Maize Genomics and Genetics 2024, Vol.15, No.1, 18-26 http://cropscipublisher.com/index.php/mgg 22 genetic markers related to vitamin content. The gene regions where these markers are located are closely related to vitamin biosynthetic pathways, providing important information for further research on key genes in these pathways (Wang, 2011, Crop Journal, 27(5): 8-12.). These case studies demonstrate the application value of GWAS methods in the study of nutritional quality traits of corn. By revealing the association between traits and specific genetic loci, GWAS can not only help scientists understand the genetic mechanisms of complex traits, but also provide precise molecular markers for corn breeding, thereby accelerating the breeding process and developing new varieties of corn with more nutrients. The application of GWAS in the study of corn nutritional quality traits provides us with a powerful tool (Figure 2) (Ruanjaichon et al., 2021), allowing us to deeply understand the genetic basis of traits from the genome level. These studies not only provide a new perspective for the scientific research of corn, but also provide a solid foundation for improving and optimizing the nutritional quality of corn. With the deepening of future research and technological advancement, GWAS will play a greater role in the genetic improvement and nutritional quality improvement of corn. Figure 2 GWAS results for sweetness trait in 250 sweet- and waxy-corn inbred and recombinant inbred lines (RILs) (Ruanjaichon et al., 2021) Note: A: Manhattan plots. Each dot represents a SNP. Bonferroni threshold of -log10 p-value=13.81 is presented by a green line on Manhattan plots; Most associated SNP AX_91849634, located 67.5 kb on chromosome 3 near the Shrunken2 gene, is indicated by a red arrow; B: Quantile-quantile (Q-Q) plots; The plot shows the expected vs. observed-log10(p) of each marker (blue dots); Red line is a guide for the perfect fit to expected-log10(p); The gray shaded area shows the 95% confidence interval for the Q-Q plot under the null hypothesis of no association between the SNP and the trait 4 Challenges and Opportunities of GWAS Research Genome-wide association studies (GWAS) play an important role in revealing the genetic basis of crop genetic traits and traits, especially in major food crops like corn. However, despite the great potential of GWAS, the method also faces various challenges during its application, while also bringing new opportunities. 4.1 Methodological challenges The success of GWAS relies heavily on sufficient sample size and genetic diversity of the samples. In crop research, especially maize, it is challenging to collect representative collections of samples from a broad range of genetic backgrounds. Insufficient sample size or poor genetic diversity will limit the ability of GWAS to discover genetic markers associated with traits, reducing the accuracy and reliability of the study. The population structure and complex genetic background of crops such as corn are also a major challenge in GWAS research (Li et al., 2009). Differences in population structure (i.e., genetic relatedness among individuals within a
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