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.
This Genome Canada supported project facilitated substantial expansion of the U.S.-led Host Genetics Consortium (PHGC) to include our colleagues in Canada, and their breeding company organization PigGen Canada. As a result, our PHGC Nursery Pig porcine respiratory and the reproductive syndrome virus (PRRSV) infection model has completed 12 infection trials of 200 pigs each at the Kansas State University biosecure animal facility using high health pigs donated by commercial breeding companies, the last three from PigGen Canada providers. Importantly these Genome Canada funds enabled the PHGC to be expanded to trials using a second virus; a 1998 PRRSV isolate was used for infections in the first 9 trials, whereas a more recent, 2006 PRRSV isolate was used for PHGC trials 10-12. Results have affirmed that there is a similar broad range of responses of swine to the 2006 PRRSV isolate as was found with the 1998 isolate. This Genome Canada project supports new approaches to assess the post-PRRSV response using next generation sequencing or RNA-seq technology. ARS scientists at Beltsville, MD, (BARC) prepared RNA from whole blood collected at different days post PRRSV infection. They worked with University of Alberta (UoA) scientists to assess gene expression using RNA-seq and analyzed results using a data pipeline developed by UoA colleagues. BARC and UoA scientists collaborated on the development of a successful method for depletion of hemoglobin RNA so that RNA-seq data will be collected more efficiently from blood samples. All PHGC data is being stored in the secure, password protected PHGC database at Iowa State University: http://www.animalgenome.org/lunney/index.php. These analyses should help to identify new genes, pathways, and mechanisms that differentiate PRRS-resistant from susceptible pigs. This will help pig breeders to select more PRRS resistant breeding stock and animal health researchers to develop alternate PRRS control strategies.