Synaptogyrin-2 influences replication of Porcine circovirus 2

Abstract

Porcine circovirus 2 (PCV2) is a circular single-stranded DNA virus responsible for a group of diseases collectively known as PCV2 Associated Diseases (PCVAD). Variation in the incidence and severity of PCVAD exists between pigs suggesting a host genetic component involved in pathogenesis. A large-scale genome-wide association study of experimentally infected pigs (n = 974), provided evidence of a host genetic role in PCV2 viremia, immune response and growth during challenge. Host genotype explained 64% of the phenotypic variation for overall viral load, with two major Quantitative Trait Loci (QTL) identified on chromosome 7 (SSC7) near the swine leukocyte antigen complex class II locus and on the proximal end of chromosome 12 (SSC12). The SNP having the strongest association, ALGA0110477 (SSC12), explained 9.3% of the genetic and 6.2% of the phenotypic variance for viral load. Dissection of the SSC12 QTL based on gene annotation, genomic and RNA-sequencing, suggested that a missense mutation in the SYNGR2 (SYNGR2 p.Arg63Cys) gene is potentially responsible for the variation in viremia. This polymorphism, located within a protein domain conserved across mammals, results in an amino acid variant SYNGR2 p.63Cys only observed in swine. PCV2 titer in PK15 cells decreased when the expression of SYNGR2 was silenced by specific-siRNA, indicating a role of SYNGR2 in viral replication. Additionally, a PK15 edited clone generated by CRISPR-Cas9, carrying a partial deletion of the second exon that harbors a key domain and the SYNGR2 p.Arg63Cys, was associated with a lower viral titer compared to wildtype PK15 cells (>24 hpi) and supernatant (>48hpi)(P < 0.05). Identification of a non-conservative substitution in this key domain of SYNGR2 suggests that the SYNGR2 p.Arg63Cys variant may underlie the observed genetic effect on viral load.

Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1

“…In the USMARC population, the genes overlapping QTL were identified in the five-SNP QTL windows extended by 300 kb in both directions (n = 222 windows) that explained the largest proportion of genetic variance for age at puberty (Nonneman et al, 2016b). Another portion of the array included SNP located in genes with ontologies associated with innate and adaptive immunity, and also SNP known to affect viral disease susceptibility (Walker et al, 2018). The immunity-related gene ontology terms were obtained from Ensemble BioMart tool (https://may2017.archive.ensembl.…”

“…The SNP array also consisted of potential loss-of-function SNP (Keel et al, 2017) as well as DNA markers for age at puberty identified in the USMARC studies (Nonneman et al, 2016a). The scaffold SNP incorporated in the SowPro90 obtained from the Porcine SNP60 BeadArray had a minor allele frequency > 0.05 in the UNL maternal crossbred data sets used for sow reproductive (Wijesena et al, 2017) and viral disease (Walker et al, 2018) research. The SowPro90 was also supplemented with SNP included in the Neogen Porcine GGPHD Array (Neogen Genomics, Lincoln, NE) if they overlapped the top 1% of the QTL for age at puberty (Wijesena et al, 2017) and SNP from the Affymetrix Axiom Pig High Density (PigHD) Array (Groenen, 2015; Thermo Fisher Scientific Inc. Waltham, MA) located in the Swine Leukocyte Antigen complex II locus ( Table 1).…”

“…Of these, 32,964 SNPs were located in 2,288 genes overlapping major QTL for age at puberty discovered in prior studies (Nonneman et al, 2016b;Wijesena et al, 2017). The SNP array was also supplemented with 16,271 SNPs located in 1,015 genes involved in innate and adaptive immunity including genes overlapping the Swine Leukocyte Antigen complex II locus and other genes influencing viral disease susceptibility (Kreikemeier et al, 2015;Walker et al 2018; Table 1). The rest of the SNPs identified were located in differentially expressed genes (including their proximal promoters) in the hypothalamic arcuate nucleus of gilts that expressed puberty early vs. late as well as their upstream regulatory genes or upstream trans modulators (Wijesena et al, 2017), SNP in genes overlapping 11 selective sweep regions for litter size traits (Trenhaile et al, 2016), and SNP in genes associated with structural soundness (Fan et al, 2009(Fan et al, , 2011.…”

“…Using multiple approaches including transcriptomic and genomic sequencing and genome-wide association study (GWAS), we have identified potential genetic variants influencing fertility (Tart et al, 2013;Nonneman et al, 2016b;Trenhaile et al, 2016;Wijesena et al, 2017), immune response (Engle et al, 2014;Kreikemeier et al, 2015;Walker et al, 2018), and SNP with predicted loss of function (Keel et al, 2017). These variants were integrated into "SowPro90," a custom Affymetrix Axiom myDesign SNP array.…”

Genome-wide association analysis for porcine reproductive and respiratory syndrome virus susceptibility traits in two genetic populations of pigs1

“…Association between phenotypic traits and major DNA markers, selected based on this research and previous studies (Boddicker et al, 2012;Serão et al, 2014;Walker et al, 2018), was assessed using a linear mixed model fit by JMP Pro 13.1 (SAS Inst. Inc.).…”