chromosome. Furthermore, linkage signals detected with SNPs on other chromosomes ranged from LOD scores 1.33 to 1.95 at different positions on chromosomes 3, 4, 7, 16, 18, and 21. The highest LOD scores from SNPs are 1.95 on chromosome 7 (Illumina) and 1.80 on chromosome 1 (Affymetrix). There were generally low linkage signal detections by microsatellites compared with SNPs across the genome. One likely reason for this poor comparative performance could be the low information content of the low-resolution microsatellite map. Since high map resolutions, such as those obtained with the two sets of SNPs in this study, also translate into increased information content, it is our belief that the use of highly dense SNP map in linkage analyses would more likely lead to detection of linkage signals that would be missed by the currently available microsatellite map.
