To avoid potential bias caused by possible genotyping errors on linkage signals, the error-checking algorithm implemented in MERLIN was applied. This algorithm identifies unlikely genotypes based on the inferred double recombination events, when erroneous genotypes can imply excessive and unlikely recombination events between tightly linked markers [3]. We used the default parameter in MERLIN, where the likelihood ratio of an erroneous genotype with p ≤ 0.025 was excluded [2]. The two whole-genome scans were carried out both with and without the erroneous genotypes to exam the effect of genotyping error on the scan results.
