Genotyping of Porcine Populations with Imputation and Quality Control

A total of 12,200 animals (10,899 sows and 1,301 boars) across the four populations were genotyped with either the PorcineSNP60K Bead Chip (Illumina Inc., San Diego, CA, USA; 61,566 SNPs) or the GGP Porcine HD v1 80K (GeneSeek Inc., Neogen Co., Lincoln, NE, USA; 68,529 SNPs). The missing genotypes were imputed using the FImpute v2.2 software (Sargolzaei et al., 2014 (link)) to the 60K Bead chip. Quality control of genotype data consisted of removing SNPs with minor allele frequency lower than 0.05, SNP call rate below 0.90 and extreme deviation from Hardy-Weinberg equilibrium (with a p-value smaller than 10⁻⁶). The total number of individuals with genotypes involved in further analyses is reported in Table 1. SPG populations had the largest number of individuals genotyped, with a total of 3,790 for SPG_LR and 5,271 for SPG_LR. TML populations had a lower number of individuals genotyped, with 1,587 for TML_LR and 1,552 for TML_YS. The final number of SNPs that passed the quality control was 48,911, 49,183, 44,824, and 44,875, for SPG_LR, SPG_LW, TML_LR, and TML_YS, respectively.