Whole Blood Transcriptome Analyses of Swine Responses to PRRSV Infection

Transcriptional changes in pig in response to Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection were studied. RNA was extracted from Tempus tube preserved porcine whole blood samples from 14 pigs at 7 time-points (0, 4, 7, 10, 14, 21 and 28 days post infection) collected in PRRS Host Genetics Consortium (PHGC) trial 5. After globin reduction, libraries were prepared and paired end sequencing performed using the Illumina HiSeq system. Following removal of low quality reads, the overall mean base quality was >35 and per base median quality >20 (100bp). An average of 58M high quality reads (per sample) were obtained, and approximately 87% of the reads could be aligned to the pig reference genome (Sus scrofa 10.2). Counts of reads mapped to each gene in each sample were imported into edgeR and normalized expression measures were generated (counts per million mapped reads, CPM). A total of 12470 genes were found expressed (CPM>1 in at least 12 samples). Previous genome-wide association studies affirmed a genomic region on swine chromosome 4 (SSC4) in controlling viral load and associated growth [B allele of WUR10000125 was assumed as favorable]. Gene expression was compared between WUR10000125 AA and AB animals with a top result highlighting a potential candidate gene near the target SNP. Additional genome-wide analysis is underway to investigate the dynamics of gene expression during infection to decipher genetic mechanisms controlling host response to PRRSV infection. This work was supported by funds from Genome Alberta, ALMA, Genome Canada, and USDA ARS and NIFA.