Samples were genotyped with the Illumina BovineSNP50 BeadChip [56] (link). Autosomal SNPs and a single pseudo-autosomal SNP were analyzed, because the data set from Gautier et al. [4] (link) excluded SNPs located exclusively on the X chromosome. We also filtered all SNPs which mapped to “chromosome unknown” of the UMD3.1 assembly [57] (link). In PLINK [58] (link), [59] , we removed SNPs with greater than 10% missing genotypes and with minor allele frequencies less than 0.0005 (1/[2*Number of Samples] = 0.000324, thus the minor allele had to be observed at least once in our data set). The average total genotype call rate in the remaining individuals was 0.993. Genotype data were deposited at DRYAD (doi:10.5061/dryad.th092) [60] .
Corresponding Organization : University of Missouri
Other organizations :
University of Vermont, Oklahoma State University, University of Córdoba, Beltsville Agricultural Research Center, University of Nottingham, Uppsala University, Texas A&M University, University of Veterinary and Animal Sciences, Brazilian Agricultural Research Corporation, Ankara University, Roman L. Hruska U.S. Meat Animal Research Center, Pennsylvania State University, Northwest A&F University, Iowa State University, University of Agriculture Faisalabad
Autosomal SNPs and a single pseudo-autosomal SNP were analyzed
SNPs located exclusively on the X chromosome were excluded
SNPs which mapped to 'chromosome unknown' of the UMD3.1 assembly were filtered out
SNPs with greater than 10% missing genotypes and with minor allele frequencies less than 0.0005 were removed
positive controls
None explicitly mentioned
negative controls
None explicitly mentioned
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