A new standard genetic map for the laboratory mouse - PubMed (original) (raw)
. 2009 Aug;182(4):1335-44.
doi: 10.1534/genetics.109.105486. Epub 2009 Jun 17.
Cheryl L Ackert-Bicknell, Beth L Dumont, Yueming Ding, Jordana Tzenova Bell, Gudrun A Brockmann, Jon E Wergedal, Carol Bult, Beverly Paigen, Jonathan Flint, Shirng-Wern Tsaih, Gary A Churchill, Karl W Broman
Affiliations
- PMID: 19535546
- PMCID: PMC2728870
- DOI: 10.1534/genetics.109.105486
A new standard genetic map for the laboratory mouse
Allison Cox et al. Genetics. 2009 Aug.
Abstract
Genetic maps provide a means to estimate the probability of the co-inheritance of linked loci as they are transmitted across generations in both experimental and natural populations. However, in the age of whole-genome sequences, physical distances measured in base pairs of DNA provide the standard coordinates for navigating the myriad features of genomes. Although genetic and physical maps are colinear, there are well-characterized and sometimes dramatic heterogeneities in the average frequency of meiotic recombination events that occur along the physical extent of chromosomes. There also are documented differences in the recombination landscape between the two sexes. We have revisited high-resolution genetic map data from a large heterogeneous mouse population and have constructed a revised genetic map of the mouse genome, incorporating 10,195 single nucleotide polymorphisms using a set of 47 families comprising 3546 meioses. The revised map provides a different picture of recombination in the mouse from that reported previously. We have further integrated the genetic and physical maps of the genome and incorporated SSLP markers from other genetic maps into this new framework. We demonstrate that utilization of the revised genetic map improves QTL mapping, partially due to the resolution of previously undetected errors in marker ordering along the chromosome.
Figures
Figure 1.—
Comparison of the original and revised genetics maps. Sex-averaged recombination rates (A) and sex-specific recombination rates (B) for the original and revised genetic maps of chromosome 1. Maps are based on data from S
hifman
et al. (2006) as described in
materials and methods
. Figures showing all chromosomes can be found in
Figure S1
.
Figure 2.—
Cumulative genetic maps of chromosome 1. Dotted lines show the original Shifman map; solid lines are from the revised Shifman map. Female, male, and sex-averaged maps are shown in red, blue, and black, respectively. See
Figure S2
for the cumulative maps for each chromosome.
Figure 3.—
Physical and genetic positions of markers. Genetic marker positions (in centimorgans) are plotted against their physical positions (in megabases) for the MGI genetic map (red) and the revised Shifman map (black). Marker-ordering errors in the MGI map are indicated by non-monotone fluctuations. In contrast, the curves for the revised map are smooth and monotone.
Figure 4.—
QTL With changes in peak shape. Seven QTL were found where the peak shape was altered due to subtle differences between the original and the revised Shifman maps. (A) The QTL for femoral BMD on chromosome 12 in the NZBxRF cross appears as a double peak when analyzed using the Mouse Genome Database (MGD)/traditional genetic map (dashed line), suggesting the presence of two closely linked QTL. When reanalyzed using the new genetic map, this double peak is collapsed into a single peak (solid line). (B) This double peak is the result of two flipped neighboring markers. Seven markers were typed in this cross for chromosome 12. The markers are placed on the centimorgan scale (center line) in relation to the MGD/traditional map (left) and the new genetic map (right). Note the difference in spacing of the markers when comparing the two maps. The other QTL with a change in peak shape were found for: (C) B6xCAST on chromosome 2, (D) B6xC3H on chromosome 2 for vBMD, (E) NZBxRF on chromosome 4 for vBMD, (F) B6xCAST on chromosome 14, (G) B6xCAST on chromosome 18, and (H) NZBxSM on chromosome 19.
Similar articles
- A High-Resolution Genetic Map for the Laboratory Rat.
Littrell J, Tsaih SW, Baud A, Rastas P, Solberg-Woods L, Flister MJ. Littrell J, et al. G3 (Bethesda). 2018 Jul 2;8(7):2241-2248. doi: 10.1534/g3.118.200187. G3 (Bethesda). 2018. PMID: 29760201 Free PMC article. - Linkage mapping bovine EST-based SNP.
Snelling WM, Casas E, Stone RT, Keele JW, Harhay GP, Bennett GL, Smith TP. Snelling WM, et al. BMC Genomics. 2005 May 19;6:74. doi: 10.1186/1471-2164-6-74. BMC Genomics. 2005. PMID: 15943875 Free PMC article. - An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus).
Ren Y, McGregor C, Zhang Y, Gong G, Zhang H, Guo S, Sun H, Cai W, Zhang J, Xu Y. Ren Y, et al. BMC Plant Biol. 2014 Jan 20;14:33. doi: 10.1186/1471-2229-14-33. BMC Plant Biol. 2014. PMID: 24443961 Free PMC article. - Genetic, physical, and comparative map of the subtelomeric region of mouse Chromosome 4.
Li X, Bachmanov AA, Li S, Chen Z, Tordoff MG, Beauchamp GK, de Jong PJ, Wu C, Chen L, West DB, Ross DA, Ohmen JD, Reed DR. Li X, et al. Mamm Genome. 2002 Jan;13(1):5-19. doi: 10.1007/s0033501-2109-8. Mamm Genome. 2002. PMID: 11773963 Free PMC article. Review. - QTL mapping using high-throughput sequencing.
Jamann TM, Balint-Kurti PJ, Holland JB. Jamann TM, et al. Methods Mol Biol. 2015;1284:257-85. doi: 10.1007/978-1-4939-2444-8_13. Methods Mol Biol. 2015. PMID: 25757777 Review.
Cited by
- Genetic background affects the strength of crossover interference in house mice.
Morgan AP, Payseur BA. Morgan AP, et al. bioRxiv [Preprint]. 2024 Aug 6:2024.05.28.596233. doi: 10.1101/2024.05.28.596233. bioRxiv. 2024. PMID: 38854148 Free PMC article. Updated. Preprint. - Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques (Macaca mulatta).
Versoza CJ, Weiss S, Johal R, La Rosa B, Jensen JD, Pfeifer SP. Versoza CJ, et al. Genome Biol Evol. 2024 Jan 5;16(1):evad223. doi: 10.1093/gbe/evad223. Genome Biol Evol. 2024. PMID: 38051960 Free PMC article. - Identification of Genomic Regions Implicated in Susceptibility to Schistosoma mansoni Infection in a Murine Backcross Genetic Model.
Hernández-Goenaga J, López-Abán J, Blanco-Gómez A, Vicente B, Burguillo FJ, Pérez-Losada J, Muro A. Hernández-Goenaga J, et al. Int J Mol Sci. 2023 Sep 30;24(19):14768. doi: 10.3390/ijms241914768. Int J Mol Sci. 2023. PMID: 37834216 Free PMC article. - Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models.
Soni V, Johri P, Jensen JD. Soni V, et al. bioRxiv [Preprint]. 2023 Jun 15:2023.06.15.545166. doi: 10.1101/2023.06.15.545166. bioRxiv. 2023. PMID: 37398347 Free PMC article. Updated. Preprint. - Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models.
Soni V, Johri P, Jensen JD. Soni V, et al. Evolution. 2023 Oct 3;77(10):2113-2127. doi: 10.1093/evolut/qpad120. Evolution. 2023. PMID: 37395482 Free PMC article.
References
- Chromosome Committee, 2000. Reports for the Mouse Genome. Mamm. Genome 11 943–960. - PubMed
- Beamer, W., K. L. Shultz, G. A. Churchill, W. Frankel, D. J. Baylink et al., 1999. Quantitative trait loci for bone density in C57BL/6J and CAST/EiJ. Mamm. Genome 10 1043–1049. - PubMed
- Beamer, W. G., K. L. Shultz, L. R. Donahue, G. Churchill, S. Sen et al., 2001. Quantitative trait loci for femoral and lumbar vertebral bone mineral density in C57BL/6J and C3H/HeJ inbred strains of mice. J. Bone Miner. Res. 16 1195–1206. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
- T32 HD007065/HD/NICHD NIH HHS/United States
- HL077796/HL/NHLBI NIH HHS/United States
- P30 CA034196/CA/NCI NIH HHS/United States
- R21 AR053992/AR/NIAMS NIH HHS/United States
- 5T32HD07065/HD/NICHD NIH HHS/United States
- GM074244/GM/NIGMS NIH HHS/United States
- CA34196/CA/NCI NIH HHS/United States
- R01 HL077796/HL/NHLBI NIH HHS/United States
- R01 GM074244/GM/NIGMS NIH HHS/United States
- 079912/WT_/Wellcome Trust/United Kingdom
- GM070683/GM/NIGMS NIH HHS/United States
- AR053992/AR/NIAMS NIH HHS/United States
- GM076468/GM/NIGMS NIH HHS/United States
- R37 HL077796/HL/NHLBI NIH HHS/United States
- P50 GM076468/GM/NIGMS NIH HHS/United States
- R01 GM070683/GM/NIGMS NIH HHS/United States
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases