A standard phenol/chloroform method was used to extract genomic DNA from muscle samples for all the pigs. The quality and concentration of genomic DNA fulfilled the requirements for the Illumina SNP genotyping platform. Samples were genotyped with GeneSeek Genomic Profiler Porcine HD BeadChip (Neogen Corporation, Lansing, MI, USA) according to the manufacturer’s protocol and genotypes were called using GenomeStudio (version 2011.1; Illumina Inc., San Diego, CA, USA).
Quality controls were implemented by Plink v1.07 [13 (link)] according to the following filtering. Firstly, SNPs with GC score below 0.2 were considered failed genotypes, and Fimpute [14 (link)] was used to impute the failed loci. Then, SNPs were excluded from the data set if i) SNPs without genome location based on the pig genome assembly Sus scrofa Build 10.2 or located on Y chromosome, ii) its minor allele frequency was <5%, or iii) it departed severely from Hardy–Weinberg equilibrium with a p-value lower than 106.
Quality controls were implemented by Plink v1.07 [13 (link)] according to the following filtering. Firstly, SNPs with GC score below 0.2 were considered failed genotypes, and Fimpute [14 (link)] was used to impute the failed loci. Then, SNPs were excluded from the data set if i) SNPs without genome location based on the pig genome assembly Sus scrofa Build 10.2 or located on Y chromosome, ii) its minor allele frequency was <5%, or iii) it departed severely from Hardy–Weinberg equilibrium with a p-value lower than 106.
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