As seen in Figure 2, the differences in map densities between Illumina and Affymetrix SNPs used in this study did not appear to confer any advantage in terms of strength of linkage signals. In fact, the Illumina map detected stronger linkage signals than the Affymetrix map on most of the chromosomes in which signals were detected (Table 1). Since it is possible that a less informative marker may be sampled at any given locus with the thinning method used in this study, the observed differences in chromosome positions for highest linkage signals for the two SNP marker sets (Table 1) could have been due to this. However, our results from using the two SNP marker sets without thinning (data not shown) indicated that the observed differences are not due to the thinning method used.
