2012 Annual Report 1a.Objectives (from AD-416): The specific objectives for this agreement are to Identify differentially expressed (DE) genes in blood in response to PRRSV infection; Determine putative gene sets and pathways that predict a pig's ability to clear PRRSV infection and maintain weight gain; and Validate utility of gene sets and pathways for prediction of responsiveness to PRRSV infections in multiple populations. Predictive blood tests of pigs with improved PRRS disease resistance and growth maintenance; increased understanding of mechanisms involved in pig responses to PRRSV infection; scientific publications. 1b.Approach (from AD-416): The University will check for differential gene expression of targeted genes e.g., CD163, SIGLEC1, PTEN, MMP9, IL10, FOXP3, TBET, GATA3, CCL21, MX1, etc., using RT-PCR on PRRS Host Genetics Consortium (PHGC) samples representing different virus/weight categories. This information that will be used in conjunction with analyses collected on the same sample sets at Michigan State University and BARC. For the third objective, the University will help identify and provide samples collected from recent U.S. PRRS infections. 3.Progress Report: 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 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. At Michigan State University (MSU) 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 have been completed at MSU and Iowa State University to identify differentially expressed (DE) genes and pathways that are associated with pigs that clear the PRRSV and that grow well despite PRRSV infection. 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 DE gene expression of targeted genes (e.g., PRRSV receptors) and critical genes controlling immune anti-viral responses, using real time-PCR. As this work progresses we expect to develop predictive gene expression pathways and classifier genes that identify pigs which resist PRRSV infection and grow normally.