It was found by Hinrichs et al. [8] that a subset of the Illumina map obtained by removing markers in high linkage disequilibrium (LD) with nearby markers provided nearly as much information as the full map and more information than the microsatellite map. In view of this, we also ran the linkage analysis using this sparser map. The marker densities for the four maps were: microsatellites, 1 per 6.03 cM; Affymetrix, 1 SNP per 0.31 cM; Illumina, 1 SNP per 0.68 cM; and sparse Illumina, 1 SNP per 1.10 cM.
