Immunogenomics for identification of disease resistance genes in pigs: a review focusing on Gram-negative bacilli.

Over the past years, infectious disease has caused enormous economic loss in pig industry. Among the pathogens, gram negative bacteria not only cause inflammation, but also cause different diseases and make the pigs more susceptible to virus infection. Vaccination, medication and elimination of sick pigs are major strategies of controlling disease. Genetic methods, such as selection of disease resistance in the pig, have not been widely used. Recently, the completion of the porcine whole genome sequencing has provided powerful tools to identify the genome regions that harboring genes controlling disease or immunity. Immunogenomics, which combines DNA variations, transcriptome, immune response, and QTL mapping data to illustrate the interactions between pathogen and host immune system, will be an effective genomics tool for identification of disease resistance genes in pigs. These genes will be potential targets for disease resistance in breeding programs. This paper reviewed the progress of disease resistance study in the pig focusing on Gram-negative bacilli. Major porcine Gram-negative bacilli and diseases, suggested candidate genes/pathways against porcine Gram-negative bacilli, and distributions of QTLs for immune capacity on pig chromosomes were summarized. Some tools for immunogenomics research were described. We conclude that integration of sequencing, whole genome associations, functional genomics studies, and immune response information is necessary to illustrate molecular mechanisms and key genes in disease resistance.

在过去的几年中，传染病给养猪业造成了巨大的经济损失。在病原体中，革兰氏阴性菌不仅会引发炎症，还会导致不同的疾病，并使猪更容易受到病毒感染。接种疫苗、使用药物和淘汰病猪是控制疾病的主要策略。遗传学方法，比如对猪进行抗病性选择，尚未得到广泛应用。最近，猪全基因组测序的完成提供了强大的工具，用于识别包含控制疾病或免疫相关基因的基因组区域。免疫基因组学结合了DNA变异、转录组、免疫反应和数量性状基因座（QTL）定位数据，以阐明病原体与宿主免疫系统之间的相互作用，它将成为鉴定猪抗病基因的一种有效基因组学工具。这些基因将是育种计划中抗病性的潜在目标。本文综述了以革兰氏阴性杆菌为重点的猪抗病性研究进展。总结了主要的猪革兰氏阴性杆菌及其引发的疾病、针对猪革兰氏阴性杆菌提出的候选基因/通路，以及猪染色体上免疫能力相关数量性状基因座的分布。描述了一些用于免疫基因组学研究的工具。我们得出结论，整合测序、全基因组关联、功能基因组学研究和免疫反应信息对于阐明抗病性的分子机制和关键基因是必要的。