Previous work identified a 1 Megabasepair region encompassing a quantitative trait locus (QTL) on Sus scrofa chromosome 4 associated with response to PRRS virus infection, in terms of weight gain and PRRS viremia. To identify candidate genes in the region responsible for these effects, we evaluated the expression of genes in the region by RNAseq using RNA isolated from whole blood taken from 8 pairs of littermates at 5 time-points following experimental infection with the PRRS virus. Each littermate pair included one individual with the favorable genotype (AB) for the SSC4 region and one with the unfavorable genotype (AA). A comparison of the gene transcript counts between AB and AA individuals was performed with a statistical model that also used sequence information to identify transcripts with allele-specific expression (A versus B) in the AB individuals. These analyses revealed a few candidate genes, with one gene in particular being differentially expressed at multiple time-points and having a high level of overall gene expression. This candidate gene is promising for follow-up functional biology studies to validate and detail its role in host response to PRRS virus infection.