Mice have some distinct advantages for use as animal models in alcohol research, particularly in genetic analyses. Over 90% of the mouse and human genomes can be partitioned into corresponding regions of conserved synteny, reflecting segments in which the gene order in the most recent common ancestor has been conserved in both species. The proportion of mouse genes without any homologue currently detectable in the human genome (and vice versa) seems to be less than 1% (Waterston et al., 2002). The first mouse genome that was fully sequenced was the C57BL/6J (B6) inbred strain, for which the physical map is readily available (http://www.ensembl.org/Mus_musculus/). Currently an additional 17 key mouse strains are being sequenced in their entirety by the Sanger Center (http://www.sanger.ac.uk/modelorgs/mousegenomes/), and all single nucleotide polymorphism (SNP) calls are publically available. For example, the QTL region of mouse distal chromosome 1 was completely sequenced for the B6 and DBA/2J (D2) strains commonly used to study alcohol related phenotypes (Walter et al., 2009). In a 3 megabase (Mb) region surveyed, 11,824 SNPs were identified between just these two strains. Additionally, mice
