Dissection of QTL on Host Chromosome 12 Uncovers Candidate Gene and Missense Polymorphism Associated with Porcine Circovirus 2 Susceptibility

Porcine circovirus 2 (PCV2) is a small single stranded DNA virus responsible for a group of detrimental diseases referred to as Porcine Circovirus Associated Diseases (PCVAD). Observed variation in incidence and severity of PCVAD between pigs suggests a host genetic role in facilitating PCV2 pathogenesis. This study builds on prior research by Engle et al. (2014), who performed a large-scale genome-wide association study of 974 crossbred pigs experimentally infected with a PCV2b isolate and provided evidence of a host genetic role in PCV2 viremia, immune response, and growth. Two major Quantitative Trait Loci (QTL) were identified for viral load located on chromosome 7 (SSC7) near the swine leukocyte antigen complex class II (SLAII) locus and the proximal end of chromosome 12 (SSC12). The SNP with largest association, UNL101 (SSC12), explained 11.1% of the genetic variance and 7.4% of the phenotypic variance for viral load. Dissection of the SSC12 QTL region using gene annotation and both genomic and RNA sequencing uncovered a novel missense polymorphism within SYG93 that exhibited the largest association with PCV2 viremia and immune response. In vitro gene silencing of SYG93 was performed on porcine kidney 15 cell line (PK15) using siRNA designed against the SYG93 mRNA sequence. A substantial decrease in SYGR93 mRNA expression (82.2%) was achieved and corresponded with a significant reduction in PCV2 titer beginning at 48 hours post infection. The novel SYG93 mutation is located within a protein domain conserved across mammals and results in an amino acid substitution unique to swine. The impact of SYG63 on PCV2 replication and location of a non-conservative substitution within a key domain provides strong evidence that the SYG93 variant underlies the observed genetic effect on viral load by potentially interfering with SYG93 activity. These findings provide important insight into the role of host genetics in PCV2 pathogenesis