Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 63-71 http://cropscipublisher.com/index.php/tgg 65 3 GWAS as a Tool for Dissecting Salt Tolerance 3.1 Advantages of GWAS over traditional QTL mapping Traditional QTL mapping is usually based on specific parent groups, and the range that can be located is often large, but the accuracy is limited (Li, 2020). The approach of GWAS is somewhat different. It directly utilizes the natural genetic diversity from vast germplasm resource banks, making it more detailed in the detection of the association between markers and traits (Huang and Lin, 2024). In this way, not only can single nucleotide polymorphisms (SNPS) significantly associated with salt tolerance traits be identified across the entire genome, but also candidate genes or alleles that are easily overlooked by traditional methods may be discovered. 3.2 Marker-trait association and identification of significant SNPs In recent barley studies, GWAS has identified many SNPS related to key traits of salt tolerance, such as Na+ and K+ contents, Na+/K+ ratio, and root and stem biomass under salt stress (Xu et al., 2023). These loci are distributed on chromosomes 2, 4, 5, 6 and 7, and some of these "hotspot" regions are concentrated with candidate genes related to ion transport, protein kinases and stress signal transduction. HKT1;5 is a typical example. It plays an important role in the transport and distribution of sodium and has a direct impact on the salt tolerance mechanism of barley (Hazzouri et al., 2018). The discovery of these marker-traits provides quite valuable genetic basis for subsequent marker-assisted selection in breeding. 3.3 Integration of GWAS with other omics approaches Although GWAS alone can identify the associated loci, the effect of screening and verifying candidate genes will be better when combined with transcriptomics and metabolomics (Gharaghanipor et al., 2022). For instance, through integrative analysis, some studies have found that in salt-tolerant and salt-sensitive barley genotypes, some differentially expressed genes (DEGs) are concentrated in pathways such as ion homeostasis, antioxidant defense, and metabolic regulation (Tu et al., 2021). Genes such as PGK2, BASS3, SINAT2, AQP and SYT3 were thus identified and further verified by qRT-PCR. The combination of such multi-omics not only enables people to have a more comprehensive understanding of the molecular mechanism of salt tolerance, but also accelerates the speed of breeding stress-resistant varieties. 4 Germplasm Resources for GWAS in Barley 4.1 Diversity of global barley collections and gene banks In national or international gene banks around the world, a large number of barley germplasms are preserved - including local varieties, wild relatives, and excellent cultivated varieties. Together, they constitute an extremely rich genetic diversity, which precisely serves as an important basis for identifying new alleles and loci related to salt tolerance during GWAS. In previous studies, some teams directly utilized hundreds or even thousands of germplasms from around the world, covering different geographical and genetic backgrounds, in order to capture as many association signals between markers and traits as possible. 4.2 Importance of landraces, wild relatives, and elite lines in salt tolerance research In terms of salt tolerance research, local varieties and wild barley (Hordeum spontaneum) have their unique value. They often adapt to regions with harsher environmental conditions and carry some alleles that are not present in modern cultivated varieties (Wu et al., 2013). Especially wild barley often outperforms cultivated varieties in terms of osmotic regulation ability and the content of compatible solutes. As for superior strains and modern cultivated varieties, although their diversity is relatively limited, they have a good agronomic background and can serve as reliable controls or references when evaluating new salt-tolerant sources. 4.3 Strategies for core set development and phenotypic screening under salinity Faced with a vast amount of germplasm resources, researchers often first establish a micro-core set or core set to cover the largest genetic and phenotypic differences with fewer samples. Then, these core sets were placed in the field or controlled environment for salt stress treatment to determine ion content, biomass, yield and some key physiological indicators (Xu et al., 2025). At the same time, by combining advanced phenotypic techniques such as ion flux measurement and transcriptome analysis, salt-tolerant genotypes and their underlying mechanisms can be identified more effectively. This approach makes GWAS more efficient and also provides a shortcut for discovering salt-tolerant candidate genes and breeding related varieties.
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