Field Crop 2024, Vol.7, No.1, 1-8 http://cropscipublisher.com/index.php/fc 4 Twelve key sites associated with SDS resistance and 12 interactions between SNPS and SNPS were identified. The additive and epistatic effects of these loci together contributed 24% to 52% of phenotypic variation. In the vicinity of these key SNPS, genes associated with disease resistance, pathogenesis, chitin response, and wound healing were also identified, in particular a trait associated SNP-locked-stress-induced receptor-like kinase gene 1 (SIK1) encoding a protein rich in leucine repeats. This study emphasizes that epistatic effects must be taken into account in breeding for SDS resistance in soybean to improve the explanation of phenotypic variation. Accordingly, the researchers also constructed a soybean root model for SDS pathogen defense (Figure 3). The findings of this study not only reveal the molecular mechanism of soybean resistance to SDS, but also provide a scientific basis for future anti-SDS breeding strategies based on genetic epistasis. Figure 3 Putative model for soybean defense against sudden death syndrome (SDS) based on the results of genome-wide association and epistasis studies (Zhang et al., 2015) 3 The Advantages and Limitations of GWAS in Crop Disease Resistance Breeding 3.1 The advantages of GWAS compared with traditional breeding methods Genome-wide association study (GWAS) has obvious advantages over traditional breeding methods in crop disease resistance breeding. GWAS has high efficiency, it can quickly identify the genetic markers and genes related to disease resistance within the whole genome in a short time, and accelerate the breeding process. There is no need for specific genetic background, and it can make use of existing natural population and variety resources for analysis (Tam et al., 2019), without the need to build specific genetic populations, reducing the cost and time of research. GWAS can also reveal the genetic structure of complex traits and identify multi-genes and inter-gene interactions that control complex traits, which is of great significance for understanding the genetic mechanism of crop disease resistance and guiding molecular marker-assisted breeding (MAS) (Tam et al., 2019). GWAS can also utilize existing natural population and variety resources without the need to construct large-scale genetic populations, thus reducing the cost and time of research, which makes GWAS an efficient breeding tool, especially suitable for research environments with limited resources. 3.2 Limitations and challenges of GWAS Although genome-wide association study (GWAS) has made remarkable progress in crop disease resistance breeding, it still faces some limitations and challenges. Population structure and linkage imbalance (LD) are major challenges for GWAS. Population structure refers to differences in genetic background in the sample, which can lead to false positive associations, and linkage imbalance refers to non-random associations between different loci,
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