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Genotypes of the two breed types were processed independently. Genotypes were first subjected to quality control (QC) filtering including 5% minor frequency allele, 5% genotype missingness, and 5% individual missingness, following PLINK (53) command plink --noweb --cow --maf 0.05 --geno 0.05 --mind 0.05. The QC for the genotypes used for association/heritability analysis (Holstein excluding farm UK2) resulted with 5377 SNPs failed missingness, 14,119 SNPs failed frequency, and 48 of 635 individuals were removed for low genotyping, resulting with 587 individuals and 121,066 remaining.

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