The conventional BXD RI strains were derived from the B6 and D2 inbred mice [104],[105]. The newer sets of advanced RI strains were derived by inbreeding intercrosses of the RI strains [57]. The parental B6 and D2 strains differ significantly in sequence and have approximately 2 million informative SNP. A subset of 14,000 SNPs and microsatellite markers have been used to genotype the BXD strains [106],[107]. We used 3,795 informative markers for QTL mapping. Thirty such informative markers are in Qrr1 and we queried these markers to identify strains with recombinations in Qrr1; genes with strong cis-QTLs (Sdhc, Atp1a2, Dfy, and Fmn2) were used as additional markers. Smaller sub-sets of markers were used to genotype the two F2 panels (total of 306 markers for the whole brain, and 75 markers for the striatum F2 datasets).
