A study of the efficacy of the BayesCπ statistical method for Genome Wide Association study of the of cellular immune response in chicken

Proportional statistical methods can help to find real relationships between genetics and phenotypes for analysis of genomic data. In recent years, various statistical methods have been used to understand these relationships. The results show that different methods have better performance, in different conditions and traits. Among these methods, it is possible to use methods based on maximum likelihood, least squares and non-parametric such as Bayesian methods. In contrast to parametric methods, in Bayesian methods, the effects of genetic variables can be analyzed in more than one statistical distribution. Considering the inheritance of quantitative traits were as the result of different effects of genetic variables the statistical distribution of these effects can be different from each other. Therefore, it seems that Bayesian methods can provide a better understanding of the effective genomic regions on quantitative traits and their effects. Thus, in the present study, cellular immunity phenotype was studied using di-Chloro Benzene injection and bird genotype with the 60k SNP chip of Ilumina Company per 198 bird of the F2 generation from the two-sided cross between Arian strain and Urmia indigenous chicken using the Bayes Cπ method. In this method, the value of π and the number of rounds of the chain were 0.1999 of 100,000 respectively. Due to the nature of the trait (low heritability) and the observation of the plot of convergence of the components of variance and π values were selected by using the test and error so that the convergence and dispersion of the effects of the markers correctly displayed. Specified SNPs were located within or close to 25 genes, among which the genes SULF2, MKNKI, LRRTM4, NCK2, CAMK1D, RBFOX1, DUSP14 provided important functions in creating the immune response through the synthesis of T cells, the formation of an immunological synapse , interfered with the formation of neutrophils and response to environmental stress considering the key role of the genes mentioned in the development of cellular immune response, the BayesCπ method can be validated for genomic scan in this trait and similar traits.