High-Throughput Porcine Genotyping

Genotyping was performed as described by Ding et al. (2017) (link). Briefly, genomic DNA was extracted from ear tissue samples using the phenol–chloroform method. Genotyping was performed using the Geneseek Porcine 50K SNP Chip (Neogen, Lincoln, NE, United States), which contains 50,703 SNPs across autosomes and sex chromosomes. Quality control of the SNP data was performed using PLINK software (Purcell et al., 2007 (link)). Animals with call rates > 0.95, and SNPs with call rates > 0.99, minor allele frequency > 0.01, and P-value > 10^-6 for the Hardy–Weinberg equilibrium test were included. Only autosomal SNPs were considered for subsequent analyses.