Porcine Reproductive and Respiratory Syndrome (PRRS) has been affecting commercial populations of pigs in the US for more than 20 years. We evaluated differences in gene expression in pigs from the PRRS Host Genetics Consortium initiative showing a range of responses to PRRS virus infection. Pigs were allocated into four phenotypic groups according to their serum viral level and weight gain. We obtained RNA at several days post-infection and hybridized it to the 20K 70 mer-oligonucleotide Pigoligoarray. We initially used plasmode datasets to select an optimal procedure for analyzing these data. We showed that the random array effects model with the moderated F statistic and significance thresholds obtained by permutation provided the most powerful analysis procedure. We then addressed global differential gene expression between phenotypic groups. We identified cell death as a biological function significantly associated with several gene networks enriched for differentially expressed genes. We found the genes interferon-alpha 1, major histocompatibility complex, class II, DR alpha, and major histocompatibility complex, class II, DQ alpha 1 differentially expressed between phenotypic groups. Finally, we used this study as pilot data to inform the design of future time-course transcriptional profiling experiments. We concluded the best scenario for investigation of early response to PRRSV infection consists of sampling at 4 and 7 days post infection using approximately 30 pigs per phenotypic group.
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