Introduction

Abiotic stresses, particularly salinity and drought, negatively impact plant growth and development, which ultimately incur significant losses in the production of essential food crops (Atkinson and Urwin 2012). Seed germination, root and shoot length, plant height, and fruit development are severely affected by salt stress (Liang et al. 2014; Sabagh et al. 2021). Salinity affects around 20% of the world’s irrigated land (Munns and Tester 2008), and this is predicted to rise to 50% in future if current scenarios prevail (Mahajan et al. 2008). Soil with electrical conductivity (EC) of 4 dS m−1 or higher (Horie et al. 2011) is saline, equating to 40-mM NaCl. Halophytes employ avoidance mechanisms, while glycophytes tolerate salinity by reducing ion imbalance and using secondary effects to withstand harsh conditions (Touchette et al. 2009). Osmotic stress and ion toxicity are the primary salt stress responses, and they cause oxidative stress followed by a series of secondary stresses and cannot maintain ion homeostasis (Munns and Tester 2008; Horie et al. 2011). As a result, plants adopted intracellular and extracellular osmoregulation processes to regulate osmotic stress and dehydration when soil environmental and salinity levels change (Rivera-Ingraham and Lignot 2017; Rahman et al. 2018). Fortunately, many naturally occurring plant events controlled different salt defense mechanisms by single or multiple genes. These defense mechanisms depend on many pathways and have been heavily investigated at the genetic, genomic, proteomic, and metabolomics levels (Gupta and Huang 2014).

A molecular understanding of the salt tolerance mechanism is essential for producing new salt-tolerant germplasms. Salt-tolerant genotypes are essential for enhancing stress tolerance in crop plants (Xu et al. 2016). Moreover, tolerance mechanisms require the coordinated actions of mechano-receptors, ion transport channels, and secondary signaling molecules to maintain ion homeostasis. Upon exposure to salt stress, plants activate a defense mechanism based on physiological and biochemical responses to coping with the abiotic stress (Pastori and Foyer 2002; Ul Hassan et al. 2021). Activation of gene cascades under saline conditions triggers hormone breakdown, signal transduction pathways, and stress perception and response genes (Silva and Gerós 2009). When stress signals are activated and transferred to cells, many other signals are activated instantly and trigger phosphorylation cascade reactions; as a result, signals are sent to specific proteins used for cell defense (transcription factors). These cell defense proteins control the expression of stress response genes, and as a result, the plant tolerates and adapts to specific mechanisms under a harsh environment (Ahanger et al. 2017).

Omics approaches like genomics, proteomics, metabolomics, and transcriptomics have been widely deployed to dissect mechanisms of salinity tolerance in plants (Cramer et al. 2011). The new genomic era includes nuclease systems with non-specific domains bonded with specific DNA sequence-binding domains help to find the genes easily and transfer them to new crop plants (Gaj et al. 2013). Applying new genome editing technologies to several crops has created opportunities for desirable traits (Jaganathan et al. 2018). However, CRISPR/Cas9 technology uses Cas9 and guides RNAs (gRNA) to target multiple sites within genomes. Genome-edited crops have advantages over transgenic plants because they contain edited DNA for specific traits (Malzahn et al. 2017). However, systematic research on the physio-chemical and biochemical variation in plant tolerance mechanisms under salt stress and genetic engineering approaches will further enhance our understanding of plant tolerance mechanisms. The techniques mentioned earlier discussed the effect of salinity on agro-morphological and physiological responses against salinity in the first section. Furthermore, the second part discussed the new breeding and omics technologies used to update the knowledge on complex pathways to overcome the salinity problems in crop plants. The implications of using these molecular processes in breeding to figure out genetic diversity gene pairs significant for salt tolerance and engineering these genes pairs in crop plants for salinity tolerance in connection to sustainable crop production in saline soils are also highlighted. The objective of the study is to conduct the systematic critical review of opportunities and challenges and further to develop potential breeding strategies for improving salt tolerance in crop plants.

Effects of Salinity on Plant Phenological Traits

Plant growth is affected by salt stress at different developmental stages: germination, seedling, growth, and development, vegetative, flowering, fruit set, and root structure. Excess salt in the soil slows down plant growth by affecting physiological and biochemical processes (Shahid et al. 2021). Further, it limits the amount of water in the root zone and upward movement to plant organs called osmotic stress. It is difficult to determine the effects of salinity by the physical or morphological characteristics of a plant, and these effects can instead be recognized using physiological and biochemical means (Munns 2002). Salinity affects plant water use, and many plants undergo osmotic regulation when exposed to salt stress by increasing the osmotic potential of the leaf sap (Gama et al. 2009). Salinity inhibits the water by imbibition seeds, as it lowers the osmotic potential of the germination media (Khan et al. 2002). Salinity also causes toxicity, restricts enzyme activity and nucleic acid metabolism, and limits the nutrients stored in seeds (Othman et al. 2019).

Salinity has been shown to affect crop plants’ germination process, i.e., in Brassica spp. (Akram and Jamil 2007), Chenopodium quinoa (Al-Barakah and Sohaib 2019), Oryza sativa (Xu et al. 2011), Triticum aestivum (Akbarimoghaddam et al. 2011; Sohaib et al. 2020), and Zea mays (Khodarahmpour et al. 2012). Khodarahmpour et al. (2012) reported that germination rate was reduced by about 32%, plumule length by 78%, seedling length by 78%, radicle length by 80%, and seed vigor by 95% in Zea mays L. when the plant was exposed to 240-mM NaCl stress. Salt stress affects plant growth in terms of plant height (ph), decreases with increased sodium chloride (NaCl) concentration (Memon et al. 2010), and the number of leaves in Kyllingia peruviana (Ha et al. 2008) was also decreased. The leaf blade is an essential parameter for Na+ toxicity in crop plants, as sodium ion is deposited in the transpiration stream rather than in the roots (Munns 2002). Salinity stress at the reproductive stage inhibits microsporogenesis and reduces the size of the stamen filaments, causing cell death, ovule abortion, and senescence of fertilized embryos (Ashraf and Harris 2004). These factors have direct physiological and biochemical effects on different growth phases during the plant life cycle (Shrivastava and Kumar 2015) and molecular level (Isah 2019). Moreover, the nutrient status of the soil is also disturbed by disrupting the osmotic and oxidative processes, which restricts water uptake from the soil. Available phosphorus is significantly reduced in saline soils because it precipitates with Ca2+ ions (Bano and Fatima 2009). Excessive accumulation of sodium ions in cell walls quickly causes osmotic stress and leads to cell death (Munns 2002). Similarly, a recent study on faba bean genotypes was evaluated to determine the salt stress effect on agronomical and physiological response. The results suggested that the salinity affects the agronomical and physiological traits under high (100 mM and 200 mM) salt stress relative to control (Afzal et al. 2022a).

Effect of Salinity on Photosynthetic Activity and Pigments

Physiological changes observed in plants experiencing salinity and ion toxicity include membrane disruption, reactive oxygenated species (ROS) production, limited photosynthetic rate, and antioxidant scavenging (James et al. 2011). (Patel et al. 2010) experimented to determine the effects of salinity (2, 4, 6, 8, and 10 dS m−1) on seed germination and other growth parameters, i.e., root length (cm), plant height (cm), Na+ concentration, Cl− concentration, proline concentration, and Na+:K+ ratio in cowpea. The results demonstrated that all cultivars were less affected at low salt concentrations (2 dS m−1), while reductions took place at 10-dS m−1 EC. Significant reductions in growth characteristics, i.e., plant height, root length, and leaf Ca+ and K+ contents were recorded at a higher salt concentration (10 dS m−1). Moreover, Na+, Cl−, and proline contents were also increased (Khosravinejad et al. 2008). Gong et al. (2018) conducted experiments to determine the effect of different salt concentrations on photosynthetic activity and chlorophyll pigments in Kalidium foliatum. Results showed that chlorophyll and carotenoid contents were higher in Kalidium foliatum when compared with the control. Salt stress also reduces leaf surface area and thus photosynthetic activity can be affected. A reduced leaf surface area leads to decreased stomata conductance and chlorophyll content and hence the efficiency of photosystem II is reduced (Netondo et al. 2004). Saravanavel et al. (2011) investigated the effect of NaCl (0–2.0%) on chlorophyll content and photosynthetic activity in Avicennia officinalis L. plants. The results suggested that maximum chlorophyll contents were accumulated at 0.75% NaCl relative to control; in addition, the photosynthetic activity were enhanced at 0.75% NaCl, while at higher concentration the photosynthetic activity was reduced.

Moreover, at high NaCl concentrations, the photosynthetic activity also increased (Munns and Tester 2008). Salinity affects a series of events in the form of oxidative and ionic stress. This reduced the water in the root zone area and limits the stomata opening and closing of stomata which in turn reduced intercellular CO2 and hence reduced photosynthetic efficiency. It has also been reported that the artificial application of NaCl (200 mM) produces a 50% reduction in the photosynthetic rate of Olea europaea. The stomata conductance (SC) and photosynthetic efficiency were decreased and limit the carbon assimilation rate because of limited stomata opening in Aegiceras corniculatum at higher salt (50–500 mM) NaCl concentration (Ball and Farquhar 1984). In short, leaf expansion is reduced due to ionic stress and, as a result, the accumulation of unexploited photosynthates in growing tissues may produce signals to down regulate photosynthesis. Under salinity stress conditions, salts can build up in leaves to excessive levels. However, deposition of salts causes dehydration in apoplasts and salt accumulation in the cytoplasm, thus limiting the activities of enzymes involved in carbohydrate metabolism. Carbohydrates may then accumulate in the chloroplast and directly affect photosynthetic processes (Munns and Tester 2008). Moreover, chlorophyll contents and relative water content are also decreased in roots and shoots under saline conditions. (Vysotskaya et al. 2010) reported that chlorophyll (a & b) contents decreased and carotenoid contents increased when barley plants were subjected to salinity stress. High NaCl concentrations damaged chloroplast electrons and mitochondria and increased reactive oxygen species (ROS). Under stress conditions, plants respond differently and produce certain antioxidant enzymes to maintain homeostasis for average plant growth. The enzymes, i.e., Superoxide dismutase (SOD) and Malondialdehyde (MDA), protect plants against ROS damage (Sen Raychaudhuri and Deng 2000). Malondialdehyde restores lipid peroxidation levels when plants suffer from salt stress. Oxidative stress occurs when plants are exposed to highly saline conditions, leading to increased MDA concentrations and significant adaptation by the plant (AbdElgawad et al. 2016). MDA level consider as biomarker for biological system in advanced oxidative states in plant: a low concentration of MDA reflects a high anti-oxidative ability and more excellent stress resistance (Hirt 2009). Rubisco activity is decreased at low NaCl concentrations (100 and 250 mM) and is increased at high NaCl concentrations (400 and 500 mM). Superoxide dismutase (SOD) levels were increased at high salt concentrations, while MDA levels were decreased at 250-mM sodium chloride salt concentration (Munns and Tester 2008). Sheldon et al. (2017) experimented to determine the effects of salt stress on water viability in wheat and chickpea cultivars. The results demonstrated that water absorption was highest under control conditions, however, somewhat reduced in wheat, and severely reduced in chickpea under salt stress treatment. From the results, it would be concluded that this may be due to Cl− toxicity at lower concentrations rather than to the osmotic effects of salinity stress. Similar results were reported by (Rivelli et al. 2002) when four wheat genotypes were examined under different salt stress conditions to determine the elimination of Na+ on water retention. The results suggested that stomata conductance was decreased under highly saline conditions but decreasing isotope discrimination ability in expanding leaves and more efficient transpiration were recorded when plants were exposed to saline conditions (Rivelli et al. 2002; Ali et al. 2022; Habib-ur-Rahman et al. 2022). Barley is considered more tolerant of salinity stress than other crops, based on its physiological behavior and water retention ability (Jamshidi and Javanmard 2018).

Mechanisms of Salt Tolerance in Plants

Salt tolerance mechanisms are processes that allow plants to resist stress, take up nutrients from the soil, and complete their life cycle under high salt concentrations in the soil. These types of plants can be obligate halophytes. Their relative growth is improved by around 50% in seawater, and they can be found in less saline habitats. Halophytes are also characterized by their physiological diversity, which permits them to adopt a variety of strategies under control and saline conditions (Parihar et al. 2015). The relative importance of the salt stress tolerance processes depends on the type of species, salinity level, the growing environment, available air moisture, evapotranspiration, and leaf water potential (Wang et al. 2009; Rahman et al. 2020b). Moreover, the salt tolerance phenotypes of these plants are incredibly complex, and studies have not yet fully explained the mechanisms behind their salt tolerance. Future research alone can shed more light on salt stress and salt tolerance mechanisms (Liang et al. 2018). For this future research, we must understand crops at the genome, transcriptome, proteome, and metabolic levels to identify components at the genetic level involved in overcoming salt stress (Inan et al. 2004). Adaptation of plant salinity response, ion toxicity, homeostasis, and tolerance for improving salt tolerance mechanism is presented in Fig. 1. Biochemical alterations involved alteration in transcription changes in physiology, as a result, the growth and development processes were altered. Transcription factors (TFs) and small RNAs (sRNAs) are backbones that control core aspects of whole-plant transcriptional responses (Sunkar and Zhu 2007).

Fig. 1
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Salt stress affects the adaptation mechanism of plant salinity, response, and tolerance mechanism in crop plants

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Strategies for Coping with Salinity Stress

As the global human population increases, the demand for food is also increasing, but agricultural production is not increasing quickly enough to meet this demand. Therefore, many attempts have been made to enhance crop salinity tolerance through conventional breeding and plant omics technologies. There are two general types of methods required to combat salinization of the soil. The first is salinity control using irrigation and drainage methods and activities to engineer the ecosystem and the other is an improvement in plant-based salinity tolerance using conventional and advanced breeding and omics technologies. There are three mechanisms involved in inducing salinity tolerance in plants which are as follows: 1. Breeding, 2. Genetic Modifications (GMOs), and 3. Application of PGPR (Plant growth-promoting rhizobacteria). Breeding and GMOs are referred to as inherited salinity tolerance, while the use of PGPR to combat salinity tolerance is referred to as induced salinity tolerance (Bashan 1998; Bashan et al. 2014). An integrated plant breeding, molecular approaches, and biotechnological approaches can be used to enhance salt tolerance mechanisms in crop plants (Fig. 2). Each way of inducing salinity tolerance in plants has its own pros and cons. The response of plants to a constraint on salinity requires multiple processes which work coordinated to minimize hyperosmolarity and restore the ionic environments of homeostatic cells. A plant genotype’s fitness to survive in saline environments, thus reducing yield loss, is called salinity tolerance. Salinity stress is a complex phenomenon that is controlled by many genes at the physiological and genetic levels. However, plant yield should be considered as the primary salinity tolerance criterion, which ultimately necessitates generating economically harvestable yield. Tolerance of salinity is a quantitatively inherited trait, highly regulated by multiple gene actions influenced by the genotypes, environment, and their interactions (G x E) (Arzani 2008). Despite its intrinsically dynamic existence of salinity tolerance in the genetic makeup, marker-assisted selection (MAS) has not done it, yet the anticipated improvement and procreation have depended primarily on the direct selection of the phenotypes. Genomic studies of tolerance to salinity in polyploid species including maize, alfalfa, cotton, and oat pose even more significant difficulties. Current crop physiology, genetics, and genomics techniques have given rise to new intuitions regarding tolerance in salinity, thereby providing a more profound knowledge of networks related to genes and new methods help to achieve the zero hunger goal (Lee et al. 2011; Rahman et al. 2019, 2020a). The biology of cellular plants strengthens our understanding of the diverse network of traits related to salinity tolerance and increases the structural genomics and functional methods suitable for use in the detection of the quantitative trait loci (QTLs) genes of interest linked with specific traits (Saradadevi et al. 2021). The genes are the key targets for transgenic generation and through molecular breeding, the QTLs can be used to improve crops. The QTLs thus help pave the path for MAS (Ashraf and Foolad 2013) and promote gene transformation (Negrão et al. 2011) and enabled researchers and scientists to make more resilient crops through genetic engineering and gene transformation technologies. Therefore, understanding salt tolerance mechanisms and analyzing salt stress-related genes and their functions will provide a theoretical basis for understanding the stress signal network and pathways for the improvement of the target crop (Zhang et al. 2018b).

Fig. 2
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Integrated plant breeding, molecular approaches, and biotechnological approaches to enhancing salt tolerance mechanisms

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Conventional Breeding Methods for Salinity Stress Tolerance

Conventional breeding methods are more powerful and efficient methods of enhancing salt tolerance. However, the success rate of conventional breeding approaches is less. Plants’ tolerance mechanism is a complex phenomenon and depends upon physiological and genetic responses. These processes involve phenotypic evaluation as well as the identification of QTLs closely related to molecular markers. Conventional plant breeding contributes to the screening genotypes to salt tolerance and involves improving crop plants through hybridization, selection, polyploidy, and introgression events. In addition, efficient biotechnology-aided modern breeding technologies are implemented for the development of salt-tolerant cultivars sustainably used in marginal and saline lands (Arzani and Ashraf 2016). A study by Thomson et al. (2010) identified the “saltol” QTL using a conventional breeding approach in rice. The “saltol” QTL controls the Na+:K+ ratio (shoot) at the seedling stage. Marker-assisted backcrossing is also an effective conventional breeding method used to transfer alleles at target loci (donor-recipient) (Hasan et al. 2022). However, conventional breeding mainly depends on genetic diversity (resources) and involves screening genotypes that confer salt tolerance. Conventional plant breeding can be replaced by genetic engineering. In many respects, plant genetic engineering is comparable to the backcross breeding method in which desirable genes are transferred (Singer et al. 2021). On the other hand, the backcross method can add one simple trait to a perfect variety/cultivar. The development of such a perfect cultivar act as a backbone to carry out conventional breeding processes. For example, for the development of a hybrid variety in the cross-pollinated crops several sequential procedures including recurrent selection, production of inbred lines (gametic selection, hybridization), or screening of the superior inbred lines based on general combining ability (GCA) and eventually superior two inbred lines (best hybrid) based on the specific combining ability (SCA) value should be selected and used to develop a hybrid variety (Janaki Ramayya et al. 2021). To identify key genes and characterize salt tolerance genes, a collective approach is required to merge genomics, molecular markers, proteomics, metabolomics, transcriptomics, and transcription factors (TFs) to engineer new crops significant for salt tolerance. Integrated plant breeding, molecular approaches, biotechnological, and new breeding technology approaches to enhancing salt tolerance mechanisms are presented in Figure.

Modern Breeding Methods for Improvement of Abiotic Stresses Tools and Approaches for Crop Improvements Against Salinity Stress

Candidate Genes for Salinity Tolerance to the Characterization of Novel Genes for Salt Tolerance

The unraveling of genes responsible for salt tolerance and their molecular mechanisms that respond to the stress of salinity in cultivated crops should help breeders accelerate genetic improvement through genetic engineering and marker-assisted selection (MAS) (Hanin et al. 2016). Identification of new QTLs may lead to the development of new salt-tolerant lines. Some important QTLs that have been identified at different growth stages of crop plants exposed to salinity are presented in Table 1. The responses caused by salinity should be tested at molecular, environment, cell, and whole-plant levels. Plant respond to salinity stress in three different ways, such as “osmotic,” “ionic-specific,” and “oxidative stress” (Roy et al. 2013). Molecular biological and omics techniques are used to identify resistance genes, introduce these genes into crop varieties through genetic engineering, and could help to resolve the salinity problem. Some important QTLs and genes related to salt tolerance in crop plants at seedling, vegetative and reproductive stages are presented in Table 1. Zhu et al. (1998) identified salt overly sensitive (SOS) Arabidopsis mutants, which are hypersensitive to high external Na+, Li+, or K+ concentrations. These mutants are mutated at three loci, namely SOS1, SOS2, and SOS3 (Martínez-Atienza et al. 2007). Shi et al. (2002) reported that SOS1 encodes a plasma membrane Na+/H+ antiporter, SOS2 encodes a serine/threonine protein kinase that activates SOS1 (Liu et al. 2000), and SOS3 encodes an EF- hand-type calcium-binding protein (Mahajan et al. 2008). The SOS3 protein regulates NA+ and K+ transport and increases the sensitivity of yeast to growth inhibition by Na+ and Li+ stress (Mendoza et al. 1994). SOS2 interacts with and activates SOS3, therefore these two mutant genes define a regulatory pathway for Na+ and K+ homeostasis and salt tolerance in plants (Halfter et al. 2000). In another study, He et al. (2005) reported that many genes responsible for salt stress responses can help to elucidate the tolerance mechanisms. The results of the study clarified that overexpression of a single gene could improve the salt tolerance of transgenic plants and that the A. thaliana SOS1 gene (encoding a plasma membrane antiporter) and the vacuolar AtNHX1 gene (encoding a Naþ/Hþ antiporter) can significantly enhance the salt tolerance of transgenic plants. Moreover, Liu et al. (2014) found that ABA-dependent regulatory pathways improved rice tolerance to high salt concentrations and extreme drought by introducing the OsbZIP71 gene in transgenic plants. P-type and H+ ATPases in the plasma membrane act as primary pumps that create a proton motive force for the active transport of solutes, such as Na+ and K+ (Sze et al. 1999). The Na+ entering the cells is also transported into the vacuole through the action of antiporters (Na+/H+) (Apse et al. 1999). Overexpression of SOS genes in transgenic Arabidopsis plants improves salt tolerance by decreasing the amount of Na+ and increasing the amount of K+ within cells (Yang et al. 2009). In another study, a high abundance of SOS pathway-related transcripts was correlated with salinity tolerance in Brassica plants (Kumar et al. 2009). Moreover, rice salt tolerance has been linked to overexpression of the three SOS loci (SOS1, SOS2, and SOS3), which is linked to its ability to exclude Na+ from the shoots to maintain a low cellular Na+/K+ ratio (Martínez-Atienza et al. 2007). Chakraborty et al. (2012) partially sequenced the cDNA of Brassica juncea genotypes and reported on the conserved nature of these genes and examined the intra- and intergenic diversity. The results showed that SOS pathway could be a factor that determines both plant salt stress tolerance and Na+:K+ ratio. Increasing the antioxidant activities of enzymes and increasing the metabolism level are other mechanisms by which plants can increase their tolerance to salt stress (Su et al. 2020). Genetic engineering can achieve a higher level of efficiency in transgenic plants and represents the best method of studying the function of antioxidant enzymes in terms of scavenging active oxygen. The activity of these enzyme has been confirmed in many transgenic plants, and the expression of the GAT, GR, SOD, and APX genes improves plant resistance to oxidative stress (Tanaka et al. 1999).

Table 1 Identification of the QTLs of salt tolerance genes in crop plants at the seedling, vegetative, and reproductive stages
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Marker-Assisted Backcross Breeding

Improving crop yield output, the primary goal of crop breeding for saline areas is under salinity stress as conventional breeding methods take the long haul for developing cultivar which tolerates salinity. Therefore, alternate approaches must be implemented effectively into the improvement program. The germplasm was genetically diverse and conventionally crossed to produce repetitive populations and selection was based on phenotypes and field data. The technique was now transformed either using MAS procedures that are connected to specific QTL or qualitative traits. Efficient application of MAS to tolerance to salinity depends mainly on a marker being closely linked to either a resistant gene or a QTL related to tolerance. Therefore, with a detailed understanding of the genetic origin of the organisms underlying in combination with the functional genomics and salinity stress is important to decide whether the MAS process has a major impact on enhancing the tolerance to salinity. As exemplified earlier, Saltol is a good QTL for ion absorption it was described in Rice (Ali et al. 2013).

A codominant-linked marker, cslinkNax2, was used successfully by a backcrossing technique in durum wheat for the TmHKT1;5 gene MAS (Munns et al. 2012). They may be used to transfer (introgress) tolerance of salinity into the elite genotype from donor, resistance, and breeding lines without passing hostile genes from donor parents after validating the main QTLs in the required germplasm for salinity tolerance. Gupta et al. (2010) proposed a method called Marker-Assisted Backcrossing (MABC). MABC was modified to integrate appropriate QTLs into genotypes using set locus with markers and background markers in the genome (Frisch et al. 1999). Given the widespread use of MABC introgress to biotic stress resistance, there has been limited use of MABC in the development of cultivars tolerant to abiotic stress and salinity stress. However, in rice, MABC’s successful application in improving abiotic tolerance was disclosed when a major QTL was used for submergence tolerance (Sub1) that was introduced to different cultivars (Singh et al. 2013). To date, there is only one known case in which a MABC strategy was used to introduce a QTL “SalTol” which was transformed into a rice cultivar (BR11) Bangladeshi and other genotype as well (Gregorio et al. 2013). Similarly, salinity-tolerant RILs line cross (Pokkali x IR29) was considered as “SalTol” parent donor for transition to BR11 (parent recipient). The authors used polymorphic markers simple sequence repeats (SSR) and sequence tags sites (STS) to validate the plants with F1 and pick genome from the foreground, recombinant, and history. This method has been used for introversion for multiple QTLs in rice root traits, and the resulting PY 84 cultivar was printed in India, with increased root growth under stress from drought (Steele et al. 2013). Similarly, MABC was also used for maize with beneficial alleles found at five loci linked with flowering days and yield components (Ribaut and Ragot 2007).

QTLs Related to Salinity Stress: Utilization of QTLs Knowledge for Salinity Stress

Salinity tolerance has already been shown to be a complex function regulated by multiple genes (Fan et al. 2016b). The QTL study was used to evaluate the positions of genomes participating in salinity tolerance. To identify the QTLs, segregating population of progeny produced by selfing or biparental cross or duplicated contrasting haploidy with parents is used in salinity response. Nevertheless, this method is time consuming in a dynamic characteristic, such as tolerance to salinity to produce population mapping, and often includes multi-locational, phenotypic data that could be reproducible and accurate. In a different method to studies of the genome-wide association (GWA), a significant number of SNPs are examined in several plant genotypes, for combination with the desired trait was employed to resolve this constraint on dissecting complex quantitative characteristics. The GWA analysis could be used to detect SNPs and the addition/deletion linked to the desired trait in germplasm collections (Mitchell-Olds 2010). In addition, the restricted availability of genomic data on minor crops makes this method more acceptable for them. Some association mapping reports exist to link different genes with salinity tolerance-associated phenotypic characteristics. Good association between AtHKT11 gene was recorded for tolerance to salinity was discovered in Arabidopsis, the findings of a GWA analysis (Atwell et al. 2010). The GWA approach was implemented in rice and 20 SNPs were identified that were significantly linked to the Na+/K+ ratio (Kumar et al. 2015). This approach was extended to barley and a QTL tolerance for salinity was identified with DArT marker at chromosome 4 (Fan et al. 2016a).

An alternative approach called linkage disequilibrium (LD) mapping or association analysis is QTL finding to identify direct phenotypic and genotypic associations (Zhu et al. 2008). It has an advantage since it does not require the creation of population mapping and may be used in many populations. In addition, association mapping may lead to a greater likelihood of identification of QTLs because of the increased variation of the alleles in the working population compared to two binding parental alleles study (Buckler IV and Thornsberry 2002). Nonetheless, the method’s limited statistical capacity, cannot detect rare alleles via linkage mapping (Lewis 2002). The association mapping method will validate the QTL-linked markers identified using classical methods (Thornsberry et al. 2001). The QTL analysis characteristics correlated with salinity tolerance performed at three growth and developmental stages in a variety of crop plants. Hence, QTL has been identified that influences directly or indirectly response differently to salinity stress, i.e., ionic status. The following information describing QTL analyzes are summarized for tolerance of salinity in the major crop species (Long et al. 2013).

Wheat, barley, and rice have been found to impart tolerance to salinity at the growth stage of seedlings (Ahmadi-Ochtapeh et al. 2015; Genc et al. 2010; Nguyen et al. 2013; Wang et al. 2012). The study results suggested that salinity tolerance is controlled by many additives and epistatic QTLs controlled different environmental activities in wheat and rice and help to enhance the salinity tolerance (Wang et al. 2012). The tolerance to salinity is also tested in rice by multiple QTLs during the reproductive stage, as Saltol QTL is closely correlated with tolerance to salinity (Ali et al. 2013; Merrium et al. 2022). The Saltol is considered best-characterized QTL responsible for both high K+/Na+ ratio and low Na+ shooting under salinity stress. In barley, five QTLs responsible for salinity tolerance are present on H chromosomes at (1, 2, 5, 6, and 7 positions) affecting more than fifty percent variability at the seedling stage (Zhou et al. 2012). In addition, many genomic regions containing candidate genes responsible for tolerance have been recognized in barley using biparental population mapping (Nguyen et al. 2013) as well as other mapping techniques for linkage were studied (Long et al. 2013). In addition, Shavrukov et al. (2010) described a solitary H-derived QTL for Na+ elimination. Analysis of QTL for leaf Na+ exclusion showed that both large QTLs (Horie et al. 2005; Shavrukov et al. 2011) and small QTLs are present in wheat (Genc et al. 2010).

A QTL named Kna1 significant for Na+ elimination, as well as involved in K+/Na+ discrimination enhancement (Dvořák et al., 1994), was linked to gene TaHKT1;5 in bread wheat (T. aestivum) improved the Na + /K + ratio(Byrt et al. 2014). Similarly, the HvCBL4 gene encoded a protein identical to calcineurin B and SOS3 homolog from Arabidopsis, mapped in rice (Rivandi et al. 2011) represents QTL for salinity tolerance genomic region. In rice, OsHKT1;5 has been linked with SKC1, which involved the absorption of K+ on chromosome 1 in the shoot (Ren et al. 2005). The SKC1 and Saltol are co-localized. OsHKT1;5, orthology of the gene AtHKT1;1, has been shown to regulate the xylem Na+ elimination (Hamamoto et al. 2015). Many other QTLs that control the homeostasis of the cellular ion have been found in rice. While considerable success in the identifying main QTL for tolerance salinity, in an empirical plant breeding, their position in MAS is not well known. However, it may also be possible to incorporate high adaptive features in the genomic era with only a relatively smaller QTL effect (Mirdar Mansuri et al. 2020). The application of next-generation sequencing (NGS) technologies allows for the rapid production of markers (indel) and SNP for specific traits, which end up and enable the pyramidization of different QTL tolerances to salinity from various sources within a single cultivar (Zhang et al. 2016). However, the integrative meta-analysis strategy led to the discovery of several intriguing genes implicated in salinity tolerance, including some of the most important genes/gene families with sufficient evidence.

Transcriptomics: Application of Transcriptomics Knowledge for Salinity Stress

Recent advances in molecular plant science have improved our collective knowledge, and transcriptomics have emerged as a powerful method of understanding differential gene responses over a specific time series. Transcriptomics is a technique used to study the whole set of RNA transcripts (coding and non-coding) of a cell at a specific time and under specific conditions (Supplitt et al. 2021). Expression analysis of tissue under different growth conditions reveals the regulatory network of responsive genes for that specific stage or condition and helps to annotate genes that were previously unannotated due to lack of information (Lowe et al. 2017). Some important transcriptomics studies revealed total clustered transcript reads, upregulated genes, and downregulated genes in salt-stressed crop plants presented in Table 2. Gene identification methods were used based on expression analysis, including subtractive hybridization (SSH) (Putney et al. 1983), expressed sequence tags (ESTs) (Diatchenko et al. 1996), microarrays, serial analysis of gene expression (SAGE) (Velculescu et al. 1995), and massively parallel sequencing (MPSS). Among the modern transcriptomics approaches, microarrays and RNA-sequencing are the dominant methodologies. Microarrays were developed in the 1990s, with the first results being published in 1995 and representing a method of gene expression analysis. One single microarray chip can investigate thousands of genes simultaneously in a sample, such as the 22 k Barley1 gene chip (Close et al. 2004) and the Model Organism Barley Gene Expression Microarray, 4 × 4 k (Agilent tech. USA) was used the first time. Initially, only one sample could be run per chip multi-sample gene chips are now available with technological advancement. Microarrays for transcriptome analysis of plants under salinity stress have been completed in crop plants, such as wheat (Peng et al. 2009), rice (Zhou et al. 2007), maize (Zheng et al. 2006), barley (Atienza et al. 2004), Arabidopsis thaliana (Liu et al. 2013), potato (Legay et al. 2009), and sorghum (Buchanan et al. 2005). RNA-sequencing (RNA seq.) is a high-throughput sequencing technology in which whole transcripts can be sequenced. It has the potential to replace microarrays analysis (Mutz et al. 2013). It is considerably more efficient than microarrays as it can detect novel transcripts even at low abundance, non-coding RNA, allele-specific expression, and alternate splice junctions. RNA- seq does not require any prior knowledge of annotations or sequence assemblies. There is no bias involved in this method of sequencing like that which occurs in probe hybridization during a microarray experiment (Zhao et al. 2014). Mutz et al. (2013) crosschecked gene expression profiles of the same sample from Illumina and a microarray analysis and concluded that RNA-seq recorded more prominent results and could also detect transcripts with very low abundances, differentially expressed genes, and identify sequence variants and new transcripts relative to microarray analysis. Different transcriptome analyses of different crops have been reported under salinity stress, i.e., rice (Mutz et al. 2013), Rosa chinensis (Tian et al. 2018), pearl millet (Shinde et al. 2018), and wild barley (H. spontaneum) leaves under salt stress (Bahieldin et al. 2015).

Table 2 Transcriptomics studies revealed total clustered transcript reads, upregulated genes, and downregulated genes in salt-stressed crop plants
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Genome-Wide Analysis Studies (GWAS) for Salt Tolerance

GWAS investigations are increasingly being utilized to identify and explain the genetic basis of agronomic features, like germination, which are generally influenced by many small genes (Naveed et al. 2018; Yu et al. 2018). GWAS uses linkage disequilibrium (LD) to find the relationships between genetic variations and phenotypes across many genotypes from natural populations. Hundreds of accessions covering thousands of gene loci can be genotyped using high-throughput markers to improve the effectiveness of present breeding procedures due to recent breakthroughs in genome-wide genotyping technology (Russell et al. 2011; Kilian and Graner 2012; Tondelli et al. 2013). To find the targeted gene, GWAS can precisely discover polymorphisms and the underlying genetic loci that are responsible for phenotypic variances under different abiotic stress conditions (Naveed et al. 2018; Xu et al. 2018; Yu et al. 2018) as well as biotic stress conditions (Afzal et al. 2022b). Aside from the high-density SNPs commonly used in GWAS, GWAS has another advantage, i.e., natural variety population selection has been done for genotyping based on phenotypic variation. The osmotic pressure in the soil is increased by high salt levels, creating a drought-like situation (Sayar et al. 2010), reducing water absorption by the seed from the soil surface, delayed seed imbibition, or even prevented for subsequent germination.

Furthermore, excess Na+ and Cl− ions create toxicity, which obstructs normal cellular functions (Hampson and Simpson 1990), resulting in a lower rate of seed germination (Luan et al. 2014). The interplay effects of ionic and osmotic stress eventually reduce the number of sprouted seeds and the germination rate (Kazemi and Eskandari 2011). Several distinct loci control salinity tolerance at this stage (Mano and Takeda, 1997). A similar study suggested by (Angessa et al. 2017) used a doubled haploid barley population developed by CM72 Gairdner cross controlled both traits by QTLs on chromosomes 2H and 3H position, respectively. Another study reported similar results and found 17 QTLs influencing ABA response on 1H, 2H, 3H, and 5H positions in the Steptoe Morex population at the germination stage (Mano and Takeda 1997). Salinity tolerance genes were tightly connected at the chromosome 5H position in both populations. A single QTL on chromosome 5H was shown to be responsible for 42% of the phenotypic variation responsive at three salt concentrations (Cattivelli et al. 2002). Some of the important are identified using GWAS analysis presented in Table 3.

Table 3 Important genes/TFs and protein families involved in salt tolerance in crop plants
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Proteomics: Utilization of Proteomics Knowledge

Salinity limits crop productivity and growth. Different complex processes occur during salt response signals in the cell, and metabolic processes take place simultaneously at the cellular and plant organ levels. The activation of transcription factors leads to the formation of specific proteins via the mechanism presented in Fig. 3. To produce effective salt tolerance mechanisms in crop plants, plant physiological and molecular processes should be investigated under different salinity levels. Nowadays, the advancement of proteomics research has provided a method of obtaining high-throughput data that are used to determine plant molecular networks (Zhang et al. 2012). Important proteins expressed under saline stress conditions at different growth stages in crop plants are presented in Table 3. Moreover, they also detected 2171 salt-responsive proteins, of which 561 were unique. These proteins were identified in leaves, roots, shoots seedlings, and other different growth stages. These proteins provide valuable a deeper insight into salt tolerance mechanisms related to photosynthesis, reactive oxygen species, signal transduction, ion homeostasis, and cytoskeleton dynamics under different salt stress conditions (Pang et al. 2010). However, the plants, i.e., glycophytes and halophytes respond differently under different salt stress conditions. Many studies have shown that A. thaliana (Pang et al., 2010), rice (Oryza sativa) (Kim et al. 2005), Triticum durum (Caruso et al. 2008), Glycine Max L. (Sobhanian et al. 2010), Tabacum (Razavizadeh et al. 2009), T. aestivum (Peng et al. 2009), A. stolonifera (Xu et al. 2010)(Xu et al., 2010), P. cathayana (Chen et al., 2012), S. Europaea (Wang et al., 2009), P. coarctata (Sengupta and Majumder 2009), and D. salina (Katz et al. 2007) induce photosynthesis-related proteins under salt stress conditions. Contrarily, salt-tolerant crops such as T. halophila (Katz et al., 2007), S. salsa (Li et al. 2011), and S. aegyptiaca (Askari et al. 2006) downregulate the expressions of salt-tolerant photosynthetic proteins under high salt stress conditions (Table 4). In some cases, proteins related to carbohydrate and energy metabolism are also induced under saline conditions in glycophytes, while the opposite is seen in halophytes (S. salsa) (Li et al. 2011).

Fig. 3
figure 3

Schematic diagram of the protein modification process that allows plants to withstand saline environments (tolerance mechanism)

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Table 4 Important proteins are expressed under saline stress conditions at different growth stages in crop plants
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Under salt stress, many proteins are expressed at the pre-transcriptional, post-transcriptional, and translational levels. The ability to distinguish plant stress proteins and identify suitable genes can enhance resistance to stress (Barkla et al. 2009). These complex regulatory pathways involve during TFs, osmolyte synthesis, ROS, kinase cascades, antioxidants, and iron homeostasis (Yin et al. 2015). The combined efforts of organ-specific and sub-cellular organelle-specific proteomic studies of the developmental mechanisms at different locations (leaf and roots) provide information on cellular and sub-cellular processes that regulate stress responses and signal transduction in various organelles (Hossain and Komatsu 2013). Proteomic approaches have been taken in studies of both halophytes and glycophytes. Plants using proteomics study include Arabidopsis thaliana (Razavizadeh et al. 2009), grass pea (Chattopadhyay et al. 2011), Populous cathayana (Chen et al. 2012), Sorghum bicolor (Ngara et al. 2012), tomato (Manaa et al. 2011), cucumber (Du et al. 2010), peanut (Jain et al. 2006), canola (Bandehagh et al. 2011), and durum wheat (Jacoby et al. 2010). Lectins are another type of protein induced by salinity and are involved in protein saccharide interactions and stress signaling. Jacalin domains work together with small lectins under stress conditions and serve as a plant tolerance mechanism (Zhang et al. 2000). Osmoticin is another type of protein that has also been linked in plants used for salt stress resilience and enhances osmotic stress in potatoes and mangroves when treated with salt stress (Tada and Kashimura 2009). Moreover, plant tolerance mechanisms include different types of proteins such as ribosomal proteins (Chattopadhyay et al., 2011), poly-A binding proteins (Witzel et al. 2009), startup translation factors (Pang et al. 2010), translation elongation factors (Sobhanian et al. 2010), tumor-controlled proteins (during translation) (Yu et al. 2011), RNA recognition motif (RRM) (Pang et al., 2010), and tRNA syntheses (Wen et al. 2010) that can help to adopt certain defense mechanism.

Transcription Factors in Crop Plants in Response to Salt Stress

Tolerance mechanisms of crops against abiotic stresses are complicated and affect plant development at different growth stages (Chinnusamy et al. 2004). Tolerance mechanisms involve changes at the cell, tissue, and whole-plant level, and it is necessary to understand the response at the physiological and molecular levels (Farooq et al. 2009). Plant responses determined using different molecular approaches provide deep insight to figure out gene expression and signal transduction pathways and helps to find the metabolic changes that occur at different stress levels. Further, this information is used to enhance the tolerance mechanism in crop plants (Amirbakhtiar et al. 2021). Transcription factors are proteins linked to transcriptional regulators involved in chromatin remodeling or protein modification (Udvardi et al. 2007). Transcription factors link cis-elements in the promoter regions of genes (which is stress induced) and trigger the upregulation of downstream genes that play an important role in abiotic stress tolerance (Agarwal and Jha 2010). Riechmann et al. (2000) identified 1500 TFs involved in stress response genes in Arabidopsis. Moreover, it has also been reported that tolerance or susceptibility is controlled at the transcriptional level, and plants respond independently to stressful conditions (Umezawa et al. 2006). Many genes are activated at the transcriptional level under salinity, which causes many metabolic proteins alteration produced under salt stress condition that regulate downstream genes and enhance stress tolerance mechanisms (Kavar et al. 2008). Vysotskaya et al. (2010) determine barley’s physiological behavior and water retention under salt conditions and found that saline conditions limit the transpiration and hydraulic conductivity (HC) in salt-tolerant barley cultivars, unlike in more sensitive cultivars. Moreover, aquaporin (AQP) downregulation was observed in salt-sensitive genotypes when salt treatment was delayed for up to 24 h. Greater tolerance was characterized by less inhibition of leaf area, greater root fresh weight, increased leaf water content, and greater chlorophyll concentration. The positive and negative effects of AQP expression have been determined at the gene expression level under saline conditions, while water transport depends on plant and cell–cell pathway interactions (López-Pérez et al. 2009). Aquaporin (HVPIP2;1) overexpression results in reduced salt sensitivity in transgenic rice at 100-mM NaCl (Katsuhara et al. 2003). Similarly, in maize, the expression of the AQP gene was enhanced by adding to a nutrient solution (Zhu et al. 2005). Fowler and Thomashow (2002) revealed that characterized gene products are of two types: genes that encode proteins and prevent water deficit within cells and genes induced by abiotic stress (regulatory proteins) that regulate stress signal transduction and alter the expressions of genes that could benefit the stress response (Shinozaki and Yamaguchi-Shinozaki 2007). Some important transcription factors (TFs) induced under salinity stress and salt related genes engineered and other abiotic stress conditions are presented in Tables 5 and 6 respectively.

Table 5 Important transcription factors (TFs) induced by salinity are used for improving salt tolerance in crop plants
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Table 6 Important genes and their function used genome editing technique for stress tolerance in crop plants
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Genome Editing and Salt Stress Tolerance

The new genomic era has brought nuclease systems with non-specific domains bonded to specific DNA sequence-binding domains. Such bonded nucleases can cut specific target genes and repair them through non-homologous end joining (NHEJ), known as genome editing (GE) (Gaj et al. 2013). First-generation GE technology includes mega-nucleases, i.e., ZFNs and TALENs, but achieving a specific target was difficult, labor exhaustive, and time consuming compared to second-generation genome editing techniques i.e., CRISPR/Cas9. Second-generation sequencing is easier to design and is easier, requires less time, and is cost effective. TALENs have greater binding specificity than ZFNs due to their length. TALENs have been successfully used in Arabidopsis sp. (Cermak et al. 2011), tobacco (Zhang et al. 2013), rice (Li et al. 2012), and Brachypodium sp. (Shan et al. 2013). New genome editing technology has provided opportunities to breed crops with desirable traits (Jaganathan et al. 2018), and CRISPR/Cas9 uses Cas9 with guided RNAs (gRNA) to target multiple sites within the genome. GE crops have advantages over transgenic plants because they transfer edited DNA for specific traits (Malzahn et al. 2017). CRISPR technology has been used in model plant species such as Arabidopsis sp., tobacco, rice, and some other crop plants are being considered for CRISPR technology (Jiang et al. 2013). A recent report also stated that around 20 crop species have been gene edited (Ricroch et al. 2017) for various agronomic traits as well as abiotic stress management so far. However, many of the published articles are proof of concept for CRISPR application, as they focused on knocking out specific genes that play important roles in biotic and abiotic stress tolerance. To enhance the resistance of rice salinity, Zhang et al. (2019) use a genome editing technique by engineering a Cas9-OsRR22-gRNA expressing vector for the rice OsR22 gene. Of 14 transgenic T0 plants, nine mutant plants have been recognized. Six mutation forms were detected at the target site by sequencing, all of which were transferred successfully to the next generations. In T1 generations, mutant plants without transfer DNA (T-DNA) have been obtained through segregation. For their salinity tolerance and agronomic characteristics, two homozygous T2 mutant lines were studied further. In the seedling stage, the results show that the T2 homozygous mutant lines have significantly increased their salinity tolerance relative to wild plants. The Dystonia (DST) knockdown mutant gene is effective in improving salt tolerance. It has a major modification in agricultural characteristics, including leaf width, plant panicle count, and panicle longitudinal (Huang et al. 2009). Likewise, another study also indicated that OsRR22, but no improvements in other agronomic features could significantly boost the salt tolerance (Takagi et al. 2015). CRISPR/Cas9 provides the potential to shorten breeder time, dramatically lowering cost compared to traditional breeding methodology (Lee et al. 2016).

Future Research Directions

Genetic engineering for tolerance to salinity shows promise when overcoming obstacles to hybridization for introgression of appropriate genes helping to interpret the results for the salinity tolerance process. In addition, the integration of the physiological, metabolic, and biochemical characteristics of salinity tolerance is important to resolve the information issues in response to the stress of the entire plant phenotype. Salinity tolerance can be enhanced using knowledge about the morphology, physiology, and genetics of the crop plant that offers a selective landscape context within which scientists must maneuver crop plants. In a way, the result after introgression of the genes responsible for salinity tolerance in crops appears to be highly divergent, especially from the establishment and evolution perspective. Much advancement in adaptation to saline conditions in crop production will be anticipated with efficient molecular-aided approaches to breeding complemented by a framework incorporating multiple components, such as molecular next-generation sequencing (NGS) technologies, cost-efficient protocols, and precise quantitative trait expression determination. High-level tolerance to salinity includes several gene modifications, such as those involving the transportation and division of KCl, NaCl, and Cl at genetic and epigenetic stages and those that include morphological and anatomical variations. Manipulation of several intervarietal crosses to pyramid QTLs by the QTL tool can be implemented in nature. Within taxonomic families of economically significant crop species, i.e., grass (Poaceae, Gramineae), wide pools of genetic variance for salinity tolerance can be exploited significantly by introgression by interspecific hybridization and transgenic approaches. Examples include genomic and multiple gene selection where it is possible to exploit the combination of MAS and traditional backcross and pedigree analysis approaches to pyramidal multiple genes responsible for tolerance. New genomics and GE technologies provide options for a biologist to enhance salt tolerance using CRISPR-based GE techniques. NBT provides a platform for scientists to identify desirable genes and insert them into target crops more quickly than conventional breeding. Knowledge about GWAS needs to expand to figure out a greater number of proteins family members, TFs, and a group of genes that played a significant role under salinity stress condition. Furthermore, the 3D protein structure deeply explained the protein structure and provides crucial information for subsequent research on biological functions. The major research aims in future should be to increase yield, nutritional factors, and biotic and abiotic stress tolerance (salinity and drought). CRISPR-based genome editing is a breakthrough technique that needs further modification to increase target efficiency. Trails from the past five years have been preliminary, and further improvement is needed to achieve a zero hunger goal and maintain food supplies for future populations.

Conclusion

Osmotic and ionic stress are caused by salt stress, and plants respond differently when salt stress occurs. Proline, ABA, and Na+:K+ ratio determination are essential, and these could be exploited to increase crop plant tolerance mechanisms. Many genes are activated that regulate plant tolerance mechanisms under salt stress. Understanding the molecular mechanisms behind salt stress is crucial for improving and introducing new salt-tolerant cultivars of crop plants into the environment. It is also essential to consider physiological, biochemical, and molecular factors for adaptation to salt stress. Furthermore, integrated plant omics approaches are crucial for genetic engineering to cope with the problem and vast knowledge for tolerance mechanisms. Due to its efficiency, simplicity, and specificity, genome editing is a valuable tool for crop development initiatives. Functional genomics and plant breeding it have opened new possibilities. Preliminary research has found that genome editing is a viable method for developing abiotic stress-resistant crops in future to combat hunger. However, significant technological and legislative barriers must be overcome before GE can be used to reshape global agriculture. It is also necessary to identify and characterize transcription factors and their products to exploit the gene products essential for salt-tolerant lines that improve adaptation under saline conditions. Moreover, TFs, as potential genes for use in breeding and crop improvement programs, provide insight into the abiotic stress mechanisms, physiological mechanisms, and molecular mechanisms (signal transduction and metabolic alteration) that could help to produce new resistant varieties and enhance salt tolerance through genetic modification.