Genomic consequences of a century of inbreeding and isolation in the Danish wild boar population
Cite this dataset
Yildiz, Beril; Megens, Hendrik-Jan; Bosse, Mirte; Hvilsom, Christina (2022). Genomic consequences of a century of inbreeding and isolation in the Danish wild boar population [Dataset]. Dryad. https://doi.org/10.5061/dryad.905qfttnc
Abstract
Methods
PLINK format genotypes
We used PAX gene blood samples that were collected from 21 wild boars in Klelund Plantation. Additionally, 11 tissue biopsies were collected from wild boars in Ulm, Germany as a part of the yearly population cull by hunters. The SNP genotyping was conducted using the Illumina Porcine 60K+iSelect Beadchip, and a total of 61,565 loci were screened for each individual. We filtered out SNPs with overall call rate less than 95%. Due to missing genotype data, 1576 SNPs were removed. The final dataset consisted of 48,227 SNPs.
We obtained the reference samples and genotype data from (Iacolina et al. 2016, 2018; Yang et al. 2017a), which contains 1263 wild boars across Eurasia as well as international commercial pig populations (Suppl. Table 4) (Ramos et al. 2009). We checked overlapping SNP markers, which corresponded to 47,325 variants in the combined dataset. From the combined dataset, a subset of only European wild boar populations consisting of 459 individuals was made to make more detailed comparisons. These datasets were used for population structure analyses (PCA and admixture).
Usage notes
PLINK format genotypes; suppl Table 4 in the main manuscript contains additional information about the samples.
Funding
Dutch Research Council, Award: 016.Veni.181.050