Analysis of Gene Expression in a Region Associated with Host Response to Porcine Reproductive and Respiratory Syndrome Virus Challenge

Previous work established a 1 Mb region on SSC4 associate with response to PRRS virus infection. We used RNAseq to identify candidate genes in this region. Blood at 0, 4, 7, 11, and 14 days post infection (dpi) from 8 litter mate pairs from trial 3 of the PRRS Host Genetics Consortium (PHGC) was collected, each pair including one pig with the favorable (AB) and one with the unfavorable (AA) QTL genotype. Samples were processed to extract RNA, deplete globin transcripts, and prepare libraries. Tuxedo software and HTseq were used to generate per-transcript read-counts, which were normalized, transformed, and analyzed with a linear model to assess differential expression (DE) between AB and AA individuals. The Genome Analysis Toolkit was used to call 136 SNPs in the SSC4 region that were consistent with the AB/AA genotype. Allele counts were obtained for each SNP and analyzed for allele specific expression (ASE) with a binomial logistic regression model. Of the 12 Ensembl reference transcripts in the region, one gene showed higher expression in AB versus AA individuals at all dpi except 0, significant (P<0.05) at 7 and 10 dpi. Other genes showed significant DE at only one time-point. Exonic SNPs for the DE gene had a higher (P <0.05) expression of the B versus the A allele. These results provide evidence of a promising candidate for further functional work to validate and detail its role in host response to PRRS. Acknowledgements: PHGC for the samples and PIC/Genus for funding the RNAseq.