Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 19-30 http://cropscipublisher.com/index.php/tgg 22 1.3 Advantages of GWAS in discovering stress tolerance trait genes in wheat crops GWAS has many advantages in discovering stress tolerance trait genes in wheat crops, making it an important method for studying the stress tolerance of wheat crops . GWAS can be analyzed at the entire genome level, covering all genes in wheat crops, not just specific candidate genes. This means it can reveal the genetic variation associated with stress tolerance traits hidden throughout the genome, thus providing a more comprehensive genetic basis. GWAS can provide high-resolution genotype-phenotype correlations and can more accurately locate genes or gene regions related to stress tolerance traits. This helps to accurately identify candidate genes, providing more reliable information for subsequent functional studies and breeding applications. GWAS usually utilizes genotype and phenotypic data from large-scale sample populations for analysis, so it has high statistical power and reliability. The application of large sample sizes can increase the chance of detecting genetic variants and reduce the occurrence of false positive results, making the results more credible (Sukumaran et al., 2018). GWAS can utilize diverse germplasm resources, including different varieties, natural germplasm and wild species, to mine potential genetic variations related to stress tolerance traits. This helps to make full use of the genetic diversity of wheat crops and provides a wider range of genetic resources for the genetic improvement of stress tolerance traits. Key genetic markers identified by GWAS can be used as molecular markers for assisted breeding. These markers can help breeders select excellent germplasm with target traits, accelerate the breeding process, improve breeding efficiency, and achieve precise selection during the genetic improvement process. Stress tolerance traits are often jointly regulated by multiple genes and have high genetic complexity. GWAS can analyze multiple genotypes and phenotypes simultaneously, reveal the genetic basis and regulatory network of complex traits, and provide deeper insights into understanding stress response mechanisms. GWAS has unique advantages in discovering stress tolerance trait genes in wheat crops, providing powerful tools and methods for analyzing the genetic basis of stress tolerance traits, accelerating crop genetic improvement, and cultivating adaptive varieties. Genomic selection has great potential in wheat improvement, but actual cases of its application in wheat breeding are currently limited, and the cost of genotyping is also a key constraint for large-scale implementation of genomic selection. In addition, the current genome-wide association studies (GWAS) of wheat use small-scale association panels, insufficient research on complex traits, and few studies focus on multiple traits. These current situations reflect the necessity of conducting overall multi-trait GWAS in a large group (Khan et al., 2022). 2 Research Progress in the Past Decade 2.1 Application cases of GWAS under different types of adversity conditions In the past decade, GWAS has been widely used to study the coping mechanisms of wheat crops under various stress conditions. For example, using a multilocus GWAS (ML-GWAS) approach, researchers successfully identified genomic regions associated with traits related to grain weight in wheat under rain-fed conditions. This method is particularly effective in dealing with complex traits. For example , in the study of Gahlaut et al. (2021), many traits usually have polygenic control, low heritability, and large genotype × environment interactions. Their study analyzed 320 spring wheat varieties and revealed multiple new molecular markers and candidate genes related to drought tolerance, providing a powerful tool for marker-assisted selection (MAS) (Figure 2). For another example, genetic relationship analysis based on markers and pedigrees identified QTL haplotype variation for salt tolerance in Chinese wheat germplasm. Yu et al. (2020) collected 5 More than 000 wheat germplasm resources, and 660 wheat The K SNP chip determined the genotypes of more than 1,500 materials. Subsequently, they selected 307 genetically representative materials, including China's modern main varieties,
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