South-east Australian Feral Pig SNPs

Methods: During feral pig control programs, either tissue or blood samples were collected from culled pigs for genetic analysis. Tissue biopsies were collected in tissue sampling unit (TSU) buffer (Allflex) or 80% ethanol. Blood sampling was undertaken using the GenoTube swab system (Thermo Fisher). Samples were extracted using the sbeadex Livestock DNA Purification Kit (Biosearch Technologies) on the Kingfisher Flex Purification System (ThermoFisher) under manufacturer’s instructions for tissue or blood extractions. SNP genotyping was conducted using the Porcine SNP60 BeadChip (v2 and v3, Illumina) containing 61,565 (v2) or 75,753 (v3) SNPs, according to the manufacturer’s protocol. After genotyping, individuals were filtered to exclude samples with less than a 99% call rate. SNPs were filtered to exclude sites with a call-rate of less than 99% (which also excluded SNPs that were only found on the v3 BeadChip), minor allele frequency of < 0.01, all unmapped SNPs and those on sex chromosomes.