Field Crop 2024, Vol.7, No.1, 1-8 http://cropscipublisher.com/index.php/fc 3 1.3 Data and technical requirements required by GWAS As a powerful genetic research tool, the application of genome-wide association study (GWAS) in crop disease resistance breeding requires certain data and technical requirements. GWAS requires large amounts of genetic variation data, typically from high-density single nucleotide polymorphism (SNP) markers or whole genome sequencing, which are used to construct genetic linkage maps (Marees et al., 2018) to identify genetic loci associated with trait phenotypes. GWAS also requires accurate phenotypic data. In crop disease resistance studies, this usually involves detailed assessment of disease responses of plants of different genotypes, and the accuracy of phenotypic data directly affects the reliability of GWAS results. GWAS also requires strong statistical analysis capabilities, association analysis requires processing large amounts of data, and mathematical control of false positive rates, the use of appropriate statistical models and correction methods (such as Bonferroni correction or false discovery rate control) is necessary (Marees et al., 2018). With the advancement of technology, the data and technical requirements of GWAS are also increasing, for example, with the reduction of sequencing costs, whole genome sequencing has gradually become an important data source for GWAS, and the development of bioinformatics tools has also provided more possibilities for the processing and analysis of GWAS data. 2 Application of GWAS in Crop Disease Resistance Breeding (A Case Study of Soybean) Soybean (Glycine max) is an important crop in the legume family, which is widely favored worldwide for its high protein and oil content. Soybean is not only an important source of human food, such as tofu, soybean milk and soybean oil, but also contains a variety of bioactive substances that are beneficial to the human body, such as isoflavones and lecithin. These ingredients have been shown to have positive effects on cardiovascular health, bone health and menopausal symptoms, and are a major component of many animal feeds, having an irreplaceable impact on the global agriculture and food industry. The origin of soybeans can be traced back to China, it has thousands of years of cultivation history, has become one of the most widely cultivated crops in the world, in agricultural production, soybeans are not only an important cash crop, but also a key component of sustainable agriculture. Major challenges include sudden death syndrome (SDS) caused by Fusarium virguliforme, one of the key diseases limiting its production. At present, the genetic mechanism of soybean resistance to SDS, especially the epistatic role between genes, is still not fully understood. Mueller and Singh's team published a paper in The Plant Journal in 2015 titled ‘Genome-wide association and epistasis studies unravel the genetic architecture of sudden death syndrome resistance in soybean’. By analyzing the genetic data of 214 soybean varieties and 31 914 single nucleotide polymorphism (SNP) markers, this study conducted a comprehensive genomic association analysis and epistatic role study (Figure 2), aiming to further explore the genetic background of soybean resistance to SDS (Zhang et al., 2015). Figure 2 Contributions of identified sudden death syndrome loci via genome-wide association studies (GWAS) and epistatic analysis to the phenotypic variance of each disease severity measurement (Zhang et al., 2015)
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