2012 Annual Report
1a.Objectives (from AD-416):
The specific objectives of this agreement includes 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):
Michigan State University (MSU) researchers will contribute to the first two objective through developing statistical methods for selecting samples for evaluation from Tempus tube preserved blood samples collected through the PRRS Host Genetics Consortium (PHGC) representing pigs in different virus/weight categories. Perform all the microarray work and transcriptional profiling for the first two objectives and analyze all microarray data (processing and normalization and use of statistical programs to identify DE genes). MSU researchers will also collaborate on planning analysis of DE gene QPCR data (generated by USDA ARS BARC) for all Objectives.
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) to use PHGC blood samples to assess 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 analyses of the data were performed at MSU using a modified version of MAANOVA and the differentially expressed (DE) gene list compiled. Bioinformatic analyses at MSU in collaboration with BARC and Iowa State University scientists identified genes and pathways that are associated with pigs that clear the PRRSV and that grow well despite PRRSV infection. As a result of analyses of data from this first set of arrays, the decision was made 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. Further analyses of DE genes and pathways were performed at MSU, and lists of genes developed for targeted quantitative polymerase chain reaction (PCR) assays to affirm which genes are correlated with viral load and/or weight gain, by comparing the data from (1) the most desirable, PRRS-resistant, low virus, high weight gain pigs and, (2) with the worst, PRRS-susceptible, high virus, low weight gain pigs. 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.