Hay El Hamidi A, Choi Igseo, Xu Lingyang, Zhou Yang, Rowland Robert R R, Lunney Joan K, Liu George E
Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
Animal Parasitic Diseases Laboratory, BARC East, USDA-ARS, Beltsville, Maryland 20705, USA.
J Genomics. 2017 May 24;5:58-63. doi: 10.7150/jgen.20358. eCollection 2017.
Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease with a significant impact on the swine industry causing major economic losses. The objective of this study is to examine copy number variations (CNVs) associated with the group-specific host responses to PRRS virus infection. We performed a genome-wide CNV analysis using 660 animals genotyped with on the porcine SNP60 BeadChip and discovered 7097 CNVs and 271 CNV regions (CNVRs). For this study, we used two established traits related to host response to the virus, i.e. viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain (WG42 from 0 to 42 days post infection). To investigate the effects of CNVs on differential host responses to PRRS, we compared groups of animals with extreme high and low estimated breeding values (EBVs) for both traits using a case-control study design. For VL, we identified 163 CNVRs (84 Mb) from the high group and 159 CNVRs (76 Mb) from the low group. For WG42, we detected 126 (68 Mb) and 156 (79 Mb) CNVRs for high and low groups, respectively. Based on gene annotation within group-specific CNVRs, we performed network analyses and observed some potential candidate genes. Our results revealed these group-specific genes are involved in regulating innate and acquired immune response pathways. Specifically, molecules like interferons and interleukins are closely related to host responses to PRRS virus infection.
猪繁殖与呼吸综合征（PRRS）是一种具有毁灭性的疾病，对养猪业造成重大影响，导致巨大经济损失。本研究的目的是检查与猪对PRRS病毒感染的群体特异性宿主反应相关的拷贝数变异（CNV）。我们使用在猪SNP60基因芯片上进行基因分型的660只动物进行了全基因组CNV分析，发现了7097个CNV和271个CNV区域（CNVR）。在本研究中，我们使用了两个与宿主对病毒反应相关的既定性状，即病毒载量（VL，感染后0至21天对数转换血清病毒血症曲线下面积）和体重增加（感染后0至42天的WG42）。为了研究CNV对宿主对PRRS不同反应的影响，我们采用病例对照研究设计，比较了这两个性状估计育种值（EBV）极高和极低的动物组。对于VL，我们从高值组中鉴定出163个CNVR（84 Mb），从低值组中鉴定出159个CNVR（76 Mb）。对于WG42，我们在高值组和低值组中分别检测到126个（68 Mb）和156个（79 Mb）CNVR。基于群体特异性CNVR内的基因注释，我们进行了网络分析并观察到一些潜在的候选基因。我们的结果表明，这些群体特异性基因参与调节先天性和获得性免疫反应途径。具体而言，干扰素和白细胞介素等分子与宿主对PRRS病毒感染的反应密切相关。
