All animals were genotyped with the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA, USA). This 50 K SNP panel contained 41,847 SNPs after the quality control following [26 (link)], with an average of 51.5 Kb spacing between SNPs. Only autosomal chromosomes and SNPs with known genome positions according to the UMD_3.1 bovine assembly map [27 (link)] were used in the present study. The imputed high-density (777 K) SNP panel contained 305,341 SNPs evenly spaced across the genome after imputation from the 50 K SNP panel genotype.
The pedigree data contained 79,613 Holstein cattle from Canada, the USA, Germany, Denmark, Spain, Finland, France, Great Britain, Italy, and the Netherlands. There were 11,227 sires, 51,350 dams, and 9363 founder animals. Within the pedigree, there were 41,264 inbred animals with an average inbreeding coefficient of 0.0441, obtained using the software CFC [28 ].
The pedigree data contained 79,613 Holstein cattle from Canada, the USA, Germany, Denmark, Spain, Finland, France, Great Britain, Italy, and the Netherlands. There were 11,227 sires, 51,350 dams, and 9363 founder animals. Within the pedigree, there were 41,264 inbred animals with an average inbreeding coefficient of 0.0441, obtained using the software CFC [28 ].
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