Tree Genetics and Molecular Breeding 2024, Vol.14, No.1, 12-21 http://genbreedpublisher.com/index.php/tgmb 15 The advantage of this method is that it does not rely on prior genetic knowledge and can discover novel genetic variations associated with traits across broad genomic regions. GWAS can also handle complex traits, which are those influenced by multiple genes as well as gene-environment interactions. 3.2 Applications of GWAS in plant breeding In plant breeding, the application of GWAS technology has primarily focused on identifying genetic markers associated with important agronomic traits. These traits span yield, disease resistance, stress tolerance (such as drought and salt stress), and nutritional quality. For instance, in a study on spring barley and winter wheat, Tsai et al. (2020) conducted genotypic and phenotypic analyses on 1 317 spring barley and 1 325 winter wheat accessions. In spring barley, GWAS identified QTLs associated with resistance to powdery mildew and leaf rust, as well as multiple SNPs related to yield. In winter wheat, GWAS revealed SNPs associated with quality traits such as grain moisture and starch content. Gutiérrez et al. (2023) conducted a genome-wide association study on 100 faba bean accessions from different geographic origins to identify traits related to drought tolerance. They identified 29 single nucleotide polymorphism (SNP) markers significantly associated with traits under drought conditions and performed genome analysis on the surrounding sequences of these markers to search for potential candidate genes. The study found that 3 SNPs associated with chlorophyll content corresponded to unknown proteins, suggesting the existence of new genes related to drought tolerance in faba beans, providing a basis for molecular-assisted breeding in faba beans. These studies not only deepened the understanding of the genetic basis of crops but also provided powerful tools for molecular breeding in practice. By utilizing the specific genetic markers discovered through GWAS, marker-assisted selection (MAS) techniques can more efficiently breed crops to improve yield and quality; furthermore, GWAS provides precise target genes for CRISPR/Cas9, further promoting directional improvement of crop traits. These advancements have not only increased the efficiency of crop breeding but also provided new strategies for coping with climate change and environmental pressures. 3.3 Special considerations and challenges of GWAS in tree research Although GWAS has achieved tremendous success in other fields, applying this technology to tree research requires considering some unique challenges. Firstly, the long lifespan and large genome sizes of trees present difficulties for genome sequencing and genetic analysis. Furthermore, the genetic diversity of tree populations is typically greater than that of crop populations, requiring larger sample sizes to ensure the accuracy and representativeness of the study. The growth and development of trees are also greatly influenced by the environment, meaning that gene-environment interactions must be considered when analyzing the associations between genes and traits. Therefore, unlike crop breeding focused on specific environments, tree breeding needs to consider the effects of genes across broader and more diverse environmental conditions. GWAS provides a powerful tool for tree genetics research and breeding, although challenges exist, its potential is immense and worth further exploration and application. Through this method, a better understanding of tree genetic diversity can be gained, providing a theoretical basis for cultivating tree species that are more adaptable to environmental changes and have higher economic value. 4 Applications of GWAS in Tree Breeding With the advancement of genomics and bioinformatics technologies, Genome-wide Association Studies (GWAS) has become an important tool in tree breeding research. Through GWAS, breeders can identify genetic markers influencing important tree traits, thereby accelerating the breeding process and promoting the protection and utilization of genetic resources. 4.1 Progress in the application of GWAS in tree breeding research The application of Genome-wide Association Studies (GWAS) in tree breeding is a relatively new field, but significant progress has been made. This technique has been primarily applied to exploring the genetic basis of
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