Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)
© Ramsdell et al; licensee BioMed Central Ltd. 2008
Received: 18 October 2007
Accepted: 26 February 2008
Published: 26 February 2008
Deer mice (Peromyscus maniculatus) and congeneric species are the most common North American mammals. They represent an emerging system for the genetic analyses of the physiological and behavioral bases of habitat adaptation. Phylogenetic evidence suggests a much more ancient divergence of Peromyscus from laboratory mice (Mus) and rats (Rattus) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest Peromyscus to be exhibit greater similarities with Rattus than with Mus.
Comparative linkage mapping of an estimated 35% of the deer mouse genome was done with respect to the Rattus and Mus genomes. We particularly focused on regions that span synteny breakpoint regions between the rat and mouse genomes. The linkage analysis revealed the Peromyscus genome to have a higher degree of synteny and gene order conservation with the Rattus genome.
These data suggest that: 1. the Rattus and Peromyscus genomes more closely represent ancestral Muroid and rodent genomes than that of Mus. 2. the high level of genome rearrangement observed in Muroid rodents is especially pronounced in Mus. 3. evolution of genome organization can operate independently of more commonly assayed measures of genetic change (e.g. SNP frequency).
The cricetid genus Peromyscus constitutes the most abundant and speciose group of North American mammals. Though superficially similar in appearance to rats and mice, deer mice represent a more distantly related lineage. Mouse and rat are thought to have diverged from each other ~10–12 million years ago (mya) while they last shared a common ancestor with the deer mouse (P. maniculatus) lineage ~25 mya . The P. maniculatus species complex is a series of semi-interfertile populations spanning nearly every habitat on the continent and is consequently an emerging tool for the study of natural mammalian genetic variation. Facilitating such research is the existence of captive stocks derived from individual populations. Utilizing two of these stocks, we have developed a comparative genomic map for the deer mouse to further research of this genus and to provide insight into the genome rearrangements seen in rats, mice, and other mammals.
Comparative genomic analyses can reveal substantial amounts of information about the biology and evolution of species and are one of the keys to deciphering the roles that genomic structure and organization play in areas such as development, gene expression, and speciation. These analyses, however, are limited to portions of the genomes that have been mapped in all the species being compared and may be compromised by uncertainty of gene orthology and order between any two species.
Although whole-genome sequences are available for many species, proper genome annotation is difficult and typically requires additional resources (e.g. meiotic linkage and radiation hybrid cell maps) . As a result, both cytogenetic methods and genetic linkage mapping are still essential tools for the analysis of genomic organization. While cytogenetic methods are effective for discerning large regions of chromosomal homology and conserved synteny, linkage maps are able to detect rearrangements of gene order within these fragments and pinpoint the locations of synteny breakpoints. Such detailed genomic comparisons require ordered linkage maps that include orthologous Type I (gene coding) loci to provide landmarks that can be identified in the genomes of multiple species. Comparative analyses using such a combined approach may reveal many more chromosomal rearrangements and novel synteny groups.
Two of the most complete mammalian genomic maps are associated with the most used biomedical models, the rat (Rattus norvegicus) and mouse (Mus musculus), which both belong to the rodent family Muridae. Rodentia is the largest mammalian order, containing > 2000 of the ~4600 recognized species and the murids constitute the majority of these . Murid genomes analyzed to date not only show more rapid nucleotide mutation rates [1, 4] but also higher rates of chromosomal rearrangement than other mammals. Murid chromosomal divergence rates are estimated to be one rearrangement per million years; ten times the rate for most mammalian genomes [5, 6]. Furthermore, such events are punctuated over time rather than having a steady-state mutation pattern . This elevated rate of rearrangement has resulted in greater karyotypic divergence between rat and mouse than between much more distantly related species (e.g., humans vs. domestic cats)  and has hampered reconstructions of ancestral rodent and mammalian genomes [9–12]. As a result, interpreting the evolutionary trajectory of chromosome segments between these model organisms and humans has proven difficult . An outgroup to the two mapped murid genomes that is less divergent than human could alleviate these problems by aiding in the construction of a more accurate ancestral rodent genome.
Here we describe the initial results of the first intermediate-density comparative genomic map for the deer mouse covering an estimated 35% of the deer mouse genome. These data suggest the deer mouse genomic organization more closely resembles that of rat than mouse, despite the much more recent common ancestor shared by the latter two species. Considered with cytogenetic data  and ancestral karyotype reconstructions [10, 12], our analysis further suggests that the deer mouse and Rattus genomes have undergone fewer large scale rearrangements than Mus.
Results and Discussion
We employed a standard backcross design for these studies utilizing P. maniculatus bairdii stock derived from Washtenaw Co. MI (BW) and P. polionotus stock derived from Ocala Nat'l forest in Florida (PO). While neither population is completely inbred, both originated from a limited number of founders and have been maintained as closed colonies. Thus, identifying fixed differences between the two (e.g., SNPs) was typically not difficult.
Markers utilized in this study, their positions in the Rattus and Mus genomes, and their source.
M. McLachlan (pers. comm.)
Our backcross panels facilitated linkage of markers at distances ranging from 1.2 cM to 35.8 cM. There are a few instances, however, where marker co-segregation occurs. These may be due to recombination "cold-spots", segmental inversions between the BW and PO strains, or simply the interval distance may be below our mapping panel resolution.
Mapping of loci from Rattus Chrs 10 and 14
To explore this possibility, we expanded the existing linkage groups using loci whose orthologs lie on Rattus Chrs 10 and 14 but are not located on Mus Chr 11 (Figure 1). For the Rattus Chr 10 homology group, we generated markers for Btbd12 and Gbl, which correspond to regions of Mus Chr 16 and 17, respectively. Single loci for each segment were sufficient because the Mus Chrs 16 and 17 segments are small and most of Rattus Chr 10 is homologous with Mus Chr 11. We found both markers to be clearly linked to the terminal locus from Rattus Chr 10, Xbp1, with very high LOD scores (>30) indicating rat genome homology. However, all three markers co-segregated. At a distance of only 1.9 Mb in the Rattus genome, these markers are likely to be closer in the deer mouse than our panel is able to resolve.
Using a similar strategy, we also expanded the Rattus Chr 14 homology group using two loci from Mus Chr 5 that have orthologs on Rattus Chr 14, Afp and Hip2. Similar to both Rattus and Mus genomes, Afp and Hip2 are linked in the deer mouse at a distance of 33.6 cM (LOD = 4.4) (Figure 1). Similar only to the Rattus genome though, we found linkage in the deer mouse between Hip2 and the Mus Chr 11 marker Xbp1 at a distance of 19.0 cM (LOD = 11.1) (Figure 1). The marker intervals for this group were larger than those of the Rattus Chr 10 markers and allowed us to map 83.0 Mb (~82%) of Rattus Chr 14 in the deer mouse with only a few markers. Our results again show a greater similarity between Peromyscus genome organization and the Rattus genome than either to the Mus genome.
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. While not comprehensive for every chromosome, this strategy accelerated our examination of chromosome evolution for the deer mouse genome and helped determine the best reference genome for future deer mouse genome mapping.
Mapping the Informative Regions of Rattus Chr 1
We next tested for linkage between the Mus Chr 17 and Mus Chr 7 homology segments of Rattus Chr 1 and found no linkage in Peromyscus between any Mus Chr 17 markers and the Mus Chr 7 marker Usp29, which is only 17.8 Mb away on Rattus Chr 1. We made no further efforts to extend the Mus Chr 7 linkage group, as Usp29 is only 5.93 Mb from the centromeric end of Mus Chr 7 and additional markers in this region were unlikely to yield a different result. We also tested for linkage between the Mus Chr 17 marker Mas1 and the Mus Chr 7 markers Usp29 and Myod1 on a PO × PO/BW backcross panel. This was to ensure that our negative linkage results were not a result of aberrant interspecific chromosomal recombination in the BW × BW/PO panel. Again, Mas1 did not link to either locus. The lack of linkage between Mus Chr 17 and Mus Chr 7 homology segments in the deer mouse genome constituted the first example of a common breakpoint between the deer mouse and Mus genomes when compared to Rattus.
Although uninformative for our comparative rearrangement analyses, we established linkage homology in the deer mouse for the large (~130 Mb) Mus Chr 7 section of Rattus Chr 1 using five markers: Usp29, Q8C5Y2, Ube3a, Rab6ip1, and H19. Althoughthe RIKEN cDNA marker Q8C5Y2 has not been accurately mapped in either Rattus or Mus, BLAST results indicated intervals between Q8C5Y2 and Usp29 at 26.4 Mb for the Rattus genome and 37.3 Mb in the Mus genome. In support of our placement, the Mus Chr 7/Rattus Chr 1 marker Ube3a co-segregated with Q8C5Y2 in the deer mouse. Our data for these five Mus Chr 7 markers showed high conservation of linkage and gene order with both Rattus and Mus genomes (Figure 2) with LOD scores all well above the 3.0 threshold. Our results for the Mus Chr 7 region were also concordant with a previous study  from which we utilized two of the same markers, Usp29 and H19.
We also found genome homology between Rattus and the deer mouse genome by markers spanning the breakpoint between the Mus Chr 7 and Chr 19 regions of Rattus Chr 1. The Mus Chr 7 marker H19 is linked to the Mus Chr 19 marker Prdx5 at a distance of 6.5 cM (LOD = 12.2). Prdx5 is also linked to a second Mus Chr 19 marker Prpf19 at a distance 4.9 cM (LOD = 13.4 cM).
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. Our results also imply that the Mus genome has been more rearranged in this region.
Breakpoint Mapping of Rattus Chr 4 and Chr 6 Loci
To broaden the scope of the deer mouse map and help reduce bias resulting from any localized phenomenon such as segmental inversions, we acquired data for markers from multiple Rattus chromosomes. Rattus Chrs 4 and 6 were priority candidates because of the simple breakpoint arrangements and well-conserved gene orders between Rattus and Mus.
The five remaining markers from Mus Chr 12 form a second linkage group in Peromyscus. Although synteny with both Rattus Chr 6 and Mus Chr 12 is conserved, we discovered an inversion with respect to both Mus and Rattus involving markers Clec14a and Pygl (Figure 4). Defining this inversion, Pygl is linked to 493504H06Rik at a distance of 4.2 cM (LOD = 9.2) while Clecl4a is linked to the more telomeric marker Pcnx at a distance of 18.2 cM (LOD = 6.3). We also found that Clec14a and Pygl have smaller distance interval at 1.3 cM (LOD = 21.2) than would have been expected from the physical intervals in Mus (11.9 Mb) and Rattus (13.4 Mb). Forming the end of the linkage group, Pcnx was linked to 1700001K19Rik at a distance of 25.3 cM (LOD = 3.9).
The spanning of two Mus genome breakpoints by the deer mouse linkage groups again indicates a more Rattus-like genome organization. However, the breakpoint between the two Peromyscus linkage groups flanked by the two Mus Chr 12 markers Allc and 493504H06Rik represents a unique rearrangement that differs from both the Rattus and Mus genomes. ZOO-FISH results from Mlynarski et al. (submitted, BMC Evolutionary Biology) also concur that Rattus Chr 6 is indeed represented by two separate chromosomes in the deer mouse.
Mapping Loci from Mus Chr 1/Rattus Chrs 5, 9, and 13
For the Rattus Chr 5 region, we detected non-segregating linkage between Oprk and Tram in the deer mouse with a strong LOD score of 20.8. To further investigate Rattus genome homology, we employed a third Rattus Chr 5 marker, Ube2j1, which is located on Mus Chr 4. Consistent with Rattus genome organization, Ube2j1 linked strongly (LOD = 23.5) but without segregation to Oprk1 and Tram1, despite a distance 35.3 Mb in the Rattus genome between Ube2j1 and Oprk1.
At the telomeric end of Mus Chr 1, we detected linkage between the Rattus Chr 13 markers Acbd3 and Glul at a distance of 21.2 cM (LOD = 9.6) and between Glul and Bcl2 at 35.8 cM (LOD = 3.8) (Figure 5). However, we did not detect linkage between Bcl2 and the Mus Chr 9 marker Fn1, as would be expected by Mus genome homology.
Mapping Loci from Mus Chr 8/Rattus Chrs 16, 17, and 19
As with the Mus Chr 1 analysis, we found linkage with highly significant LOD scores but only within the individual Rattus chromosomal groups, not between them. For the Rattus Chr 16 segment, Adam3 and Mtus1 are linked at distance of 8.4 cM (LOD = 14.8) and Mtus1 is linked to Spata4 at a distance of 16.9 cM (LOD = 9.3). Spata4 is also linked to the terminal marker 9130404D08Rik at a distance of 7.0 cM (LOD = 16.4). The two markers from Rattus Chr 19, Elmod2 and Pmfbp1, are linked 10.3 cM (LOD = 12.5).
Based on suggestions from ZOO-FISH results (Mlynarski et al., submitted BMC Evolutionary Biology), we also examined an additional chromosomal segment for linkage. Representing Rattus Chr 17 and Mus Chr 2, Sec61a2 links to the Rattus Chr 19/Mus Chr 8 marker Pmfbp1 at a distance of 30.1 cM (LOD = 3.7). This linkage indicates a clear deviation from both the Rattus and Mus genomes by the deer mouse genome and highlights the benefit of performing cytogenetic analyses in tandem with meiotic linkage mapping.
Linkage Testing of Mus Chrs 17, 5, and 13 Loci
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. No linkage was found other than that which already existed amongst the Rattus Chr 1 markers Tcp10b, Pacrg, and Mas1 (Figure 8).
We conducted a similar test for several markers from Mus Chr 5 (Figure 9). Eleven markers representing five Rattus chromosomes were tested for linkage. As in the Mus Chr 17 analysis, linkage was found only between markers located on the same Rattus chromosomes.
Two Mus Chr 13 markers, Clptml1 and Spz, also failed to show linkage despite being only about 19.6 Mb apart in the Mus genome, thus further reinforcing the linkage group disparities between the deer mouse and Mus genomes. Clptml1 is located in Rattus Chr 1 and Spz1 is on Rattus Chr 2 (Figure 10).
Genome Mapping and Genomic Evolution
Development and availability of multiple mapping tools is essential for accurate and timely exploration of any species' genome. Three methods have already been employed in mapping small portions of the deer mouse genome in the form of cytogenetics [14, 20], meiotic segregation analysis [17, 21–25], and a whole-genome radiation hybrid cell panel . These tools are most powerful when used in combination, as exemplified by Rowe et al.  for Mus and by Menotti et al.  for the cat.
Here we significantly expand the Peromyscus meiotic segregation mapping data using two P. maniculatus × P. polionotus interspecific backcross panels and present the most comprehensive comparative linkage mapping data for the deer mouse to date using Type I gene markers. In addition to providing an important genetic tool for Peromyscus research, we tested whether the deer mouse genome displayed organizational homology to that of Mus musculus, Rattus norvegicus, or a combination of both. Our results indicate a large degree of gene order and synteny conservation by the deer mouse genome with that of Rattus.
Our analysis was done by establishing linkage over approximately 35% of the deer mouse genome using gene markers that predominantly spanned junctions of large-scale genome rearrangements between the Rattus and Mus genomes. While using the Rattus genome as the reference, we tested 13 Mus genome breakpoints. Ten of the 13 breakpoints spanned by the Rattus genome were similarly linked in the deer mouse genome. In contrast, only one of 12 Rattus genome breakpoints that we examined while using the Mus genome as a reference closely coincided with any linkage breakpoints that we found in deer mouse genome. These data demonstrate that the organization of the deer mouse and Rattus genomes are more similar to each other than either is to Mus.
There are three instances, however, where the deer mouse map differs from both the Rattus and Mus maps. Two examples are located between markers Allc and 493504H06Rik (Figure 4) and between markers Col9a1 and Col3a1 (Figure 6). Approximately 21 Mb separates the latter pair in both Rattus and Mus, so additional markers will need to be applied to the deer mouse panel to better pinpoint the location of this breakpoint. The third instance is the unique deer mouse linkage of Sec61a2 to Pmfbp1. Collaborative efforts have also helped to inform, as well as confirm, some of these data using additional tools such as ZOO-FISH analyses using flow-sorted whole chromosome probes (Mlynarski et al., submitted BMC Evolutionary Biology). The strong organizational similarity of the deer mouse genome with the Rattus genome rather than the more morphologically similar Mus musculus suggests that a significant amount of rearrangement occurred in the Mus genome after the divergence of the cricetid and murid lineages. Concomitantly, our results suggest that the genomic organizations of Rattus and Peromyscus are more representative of the ancestral muroid genome than the Mus genome, which is in agreement with previous literature that indicated a higher rate of genome rearrangement for Mus [5, 6]. Most eutherian genomes have 30 to 40 blocks of homology with the human genome while the Mus genome is extraordinary with approximately 200 homology blocks. However, the Mus genome is not unique in having higher relative rearrangement rates, as the canine and gibbon genomes have approximately twice the average number of homology blocks .
Our results also show that genome rearrangement can act independently from other forms of genome evolution, such as sequence mutation. Although rodent sequence mutation rates are higher compared to other mammals, such measurements of genome evolution show Mus and Rattus shared a common ancestor significantly more recently than either have with Peromyscus. Our data does not propose to change this phylogeny but rather merely highlights that DNA sequence variation and chromosome rearrangement are independent processes and greater understanding of both processes can provide different insights into the evolution of the structure and function of the eukaryotic genome.
Development of a P. maniculatus Backcross Panel
We chose interspecific backcross analysis in order to maximize genetic polymorphism and for the ease of linkage analysis . The two species used in the cross were the deer mouse (P. maniculatus bairdii; BW) and the old field mouse (P. polionotus subgriseus; PO) and were obtained from the Peromyscus Genetic Stock Center at the University of South Carolina . We set up the initial crosses in only one direction, BW females × PO males, to generate interspecific hybrid F1's. The direction of this cross is essential, as the reciprocal cross results in lethal overgrowth of the offspring .
We created two separate backcross panels, BX116 and BX2, for the linkage analysis. For the BX116 panel, we bred twelve hybrid (plt BW × PO) F1 animals with 12 unrelated plt BW animals to generate 116 backcross progeny. Backcrosses to BW can be performed using both female and male F1 hybrid animals, as both matings will give viable offspring. However, all but one of the matings used for this panel were F1 × BW (♀ × ♂).
We used a similar strategy for the BX2 panel but the plt BW stock was substituted with wild-type BW stock. The plt allele originated in a different subspecies of P. maniculatus than the BW stock to which it was crossed. This additional backcross panel was designed to circumvent intraspecific SNP variation and possible recombination problems due to chromosomal inversions that are known to exist within some P. maniculatus sub-species.
To create the BX2 panel, we crossed four F1 males from separate unrelated ♀ BW × ♂ PO matings to non-sibling BW females, which were generated from separate matings. This resulted in four unrelated backcross families. We obtained twenty-two ♀ BW × ♂ F1 offspring from each of three of these backcross matings and 20 offspring were obtained from the fourth for a total of 86 backcross animals. These were grouped in a 96-well tray along with the eight parentals and a positive and a negative control. We employed this strategy to minimize variation within families while maximizing information between families. Similarly, the strategy of crossing F1 hybrid males with BW females minimized variation due to gender-based differences in recombination frequency.
We extracted genomic DNA from all backcross parents and progeny for the BX116 panel from 1.0 cm tail snips with the Qiagen DNEasy Tissue Kit using the manufacturers protocol (Qiagen, Inc.). Genomic DNA for the BX2 panel animals was extracted using a phenol/chloroform/isoamyl alcohol extraction method to increase yields.
We obtained primer sequences for some Type I markers from published sets of orthologous gene markers. These are termed UMPS, CATS, and TOASTs [31–33]. Primer sequences for Il23a, Mas1, H19, Sos1, and Grb10 were developed or obtained from published Peromyscus data [34–36]. Trp53 primers were developed from P. maniculatus sequence and were kindly provided by Michael McLachlan. We developed all other primers from P. maniculatus EST sequences (Weston Glenn et al., submitted BMC Genomics). Deer mouse EST clones were used for marker design because of greater PCR amplification success (>80% versus ~60% for the published sets).
We designed all the markers to be ~400 bp–1500 bp and to span an intron to increase polymorphism detection. This was done by aligning deer mouse DNA sequences to Mus musculus genomic sequences using cross-species megaBLAST (NCBI). Some critical markers however, spanned larger introns and resulted in amplicons slightly larger than the ideal size parameters.
PCR cycling conditions for all Type I markers were optimized for P. maniculatus and P. polionotus DNA using a MJ Research PTC-200 DNA Engine gradient thermal cycler and are defined as follows: 1) Standard: 95°C for 14.5 min followed by 35 cycles of (95°C for 30 s, 48–65°C for 30 s, 72°C for 30 s per 0.5 kb), 72°C for 10 min, 4°C hold. 2) Touchdown65 (TD65): 95°C for 14.5 min followed by 20 cycles of (95°C for 30 s, 65°C for 30 s minus 0.5°C/cycle for 20 cycles, 72°C for 30 s per 0.5 kb) followed by 15 cycles of (95°C for 30 s, 55°C for 30 s, 72°C for 30 s per 0.5 kb), 72°C for 10 min, 4°C hold. If no product was obtained using Touchdown65, the starting annealing temperature was changed to 60°C or 55°C, with the final annealing temperature remaining 10°C lower than the starting temperature.
PCR was performed using 20 ng of genomic DNA in a 10 μl reaction containing 1 μl 10× Qiagen HotStar buffer (1.5 mM MgCl2), 200 μM each dNTP, 0.4 μM forward primer, 0.4 μM reverse primer, and 1 unit Qiagen HotStar Taq polymerase. Some difficult templates required the use of Qiagen Q-solution at either 1× or 0.5× strength. Four markers, Sparc, Xbp1, Grb10, and Ugp2 required 2.0 mM MgCl2.
For all markers, 5 μL of each amplification product was visualized by gel electrophoresis. The remaining 5 μL portion of the PCR products was treated for sequencing with 5 units Exonuclease I and 0.75 units Shrimp Alkaline Phosphatase (SAP) and incubated at 37°C for 15 minutes followed by heat-inactivation at 80°C for 15 minutes. For sequencing reactions, 2.0μL of purified PCR product was direct sequenced with BigDye (v3.1) (ABI) on an ABI 3130 × l according to the manufacturer's protocol.
Sequence identities were verified by cross-species megaBLAST or BLASTN search to the Mus musculus genome. Any predicted simple size polymorphisms between BW and PO were tested by gel electrophoresis using amplification products from BW, PO, and BW/PO mix (equal ratio) DNAs. Markers not showing size polymorphisms were further analyzed for species-specific RFLPs by sequence comparison using Sequencher software (Gene Codes Corporation), the TCAG program available as part of the Biology Workbench software utilities provided at the San Diego Supercomputer Center , or with the SNP-RFLPing program . Candidate enzymes were chosen from those predicted by the software. RFLP tests for each marker and enzyme were conducted according to manufacturer's protocols on 10 μL PCR products from a template test panel consisting of DNA from BW, PO, a BW/PO mix (equal ratio), and a negative using only TE. All RFLP products were analyzed by gel electrophoresis. Any essential markers that could not be genotyped by either size polymorphism or RFLP were sequenced on all the backcross animals and their parents.
PCR Typing of the Backcross Panel
We tested the backcross panel parental mice with each marker prior to use on the backcross panel. We typed then typed the markers on all possible backcross animals whose parents exhibited the expected genotype. On the BX116 panel, no fewer than 73 animals were used for data to establish linkage between any two markers with exception of Gbl to Hba and Hba to Canx, of which both only used 39 animals due to the small usable data set for Hba. For the BX2 panel, no fewer than 60 animals were typed between any two markers with the exception of Mut and Col9a1, for which only 40 animals could be genotyped in common.
We performed backcross linkage analysis using Map Manager QTX software . A minimum LOD score of 3 was used to establish linkage. Ordering of markers typed on the backcross data was determined by subjecting the data to the "ripple test", which evaluated local permutations and selected the optimal order based on minimum breakage. Once linkage and gene order was established with high degree of confidence, omitted or unavailable genotypes could sometimes be inferred by Map Manager, as double crossovers between closely linked markers are rare. The procedure of inferring genotypes did not change any gene orders but typically tightened linkages slightly and raised LOD scores.
Basic Local Alignment Search Tool
Peromyscus maniculatus bairdii
Comparative Anchor Tag Sequences
distilled deionized water
ethylenediaminetetraacetic acid-disodium salt
expressed sequence tag
logarithm of the odds (to the base 10)
million years ago
New England Biolabs
polymerase chain reaction
- plt :
platinum coat-color mutation
Peromyscus polionotus subgriseus
restriction fragment length polymorphism
shrimp alkaline phosphatase
single nucleotide polymorphism
simple sequence length polymorphism
Tris-EDTA (10 mM Tris, 1 mM EDTA)
Tris-low EDTA (10 mM Tris, 0.1 mM EDTA)
traced orthologous amplified sequence tags
universal mammalian primer sequence
cross-species fluorescence in-situ hybridization
This manuscript is dedicated to Dr. Wallace D. Dawson, a pioneer in Peromyscus research. Wally led the way in recognizing and exploiting the unique potential offered by the genus to study the genetic underpinnings of mammalian biology, including speciation, habitat adaptation, and behavior. Herein is presented a continuation of his initial work developing a Peromyscus linkage map. We would also like to thank Gabor Szalai, Michael Felder, Travis Glenn, and Fernando Pardo-Manuel de Villena for their valuable comments and suggestions. Support for this work was provided by grants from the American Cancer Society (RSG-03-070-01-MGO), NSF (MCB-0517754) (PBV); UCONN Research Advisory Council, (RJO); and NSF (DEB-0344710) and NIH (P40-RR14279 and RO1-M069601), (MJD).
- Steppan SJ, Adkins RM, Anderson J: Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes. Syst Biol. 2004, 53: 533-553. 10.1080/10635150490468701.View ArticlePubMedGoogle Scholar
- Rowe LB, Barter ME, Kelmenson JA, Eppig JT: The comprehensive mouse radiation hybrid map densely cross-referenced to the recomination map: a tool to support the sequence assemblies. Genome Res. 2003, 13: 122-133. 10.1101/gr.858103.PubMed CentralView ArticlePubMedGoogle Scholar
- Wilson DE, Reeder DAM: Mammal species of the world : a taxonomic and geographic reference. 1993, Washington , Smithsonian Institution Press, xviii, 1206 p.-2ndGoogle Scholar
- Adkins RM, Gelke EL, Rowe D, Honeycutt RL: Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol Biol Evol. 2001, 18 (5): 777-791.View ArticlePubMedGoogle Scholar
- O'Brien SJ, Menotti-Raymond M, Murphy WJ, Nash WG, Wienberg J, Stanyon R, Copeland NG, Jenkins NA, Womack JE, Marshall Graves JA: The promise of comparative genomics in mammals. Science. 1999, 286 (5439): 458-62, 479-81. 10.1126/science.286.5439.458.View ArticlePubMedGoogle Scholar
- Cavagna P, Menotti A, Stanyon R: Genomic homology of the domestic ferret with cats and humans. Mamm Genome. 2000, 11 (10): 866-870. 10.1007/s003350010172.View ArticlePubMedGoogle Scholar
- Ruvinsky A, Graves JAM: Mammalian genomics. 2005, Wallingford, Oxfordshire, UK ; Cambridge, MA, USA , CABI Pub., x, 600 p.View ArticleGoogle Scholar
- Stanyon R, Yang F, Cavagna P, O'Brien PC, Bagga M, Ferguson-Smith MA, Wienberg J: Reciprocal chromosome painting shows that genomic rearrangement between rat and mouse proceeds ten times faster than between humans and cats. Cytogenet Cell Genet. 1999, 84 (3-4): 150-155. 10.1159/000015244.View ArticlePubMedGoogle Scholar
- Bourque G, Pevzner PA, Tesler G: Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res. 2004, 14 (4): 507-516. 10.1101/gr.1975204.PubMed CentralView ArticlePubMedGoogle Scholar
- Murphy WJ Larkin D. M., Everts-van der Wind A., Bourque G., Tesler G., Auvil L., Beever J. E., Chowdary B. P. Galibert F., Gatzke L., Hitte C., Meyers S. N., Milan D., Ostrander E. A., Pape G., Parker H. G., Raudsepp T., Rogatcheva M. B., Schook L. B., Skow L. C., Welge M., Womack J. E., O'Brien S. J., Pevsner P. A., Lewin H. A.: Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps. Science. 2005, 309: 613-617. 10.1126/science.1111387.View ArticlePubMedGoogle Scholar
- Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ: Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum Genomics. 2003, 1 (1): 30-40.PubMed CentralView ArticlePubMedGoogle Scholar
- Murphy WJ, Stanyon R, O'Brien SJ: Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biol. 2001, 2 (6): REVIEWS0005-10.1186/gb-2001-2-6-reviews0005.PubMed CentralView ArticlePubMedGoogle Scholar
- Pevzner P, Tesler G: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc Natl Acad Sci U S A. 2003, 100 (13): 7672-7677. 10.1073/pnas.1330369100.PubMed CentralView ArticlePubMedGoogle Scholar
- Dawson WD, Young SR, Wang Z, Liu LW, Greenbaum IF, Davis LM, Hall BK: Mus and Peromyscus chromosome homology established by FISH with three mouse paint probes. Mamm Genome. 1999, 10 (7): 730-733. 10.1007/s003359901080.View ArticlePubMedGoogle Scholar
- Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ: The Rat Genome Database, update 2007--easing the path from disease to data and back again. Nucleic Acids Res. 2007, 35 (Database issue): D658-62. 10.1093/nar/gkl988.PubMed CentralView ArticlePubMedGoogle Scholar
- Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA: The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. 2008, 36 (Database issue): D724-8.PubMed CentralPubMedGoogle Scholar
- Ramsdell CM, Thames EL, Weston JL, Dewey MJ: Development of a deer mouse whole-genome radiation hybrid panel and comparative mapping of Mus chromosome 11 loci. Mamm Genome. 2006, 17 (1): 37-48. 10.1007/s00335-005-0051-x.View ArticlePubMedGoogle Scholar
- Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O'Brien S J, Pevzner PA, Lewin HA: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 2005, 309 (5734): 613-617. 10.1126/science.1111387.View ArticlePubMedGoogle Scholar
- Loschiavo M, Nguyen QK, Duselis AR, Vrana PB: Mapping and identification of candidate loci responsible for Peromyscus hybrid overgrowth. Mamm Genome. 2007, 18 (1): 75-85. 10.1007/s00335-006-0083-x.PubMed CentralView ArticlePubMedGoogle Scholar
- Wang Z, Young SR, Liu L, Dawson WD: Assignment of Tp53 and Tk1 to chromosome 13 in Peromyscus by fluorescence in situ hybridization. Cytogenet Cell Genet. 1995, 69 (1-2): 97-100.View ArticlePubMedGoogle Scholar
- Bowen WW, Dawson WD: Genetic analysis of coat pattern variation in oldfield mice (Peromyscus polionotus) of western Florida. Journal of Mammalogy. 1977, 58: 521-530. 10.2307/1380000.View ArticleGoogle Scholar
- Dawson WD: Protein polymorphisms in American deermice (Peromyscus) and genetic linkage homology. Acta Theriologica. 1982, 16: 213-230.View ArticleGoogle Scholar
- Dawson WD, Huang LL, Felder MR, Shaffer JB: Linkage relationships among eleven biochemical loci in Peromyscus. Biochem Genet. 1983, 21 (11-12): 1101-1114. 10.1007/BF00488462.View ArticlePubMedGoogle Scholar
- Robinson R: Linkage in Peromyscus. J Hered. 1964, 19: 701-709.View ArticleGoogle Scholar
- Snyder LR: Evolutionary conservation of linkage groups: additional evidence from murid and cricetid rodents. Biochem Genet. 1980, 18 (3-4): 209-220. 10.1007/BF00484237.View ArticlePubMedGoogle Scholar
- Menotti-Raymond M, David VA, Roelke ME, Chen ZQ, Menotti KA, Sun S, Schaffer AA, Tomlin JF, Agarwala R, O'Brien SJ, Murphy WJ: Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus). J Hered. 2003, 94 (1): 95-106. 10.1093/jhered/esg008.View ArticlePubMedGoogle Scholar
- Ferguson-Smith MA, Trifonov V: Mammalian karyotype evolution. Nat Rev Genet. 2007, 8 (12): 950-962. 10.1038/nrg2199.View ArticlePubMedGoogle Scholar
- Copeland NG, Jenkins NA: Development and applications of a molecular genetic linkage map of the mouse genome. Trends Genet. 1991, 7 (4): 113-118. 10.1016/0168-9525(91)90455-Y.View ArticlePubMedGoogle Scholar
- Peromyscus Genetic Stock Center. [http://stkctr.biol.sc.edu/]
- Dawson WD: Fertility and size inheritance in a Peromyscus species cross. Evolution. 1965, 19: 44-55. 10.2307/2406294.View ArticleGoogle Scholar
- Venta PJ, Brouillette JA, Yuzbasiyan-Gurkan V, Brewer GJ: Gene-specific universal mammalian sequence-tagged sites: application to the canine genome. Biochem Genet. 1996, 34 (7-8): 321-341. 10.1007/BF02399951.View ArticlePubMedGoogle Scholar
- Lyons LA, Laughlin TF, Copeland NG, Jenkins NA, Womack JE, O'Brien SJ: Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nat Genet. 1997, 15: 47-56. 10.1038/ng0197-47.View ArticlePubMedGoogle Scholar
- Jiang Z, Priat C, Galibert F: Traced orthologous amplified sequence tags (TOASTS) and mammalian comparative maps. Mamm Genome. 1998, 9: 577-578. 10.1007/s003359900821.View ArticlePubMedGoogle Scholar
- Schountz T, Green R, Davenport B, Buniger A, Richens T, Root JJ, Davidson F, Calisher CH, Beaty BJ: Cloning and characterization of deer mouse (Peromyscus maniculatus) cytokine and chemokine cDNAs. BMC Immunol. 2004, 5: 1-10.1186/1471-2172-5-1.PubMed CentralView ArticlePubMedGoogle Scholar
- Vrana PB, Fossella JA, Matteson P, del Rio T, O'Neill MJ, Tilghman SM: Genetic and epigenetic incompatibilities underlie hybrid dysgenesis in Peromyscus. Nat Genet. 2000, 25 (1): 120-124. 10.1038/75518.View ArticlePubMedGoogle Scholar
- Vrana PB, Guan XJ, Ingram RS, Tilghman SM: Genomic imprinting is disrupted in interspecific Peromyscus hybrids [see comments] [published erratum appears in Nat Genet 1999 Feb;21(2):241]. Nat Genet. 1998, 20 (4): 362-365. 10.1038/3833.View ArticlePubMedGoogle Scholar
- Biology Workbench. [http://workbench.sdsc.edu]
- Chang HW, Yang CH, Chang PL, Cheng YH, Chuang LY: SNP-RFLPing: restriction enzyme mining for SNPs in genomes. BMC Genomics. 2006, 7: 30-10.1186/1471-2164-7-30.PubMed CentralView ArticlePubMedGoogle Scholar
- Manly KF, Cudmore RH, Meer JM: Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome. 2001, 12 (12): 930-932. 10.1007/s00335-001-1016-3.View ArticlePubMedGoogle Scholar
- Duselis AR, Wiley CD, O'Neill MJ, Vrana PB: Genetic evidence for a maternal effect locus controlling genomic imprinting and growth. Genesis. 2005, 43 (4): 155-165. 10.1002/gene.20166.View ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.