2012 Annual Report
1a.Objectives (from AD-416):
This proposed Alberta Livestock Genomics Program project will build a Canadian component to the PRRS Host Genetics Consortium (PHGC) project. This involves Canadian researchers, laboratories and companies thereby adding significant value to the Canadian industry and providing a significant leverage of ALGP and Canadian company funding. The project addresses two of the ALGP research areas: 1. Genomics supported Expected Progeny Differences (EPD’s) for bovine or porcine (including potential marker validation studies), and 2. Genomics of livestock health. The three objectives of this project are:.
1)Enhance the development of Genomic Estimated Breeding Values;.
2)Enhance the planned transcriptome analysis by incorporating Next-gen sequencing technology; and.
3)Enhance the proteomic analysis to increase the number of samples using high throughput immune assays developed by Dr. Lunney at USDA-ARS. The Cooperator has the expertise and infrastructure to effectively perform single nucleotide polymorphism (SNP) and Transcriptome Sequencing (RNA-seq) analyses and will collaborate on proteomic fluorescent microsphere immunoassays (FMIAs).
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 porcine respiratory and the reproductive syndrome virus (PRRSV) infection. Many of these studies have been performed with pigs from Canadian sources. This information will be used by both parties and members of the PHGC determine genetic alleles and gene and protein expression differences that are associated with PRRS resistance/susceptibility. The COOPERATOR will genotype PHGC DNAs and perform RNA-seq and FMIA analyses to identify genes and proteins that differentiate PRRS resistant from susceptible pigs.
This project, supported by the Alberta Livestock Genomics Program (ALGP), under Genome Alberta funding, expanded our efforts and built a Canadian component to the U.S. PRRS Host Genetics Consortium (PHGC) project. This project involves Canadian researchers, and PigGen Canada, which represent the Canadian swine genetics industry and whose goal is to seize new opportunities from developments that are taking place in the field of genomics. A PigGen Canada CRADA provides matching funds for this ALGP project. The first target for this project was to complete genotyping of genomic DNAs from PHGC trials 6-8. Genomic DNAs were prepared by ARS scientists at Beltsville, MD, (BARC), and were genotyped with the 60K single nucleotide polymorphism (SNP) chip, the Porcine SNP60 BeadChip. All data will be entered into the PHGC relational database. This data is now being used for the more detailed genome wide association studies (GWAS) to generate predictive breeding values. The second target of this collaboration is to characterize the immune response to porcine respiratory and reproductive syndrome virus (PRRSV) infection using sera collected during PHGC trials. Our lab has performed proteomic fluorescent microsphere immunoassays (FMIAs) testing for a panel of cytokines, i.e., those involved in:.
2)adaptive anti-viral responses T helper 1 (Th1) immunity;.
3)prevention of Th2 responses;.
4)chemokine responses; and,.
5)negative regulatory cytokine production. Results affirmed that early increases in interleukin-1 beta (IL-1b), and IL-8 were correlated with PRRS vaccinated, but not infected, pigs, suggesting them as markers for protective immunity. The third target of this ALGP project is training Canadian scientists in FMIA technology. This was accomplished by visits of Canadian scientists to BARC as well as follow-up conference calls aimed at improving their use of this technology. Overall these immune protein analyses should help to identify proteins and mechanisms that differentiate PRRS-resistant from susceptible pigs.