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United States Department of Agriculture

Agricultural Research Service

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Research Project: Genome Canada

Location: Animal Parasitic Diseases Laboratory

2013 Annual Report

1a. Objectives (from AD-416):
The Cooperator and the assembled team of researchers has the expertise and infrastructure to 1) perform new porcine respiratory and the reproductive syndrome virus (PRRSV) infection trials in nursery pigs and pregnant gilts and porcine circovirus (PCV2) infection trials in nursery pigs; 2) perform gene expression Transcriptome Sequencing (RNA-seq) analyses of relevant samples; 3) perform single nucleotide polymorphism (SNP) analyses on genomic DNA from samples; 4) use bioinformatic resources to process genomic data for these analyses; and 5) collaborate on proteomic fluorescent microsphere immunoassays (FMIAs). An industry component for targeted gilt monitoring, sampling and application of results is included in the application.

1b. Approach (from AD-416):
ARS has led the PRRS Host Genetics Consortium (PHGC) Project the goal of which is to identify genetic determinants of resistance/susceptibility of commercial swine to PRRSV infection. Many of these studies have been performed with pigs from Canadian sources. The information generated in this Genome Canada proposal will extend the deep phenotyping of existing PHGC samples, will add samples from nursery infection trials with a 2nd PRRSV isolate, and will add a gilt PRRS model. These data will be used by both parties and members of the PHGC to determine genetic alleles and gene and protein expression differences that are associated with PRRS and PCV2 resistance/susceptibility. The Cooperator will perform new PRRSV and PCV2 infection trials, genotype new sets of genomic DNAs and perform RNA-seq and FMIA analyses to identify genes and proteins that differentiate PRRS resistant from susceptible pigs. The Cooperator will apply for funding through the Alberta Livestock Genomics Program grant program.

3. Progress Report:
Alternate approaches to evaluate swine health have been advanced by this U.S. Canadian effort that addresses the major disease of swine worldwide porcine respiratory and reproductive syndrome (PRRS). ARS researchers at the Beltsville Agricultural Research Center (BARC) in Beltsville, Maryland partnered with scientists from Iowa State and Kansas State universities in the U.S. and the University of Alberta (UoA) and Saskatchewan in Canada and their breeding company organization, PigGen Canada, to characterize host factors that contribute to PRRS disease resistance and growth losses. Unique swine responses to PRRS virus infection are being analyzed using RNA collected from blood of infected pigs. Because of high amounts of hemoglobin RNA in blood samples BARC and UoA scientists had to first develop new pretreatment protocols for reduction of globin RNA. With that accomplished efforts are now aimed at using next generation sequencing technology and bioinformatic pipelines to probe the complexity of swine responses at multiple days post PRRSV infection. We expect to reveal differential transcripts and unique immune pathways expressed by pigs which are genetically more resistant to PRRSV infection.

4. Accomplishments

Last Modified: 08/19/2017
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