2012 Annual Report
1a.Objectives (from AD-416):
The specific objectives will be.
1)Identify differentially expressed (DE) genes in blood in response to PRRSV infection;.
2)Determine putative gene sets and pathways that predict a pig’s ability to clear PRRSV infection and maintain weight gain; and.
3)Validate utility of gene sets and pathways for prediction of responsiveness to PRRSV infections in multiple populations.
1b.Approach (from AD-416):
The proposed studies will identify functional genomic determinants, and potential “classifier genes” that predict resistance/susceptibility of commercial U.S. swine to PRRSV infection and associated growth losses. Such gene-specific information will directly complement the genetic variation and QTL mapping data being developed in the PHGC, to provide an integrated view of the molecular genetic architecture of PRRSV resistance. All information will be disseminated to swine researchers and breeders, as well as genetics companies and genotyping services so that these recommended genes can be targeted in future breeding programs to increase resistance to PRRS, the most economically important disease affecting the U.S. pork industry.
This functional genomics project uses samples collected from pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV), a major swine pathogen causing losses to the U.S. pig industry of $664 million per year. The goal is to determine which anti-viral response pathways differ in PRRS-resistant versus PRRS-susceptible pigs using samples collected as part of the PRRS Host Genetics Consortium (PHGC). ARS Researchers at Beltsville, Maryland (BARC) have partnered with Michigan State University (MSU), Iowa State University (ISU), Washington State University (WSU), and Purdue University (PU) scientists to use PHGC samples to assess blood gene expression responses. To date, sets of blood RNA samples have been prepared at BARC from 120 pigs from three different PHGC trials. The Swine Protein-Annotated Oligonucleotide Microarray, or Pigoligoarray (www.pigoligoarray.org), was used to evaluate changes in gene expression of blood RNA from 12 pigs collected at 0, 4, 7, 11, 14, 28, and 42 days post infection (dpi). Biostatistical and bioinformatic analyses were performed at MSU with interactions from both MSU and ISU scientists. Sophisticated statistical tools were used to generate informative gene networks that differentiate the PRRSV response patterns in pigs representing different virus/weight categories. Analyses of data from this first set of arrays has resulted in the decision to focus on 0, 4, and 7 dpi samples so that gene expression of early anti-PRRSV infection can be evaluated in a more robust statistical manner. Targeted quantitative polymerase chain reaction (PCR) assays will help to affirm which genes are correlated with viral load and/or weight gain by comparing the (1) most desirable, PRRS-resistant, low virus, high weight gain pigs with the (2) worst, PRRS-susceptible, high virus, low weight gain pigs. At PU, scientists used quantitative PCR analyses to affirm differential gene expression of targeted genes, e.g., the PRRSV receptors and critical genes controlling immune anti-viral responses, using real time PCR. As this work progresses, systems biology based analyses at ISU will be used to develop predictive gene expression pathways and classifier genes that identify pigs which resist PRRSV infection and grow normally.