Bovinesnp50 beadchip version 1

The analyzed datasets comprised 2243 Polish and 2294 German Holstein-Friesian bulls. Both groups were defined as bulls for which EBVs on a national basis were available only for one of the countries. For each bull, EBVs calculated based on the national routine genetic evaluation models and corresponding effective daughter contributions were available for milk (MY), protein (PY), and fat (FY) yields, as well as for somatic cell score (SCS). Moreover, each individual was genotyped using the Illumina BovineSNP50 BeadChip version 1. Separately for each dataset, SNPs were filtered based on two criteria: the minor allele frequency (MAF) had to be ≥ 0.01 and the call rate ≥ 90%. Only SNPs that were present in both populations after filtering were kept, resulting in a final list comprising 39,557 SNPs representing an intersection of markers in the German and Polish datasets.

Genome-wide SNP genotype data from the Illumina BovineSNP50 BeadChip version 1 [25 (link)] for 20 East African taurine Sheko, 25 West African taurine N’Dama and 21 Asian zebu Nelore cattle were obtained from the Bovine HapMap consortium [26 (link)]. Quality control analyses were carried out on 54,334 autosomal SNPs mapped to the UMD3.1 bovine reference genome using the check.marker function of the GenABEL package [27 (link)] for R software version 3.2.2 [28 ]. In total, 19,417 SNPs with minor allele frequency less than 0.05 and 6,886 SNPs with call rate less than 0.95 were removed. Among these, 5,766 SNPs failed both criteria, leaving 33,797 SNPs for downstream analyses. None of the samples had a SNP call rate < 0.95 or identity-by-state (IBS) > 0.95.