the detection of linkage evidence that was missed by the microsatellite screen. To examine this hypothesis, we compared the locations of the trait-linked SNP markers on chromosomes 2 and 7 to the locations of the microsatellite markers using integrated map information from the National Center for Biotechnology Information (NCBI) [6], specifically, the NCBI build 35.1 reference assembly. This assembly places the peak SNP on chromosome 7, rs322812, at 127.338 Mb. This falls near the midpoint of the flanking microsatellites, which are located at 122.205 Mb and 131.736 Mb of the same build, indicating a modest gap, which is also borne out by the genetic positions of these microsatellites at 146.7 cM and 156.2 cM on the GAW14 map. However, for some of the other trait-linked SNPs, there do appear to be microsatellites positioned relatively close by. Other possible explanations for the higher LOD scores in the SNPs could be higher genotyping success rates in the SNPs or greater genotyping error in the microsatellites. The discrepancy could also be due to chance, for example if less informative SNPs resulted in some families being uninformative for linkage who might otherwise have contributed evidence against linkage.
