Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 63-71 http://cropscipublisher.com/index.php/tgg 68 6.3 Practical applications of findings in regional breeding programs For regional breeding, these salt-tolerant genotypes and the corresponding genetic markers are not "paper achievements", but tools that can be directly applied. Through marker-assisted selection, favorable alleles in genes such as HvHKT1;5 and HvNHX1 can be introduced into superior varieties that adapt to saline-alkali environments. Meanwhile, some phenotypic characteristics - such as the biomass in the upper highlands, higher grain yield, and maintaining strong antioxidant enzyme activity under saline-alkali conditions - can also serve as reliable selection criteria (Allel et al., 2019). This approach not only benefits local breeding but also provides reference and support for other regions with increasingly severe salinization, helping to achieve sustainable agriculture and food security. 7 Challenges and Limitations in GWAS for Salt Tolerance 7.1 Population structure and false-positive associations A common problem when conducting GWAS is the confounding effect brought about by the population structure. When genetic relationships are too close or there are significant differences among different subgroups, and these have not been fully incorporated into the analysis, it is very easy to have some "seemingly related" markers and trait associations that are actually false (Li, 2020). Hybrid linear models and more refined statistical methods can alleviate this situation, but it is almost impossible to completely eliminate it. 7.2 Limited resolution in complex trait mapping under environmental interaction Salt tolerance itself is a complex quantitative trait, involving not only multiple genes but also having a strong interaction with the environment (Thabet et al., 2025). When the environment fluctuates greatly or the effect of a single site is small, it is very difficult for GWAS to precisely analyze the genetic structure of this trait (Kumar et al., 2015). In this case, the result might merely be the delineation of a larger genomic region rather than directly locking onto a specific pathogenic gene. Even some loci that are crucial to overall tolerance but have a relatively small effect may be overlooked. 7.3 Need for high-quality phenotyping and environmental standardization The salt tolerance phenotype is highly sensitive to external conditions. A slight difference in the growth environment or a slight change in the measurement method may lead to different results (Hu and Schmidhalter, 2023). Differences in salinity levels, planting conditions, and measurement methods will all increase noise, making true associated signals more difficult to identify. New phenotypic analysis techniques such as high-throughput imaging and sensor-based automatic measurement seem promising, but they are costly and not easy to popularize, especially in the early breeding stage or in areas with limited conditions. To enhance the reliability of GWAS in salt tolerance studies, the standardization of environmental conditions and phenotypic analysis methods remains a problem that must be addressed. 8 Integration of GWAS with Genomic Selection and Molecular Breeding 8.1 Use of significant GWAS markers for marker-assisted selection (MAS) Significant SNPS or loci identified in GWAS can often be put to use directly - they can serve as molecular markers to help breeders more quickly identify materials with superior salt-tolerant alleles (Liu et al., 2024). Especially those markers closely linked to key genes can be easily embedded into the breeding process to track and combine beneficial traits (He et al., 2014). In this way, the screening becomes more targeted and the steps for cultivating high-quality seeds can also be simplified. 8.2 Potential of genomic prediction models to improve breeding efficiency The greatest advantage of genomic selection (GS) is that there is no need to wait until the traits are fully manifested before drawing a conclusion. It relies on genome-wide marker data to predict an individual's breeding value in advance (Spindel et al., 2015; 2016; Li et al., 2017). If the results of GWAS are incorporated into the GS model, such as weighting significant markers or directly setting them as fixed effects, the prediction accuracy tends to be higher (Wang et al., 2024; Pang et al., 2025). Traits such as salt tolerance, which are jointly controlled by multiple genes, are particularly suitable by this method - it can not only increase the genetic gain in each breeding cycle, but also facilitate the faster screening of dominant genotypes from large populations (Zhang et al., 2023; Meuwissen et al., 2024).
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