Genome-Wide Association Study on Two Immune-Related Traits in Jinghai Yellow Chicken

ABSTRACT This study was designed to discover molecular marker associated with the interferon INF-γ and avian influenza (AI) antibody titer traits in Jinghai Yellow chicken (Gallus gallus). Serum samples were taken from 400 female chickens and the INF-γ concentrations and AI antibody titer levels were measured. A genome-wide association study was carried out using specific-locus amplified fragment (SLAF) sequencing. Bioinformatics analysis was applied to detect single-nucleotide polymorphisms (SNPs) associated with the two traits. After sequencing and quality control, 103,680 SLAFs and 90,961 SNPs were obtained. The 400 samples were divided into 10 subgroups to reduce the effects of group stratification. The Bonferroni adjusted P-value of genome-wide significance was set at 1.87E−06 according to the number of independent SNP markers and linkage disequilibrium blocks. A SNP that was significantly associated with INF-γ concentration was detected in the myomesin 1 (MYOM1) gene on chromosome 2, and another SNPthat was significantly associated with the AI antibody titer level was detected in an RNA methyltransferase gene (Nsun7), which was found to have an important biological function. We propose that MYOM1 and Nsun7 are valuable candidate genes that influence the disease resistance characters of chicken. However, in-depth investigations are needed to determine the essential roles of these genes in poultry disease resistance and their possible application in breeding disease resistant poultry.

摘要 本研究旨在挖掘与京海黄鸡（Gallus gallus）干扰素γ（interferon INF-γ）及禽流感（avian influenza, AI）抗体滴度性状相关的分子标记。研究采集了400只母鸡的血清样本，测定了其中干扰素γ浓度与禽流感抗体滴度水平。采用特异性位点扩增片段（specific-locus amplified fragment, SLAF）测序技术开展全基因组关联分析（genome-wide association study），并通过生物信息学分析筛选与这两个性状相关的单核苷酸多态性（single-nucleotide polymorphisms, SNPs）。经测序与质量控制后，共获得103,680个SLAF标签与90,961个SNPs。为降低群体分层的影响，将400份样本划分为10个亚群。根据独立SNP标记数量与连锁不平衡区块数量，将全基因组显著性的Bonferroni校正P值设定为1.87×10⁻⁶。在2号染色体的肌间线蛋白1（myomesin 1, MYOM1）基因中，检测到1个与干扰素γ浓度显著关联的SNP；另在RNA甲基转移酶基因（RNA methyltransferase gene, Nsun7）中，检测到1个与禽流感抗体滴度水平显著关联的SNP，该基因已被证实具有重要的生物学功能。本研究提出，MYOM1与Nsun7可作为影响鸡抗病性状的极具价值的候选基因。不过，仍需开展深入研究以明确这两个基因在家禽抗病过程中的核心作用，以及其在抗病家禽育种中的潜在应用价值。