Development of B6.CAST and HG.CAST MMU2 speed congenic strains
All speed congenic strains were developed starting with an initial cross between a CAST male and HG females (Figure 1) [5,6]. Male F1 mice were then backcrossed to HG females. All agouti (the dominant nonagouti (a) locus is located at 154.8 Mbp on MMU2) N2 males were genotyped for 79 microsatellite markers (Additional File 1). These markers were evenly spaced across the genome, except in regions previously identified as harboring QTL [1], which were more densely screened. The "best" N2 agouti male with the lowest level of genome-wide unwanted heterozygosity while maintaining CAST alleles for all MMU2 markers was selected for breeding. This selection scheme was used at each generation until a N4 male was identified as homozygous HG for all markers typed outside MMU2. After an additional backcross to HG females, recombinant males were identified providing the foundation for the four overlapping donor regions. Selected recombinant males were then backcrossed to both B6 and HG females to create strains, which were B6 (+/+) or HG (hg/hg) and heterozygous congenic. These mice were intermated to produce homozygous founders for each strain. This novel breeding scheme created four identical founder congenics on two backgrounds B6 (+/+) and HG (hg/hg), which formed the basis for our examination of interactions caused by the presence of the hg deletion. MMU2 speed congenic strains were maintained through brother-sister mating. Once each congenic was stabilized, 20 additional microsatellite markers were used to refine the position of each congenic recombinant end point (Additional File 2).