Animal Molecular Breeding 2024, Vol.14, No.1, 36-44 http://animalscipublisher.com/index.php/amb 39 it is expected to breed poultry breeds with high egg-laying performance and other economic traits to meet the growing demand for food. 2 Principles and Applications of Genome-Wide Association Analysis (GWAS) 2.1 Principles and methods of GWAS Genome-wide association analysis (GWAS) is based on finding associations between specific traits and genetic markers. The process begins with the collection of samples of individuals with or without a particular trait, which are then extensively genotyped to identify tens of thousands of single nucleotide polymorphisms (SNPs). By comparing the difference in frequency of SNPs between individuals with a particular trait and those without that trait, GWAS aims to discover genetic variation associated with the trait. The advantage of this approach is that it does not require prior in-depth knowledge of the genetic background, making it a powerful tool for exploring genetic causes and traits. As technology has evolved, the analytical power of GWAS has increased dramatically. The use of high-throughput sequencing technology and high-density microarrays has allowed researchers to more accurately cover the entire genome, thereby increasing the chances of discovering genetic markers associated with target traits. The success of this approach relies on large sample sizes, as large-scale samples increase the accuracy and reliability of discovering truly relevant genetic variants. 2.2 Application of GWAS in poultry genetic studies Emrani et al. (2017) team conducted GWAS in 2017 using an F2 generation chicken population derived from a fast growing line and a local slow growing chicken crossed with each other to look for genes and genomic regions affecting growth traits. This study identified nine SNPs significantly associated with body weight traits. The research team of Khalil et al. (2021) in 2021 reviewed molecular approaches in poultry genetic improvement programs emphasizing the use of GWAS to identify causative genes affecting economic traits in poultry. This included the identification of many genes that affect growth and egg production. Wang et al. (2020) performed GWAS and pathway analyses to identify biological mechanisms involved in the heterophilic lymphoid ratio (H/L) of chickens, which reflects the state of their immune system. The study identified SNPs that were significantly associated with the Heterophilic lymphoid ratio in chickens, contributing to the understanding of the genetic regulation of this trait (Figure 3). Figure 3 Quantile–quantile (Q–Q) plot of the GWAS results with GAPIT 3.0 (Wang et al., 2020) Note: The x-axis shows the expected p-values under the null hypothesis and the y-axis shows the observed p-values Using the GWAS approach, researchers have identified genetic markers that affect eggshell quality and egg size, which has significant implications for improving egg quality and reducing losses. GWAS has also been used to explore the genetic basis of disease resistance in poultry, which is valuable for breeding healthier poultry breeds and reducing the use of antibiotics.
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