Genetic Diversity Analysis of Wild and Domestic Pigs

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