DNA was extracted as described elsewhere (Malmanger et al. 2006). Mice were genotyped using a custom single nucleotide polymorphism (SNP) array and the Illumina Golden Gate Assay (San Diego, CA, USA). A description of the array is found in Hitzemann et al. (2008). Samples were run locally using procedures exactly as described by the manufacturer. The SNP data for the High and Low lines were analyzed using a marker-by-marker C2 analysis. In the absence of a correction for drift, the nominal LOD threshold (4.2) is obtained by correcting for the number of multiple comparisons. The drift correction was patterned after that of Belknap et al. (1997); details of how the correction was calculated are found in Hitzemann et al. (2008). For the experiments described here, the estimated −LogP threshold for a significant QTL was 10.5.
