Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 63-71 http://cropscipublisher.com/index.php/tgg 66 5 Major Findings from GWAS on Salt Tolerance 5.1 Identified loci and candidate genes associated with salt-responsive traits In GWAS analysis, researchers have identified many SNPS and candidate genes related to salt tolerance. These traits include Na⁺, K⁺ content, Na⁺/K⁺ ratio, and biomass changes under salt stress. Among them, the HKT1;5 gene located on chromosome 4 has attracted much attention - it is directly involved in the transport of sodium, can reduce the accumulation of Na⁺ in leaves, and thus improve the salt tolerance of plants (Hazzouri et al., 2018). In addition, 54 significant SNPS distributed on chromosomes 2, 4, 5, 6 and 7, as well as 616 candidate genes involved in transport, signal transduction and stress response, were recorded. Genes such as PGK2, BASS3, SINAT2, AQP and SYT3, which have been verified in combination with transcriptome data, are also closely related to maintaining ion balance and adapting to stress. 5.2 Chromosomal hotspots and pleiotropic regions relevant to salinity stress On multiple chromosomes, especially on chromosomes 4, 6 and 7, research has identified regions where SNPS are highly concentrated and overlap with the positions of key candidate genes. These places are often referred to as "hotspots", which not only control ion homeostasis but may also simultaneously affect properties such as antioxidant activity and yield (Alqudah et al., 2024). Take chromosome 7H as an example. Some loci on it are related not only to the activity of antioxidant enzymes under salt stress but also to morphological traits, indicating that these loci have a wide range of roles in stress adaptation. 5.3 Functional annotations of genes involved in ion homeostasis, osmoprotection, and signaling When performing functional annotations on the genes identified by GWAS, some results are quite intuitive - many genes precisely fall into the crucial aspects of salt tolerance. For example, HKT1;5 and NHX1 are mainly responsible for expelling Na⁺ or isolating it to specific positions within the cell, thereby maintaining ionic balance (Soud et al., 2024). Aquaporin (AQP) acts like a "waterway", helping water flow rapidly. There is another type of gene that encodes antioxidant enzymes - peroxidase, catalase, and ascorbic acid peroxidase - whose task is to eliminate reactive oxygen species and reduce the oxidative stress of cells. On the other side, genes related to signal transduction, such as LRR-KISS, CML, and SINAT2, enable plants to respond rapidly and coordinate various defense mechanisms when exposed to high salt levels (Chang et al., 2024). This information does not merely remain at the research level; it also provides a readily available genetic basis for breeding salt-tolerant barley varieties. 6 Case Study 6.1 Selection of diverse accessions from Tunisia and Algeria for association mapping In North Africa, the local varieties and genotypes of barley in Tunisia and Algeria have long been systematically collected and evaluated under salt stress conditions. The genetic background of these materials is very broad, and the differences in traits are also considerable - whether it is agronomic traits, morphological characteristics or yield-related indicators, they all show obvious differentiation in the high-salt environment (Allel et al., 2016). Among them, some strains have demonstrated outstanding salt tolerance, such as Tozeur2, Tichedrett, Kerkena and Kebelli2, which can maintain high yields even under high-salt conditions. This makes them particularly valuable in association mapping and breeding. 6.2 Key SNPs and genes (e.g., HvHKT1;5, HvNHX1) discovered under controlled salinity trials In the study of barley in North Africa, GWAS and physiological experiments together revealed many loci and genes closely related to salt tolerance. HvHKT1;5 on chromosome 4 is the key point among them. It plays a core role in the transport and excretion of sodium ions and can significantly reduce the accumulation of Na+ in leaves, thereby enhancing the salt tolerance of the plant (Figure 2). HvNHX1 is also worth mentioning. Such genes are responsible for the regionalization of Na+ and the maintenance of ion balance, and are closely related to the adaptability of plants under salt stress (Xu et al., 2025). In addition, there are some loci related to antioxidant defense and accumulation of osmotic regulatory substances, which provide more clues for understanding the genetic basis of salt tolerance in these germplasms (Alqudah et al., 2024).
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