Porcinesnp60 beadchip

The dataset we analyzed here was taken from publicly available data (Iacolina et al. 2016 (link); Yang et al. 2017 (link); Scandura et al. 2022 (link)), comprising various WB, DP, and outgroup species, all genotyped with the Illumina Porcine SNP60 Beadchip (Ramos et al. 2009 (link)), that is mapped onto the pig reference genome Sscrofa10.2 (Groenen et al. 2012 (link)). In particular, we selected the SarWB samples, together with a reference set of commercial European pig breeds (Berkshire (BK), Duroc (DU), Large White (LW), Pietrain (PI), Yorkshire (YO), Sardinian local pigs (SarDP)), and Italian WB that are assumed to be free of recent domestic introgression (ItaWB), and finally an outgroup — here represented by S. barbatus (SB; Bornean bearded pig). The merged dataset (Table 1) underwent a quality control (QC) step in PLINK 1.9 (Purcell et al. 2007 (link)) to remove the sites with at least 10% missing genotype rate, with low allele frequency (MAF < 0.05), and in linkage disequilibrium (LD, r² < 0.5). We retained 38K SNPs to use in the structure analyses.Table 1

The merged dataset gathered for this study

Population	Type	Sample size
SarWB	Wild boar	96
ItaWB	Wild boar	19
BK	Domestic pig	10
DU	Domestic pig	10
LW	Domestic pig	10
PI	Domestic pig	10
YO	Domestic pig	10
SarDP	Domestic pig	8
SB	Outgroup	11

To detect QTLs associated with S. aureus carrier status, we genotyped all pigs using diagnostic blood samples collected in EDTA tubes (VWR, USA). DNA was extracted using either a salting out procedure with minor modifications [26 (link)] or MasterPure™ Complete DNA and RNA Purification Kit (Epicentre Biotechnologies, USA) according to the manufacturer’s instructions. The concentration and purity of DNA was measured on a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, USA). 2500 ng of each sample was submitted for genotyping to GeneSeek, Inc. (http://www.neogeneurope.com). Samples were genotyped for 61,565 SNPs using Illumina’s Porcine SNP60 beadchip [25 (link)].

Genotyping was performed mainly using the Illumina Porcine SNP60 Beadchip, but some animals from all populations were genotyped using the Illumina Porcine SNP60 v2 Beadchip. Genotypic data were available on 3723 LW, 3291 LR, and 1126 F1 animals (Table 1). In the purebred populations, both males and females were genotyped. In the F1 population, only females were genotyped. Genotypes of all animals were imputed to the SNP60 Beadchip for all SNPs that passed the quality control. The quality control excluded SNPs with a GenCall lower than 0.15, a call rate lower than 0.95, a minor allele frequency lower than 0.01, and SNPs that deviated significantly from Hardy–Weinberg equilibrium (χ² > 600). SNPs located on the sex chromosomes and unmapped SNPs were also excluded. Positions of the SNPs were based on the Sscrofa10.2 assembly of the reference genome [22 (link)]. All genotyped animals had a frequency of missing genotypes below the threshold of 0.05 in order to exclude poorly genotyped animals. After quality control and imputation, 39,788 SNPs for LW, 41,299 SNPs for LR, and 45,515 SNPs for F1 were available for further analyses.

DNA was extracted from ear tissue using the phenol-chloroform method [17 (link)]. The quality and quantity of the DNA extracted was checked with a NanoDrop™ 2000 (Thermo Fisher Scientific Inc., USA). DNA quality was measured by retaining samples with concentrations >50 ng/μl, total volume >50 μl, and a ratio of light absorption (A260/280) between 1.8 and 2.0. Genotyping was conducted using the Illumina Porcine SNP60 BeadChip by the company (DNA LandMarkers, Canada) Genotypes were called with GenomeStudio (Illumina, USA). Data mining was performed in our lab.
To reduce the false-positive associations resulting from genotyping, we controlled our SNP analysis with a genotyping call rate ≥ 95% and a Hardy–Weinberg equilibrium (HWE) p ≥ 10⁻⁴. Considering that rare SNPs have lower statistical power, SNPs with a minor allele frequency (MAF) ≥ 1% were selected for further analysis. Moreover, all of the SNPs located on the sex chromosome were removed.

The data used in this study were from two unrelated pig lines provided by Genus plc (Hendersonville, TN, USA). Genotypes for all sows were generated using the Illumina PorcineSNP60 BeadChip (Illumina, San Diego). After quality control, i.e. excluding genotypes from single nucleotide polymorphisms (SNPs) with a minor allele frequency lower than 0.05 and a call rate lower than 0.95 in each population, 37,900 and 37,011 genotypes for SNPs remained for lines 1 and 2, respectively. Individuals with a call rate lower than 0.95 were also removed. Finally, the number of sows included in the analysis were 3631 and 2612 for lines 1 and 2, respectively. In total, 13,449 and 11,581 records on litter size (number of piglets born alive) were available for these sows, with an average litter size of 11.7 ± 2.9 and 12.4 ± 3.0 for lines 1 and 2, respectively.

Animals were genotyped using the Illumina Porcine SNP60 BeadChip (Illumina Inc., San Diego). Assuming an additive allele substitution effect, genotypes were arbitrarily coded to 0, 1, and 2 for the homozygote for the minor allele, heterozygote, and other homozygote, respectively. SNPs with a call rate lower than 0.90 and a minor allele frequency lower than 0.05 were removed. Boars with a call rate lower than 0.90 and parent-offspring pairs that displayed Mendelian inconsistencies were discarded. After this quality control, 46,610 SNPs were retained to pursue the analyses. Zero and near-zero-variance SNPs were identified and removed with the “nearZeroVar” function which removes predictors that have a unique value or have very few unique values relative to the number of samples, and the ratio of the frequency of the most common value to the frequency of the second most common value is 95/5 (Caret R package, Kuhn, 2008 (link)). Subsequently, the “findCorrelation” function (Caret R package, Kuhn, 2008 (link)) with a cut-off = 0.8 was used to diminish high pair-wise correlations between features. After this genotype edition, 9,523 SNPs were retained.