**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 salttolerant 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<sup>+</sup> 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.


#### **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

### *Achieving Salinity-Tolerance in Cereal Crops: Major Insights into Genomics-Assisted Breeding… DOI: http://dx.doi.org/10.5772/intechopen.112570*

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<sup>+</sup> / 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<sup>+</sup> , Li<sup>+</sup> , or K<sup>+</sup> 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**).

### **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


**Table 2.**

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


*Achieving Salinity-Tolerance in Cereal Crops: Major Insights into Genomics-Assisted Breeding… DOI: http://dx.doi.org/10.5772/intechopen.112570*


#### **Table 3.**

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

*Achieving Salinity-Tolerance in Cereal Crops: Major Insights into Genomics-Assisted Breeding… DOI: http://dx.doi.org/10.5772/intechopen.112570*

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].
