DOI: 10.5061/dryad.zgmsbccjh
title: Genomic regions associated with pseudorabies virus infection status in naturally infected feral swine (Sus scrofa)

description: Pseudorabies virus (PRV) – the causative agent of Aujeszky’s disease – was
 eliminated from commercial pig production herds in the United States (US)
 in 2004; however, PRV remains endemic among invasive feral swine (Sus
 scrofa). The circulation of PRV among abundant, widespread feral swine
 populations poses a sustained risk for disease spillover to production
 herds. Risk–based surveillance has been successfully implemented for PRV
 in feral swine populations in the US. However, understanding the role of
 host genetics in infection status may offer new insights into the
 epidemiology and disease dynamics of PRV that can be applied to management
 strategies. Genetic mechanisms underlying host susceptibility to PRV are
 relatively unknown; therefore, we sought to identify genomic regions
 associated with PRV infection status among naturally infected feral swine
 using genome–wide association studies (GWAS) and gene set enrichment
 analysis of single nucleotide polymorphism data (GSEA–SNP). Paired
 serological and genotypic data were collected from 6,081 feral
 swine distributed across the invaded range within the contiguous US. Three
 complementary study populations were developed for GWAS: 1) comprehensive
 population consisting of feral swine throughout the invaded range within
 the contiguous US; 2) population of feral swine under high, but temporally
 variable PRV infection pressure; and 3) population of feral swine under
 temporally stable, high PRV infection pressure. We identified one intronic
 SNP associated with PRV infection status within candidate
 gene AKAP6 on autosome 7. Various gene sets linked to metabolic
 pathways were enriched in the GSEA–SNP. Ultimately, improving disease
 surveillance efforts in feral swine will be critical to further
 understanding of the role host genetics play in PRV infection status,
 helping secure the health of commercial pork production.
description: <strong>Sample
 Collection<br></strong>Between 2012 and 2020, blood, hair, and
 tissue samples were collected from adult feral swine (n = 2,490)
 throughout the invaded range within the contiguous United States as an
 extension of damage management efforts led by the United States Department
 of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS)
 Wildlife Services (WS).<br><br><strong>Serological
 Assay<br></strong>Serum samples were tested for PRV antibodies
 at the Kentucky Federal Brucellosis Laboratory (Frankfort, Kentucky, USA)
 using the "short protocol" for Pseudorabies–gB Enzyme–Linked
 Immunosorbent Assay (PRV–gB ELISA; IDEXX Laboratories Inc., Westbrook,
 Maine, USA). Samples were considered positive for PRV if the S/N value ≤
 0.60 and negative if the S/N value &gt; 0.70.
 <strong>Genotype Data<br></strong>DNA
 extraction and genotyping were conducted at GeneSeek (Neogen Corporation,
 Lincoln, Nebraska, USA). DNA extraction was performed using the MagMAX™
 DNA Multi-Sample Ultra Kit (Thermo Fisher Scientific Inc., Waltham, MA,
 USA) and genotyping was completed using the GeneSeek Genomic Profiler
 (GGP) for Porcine 80k array (68,516 loci; Illumina BeadChip microarrays
 [San Diego, California, USA] licensed exclusive to GeneSeek, Neogen
 Corporation, [Lincoln, Nebraska, USA]). Bi–allelic SNP were mapped to the
 Sscrofa11.1 reference genome assembly (Warr et al., 2020), and unmapped
 and non–autosomal markers were removed, leaving 62,128 loci for further
 consideration. Standard quality control filters for genotype data were
 implemented using SNP & Variation Suite (SVS; version 8.9.0;
 Golden Helix, Bozeman, Montana, USA), specifically removing samples with
 call rates &lt; 0.90 and then pruning loci with call rates &lt;
 0.90 or minor allele frequency &lt; 0.05. Following quality control
 measures, 56,024 SNP were retained. <strong>True
 Seroprevalence for PRV<br></strong>True seroprevalence for
 PRV, accounting for imperfect detection was predicted for each year in
 each watershed (hydrological unit code [HUC] eight). Predictions were made
 using a hierarchical Bayesian model with 28,030 feral swine sampled across
 37 states in the contiguous United States between 2010 and 2020. Similar
 to the paired genetic and serological samples that serve as the focus of
 this study, these samples were more broadly collected (temporally and
 spatially) by USDA APHIS Wildlife Services as a component of disease
 surveillance and population control efforts.
 <strong>Percent European Wild Boar
 Ancestry<br></strong>The methods described in Smyser et al.
 (2020) were used to estimate the percent European wild boar ancestry of
 individual feral swine included in our analysis. Briefly, ADMIXTURE
 (Alexander et al. 2009) was used in a supervised framework to query an
 individual genotype against a comprehensive reference set
 for <em>Sus scrofa</em>, comprised of 105 domestic breeds, 23
 wild boar populations, and 4 sister taxa. This method proportionately
 associates the origin of individual feral swine genotypes among the 17
 ancestry groups that comprise the <em>Sus scrofa</em>
 wild–domestic species complex reference
 set.<br>
 <strong>References</strong> Alexander,
 D.H., Novembre, J., and Lange, K. (2009). Fast model-based estimation of
 ancestry in unrelated individuals. <em>Genome Res</em>
 19(9)<strong>,</strong> 1655-1664. doi:
 10.1101/gr.094052.109.<br><br> Smyser,
 T.J., Tabak, M.A., Slootmaker, C., Robeson, M.S., Miller, R.S., Bosse, M.,
 et al. (2020). Mixed ancestry from wild and domestic lineages contributes
 to the rapid expansion of invasive feral swine. <em>Molecular
 ecology</em> 29(6)<strong>,</strong> 1103-1119. doi:
 https://doi.org/10.1111/mec.15392.<br><br> Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., et al. (2020). An improved pig reference genome sequence to enable pig genetics and genomics research. <em>GigaScience</em> 9(6)<strong>,</strong> giaa051. doi: https://doi.org/10.1093/gigascience/giaa051.
description: # Genomic regions associated with pseudorabies virus infection status in
 naturally infected feral swine (*Sus scrofa*)
 Paired genotypic and
 serological data collected from 2,490 adult feral swine (*Sus scrofa*)
 throughout the invaded range in the contiguous United States as an
 extension of damage management efforts led by the United States Department
 of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS)
 Wildlife Services (WS). Associated metadata includes sample ID,
 hydrological unit code [HUC] eight, sample collection year, sex of the
 animal, percent European wild boar ancestry, true seroprevalence of
 pseudorabies virus (PRV), and infection status as determined by
 Pseudorabies-gB Enzyme-Linked Immunosorbent Assay (PRV-gB ELISA). ##
 Description of the data and file structure **Genotypes** Feral swine
 genotypes generated using the GeneSeek Genomic Profiler (GGP) for Porcine
 80k array provided in BED format (description provided below). Genotypes
 are mapped to the Sscrofa11.1 reference genome assembly. .bed - binary
 bi-allelic genotypes .bim - text file with no header. One line per SNP
 with the following fields: 1. Chromosome. 2. SNP identifier 3. Position in
 morgans or centimorgans. Dummy value '0' is used. 4. Base-pair
 coordinate 5. Allele 1 6. Allele 2 .fam - text file with no header. One
 line per sample with the following fields: 1. Family ID. Dummy value
 '0' is used for unknown. 2. Sample ID 3. Paternal ID. Dummy
 value '0' is used for unknown. 4. Maternal ID. Dummy value
 '0' is used for unknown. 5. Sex code. Dummy value '0'
 is used. This information is provided in the .txt file described below. 6.
 Phenotype value. Dummy value '-9' is used. This information is
 provided in the .txt file described below. **Metadata** Metadata for
 individual feral swine provided in a tab delimited text file
 (FS_PRV_Metadata_2490.txt). One line per sample with the following fields:
 1. SampleID 2. HUC8ID - Hydrological unit code eight in which the sample
 was collected. 3. CollectionYear - Year the sample was collected. 4. Sex -
 Sex of the animal. 5. PercentEuropeanWildBoar - Percent European wild boar
 ancestry. 6. TrueSeroprevalencePRV - True seroprevalence of PRV. 7.
 PRVgBELISA - Infection status as determined by Pseudorabies-gB
 Enzyme-Linked Immunosorbent Assay (PRV-gB ELISA).