The presence of these recent polymorphisms creates a challenge illustrated by our analysis of the tail clip phenotype. The QTL detected in the full expanded RI panel have higher LOD scores than those detected in the earlier panels. Further, these QTL appear to be more distinct from what may be ‘mirror’ loci, peaks of similar height because of non-unique strain distribution patterns when only a limited number of strains are tested, often observed when just the early set is used. Interestingly, not all loci detected in earlier panels were detected when combining these lines with the new, expanded panel. For example, the locus on chromosome 9 that was suggestive when mapped in Taylor I females had an LOD score below the suggestive threshold when mapped using the recent BXD RI set (Fig. 2a,b). Of particular interest is the locus on Chr 1, which was also suggestive in the original panel but dropped below the suggestive level in the recent BXD RI set. This could be due simply to sample size, which for RI panels is still quite low compared with
