Bovinesnp50 v3

Genotypic data were obtained using two SNP panels: BovineSNP50 v2 and BovineSNP50 v3 (Illumina Inc., USA). These two SNP panels were imputed to BovineSNP50 version 3 using Fimpute version 2.2 [12 ]. After excluding unmapped SNPs and SNPs on sex chromosomes, the available number of SNP markers was 54,931. After performing marker quality control, genotypes at each locus were excluded based on the following criteria: average call rate lower than 0.90; minor allele frequency less than 0.01; markers not in Hardy–Weinberg equilibrium, with a chi-square value (χ²) greater than 95%; and SNPs in extreme linkage disequilibrium (LD, r² >0.99). After editing, 50,765 SNP genotypes were available for analysis. Furthermore, genotyped animals were excluded from analysis based on the following criteria: duplicate animals, twin animals, and animals that failed parentage tests. Duplicate animals and twin animals were removed based on marker call rates. Furthermore, genotype identification that could not be matched to the corresponding animal in the phenotypic data set was removed from a total of 2,032 Holstein dairy cattle. Finally, for ss-GBLUP for all traits, the genotype data set comprised 1,919 animals, whereas for Bayes-B, the number of animals available for MY305, FY305, and PY305 was 963, 943, and 946, respectively.

In total, 192 Canadienne samples (two of the 190 animals were genotyped twice as quality control replicates) were genotyped using the Affymetrix/ThermoFisher Axiom BOS1 platform targeting 648,874 SNPs. Canadian Holstein genotypes were acquired within the context of a different project on the Illumina Bovine SNP50 v3 platform targeting 53,218 SNPs. All sample hybridizations were performed at the Centre d’expertise et de services Génome Québec (Montréal, QC, Canada).