Genotyping and Quality Control of Pigs

A total of 364 pigs, including their F0, F1 and F2 founder generations (72 animals), were genotyped with the Porcine SNP60K BeadChip [75] (link) following the Infinium HD Assay Ultra protocol (Illumina Inc.; San Diego, CA, USA) and the genotypes were visualized with the GenomeStudio software (Illumina Inc.; San Diego, CA, USA). The quality control of the 62,163 SNPs was performed by using Plink [76] (link) software removing markers with a minor allele frequency (MAF) <5% and animals with missing genotypes>5%. The SNP mapping and annotation was performed by using the pig assembly 10.2 [ftp://ftp.ncbi.hlm.nih.gov/genomes/Sus_scrofa/GEF/]. We also excluded markers which did not map in the Sscrofa10.2 version assembly. Pedstats program [77] (link) was used to check Mendelian inheritance errors.