Challenges remain to the use of BXD lines including lower precision, potential of false positives due to linkage disequilibrium, finite statistical power and a limited pool of polymorphisms. These challenges are far outweighed by the ability to undertake integrative data analysis within the BXD RI lines as they serve as a common reference population. Executing similar phenotypic analysis in the Collaborative Cross (Chesler et al. 2008; Churchill et al. 2004; Iraqi et al. 2008; Morahan et al. 2008) will help address these issues and give positional refinement to the QTL identified in this study. Large cohorts of the Collaborative Cross population have been simultaneously bred, with the goal of creating well-randomized, independent RI lines.
