error rate (0.37% for the microsatellites and 0.20% for the SNPs) and may not be generalized to other data sets. It is worth noting that for the full SNP set with an average spacing of 0.35 cM, it is highly possible that there is LD between SNPs, which may influence the linkage results from MERLIN since MERLIN assumes linkage equilibrium between all markers. John et al. [2] explored the possible effect of LD on the two scans by keeping one SNP from a group of SNPs in LD, or by assigning haplotypes to individuals for clusters of SNPs in LD and treating them as multi-allelic markers. They found that for both cases, there were losses in IC, which made it difficult to assess whether the difference observed in the two scans were due to LD or to losses in IC. They concluded that overall the results were qualitatively similar when SNPs in LD were included or excluded.
