Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 63-71 http://cropscipublisher.com/index.php/tgg 63 Case Study Open Access Genome-Wide Association Mapping of Salt Tolerance in Barley Germplasm Jiamin Wang, Xian Zhang, Xuemei Liu Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding email: xuemei.liu@hitar.org Triticeae Genomics and Genetics, 2025, Vol.16, No.2 doi: 10.5376/tgg.2025.16.0007 Received: 16 Jan., 2025 Accepted: 28 Feb., 2025 Published: 20 Mar., 2025 Copyright © 2025 Wang et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wang J.M., Zhang X., and Liu X.M., 2025, Genome-wide association mapping of salt tolerance in barley germplasm, Triticeae Genomics and Genetics, 16(2): 63-71 (doi: 10.5376/tgg.2025.16.0007) Abstract Salt stress is the main abiotic factor that limits the productivity of barley (Hordeum vulgare L.) in global saline-alkali regions. This study employed genome-wide association analysis (GWAS) methods to reveal the genetic basis of salt tolerance in different barley germplasm resources. We evaluated a group of core germplasm resources under controlled salinity conditions and conducted high-resolution GWAS analysis using single nucleotide polymorphism (SNP) markers. Our analysis identified several loci and candidate genes significantly associated with salt stress traits, including those involved in ion homeostasis, osmotic regulation, and stress signaling pathways. A case study focusing on North African germplasm resources highlighted key salt-tolerant genes, such as HvHKT1;5 and HvNHX1, which further emphasizes their significance in breeding projects. Despite the challenges related to population structure and environmental variations, our research results demonstrate the practicality of GWAS in analyzing complex traits and guiding marker-assisted selection (MAS). This study laid the foundation for breeding salt-tolerant barley varieties and emphasized the value of integrating genomic tools into climate-adaptive agricultural breeding strategies. Keywords Barley germplasm; Salt tolerance; GWAS; Candidate genes; Marker-assisted selection 1 Introduction In some areas with high soil salinity, barley is often regarded as a "safe grain" for food security. It's not because its yield is necessarily the highest, but because it can tolerate salt more than many crops. Salinization is now spreading worldwide, and the area of affected cultivated land is still expanding. However, a salt environment does not mean that crops will be safe and sound - salt stress can disrupt the ionic balance of plants, reduce biomass, and also impact germination, chlorophyll levels, and antioxidant defense processes. As a result, the growth of the plants is often weakened, and the yield declines accordingly. Sometimes, even quite serious losses occur (Sonia et al., 2023; Thabet and Alqudah, 2023). It is not an easy task to enhance salt tolerance through traditional breeding. Not only is the genetic structure complex, but it also involves multiple physiological and molecular pathways. In contrast, genome-wide association studies (GWAS) have been proven useful in understanding the genetic basis of salt tolerance. It can identify quantitative trait loci (QTLS), single nucleotide polymorphisms (SNPS), and candidate genes related to key traits, including ion transport, antioxidant capacity, and stress response gene expression, etc. (Việt et al., 2013; Mwando et al., 2020). Previous studies have mapped important QTLs on chromosomes 2H, 4H, 6H, and 7H, and have also identified genes such as HKT1;5 that regulate sodium ion transport, as well as other genes involved in ion homeostasis and antioxidant defense. (Huang et al., 2008; Mwando et al., 2021). This study intends to use GWAS to screen out salt-tolerant gene loci and candidate genes in different barley germplasms, and combine genomic, physiological and transcriptomic information to provide genetic markers and resources that can be used for breeding. In this way, the efficiency of mark-assisted selection can be enhanced, and the breeding of salt-tolerant varieties will also be accelerated. Not only that, these achievements are helpful for the sustainable development of saline-alkali land agriculture and can also provide a reference framework for similar research on other crops.
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