The BXD CNS datasets were generated from a combined panel of conventional RI strains and advanced RI strains that were derived by inbreeding advanced intercross progeny. The advanced RIs have approximately twice as many recombinations compared to standard RIs and the merged panel offers over a 3-fold increase in mapping resolution [57]. This expanded RI set combined with the relatively high intrinsic recombination rate within Qrr1 [58] provides comparatively high mapping resolution. Mapping precision can be empirically determined by analyzing cis-QTLs in multiple large datasets, particularly the BXD Hippocampus Consortium, UMUTAffy Hippocampus, and Hamilton Eye datasets. These three datasets were selected because they have expression measurements from six BXD strains with recombinations in Qrr1. These strains—BXD8, BXD29, BXD62, BXD64, BXD68, and BXD84—collectively provide six sets of informative markers and divide Qrr1 into six non-recombinant segments, labeled as segments 1–6 (haplotype structures shown in figure 2).
