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

Abstract

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.

Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish

“…However, performance and production traits are often highly complex and the outcome of agricultural operations is affected by variations at all levels. For example, genetic background is very important because disease resistance genes allow the organism to survive the serious infections [ 12 , 13 ]. In most cases, disease resistance genes have been studied through genetic linkage and QTL analyses that allow the identification of genomic regions containing disease resistance genes to be identified.…”

“…Even with the most powerful molecular approaches, analysis of complex traits such as disease resistance can be extremely challenging. In 1991, Michelmore et al developed a method called bulked segregant analysis (BSA) to study disease resistance in plants [ 13 - 20 ]. The basic idea of BSA was that phenotypic extremes should have drastic differences in genotypes.…”

Comparative transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine–cytokine receptor interaction pathway related to health status

“…In the US, porcine reproductive and respiratory syndrome virus (PRRSV) alone costs swine producers millions of dollars per year (Brito et al, 2014). In China, the annually economic loss caused by infectious disease in the pig industry is estimated to be RMB 40 billion (equivalent to > $6Bn) (Zhao et al 2012). The main approaches for prevention and control of diseases include vaccination and medication, elimination of sick animals, the maintenance of high levels of bio-security, and all-in-all-out production.…”

Investigation of single nucleotide polymorphisms in porcine candidate genes for blood component traits in pigs

“…Recent research using these methods has identified critical candidate genes through gene network and pathway analysis in immune response experiments related to PRRSV resistance and gram-negative Bacillus resistance in pigs (Wysocki et al, 2012;Zhao et al, 2012).…”