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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: FUNCTIONAL GENOMIC APPROACHES FOR CONTROLLING DISEASES OF SWINE

Location: Animal Parasitic Diseases Laboratory

2012 Annual Report


1a. Objectives (from AD-416):
Objective 1: Identify genetic variations associated with disease resistance to PRRS virus and identify biological determinants associated with anti-PRRS virus host responses to discover genetic and biological determinants associated with disease resistance to infectious diseases of swine. Objective 2: Discover effective immune intervention strategies to prevent and control infectious diseases of swine by developing immunologic tools to enhance our understanding of swine immune system development and novel assays to evaluate pig responses to infectious diseases; and by assessing differential responses to infection versus vaccination to determine what pathways are associated with protective responses of pigs to respiratory pathogens.


1b. Approach (from AD-416):
Assess whether genomic variation in pigs is associated with differential PRRS resistance/susceptibility and biologic responses to PRRSV infection. The PRRS Host Genetics Consortium (PHGC) was developed to assess the genomic basis of PRRS disease resistance. The PHGC is a national effort to assess pig resistance/susceptibility to primary PRRSV infection and associated growth effects. Our research will focus on the PHGC objectives: 1) use genotyping and phenotyping tools to determine if there are host genes that control resistance/susceptibility to PRRSV infection; 2) verify genetic variation in response to PRRSV, via improved health, survivability and growth; and 3) identify relative importance of different phenotypes, and their heritability, that predict response to PRRSV infection. Identify biological determinants associated with anti-PRRS virus host responses. We hypothesize that there will be functional genomic and proteomic differences that correlate with resistance to PRRSV infections. Using PHGC samples, functional analyses will be performed to identify gene networks and resistance associated biomarkers that differ in high versus low viral load pigs. Our goal would be to identify markers expressed pre-infection, e.g., serum biomarkers in uninfected pigs. Develop immunologic tools to enhance our understanding of swine immune system development and novel assays to evaluate pig responses to infectious diseases. A portion of the time devoted to this project will involve research to develop and improve immune reagents available to characterize swine immune responses and regulation. Numerous commercial sources provide reagents for swine immunity research; yet, compared to human and mouse, these resources are limited. Working with the U.S. Veterinary Immune Reagent Network (VIRN) we will develop new immunologic reagents and assays to measure swine cytokines, chemokines, and immune cell surface molecules. These will help identify key features of an effective swine immune response to infectious pathogens Assess differential responses to infection versus vaccination to determine what pathways are associated with protective responses of pigs to respiratory pathogens. Biomarkers are present in pigs that correlate with protective immunity to respiratory pathogens. Determining whether a response to infection or vaccination is protective or pathologic is essential for the design of new vaccines, diagnostics and therapeutics. For pigs this means understanding the genes and proteins, networks and pathways involved in these responses. Based on the newly finished swine genome sequence, we will identify and annotate some of the numerous genes and regulatory sequences encoded in the swine genome. With that information, functional genomic tools will be applied to assess infection or vaccination responses. Research targets will be infection and vaccination of pigs with respiratory pathogens, particularly PCV2b and PRRSV.


3. Progress Report:
This project investigated swine immunity to viral infectious diseases, targeting the most economically important swine pathogen, Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). With National Pork Board (NPB) funding, ARS scientists at Beltsville, MD, working with scientists at Kansas State University (KSU), Iowa State University (ISU), and commercial pig breeding and animal health companies, established the PRRS Host Genetics Consortium (PHGC). This Consortium has now completed 12 infection trials of 200 commercial pigs each with a goal of determining the role of host genetics in resistance/susceptibility to PRRSV infection and associated growth effects. All PHGC data is stored in the secure, password protected PHGC database at ISU: http://www.animalgenome.org/lunney/index.php Access to the PHGC database is open to Consortium members who have signed a Cooperative Research and Development Agreement (CRADA) Material Transfer Agreement (MTA) #58-3K95-9-1319 organized by ARS. This CRADA MTA was updated in FY12 (#58-3K95-1-1518-MTA). Other grants associated with this effort and with this ARS project have completed single nucleotide polymorphism (SNP) chip typing of all PHGC pigs and the first genome wide association studies (GWAS) that have already mapped several PRRS resistance genes. In fact a major gene on swine chromosome 4 has been identified as accounting for 15% of viral load variation and 11% of weight gain after PRRSV infection. Separate analyses of whole blood RNA and serum are probing for differences in gene and protein expression following PRRSV infection. The PHGC has identified host genes involved in PRRSV resistance or susceptibility, as well as in the ability of some pigs to grow normally despite being PRRSV infected. Results should help pig breeding companies to identify and provide more disease resistant pigs to producers. In addition these studies should provide new alternatives to address immunity to PRRSV infection resulting in improved biotherapeutics and vaccines. This project has focused on immune studies, targeting the role of cytokines and chemokines in stimulating immune, disease and vaccine responses, assessing gene and protein responses. Major efforts include leading the swine team of the U.S. Veterinary Immunological Reagents Network (VIRN) and using recombinant protein and hybridoma technologies to address the dearth of immune reagents for the pig, as noted at www.vetimm.org. Genomic and protein tools, as well as microarrays and proteomics, initiated through this project are now actively used by researchers worldwide. Validation of the our Fluorescent Microsphere Immune Assay (FMIA), to measure 8 swine cytokines and chemokines simultaneously in pig sera, oral fluids, and cell supernatants, has opened up major routes for examining infection and vaccine responses and predicting protective versus pathologic immune responses.


4. Accomplishments


Review Publications
Bishop, S.C., Lunney, J.K., Pinard-Van Der Laan, M., Gay, C.G. 2011. Report from the Second International Symposium on Animal Genomics for Animal Health: Critical Needs, Challenges and Potential Solutions. Review Article. 5 Suppl 4:S1.

Lunney, J.K. 2012. Genomics and Animal Health. Advances in Pork Production. 23:155-166.

Last Modified: 10/16/2017
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