between N forms despite a higher shoot Na⁺ accumulation and lower root Na⁺ efflux. Genes related to cell wall synthesis, K⁺ and Na⁺ transporters, and denaturized protein scavenging in the barks showed differential expression between females and males in response to salt stress under both N forms. These results suggested that the regulation of N forms in salt stress tolerance was sex-dependent, which was related to the maintenance of the K⁺ /Na⁺ ratio in tissues, the ability of Na⁺ translocation to the shoots, and the transcriptional regulation of bark cell wall and proteolysis profiles.

Analysis of Salinity Tolerance in Tomato Introgression Lines Based on Morpho-Physiological and Molecular Traits

The development of salt-tolerant tomato genotypes is a basic requirement to overcome the challenges of tomato production under salinity in the field or soil-free farming. Two groups of eight tomato introgression lines (ILs) each, were evaluated for salinity tolerance. Group-I and the group-II resulted from the following crosses respectively: Solanum lycopersicum cv-6203 × Solanum habrochaites and Solanum lycopersicum M82 × Solanum pennellii. Salt tolerance level was assessed based on a germination percentage under NaCl (0, 75, 100 mM) and in the vegetative stage using a hydroponic growing system (0, 120 mM NaCl). One line from group I (TA1648) and three lines from group II (IL2-1, IL2-3, and IL8-3) were shown to be salt-tolerant since their germination percentages were significantly higher at 75 and 100 mM NaCl than that of their respective cultivated parents cvE6203 and cvM82. Using the hydroponic system, IL TA1648 and IL 2-3 showed the highest value of plant growth traits and chlorophyll concentration. The expression level of eight salt-responsive genes in the leaves and roots of salt-tolerant ILs (TA1648 and IL 2-3) was estimated. Interestingly, SlSOS1, SlNHX2, SlNHX4, and SlERF4 genes were upregulated in leaves of both TA1648 and IL 2-3 genotypes under NaCl stress. While SlHKT1.1, SlNHX2, SlNHX4, and SlERF4 genes were upregulated under salt stress in the roots of both TA1648 and IL 2-3 genotypes. Furthermore, SlSOS2 and SlSOS3 genes were upregulated in TA1648 root and downregulated in IL 2-3. On the contrary, SlSOS1 and SlHKT1.2 genes were upregulated in the IL 2-3 root and downregulated in the TA1648 root. Monitoring of ILs revealed that some of them have inherited salt tolerance from S. habrochaites and S. pennellii genetic background. These ILs can be used in tomato breeding programs to develop salt-tolerant tomatoes or as rootstocks in grafting techniques under saline irrigation conditions.