Identification of a Putative Quantitative Trait Nucleotide (QTN) for Host Response to Porcine Respiratory and Reproductive Syndrome (PRRS) Virus Infection

Previously, we identified a major quantitative trait locus (QTL) on Sus scrofa chromosome 4 (SSC4) for host response to PRRS virus infection, as part of the PRRS Host Genetics Consortium (PHGC).  Recent RNAseq analyses identified a strong candidate gene in the QTL region based on differential expression (DE) due to QTL genotype (WUR0000125 AA and AB genotypes) at several days post infection (dpi) with with NVSL97-7985 PRRSV isolate in growing pigs. A whole-transcriptome assembly from Velvet-Oases revealed three splice isoforms for the candidate gene. In addition, an intronic mutation was identified that would alter splicing and explained one of these isoforms.  This isoform encodes a frame-shifted protein that introduces an early stop codon. This mutation was in perfect linkage disequilibrium with the SSC4 QTL.  Altered splicing was observed to segregate consistently with the AA and AB WUR0000125 genotypes by evaluation of RNAseq reads. Expression of the three isoforms was quantified using RNAseq data and validated by quantitative capillary electrophoresis.  Statistical analysis of RNAseq data revealed that differential splicing was associated with the splice site genotype at 14 dpi (p<0.0001).  This result was further validated in a combined analysis across five dpi (p<0.0001).  The wild-type isoform was more highly expressed in AB vs. AA genotype animals.  In contrast, the frame-shifted allele was more highly expressed in the AA vs. AB genotype animals.  These findings make this mutation a strong positional and biological candidate QTN for host response to PRRS virus infection.  Acknowledgements: PHGC for samples and PIC/Genus for funding the RNAseq.