Animal Molecular Breeding 2024, Vol.14, No.1, 10-18 http://animalscipublisher.com/index.php/amb 16 4 Challenges and Limitations of GWAS 4.1 Limitations of sample size and genetic diversity Although genome-wide association studies (GWAS) have achieved remarkable results in revealing the genetic basis of disease resistance in poultry, a series of challenges and limitations have been encountered in their application. These challenges involve not only technical and methodological issues, but also the complexity of statistical analysis and bioinformatics. The effectiveness of GWAS largely depends on a sufficiently large sample size to ensure the strength of statistical analysis and the reliability of results. In the study of disease resistance in poultry, it is often difficult to obtain a large number of samples due to high costs and limitations in experimental conditions. Insufficient sample size may lead to bias in the results, increasing the risk of discovering false positive associations. The genetic diversity within poultry populations also has a significant impact on the outcomes of GWAS. The genetic differences between different poultry breeds may lead to confusion of association signals, making it more difficult to identify genetic variations directly related to disease resistance (Żbikowska et al., 2020). 4.2 Consideration of the interaction between environmental factors and genetics Poultry disease resistance is not only influenced by genetic factors, but also closely related to environmental factors. Environmental factors such as feeding conditions, nutritional status, and exposure to pathogens can all affect the resistance phenotype of poultry to diseases. In GWAS, it is often difficult to fully control these environmental variables, making it difficult to distinguish the interaction effects between genetics and environment. This complex genetic environmental interaction increases the difficulty of GWAS analysis and also affects the interpretation of the results. There may be interactive effects between environmental factors and genetic factors. Environmental factors may alter the expression patterns of genetic factors on poultry disease resistance, or affect the phenotypic expression of specific genotypes. Some genotypes may exhibit different levels of disease resistance under different environmental conditions, and this environmental interaction effect may mask or amplify genetic effects, affecting the interpretation of genome-wide association studies. It is necessary to consider the interaction between environmental and genetic factors in research design and data analysis to more accurately evaluate their impact on poultry disease resistance. There is a complex interaction between environmental factors and genetic factors, which must be considered in the genetic analysis of disease resistance in poultry. By comprehensively considering the influence of environmental and genetic factors, the disease resistance level of poultry can be more accurately evaluated, and more effective strategies and methods can be provided for disease prevention and treatment (Figure 4). Figure 4 The interaction effect between environmental factors and genetic factors 4.3 The complexity of data interpretation and validation Even if GWAS successfully identifies genetic markers associated with disease resistance in poultry, interpreting these data correctly remains a challenge. Association discovery is not directly equivalent to causal relationships, and subsequent biological experiments are needed to verify the functions and mechanisms of these genetic
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