#07-062

Complete

Date Full Report Received

08/01/2008

Date Abstract Report Received

08/01/2008

Investigation

Institution:
Primary Investigator:
Co-Investigators: Annette O’Connor, Jack C.M. Dekkers, James McKean, Shawn Bearson

The long-term goals of this project are to use genomics tools to identify genetic variants associated with decreased Salmonella shedding on farms; and to use these variants to select for animals that shed fewer bacteria and so are less likely to cause abattoir carcass contamination and thus improve pork safety. To achieve these long term goals, we worked on 4 specific objectives: 1) generate a large bank of Salmonella fecal shedding data and matched DNA samples using US industry pigs; 2) create DNA tests for genetic variation at candidate genes, selected based on our previous data on gut lymph node gene expression patterns in response to Salmonella infection; 3) using new and established DNA tests, perform genotyping on US industry Salmonella-positive–control groups and laboratory challenge populations; 4) test associations of genotypes with Salmonella incidence and integrate data from epidemiology and genomics projects to understand Salmonella contamination.
For objective 1, during a 15-month period a total of 178 belly flap pig tissue samples from 33 farms have been collected that includes 59 Salmonella positive and 119 negative samples as determined by qualitative fecal testing. Objective 1 is an ongoing project performed in collaboration with a large epidemiology study funded by USDA-NRI. In our laboratory, DNA from Salmonella-positive and negative-control pig tissue is being isolated as soon as samples are collected. In objective 2 we confirmed 11 new genetic variants (single nucleotide polymorphisms, SNPs). To analyze genetic variants in the objective 3 work, three porcine populations with Salmonella shedding data were used: 1) the field pig population (objective 1); 2) a 40 pig NADC Salmonella Typhimurium challenge population; and 3) a 228 pig Compton Salmonella Choleraesuis challenge population. In addition to confirmed SNPs we also selected to be genotyped 38 new putative SNPs in 25 genes involved in regulation of porcine response to Salmonella. To genotype this larger number of SNPs, we adopted Sequenom technology due to its increased throughput and reduced cost. For the first round of genotyping, a total of 29 selected SNPs have been combined and will be genotyped using all 3 porcine populations, a total of 378 DNA samples. The objective 4 statistical association analysis will be performed upon completion of this genotyping project. The genotyping and statistical analysis data will be used to generate genetic markers useful in selecting animals that shed fewer bacteria and are less likely to cause pen-mate Salmonella contamination in a farm and on a slaughter plant, thus providing novel information for the pig industry to implement in strategies for selecting pigs with reduced shedding and/or disease susceptibility. Contact: Christopher K. Tuggle, 515-294-4252, email: cktuggle@iastate.edu