Achieving Salinity-Tolerance in Cereal Crops: Major Insights into Genomics-Assisted Breeding (GAB)

Abstract

Cereal crops including rice, wheat, corn, sorghum, pearl millet and small millet, are grown for food, feed and fuel in crop-livestock based agricultural systems around the world. Soil salinity occupies an important place among the soil problems that threaten the sustainability of agriculture in a wide area around the world. Salinity intensity is predicted to exacerbate further due to global warming and climate change, requiring greater attention to crop breeding to increase resilience to salinity-induced oxidative stress. Knowledge of physiological responses to varying degrees of oxidative stress has helped predict crop agronomic traits under saline ecosystems and their use in crop breeding programs. Recent developments in high-throughput phenotyping technologies have made it possible and accelerated the screening of vast crop genetic resources for traits that promote salinity tolerance. Many stress-tolerant plant genetic resources have been developed using conventional crop breeding, further simplified by modern molecular approaches. Considerable efforts have been made to develop genomic resources which used to examine genetic diversity, linkage mapping (QTLs), marker-trait association (MTA), and genomic selection (GS) in crop species. Currently, high-throughput genotyping (HTPG) platforms are available at an economical cost, offering tremendous opportunities to introduce marker-assisted selection (MAS) in traditional crop breeding programs targeting salinity. Next generation sequencing (NGS) technology, microenvironment modeling and a whole-genome sequence database have contributed to a better understanding of germplasm resources, plant genomes, gene networks and metabolic pathways, and developing genome-wide SNP markers. The use of developed genetic and genomic resources in plant breeding has paved a way to develop high yielding, nutrient-rich and abiotic stress tolerant crops. Present chapter provides an overview of how the strategic usage of genetic resources, genomic tools, stress biology, and breeding approaches can further enhance the breeding potential and producing salinity-tolerant crop varieties/lines.

1. Introduction

Food is one of the basic needs of every organism including human being to survive hence its importance cannot be exaggerated. Beyond the need to quench appetite, food is extremely essential for optimal functioning of the entire body physiology and metabolism. All requirements meet out by a balanced diet that comprise essential macro and micro nutrients available in several types of food ingredients (i.e., carbohydrates, proteins, lipids, mineral and vitamins, and dietary fibers) consumed as daily meal [1]. Among all the necessary food ingredients, carbohydrates are the key ingredients occurring in balanced diets as a primary source of energy required to perform routine workout and other physical actions. Most of the carbohydrates are supplied by cereal grains of the grassy crops [2]. Cereals which include; rice, wheat, corn, sorghum, pearl millet and small millets have been grown since time immemorial for food, fodder and fuel in crop-livestock based agricultural systems around the world [3]. Most of the cereals have predominantly been considered as a staple foods in every agro-ecology and promoted as a healthy food in body weight management, however each cereal contribute in different ways. Plant based foods in various forms are an essential components in human diets which contain essential ingredients. For instance, millets are high-quality alternative to major cereals (rice, wheat, and maize) owing to their greater minerals and proteins contents. In addition, statistical studies have shown that half of the total percentage of calories consumed by human population comes from cereals which are the most traded agricultural commodity in international markets [4].

Global cereal growing area is projected to increase by 14 million hectares between 2020 and 2030 and harvested area over developed countries projected to grow by 4 million hectares, in Russia, Ukraine and Australia, as well as in developing countries using about 10 million hectares, mainly in Asian and Latin American countries. Arable land area under wheat and corn is expected to be raised by ~3% and 4%, however other areas under coarse grains and rice expected to remain unchanged. As land expansion is constrained by limited arable land accessibility compared to the previous decade, resulting restrictions placed on the conversion of forests or pastures to cropland, and continued urbanization, worldwide production growth is predictable to be driven mostly by intensification. Yield growth due to improved cultivation technology and methods, particularly in developing countries, is predicted to support prospect cereal production. Thus, the upward trend in cereal production observed in recent decades is indicative of the progress made in the agricultural sector around the world (Figure 1). Global yields are expected to increase between the base period and 2030 by approx 9% for wheat and other coarse grains, 10% for corn and 12% for rice. World wheat production is anticipated to hike by 87 million tons to 840 million tons by 2030, a moderate pace in relative terms compared to the past decade. India is the world’s third-largest wheat producer, expected to provide the largest share of additional wheat supplies, boosting production by 18 million tonnes by 2030 and expanding acreage in response to a national policy to increase self-sufficiency in wheat. Nevertheless, consumption of the cereal grains is greater than the production; hence a higher cereal production with improved nutritional values will need to meet out increasing demands due the burgeoning population. Global cereal production predicted to be lesser than consumption requirements in future due to several environmental stresses in the wake of climate change that may lead to drawdown in cereal stock globally.

Figure 1.

Bar diagram illustrating the year wise production and consumption of cereal grains globally.

Among all the cereal, rice (Oryza sativa) is major staple food grain belongs to family Poaceae worldwide and has extensive economic importance. Rice provides feed to more than 50% of world’s population predominantly in Asia where the population is expected to rise from 4.3 to 5.2 billion by 2050. Wheat (Triticum aestivum L.) is the second most important staple cereal crop grown all over the world contributing substantially to the world’s food and nutritional security world [5]. About 20–30% daily calorie intake [6] and 55% of carbohydrates are provided by wheat worldwide [7]. Wheat bread has high vitamins B, thiamine, and B2-riboflavin content with other several minor nutrients [8]. Worldwide estimated annual production of wheat is about 768.90 million metric tons whereas; India’s contribution is about 107.6 million metric tons [9]. Maize (Zea mays) is a cereal grain belongs to family Poaceae, cultivated throughout the world. The maize production globally in the year 2020–2021 was 1.2 billion tonnes led by India with 30.2 million metric tonnes [9]. Maize is a staple food plays an important role in food and nutritional security worldwide. Sorghum (Sorghum bicolar) is a cereal crop used for grain, fiber and fodder. Sorghum is cultivated in warmer climates worldwide and nutritional profile includes several minerals like phosphorous, iron zinc and copper it is also a good source of b-complex and vitamins. It estimated that the world sorghum production in year 2021–2022 was 60.32 million tons whereas; India’s contribution in total production was 4.7 million tons. Pearl millet (Pennisetum glaucum L.) has been widely grown in Sub-Saharan Africa, South Asia and Indian subcontinent. Archeological proof and modern genome sequence analysis showed that pearl millet originated and domesticated about 4000 to 5000 years ago in West Africa [10]. The global millet production in the year 2020–2021 was 30.5 million metric tonnes led by India with 41% (12.5) million metric tons [11]. Pearl millet is one the most important eco-friendly field crop in conventional farming system, plays an important role in food and nutritional security [3].

However, multiple types of environmental stresses (abiotic and biotic) are affecting holistic growth and plant health which ultimately leads to low crop productivity globally. Among the abiotic stresses, soil salinity or salt stress is one the most brutal environmental stresses adversely affecting sustainable crop yield and productivity globally. Hence, a comprehensive research on abiotic stresses in cereals has been experienced to cope with such a crucial salinity problem and related breakthroughs have been conducted and proved to be as one of the key activities to obtain higher genetic gains in terms of adaptability in changing climatic scenarios. Salinity adversely impacts on plant growth and development by exerting ion cytotoxicity, osmotic shock, nutrient imbalance, and oxidative stress [12]. The influence of soil salinity leads to impaired plant physiology, biochemistry and metabolism, hormonal imbalance, and regulatory pathways at cellular or entire plant structure. Plants response to the access salt stress comprised of several physiological and molecular approaches operates in cells in a coordinated fashion to cope with ion toxicity and hyperosmolarity [13]. A plenty of conventional as well as advanced molecular approaches have been developed and employed to breed the salinity tolerant varieties of the different cereal crops [14].

2. Abiotic stresses

Multiple abiotic (including; drought, heat, salinity, flood, harmful radiation, heavy metals, gaseous pollutants) and biotic stresses that are attacks of different microbial pathogens (e.g., fungi, bacteria, viruses, viroids, oomycetes, nematodes, and phtyotoplasma) causing adverse effects on morphology, physiology and metabolism leads to impaired plant growth and yield potential. Abiotic stress is progressively predominant in the wake of climate change and global warming affecting overall plants growth at different developmental stages such as germination, vegetative, and reproductive phase [15]. Total yield of crop is immensely affected by various factors like climatic fluctuations, insect incidents, agronomic factors, and nutrient availability in the soil. Stress is the any adverse environmental condition that hampers optimal growth and development of the plants [16]. Crop productivity and adaptability is affected by mainly physiological heat, drought, salinity and cold oxidative stresses. According to statistical estimates, approximately 20% of agricultural land is under salt stress, which negatively affects plant physiology and, ultimately, yield and nutritional value. The role of identified germplasm has been emphasized for drought breeding as the measured performance under drought stress is largely a result of adaptation to stress conditions. Hybridization of adapted landraces with selected elite genetic material has been testified to amalgamate adaptation and productivity. Abiotic stress is governed by quantitative trait hence genes linked to these traits have been identified and used to select desirable alleles responsible for stress tolerance in plant. Abiotic stress reduce water availability to plant roots by increasing water soluble salts in soil and plants suffer from increased osmotic pressure outside the root. Physiological changes include lowering of leaf osmotic potential, water potential and relative water content, creation of nutritional imbalance, enhancing relative stress injury or one or more combination of these factors. Plants operate a number of molecular, cellular and physiological modifications to overcome abiotic stresses [13]. Morphological and biochemical changes include changes in root and shoot length, number of leaves, secondary metabolite (glycine betaine, proline, malondialdehyde (MDA), abscisic acid) accumulation in plant, source and sink ratio.

Plants have developed various mechanisms in order to overcome these threats of biotic and abiotic stresses. They sense the external stress environment, get stimulated and then generate appropriate cellular responses. They perform this by stimuli received from the sensors located on the cell surface or cytoplasm and transmitted to transcriptional machinery situated in nucleus through various signal transduction pathways. This leads to differential transcriptional changes making plant tolerant against stress. Signaling pathways act as a connecting link and play an important role between sensing stress environment and generating an appropriate biochemical and physiological response.

2.1 Salinity stress

Soil salinity or salt stress refers to concentrations of salts in soils that affect physiological, biochemical process, growth and productivity of crops [17]. Salinity is one of the most important challenges which induce various physiological, molecular and cellular responses in plants [12]. Salt stress leads to loss of production by aggregation of soluble salts in the soil of root zone (18) which finally cause about 10 mha annual losses of arable land. A large number of sodium ions (Na⁺), carbonate and bicarbonate anions present in exchange sites affecting pH ranges [18]. Approximately 900 million hectares of agricultural land are affected by salinity globally, with India contributing 7 million hectares [19]. Salt stress affects approx 32 million hectares out of 1500 million hectares of dry agriculture land and 45 million hectares of irrigated land [20]. Therefore, yield reduction because of the increase in salt stress will have a disproportionately large effect.

Based on the salinity stress, three types of the soils are found in different geographical areas [21], which includes; (i) Saline soils which contains high level of water-soluble salt and electro-conductivity (EC) exceeded up to 4ds/m. By definition, saline soil has EC ≥ of 4 dSm⁻¹ (equal to approximately 40 mM NaCl), whereas soils are considered strongly saline if the EC ≥ of 15 dSm⁻¹. (ii) Sodic soils contain high contents of exchangeable sodium on the cation-exchange sites and usually have pH values ranges from 7.0 to 8.5. There are high accumulation of Na⁺ which cause soil collides to disperse cations (Ca⁺² and Mg⁺²) insufficiently. Distributed collides clog the soil’s pore and reduce the ability to transport water and air. Sodic soils have the tendency to extreme swelling and shrinking during moist and dry conditions respectively. (iii) Saline-sodic soil which is known for high producing soil at the arid and semi-arid area. This soil shows dual nature that associates with high EC (>4 dSm⁻¹) and low pH (below 8.5), hence both excess salts and Na⁺ affects plant growth under in saline-sodic soil conditions. Under salinity, plant growth is affected by two-phase salt stress.

2.1.1 Phases of salt stress

2.1.1.1 Osmotic phase

In osmotic phase, the excess soil salt concentration reduced water potential in root zone causing water scarcity results in impaired plant growth. Growth reduction in osmotic phase rely only on the outer surface of salt concentration not in inside the plant tissues. A primary cause of reduced growth is that plant has to expense major portion of energy to acquire water from salty soil for routine metabolic process (Figure 2). Due to osmotic stress low water potential occurs in salty soil for plant uptake even if the volumetric soil water content is higher as field capacity. Osmotic stress initially causes numerous physiological changes, like membranes disruption, nutrient imbalance, decreased photosynthetic activity, and reduction of the stomatal aperture [12].

Figure 2.

Diagram displaying plant responses and mechanism of salt tolerance showing ion exclusion, osmotic tolerance and tissue tolerance in crops.

2.1.1.2 Ion phase

Reduction of plant growth in the ionic phase is mainly due to internal tissue injury caused due to high accumulation of toxic Na⁺. In addition, salt stress leads to reduced plant growth due to higher intake of certain ions (Na⁺ and Cl⁻) which is known as ion toxicity [22]. Accumulation of Na⁺ and Cl⁻ in higher concentration delays the growth and negatively affects the metabolic processes in plants. The Na⁺ ions inhibits K⁺ ion uptake in plants and disturbs stomatal regulation which is the reason for water loss and necrosis. The Cl⁻ ions stimulates chloride toxicity due to defective production of chlorophyll.

2.1.2 Mechanism of salt tolerance in plants

Tolerance to salt stress varies on species and variety and it also varies at growth stages of plants. A wide spectrum of responses against salt stress shown by plant gives warranty of a broad range of adaptations at the entire plant level [23]. Many crops tolerate negative effect of salinity and could survive with their routine function and metabolisms. Salt tolerance is associated with accumulation of compatible osmolytes and exclusion of Na⁺ while entering into the plant or tissue tolerance to high Na⁺ [24]. To grow and reproduce in high salt stress conditions plants had developed several mechanisms (Figure 2) these mechanisms can be categorized into three steps [25]; (i) ions exclusion, it regulates Na⁺ and Cl⁻ uptake. it prevent the accumulation of toxic ions into leaves (ii) osmotic stress tolerance, limits the growth of stems which is controlled by long-distance signals and is activated prior shoot Na⁺ accumulation; and (iii) tissue tolerance, tolerance power of tissues against accumulated Na⁺ or Cl⁻. When Na⁺ or Cl⁻ ions get succeeded to enter inside the plant tissue it grouped in leaf vacuole to prevent it from salt injury of thylakoid membrane.

2.1.2.1 Ion exclusion

Intercellular compartmentalization of Na⁺ ion is a main tolerance mechanism, which provides the ability to leaves to bear with high Na⁺ concentration (Figure 3). Salt stress imbalance the ion ratio by altering the pathway of sodium intake in place of potassium acquisition. There are four mechanisms for Na⁺ exclusion [26]; (i) Selective permeability of ions in cortex and stele by root cells, (ii) Stocking of xylem in root by xylem parenchyma cells, (iii) Elimination of salt from the stem by xylem parenchyma cells and, (iv) phloem stacking. Salt entering through root system can be excluded, or inside the plant system salt can be barred from entering sensitive organs. Most of the plant species grown under salt stress, Na⁺ ion competes with Cl⁻ to reach a concentration of toxic level. Therefore, the main focus of the researcher is on Na⁺ exclusion and transport within plant. Na⁺ exclusion by roots regulates toxicity level of Na⁺ within leaf blade; however, fails to do that induce Na⁺ toxicity after a short or long period, and cause death of older leaves. Exclusion of Na⁺ at root level occurs as a result of ion selectivity. A mechanism that operates for uptake of Na⁺ and K⁺ ions reported earlier by Schachtman and Schroeder [27]. Salt tolerance in many species is associated with a high concentration of K⁺ in young expanding leaf tissues. So it clearly shows the possibility of association of Na⁺/K⁺with salt tolerance. The control of Na⁺ uptake and better maintenance of the K+/Na⁺ ratio can be considered as key cellular mechanism to maintain osmotic potential for optimum cell activities, which contributes provides better adaptation capacity in plant under stress conditions [28, 29].

Figure 3.

Diagrammatic representation of all the abiotic stress tolerance mechanisms operated in plants.

2.1.2.2 Tolerance to osmotic stress

Osmotic tolerance is reducing the osmotic potential due to solute accumulation in response to water stress, plays key role in plant adaptation to dehydration by maintaining turgor pressure, relative water content, and high stomatal conductance [30]. The osmotic effect is measured by growth rate and stomatal conductance of plants. Proline is a widely distributed osmolyte which protects the plant cells against salt stress. Proline acts as osmolyte that protects subcellular structure and biomolecules and chelate metal ions under osmotic stress [31]. In drought conditions, the delayed stomatal closure caused mainly by higher osmotic adjustment led to elevated assimilation rate and assimilates production [32]. In addition, increase in polyphenol content, glycine betaine and antioxidant enzymes activities have been reported associated with stress tolerance in plants providing protection against reactive oxygen species (ROS) [33]. All the possible mechanisms of salt tolerance operate at cellular levels in plants are depicted in Figure 3.

2.1.2.3 Tissue tolerance

Third mechanism, as tissue tolerance is increases the shelf-life of older leaves, where it distributes Na⁺ and Cl⁻ at intercellular level to remove toxic levels of ions from cytoplasm and leaf mesophyll cells and to avoid detrimental effect on cellular process [25]. It synthesizes compatible solutes and controls transport and biochemical processes in cytoplasm and thus has dual function as osmoprotectant and osmotic adjustment (lowering of osmotic potential) [34]. These compatible solutes regulate osmotic tolerance in plants through different pathways such as it protects enzyme to get denature, stabilize plasma membrane and regulate macromolecules by osmotic adjustment [35].

3. Breeding approaches for salinity tolerance

Plants adapted specific mechanisms to tolerate saline conditions and activate various genes for salt tolerance to counter osmotic and oxidative stresses induced by salinity. Genetic evolution of salt tolerance is quite complex, while improvement has made less progress than anticipation over the past few decades. The explosive generation of information and technology related to genetics and genomics over the past decades pledge to deliver innovative and advanced resources for the potential production of tolerant genotypes. Although considerable progress in defining the primary mechanisms of salt tolerance, key hurdles are yet to be resolved in the translation and combination of the resulting molecular information into the plant breeding activities. Availability of the wide range genetic resources in cereals along with the implementation of advanced mechanisms like ion exclusion, osmatic tolerance, and tissue tolerance have been continuously improving screening procedures for salt tolerance genotypes. It could be enhanced via using traditional breeding or molecular breeding techniques such pyramiding, introgression by employing the genes or alleles which are already reported to have the potential of salt tolerance in the crop plants. Thus, considering these advantages, several breeders have been employed the techniques in cereal crop for salt tolerance enhancement.

3.1 Traditional cereal breeding for salinity tolerance

Plant breeding is decisive manipulation of plant species to produce desired plant accessions that are better suited for cultivation, produce higher yields, and stress resistance. Breeders selected edible plants with certain desirable traits and over time these valuable traits accumulated. Initial period of plant breeding spans from beginning of agriculture until the first hybridization investigation carried out by Kölreuter [36]. With the discovery of the laws of heredity, in turn from 19th to 20th century, importance of hybridization in plant breeding became widely recognized. Therefore, understanding the environmental stress effects becomes vital for different cereal crop improvement programs which have depended mainly on the genetic variations present in the genome through conventional breeding. The development of elite salt-tolerant varieties of grain is considered the most cost-effective and environmentally safe method for further effective use of saline-alkali soils, it is important to maintain and preserve the genetic resources of agricultural crops.

Conventional breeding strategies are effective for improving tolerance to salinity, though success rate is low using traditional breeding methods. The mechanism of plant tolerance depends on physiological and genetic responses and involves screening genotypes that confer salt tolerance. Conventional breeding of crops play an important role in screening of genotypes for salinity tolerance and implicates crop improvement using selection, hybridization, polyploidy, and introgression proceedings. We can add simple trait with the help of backcross method to make an elite variety/cultivar and development of such an elite variety act like a backbone to perform conventional breeding processes. For instance, to develop a hybrid variety of the cross-pollinated crops numerous progressive methods are used like, recurrent selection, production of inbred lines, screening of the superior inbred lines and finally superior two inbred lines based on specific combining ability value [37]. Convention breeding has pre-requisite of the natural genetic variation existed for the desired trait. In cereals wheat is known for its diversity for the ion exchange mechanism of Na⁺ and K⁺/Na⁺ ratio that exits in the form of landraces, progenitors [38], and other species having halophytic relationship in the family triticeae [39].

Targeted breeding for salt tolerance is done under coordinated wheat and barley program in India. However, there is a need to develop and exploit new sources of salt tolerant germplasm. Kharchia 65 is widely exploited genotype in India for the development of wheat varieties for salt tolerance and utilized as a donor parent for many wheat improvement programs globally [40]. However, it is not enough to consistently sustain the salt toxicity problem in all types of saline soils. The HD 2009 cultivar is considered as a susceptible parent to salinity that was released in 1975 for cultivation in North Western Plains of India grown under irrigated and timely sown conditions. In the recent past, wheat germplasm was screened for the identification of salt tolerant genotypes and only a few genotypes were identified in screening that imparts a significant level of tolerance against salt toxicity. Many wheat varieties were developed by employing identified tolerant genotypes and successfully cultivated throughout the world (Table 1). While, first salt tolerant variety of rice was basmati CSR 30 (Yamini) derived from the cross BR4-10/Pakistan Bas1, the donor BR4-10 from costal saline areas in state of Maharashtra, India.

Variety/line	Parents	Year	Developed by	Area of suitability	Reference
KH 65	Kharchia local/EG953	1970	Indian farmers through selection on sodicsaline Soil	Salinity soil of Durgapur, Rajasthan, India	[41]
Sakha 8	CNO67//SN64/KLRE/3/8156	1976	Agricultural Research Centre, Giza, Egypt	All saline soils	[42]
KRL1-4	WL711/Kharchia 65	1990	Central Soil Salinity Research Institute, Karnal, India	Saline/ sodic soils of Northern India	[43]
KRL 19	PBW255/KRL 1-4	2000	Central Soil Salinity Research Institute, Karnal, India	Saline/sodic soils of Northern India	[43]
KRL 210	PBW65/2*PASTOR	2010	Central Soil Salinity Research Institute, Karnal, India	Sodic soil of Northern India	[44]
KRL 213	CNDO/R143//ENTE/MEXI_2/3/Aegilops squarrosa TAUS) /4/WEAVER/5/2*KAUZ	2010	Central Soil Salinity Research Institute, Karnal, India	Sodic soil of Northern India	[44]

Table 1.

Brief description about the development of salt tolerant wheat variety for using conventional breeding.

3.2 Molecular breeding approaches for salinity tolerance

To understand the inheritance and genomics, molecular breeding started by artificial crossing of parental lines. In modern breeding, several alleles are mixed together from different germplasm, and useful wild alleles are added to elite variety. In consort with the advances in high-throughput genotyping technology have enabled direct observation of alleles at loci. This permits understanding of allele’s effects on particular phenotypes. Furthermore, it allows phenotypes prediction on the basis of genotypes with a genomic selection scheme. Finally, understanding the architecture of genome will help frame a precise breeding approach to deal with changes. On the other hand, polymorphic genetic factors numbers is too high in the genome to clarify their individual effects, particularly for quantitative traits. This confine power of genome-wide association studies to discover main quantitative trait loci. Genes and their molecular mechanisms for salt tolerance in cultivated crops should help breeders speed up genetic improvement of crop using marker-assisted selection (MAS) and genetic engineering [45]. Discovery of molecular markers is one of the most significant achievements of the biotechnology. They are extensively utilized to explore the DNA polymorphisms in the plant system and extremely useful for plant researchers and breeders to identify a particular trait linked with molecular markers at early stages of plants without doing phenotyping screening experiment [46]. To develop an elite line for salinity tolerance, identification of new QTLs is a key point. Salt tolerance is governed by more than one gene and is controlled by different QTL (quantitative trait loci) which are largely influenced by the environmental conditions. Thomson et al. [47] identified the “saltol” QTL that is involve into controls the Na⁺/K⁺ ratio at the seedling stage in shoot using a conventional breeding approach in rice. According to Hasan et al. [48] one method of effective conventional breeding is marker-assisted backcrossing used to transfer alleles at target loci. Hence, the implementation of conventional breeding approaches shows limitations to handle the QTL character like salt tolerance in wheat crop improvement programs. Molecular markers are not influenced by the environmental conditions and they have been widely used for the QTL analyses in various mapping populations [49]. Molecular breeding approaches have different steps to go for the final level and track-down a single gene or QTL having linkage with the desired trait.

Some main QTLs and genes in crop plants associated with salinity tolerance are salt overly sensitive (SOS) at seedling, vegetative and reproductive stages which are hypersensitive to high external Na⁺, Li⁺, or K⁺ concentrations. These mutants are mutated at three loci SOS1, SOS2, and SOS3 [50]. The SOS1 encodes a plasma membrane Na^+/H⁺ antiporter, SOS2 activates the SOS1 and encodes a serine/threonine protein kinase, and finally, SOS3 gene encodes calcium-binding protein [51]. Single gene over expression could improve the tolerance to salinity of transgenic plants for example; A. thaliana SOS1 and the vacuolar AtNHX1 gene can considerably boost the salt tolerance of transgenic plants (Table 2). Moreover, at high salinity rice tolerance can improve using ABA-dependent regulatory pathways and high drought using OsbZIP71 gene introducing the in transgenic plants. As per Su et al. [66], plant tolerance for salinity can improve by increasing the enzymes antioxidant activities and metabolism level of other mechanisms. The enzyme activity has also been confirmed in various transgenic plants by transferring bacterial genes. Plant resistance to oxidative stress improved through gene expression including; GAT, GR, SOD, and APX genes. The QTLs linked with grain yield were identified on chromosomes 1A, 1B, 2D, 3B, 4A, 4D, 6A, 6D, 7A and 7D tightly linked with different SSR marker in wheat for salt tolerance. The QTLs for TGW were identified on chromosomes 2B, 2D, 3B 7A and 7D. The QTL for tiller number (TN) and number of earhead (NE) identified on 4B, 4D and 1A, 2A, 2D, 4D, 5B 7A respectively tightly linked with SSR marker in wheat for salt tolerance (Table 3).

Crop	Gene family	Locus name/Gene	Function/Cellular response	Linked marker to gene	Reference
Transporters
Wheat (Triticum; aestivum L.)	HKT family	Nax1(HKT7, TmHKT1;4)-2AL chromosome	Involved in remove of Na^+ from xylem in roots and leaf sheath	Gwm312	[52, 53]
		Nax2 (HKT8, TmHKT1;5)-5AL chromosome	removes Na^+ from the xylem in the roots and enhancing K^+ loading into the xylem	gwm291, gwm410, gpw2181	[54]
		Kna1 (HKT8, TaHKT1;5)-4DL chromosome	Removes Na^+ from the leaves. Controls the selectivity of Na^+ and K^+ transport from root to shoot and maintains high K^+/Na^+ ratio	Xwg199, Xabc305, Xbcd402, Xpsr567 and Xpsr375	[55, 56]
		HKT1	Na^+-K^+-symporter, Salt stress		[57]
Rice; (Oryza sativa)	Na^+-K^+-symporter	HKT1	Salt stress		[58]
Maize; (Zea mays L.)	Na^+-H^+-dependent K^+ transporter	ZmHKT1	Salt stress		[59]
Antioxidants
Wheat	Catalase	CAT	Drought stress		[60]
Rice	Ascorbate peroxidase	APX	Drought, Salt and Cold		[61]
	Superoxide dismutase	SOD	Abiotic stress		[62]
Osmolytes
Wheat	Proline	P5CS	Drought		[63]
Rice	Glycine betaine	BADH	Heavy metal stress		[64]
Maize	Glycine betaine	bet A	Abiotic stress		[65]

Table 2.

Brief description about the genes underlying salt tolerance in cereal crops.

Traits	Chromosome	Markers name	Markers type	Population	Reference
Na^+	2A	Jagger_c4026_328	SNP	Genotype	[67]
	2A	Wmc272/Barc349	SSR		[68]
	2B	cfd73.1	SSR	RIL	[69]
	2B	wPt-4647/wmc147	SSR		[68]
	3A	wsnp_Ex_rep_c106152_90334299	SNP	Genotype	[67]
		wpt-666,438	DArt	RIL	[70]
	3B	gwm493	SSR	RIL	[69]
		wpt-8303	DArt	RIL	[71]
	4B	gwm368	SSR	RIL	[72]
	5A	gwm205	SSR	RIL	[71]
	5B	RAC875_c28831_558	SNP	Genotype	[67]
	5D	gwm174	SSR	RIL	[72]
	6B	wsnp_Ex_c45713_51429315	SNP	Genotype	[67]
	7A	barc121	SSR	RIL	[69]
		gwm282	SSR	RIL	[71]
		wmc0017	SSR	DH	[73]
K^+	1D	RAC875_c14137_994	SNP	Genotype	[67]
		barc169	SSR	RIL	[69]
	2A	wpt-1142, wpt-4199	DArt	RILs	[71]
		wpt-4559, wpt-3378	DArt	RILs	[70]
		barc1155	SSR	RILs	[69]
		X1103701.44AG	SNP	DH	[73]
	2D	gwm132	SSR	RIL	[72]
		gwm261	SSR	RIL	[74]
	3B	wpt-0302, wpt-0895	DArt	RILs	[71]
		barc251	SSR	RIL	[69]
	3D	gwm191	SSR	RIL	[72]
	4B	barc193	SSR	RIL	[69]
	5A	IAAV8258	SNP	Genotype	[67]
		Vrn-A1	SNP	DH	[73]
		barc151	SSR	RIL	[69]
	5D	RAC875_rep_c70595_321	SNP	Genotype	[67]
		gwm174	SSR	RIL	[72]
	6B	Kukri_c49331_77	SNP	Genotype	[67]
	7D	Excalibur_c13094_523	SNP	Genotype	[67]
TN	4B	gwm6	SSR	Genotype	[68]
	4D	cfd84	SSR	RIL	[74]
NE	1A	gwm71, wmc59	SSR	DH	[75]
	2A	gwm71	SSR	DH	[75]
	2D	cfd53	SSR	DH	[75]
	4D	cfd84	SSR	RILs	[74]
	5B	gwm 499	SSR	RILs	[72]
	7A	gwm635	SSR	DH	[76]
DTH	2A	wmc177(Drought stress)	SSR	RIL	[77]
	2D	wmc112	SSR	RIL	[73]
	7D	XC29-P13(Drought stress)	SNP	RIL	[78]
DTA	7D	X7D-acc/cat-10(Drought stress)	SNP	RIL	[78]
	2D	wmc112	SSR	RIL	[74]
TGW	2B	gwm55	SSR	DH	[75]
	2D	wPt-8330, wPt-666,857	DArt	RILs	[71]
		cfd53	SSR	DH	[75]
		gwm 296 and wmc 601	SSR	DH	[53, 76]
	3B	gwm383	SSR	DH	[53, 76, 79]
		gwm 247	SSR	RIL	[80]
	7A	gwm282	SSR	DH	[76, 80]
	7D	barc 172	SSR	DH	[79, 81]
GY	1A	gwm 357	SSR	RIL	[80]
	1B	gwm11	SSR	DH	[81]
	1D	gwm642	SSR	RIL	[72]
	2D	gwm311	SSR	DH	[81]
		wmc41	SSR	RIL	[82]
		gwm261	SSR	RIL	[82]
		wPt-4413	DArt	RIL	[80]
		wmc601	SSR	RIL	[74]
	3B	gwm566,Gwm247	SSR	RILs	[72, 80]
		gwm 247	SSR	RIL	[80]
	3D	gwm314, gwm645	SSR	DH, RILs	[72, 81]
	4A	wpt-4620	DArt	RIL, Germplasm	[80]
	4D	Gwm194	SSR	DH	[81]
	6A	XP02m22-3, gwm169	RFLP, SSR	DH	[75]
	6D	gwm469	SSR	DH	[75]
	7A	gwm282	SSR	RIL	[79, 80, 82]
	7D	gwm437	SSR	RIL	[74]

Table 3.

Brief description about the identified QTLs linked to salt stress tolerance in wheat.

3.3 Genome-wide studies (GWAS) for salt tolerance

Genome wide analysis studies (GWAS) approach for tolerance to abiotic stress has popular in last couple of years [67, 83]. GWAS is frequently being used to find and describe genetic basis of agronomic traits, which are generally influenced by numerous small genes [84]. GWAS identify single nucleotide polymorphism (SNP) variations and functional effects that best way to develop elite variety for salinity [85]. GWAS used to selection for natural variety population for genotyping on the basis of phenotypic variation. To find out the association among genetic loci and phenotypic variations in natural populations genotype, linkage disequilibrium (LD) analysis uses and it provide an important alternative to linkage mapping. In different abiotic and biotic stress conditions to discover the targeted gene using GWAS approach has led to identify the polymorphisms and identify the genetic loci which are accountable for phenotypic variances [57, 86]. High salinity increased osmotic pressure into the soil and cause drought condition dropping, water absorption by the seed to the soil resulting, delayed seed germination [87]. Using different sequencing platform development of SNP marker is a modern technology for crop improvement. More than thousands SNPs are available has directed to the use of GWAS method in cereal crops to dissever traits. Association mapping based on candidate gene (CG) have targeted grain yield and yield related traits and physiological traits [88]. Edae et al. [89] identified three candidate (i.e. DREB1A, ERA1 and 1-FEH) genes in wheat with multiple agronomic and physiological traits using SNPs association and CG-association mapping. Moreover marker trait association (MTAs) for heat tolerance in wheat at seedling stage first reported by Maulana et al. [90] and found QTL on chromosomes 3B and 4B. Schmidt et al. [91] identified QTL for heat and drought tolerance in spring wheat using GWAS. Qaseem et al. [92] reported stable association on 5A and 7D chromosome for drought tolerance. Furthermore, significant association of yield traits for drought and heat tolerance was identified on 6A chromosome [91]. Qaseem et al. [92] find out three haplotypes on 1A, 3B and 6B chromosomes for salt tolerance index in 307 wheat accessions by affymetrix wheat 660 K SNP array. The QTLs for yield and other associated traits identified on 4A, 5A, 5B, 6B and 7A chromosome for salt tolerance [93].

4. Conclusion and future perspectives

In the wake of global warming and climate change, abiotic stresses like salinity is a major constrain to agriculture and allied sector which affects sustainable food and nutrition security. During last decades considerable efforts have been made to decipher mechanism of stress resistance and metabolic processes against various environmental factors affecting plant growth and yield potential (Figure 3). The degree of salt stress and plant growth stage are mainly responsible for foreseeing how plants defend and respond to prevailing stress conditions. In terms of drought, stomata close progressively along with a parallel reduction in water-use efficiency and net photosynthetic activity. Under drought conditions, lower stomatal conductivity and moisture use-efficiency leads to the impaired photosynthetic potential and overall growth in plants. In addition to several aspects, changes of plant pigments were found to be closely related to salinity tolerance in crops. In plants, self-defense mechanism operated at cellular level in leaf is triggered frequently to protect entire solar energy trapping system existing in the form of photosynthetic machinery from permanent damage. Removal of reactive-oxygen species through multiple enzymatic and non-enzymatic antioxidant defense pathways, cellular transportation and membrane stability, expression of underlying genes networks, and biosynthesis of array of defensins are key mechanisms of salinity tolerance.

Several plant genetic and genomic resources have been generated to address the abiotic stresses by different scientific groups under independent and coordinated research programs globally. With the use of conventional plant breeding approaches, multiple crop varieties, elite cultivars, promising lines and germplasm collections and gene bank accessions have been developed and preserved for cereal crop species. To support the traditional phenotypic selection-based breeding, advanced high-throughput phenotypic tools have also been devised and being utilized in phenotyping of various phenotypic traits manifested under stress conditions. Similarly, with advancement and availability of the next-generation sequencing technology at affordable cost, has paved the way to develop high-throughput genotyping platforms that used in whole-genome sequencing. The NGS-based genomic tools including SNP markers, genome maps, genome-wide QTLs and MTAs and gene networks underlying abiotic stress resistance have been deciphered and implemented in crop improvement programs to achieve higher genetic gains. Despite of technological advancements and resource mobility, usually a significant gap in terms of mutual cooperation and liaising needed in lab to land technology transfer have been witnessed at both institutional and scientific levels. Moreover, the potential of untapped alleles occurring in wild genetic stocks and genomic advancement are yet to be realized adequately in plant breeding.