The high degree of Rattus genome similarity that we found for these two deer mouse linkage groups warranted examination of additional informative regions where synteny breakpoints occur between the Mus and Rattus genomes.
The third instance is the unique deer mouse linkage of Sec61a2 to Pmfbp1.
We selected markers in each group that are less than 20.Mb apart in the Rattus genome to facilitate deer mouse linkage detection.
This approach circumvents the obstacles associated with human studies (namely, environmental heterogeneity) and mouse linkage analyses (namely, poor mapping resolution).
The spanning of two Mus genome breakpoints by the deer mouse linkage groups again indicates a more Rattus-like genome organization.
The deer mouse linkage group homologous to the centromeric end of Rattus Chr 6 consists of five loci and represents three different chromosomes in Mus.
Our previous analysis of the Peromyscus genome using loci from Mus Chr 11 [ 17] indicated that there are two separate deer mouse linkage groups.
In contrast, mouse linkage studies often have high statistical power to detect genetic effects but lower genetic resolution, producing loci that include hundreds of genes [ 19, 20].
Overall, our data for Rattus Chr 1 loci show that the two deer mouse linkage groups span two Mus genome breakpoints but only one Rattus genome breakpoint, which shows a continued bias towards similarity with the Rattus genome.
The spatial distribution of crossover density estimated over large windows (for example, 5 Mbp; see panel 1 in Figure S2) in the G2 F1 population is qualitatively similar to that of the most current mouse linkage map (Cox et al. 2009).
For Mus Chr 17, six markers (Tcp10b, Mas1, and Pacrg from Rattus Chr 1; Gbl from Rattus Chr 10; Lama1 from Rattus Chr 9; and Sos1 from Rattus Chr 6) were tested for linkage in all possible arrangements despite having already been assigned to other deer mouse linkage groups.
