Raeesi V, Ehsani A, Torshizi R V, Sargolzaei M, Masoudi A A, Dideban R
Department of Animal Science, Tarbiat Modares University, Tehran, Iran.
Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
J Anim Breed Genet. 2017 Oct;134(5):405-411. doi: 10.1111/jbg.12265. Epub 2017 Mar 10.
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 SNPs (FDR < 0.05) on chromosome 24 and linkage group E22C19W28_E50C23, and three suggestively associated SNPs (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 SNPs, and their influences were mostly on antigen processing and presentation, and cellular structure.
细胞介导的免疫（CMI）导致抗原在细胞内被破坏或宿主细胞被清除，从而使动物对外源抗原和癌症具有抵抗力。在本研究中，利用鸡60k高密度单核苷酸多态性（SNP）芯片开展了全基因组关联研究（GWAS），以鉴定鸡中与CMI相关的基因组区域。考虑了基因组关系以校正群体结构。为了应对多重检验问题，将染色体水平的错误发现率控制在5%和10%的水平。此外，基于基因组膨胀因子对固定线性模型和混合线性模型的效能进行了比较。混合线性模型（MLM）具有更好的膨胀率，因此将MLM的结果用于后续分析。在24号染色体和连锁群E22C19W28_E50C23上鉴定出3个显著相关的SNP（FDR < 0.05），在1号、5号和16号染色体上鉴定出3个暗示性相关的SNP（FDR < 0.1）。通路分析表明，两条与免疫反应相关的生物学通路与所鉴定SNP周围的候选基因密切相关，其影响主要体现在抗原加工与呈递以及细胞结构方面。
