A genetic map of Peromyscus with chromosomal assignment of linkage groups (a Peromyscus genetic map)

Abstract

The rodent genus Peromyscus is the most numerous and species-rich mammalian group in North America. The naturally occurring diversity within this genus allows opportunities to investigate the genetic basis of adaptation, monogamy, behavioral and physiological phenotypes, growth control, genomic imprinting, and disease processes. Increased genomic resources including a high quality genetic map are needed to capitalize on these opportunities. We produced interspecific hybrids between the prairie deer mouse (P. maniculatus bairdii) and the oldfield mouse (P. polionotus) and scored meiotic recombination events in backcross progeny. A genetic map was constructed by genotyping of backcross progeny at 185 gene-based and 155 microsatellite markers representing all autosomes and the X-chromosome. Comparison of the constructed genetic map with the molecular maps of Mus and Rattus and consideration of previous results from interspecific reciprocal whole chromosome painting allowed most linkage groups to be unambiguously assigned to specific Peromyscus chromosomes. Based on genomic comparisons, this Peromyscus genetic map covers ~83% of the Rattus genome and 79% of the Mus genome. This map supports previous results that the Peromyscus genome is more similar to Rattus than Mus. For example, coverage of the 20 Rattus autosomes and the X-chromosome is accomplished with only 28 segments of the Peromyscus map, but coverage of the 19 Mus autosomes and the X-chromosome requires 40 chromosomal segments of the Peromyscus map. Furthermore, a single Peromyscus linkage group corresponds to about 91% of the rat and only 76% of the mouse X-chromosomes.

Figure 1. Peromyscus genetic linkage map

Type I genetic markers are shown in black and microsatellite loci are indicated in red. The linkage groups are associated with the Peromyscus chromosomes according to the standardized nomenclature of the karyotype. Two linkage groups are assigned to chromosome 8.

Figure 2. Linkage groups 8a and 8b are both located on Peromyscus Chromosome 8

(A). The two linkage groups are aligned according to their location on Chromosome 8. BAC clones containing different genes were fluorescently labeled as described in Materials and Methods. (B). FISH to Peromyscus metaphase chromosomes with BACs harboring the Hba (red) and the Pacrg (green) genes. (C). Results of hybridization with BACs harboring the Hba (red) and Mpo (aqua) genes. (D). Merged hybridization results showing that the Pacrg and Mpo genes are close together while Hba is more proximal to the centromere of Chromosome 8.

Figure 3. Comparative relationships of the genetic map of Peromyscus with the molecular map of Rattus and Mus

For Rattus and Mus segments the numbers in parentheses indicate the molecular position at the ends of the chromosomal segment. The Rattus and Mus chromosomes are indicated in bold. Molecular locations of Mus loci come from Genome Reference Consortium Mouse Build 38 (GRCm38) and Rattus gene positions are from RGSC Genome Assembly v3.4. Fig. 3A. Peromyscus chromosomes 1-6 compared to Mus and Rattus. Fig. 3B. Peromyscus chromosomes 7-14 compared to Mus and Rattus. Fig. 3C. Peromyscus chromosomes 14-23 and the X compared to Mus and Rattus. The M33 locus (Vrana et al. 2000) on the Peromyscus X chromosome is not orthologous to Hprt but its sequence is found very near this gene in both Mus and Rattus.

Figure 3. Comparative relationships of the genetic map of Peromyscus with the molecular map of Rattus and Mus

For Rattus and Mus segments the numbers in parentheses indicate the molecular position at the ends of the chromosomal segment. The Rattus and Mus chromosomes are indicated in bold. Molecular locations of Mus loci come from Genome Reference Consortium Mouse Build 38 (GRCm38) and Rattus gene positions are from RGSC Genome Assembly v3.4. Fig. 3A. Peromyscus chromosomes 1-6 compared to Mus and Rattus. Fig. 3B. Peromyscus chromosomes 7-14 compared to Mus and Rattus. Fig. 3C. Peromyscus chromosomes 14-23 and the X compared to Mus and Rattus. The M33 locus (Vrana et al. 2000) on the Peromyscus X chromosome is not orthologous to Hprt but its sequence is found very near this gene in both Mus and Rattus.

Figure 3. Comparative relationships of the genetic map of Peromyscus with the molecular map of Rattus and Mus

For Rattus and Mus segments the numbers in parentheses indicate the molecular position at the ends of the chromosomal segment. The Rattus and Mus chromosomes are indicated in bold. Molecular locations of Mus loci come from Genome Reference Consortium Mouse Build 38 (GRCm38) and Rattus gene positions are from RGSC Genome Assembly v3.4. Fig. 3A. Peromyscus chromosomes 1-6 compared to Mus and Rattus. Fig. 3B. Peromyscus chromosomes 7-14 compared to Mus and Rattus. Fig. 3C. Peromyscus chromosomes 14-23 and the X compared to Mus and Rattus. The M33 locus (Vrana et al. 2000) on the Peromyscus X chromosome is not orthologous to Hprt but its sequence is found very near this gene in both Mus and Rattus.

Figure 4. Coverage of the Peromysus genetic map revealed by comparison to the Rattustus and Mus genomes

The length of the corresponding Peromyscus mapped segments containing homologous Mus or Rattus chromosomes are indicated. The vertical mark at the end of each chromosome indicates the full length of the Rattus or Mus chromosome. The numbers at the end of the linkage segments are the Peromyscus chromosomal linkage group segments in order corresponding to the Rattus or Mus chromosomes. In cases of overlap of corresponding Peromyscus linkage segments (Rattus 7, 16 and Mus 17) the number(s) before the slash represent segment(s) on the bottom and those after the slash represent the segment(s) on the top.