Genotypic Data Analysis of Pig Populations

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.