Genotyping and quality control
In total, 192 animals representing 5 cattle populations of Ethiopia were genotyped for 8,773 SNPs with the Illumina Bovine 8K SNP BeadChip (Illumina, San Diego, CA, USA) according to Illumina protocols [9]. Over the loci, the average GenTrain score, 10% GenCall (10% GC) score, and 50% GenCall (50% GC) score were 0.86, 0.87, and 0.83, respectively. In this experiment, about 99.91% of the markers identified had a GenTrain score greater than the minimum acceptable value (0.25) (http://www.illumina.com). All of the samples had at least a 0.20 or greater 10% GC score, while the 50% GC score ranged from 0.75 to 0.91, with the average call rate of 0.913. For Hanwoo cattle, about 51,162 SNPs were genotyped using the Illumina Bovine 50K SNP BeadChip [10]. 8K and 50K genotypes were merged using Golden Helix SNP Variation Suite software version 7 (Golden Helix, Inc., Bozeman, MT, USA). To ensure the highest quality of data from the 8K and 50K SNP BeadChips, duplicate marker genotypes were identified and dropped. Finally about 7,045 SNPs that were common for both Bead-Chips were subjected to analysis. Markers selected for diversity analysis were all located on autosomal chromosomesand had at least an 80% call rate.