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Genome‐wide association study of cell‐mediated immune response in chicken
Author(s) -
Raeesi V.,
Ehsani A.,
Torshizi R.V.,
Sargolzaei M.,
Masoudi A.A.,
Dideban R.
Publication year - 2017
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12265
Subject(s) - single nucleotide polymorphism , biology , genome wide association study , genetics , genetic association , snp , chromosome , population , immune system , genome , genetic linkage , gene , genotype , medicine , environmental health
Summary Cell‐mediated immunity ( CMI ) causes the intracellular destruction of the antigen or elimination of the host cell to make animals resistant against exogenous antigens and cancers. In this study, a genome‐wide association study ( GWAS ) was carried out to identify genomic regions associated with CMI in chicken using chicken 60k high‐density single nucleotide polymorphism ( SNP ) array. Genomic relationships were taken into account to adjust for population structure. In order to account for multiple testing, chromosome‐wise false discovery rate was controlled at 5% and 10% levels. Moreover, a comparison of the power of fixed and mixed linear models based on genomic inflation factor was carried out. Mixed linear model ( MLM ) had better inflation rate, and therefore the results from MLM were used for subsequent analysis. Three significantly associated SNP s ( FDR < 0.05) on chromosome 24 and linkage group E22C19W28_E50C23, and three suggestively associated SNP s ( FDR < 0.1) on chromosome 1, 5 and 16 were identified. Pathway analysis showed that two biological pathways, which are related to immune response, were strongly associated with the candidate genes surrounding identified SNP s, and their influences were mostly on antigen processing and presentation, and cellular structure.