Genetic, physical, and comparative map of the subtelomeric region of mouse Chromosome 4
- PMID: 11773963
- PMCID: PMC1994206
- DOI: 10.1007/s0033501-2109-8
Genetic, physical, and comparative map of the subtelomeric region of mouse Chromosome 4
Abstract
The subtelomeric region of mouse chromosome (Chr) 4 harbors loci with effects on behavior, development, and disease susceptibility. Regions near the telomeres are more difficult to map and characterize than other areas because of the unique features of subtelomeric DNA. As a result of these problems, the available mapping information for this part of mouse Chr 4 was insufficient to pursue candidate gene evaluation. Therefore, we sought to characterize the area in greater detail by creating a comprehensive genetic, physical, and comparative map. We constructed a genetic map that contained 30 markers and covered 13.3 cM; then we created a 1.2-Mb sequence-ready BAC contig, representing a 5.1-cM area, and sequenced a 246-kb mouse BAC from this contig. The resulting sequence, as well as approximately 40 kb of previously deposited genomic sequence, yielded a total of 284 kb of sequence, which contained over 20 putative genes. These putative genes were confirmed by matching ESTs or cDNA in the public databases to the genomic sequence and/or by direct sequencing of cDNA. Comparative genome sequence analysis demonstrated conserved synteny between the mouse and the human genomes (1p36.3). DNA from two strains of mice (C57BL/6ByJ and 129P3/J) was sequenced to detect single nucleotide polymorphisms (SNPs). The frequency of SNPs in this region was more than threefold higher than the genome-wide average for comparable mouse strains (129/Sv and C57BL/6J). The resulting SNP map, in conjunction with the sequence annotation and with physical and genetic maps, provides a detailed description of this gene-rich region. These data will facilitate genetic and comparative mapping studies and identification of a large number of novel candidate genes for the trait loci mapped to this region.
Figures
![Fig. 1](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/1994206/bin/nihms26596f1.gif)
![Fig. 2](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/1994206/bin/nihms26596f2.gif)
![Fig. 3](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/1994206/bin/nihms26596f3a.gif)
![Fig. 3](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/1994206/bin/nihms26596f3a.gif)
![Fig. 3](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/1994206/bin/nihms26596f3a.gif)
Similar articles
-
Generation of a 5.5-Mb BAC/PAC contig of pig chromosome 6q1.2 and its integration with existing RH, genetic and comparative maps.Cytogenet Genome Res. 2003;102(1-4):116-20. doi: 10.1159/000075735. Cytogenet Genome Res. 2003. PMID: 14970689
-
A sequence-ready BAC contig of the GABAA receptor gene cluster Gabrg1-Gabra2-Gabrb1 on mouse chromosome 5.Genome Res. 1999 Aug;9(8):732-8. Genome Res. 1999. PMID: 10447508 Free PMC article.
-
Congenic mapping of the type 1 diabetes locus, Idd3, to a 780-kb region of mouse chromosome 3: identification of a candidate segment of ancestral DNA by haplotype mapping.Genome Res. 2000 Apr;10(4):446-53. doi: 10.1101/gr.10.4.446. Genome Res. 2000. PMID: 10779485 Free PMC article.
-
The Human Genome Project--an overview.Med Res Rev. 2000 May;20(3):189-96. doi: 10.1002/(sici)1098-1128(200005)20:3<189::aid-med2>3.0.co;2-#. Med Res Rev. 2000. PMID: 10797463 Review.
-
The horse genome derby: racing from map to whole genome sequence.Chromosome Res. 2008;16(1):109-27. doi: 10.1007/s10577-008-1204-z. Chromosome Res. 2008. PMID: 18274866 Review.
Cited by
-
Genetic controls of Tas1r3-independent sucrose consumption in mice.Mamm Genome. 2021 Apr;32(2):70-93. doi: 10.1007/s00335-021-09860-w. Epub 2021 Mar 12. Mamm Genome. 2021. PMID: 33710367
-
Genetics of Amino Acid Taste and Appetite.Adv Nutr. 2016 Jul 15;7(4):806S-22S. doi: 10.3945/an.115.011270. Print 2016 Jul. Adv Nutr. 2016. PMID: 27422518 Free PMC article. Review.
-
Genetics of taste receptors.Curr Pharm Des. 2014;20(16):2669-83. doi: 10.2174/13816128113199990566. Curr Pharm Des. 2014. PMID: 23886383 Free PMC article. Review.
-
Genetics of sweet taste preferences.Flavour Fragr J. 2011 Jul;26(4):286-294. doi: 10.1002/ffj.2074. Flavour Fragr J. 2011. PMID: 21743773 Free PMC article.
-
Behavioral discrimination between sucrose and other natural sweeteners in mice: implications for the neural coding of T1R ligands.J Neurosci. 2007 Oct 17;27(42):11242-53. doi: 10.1523/JNEUROSCI.1227-07.2007. J Neurosci. 2007. PMID: 17942718 Free PMC article.
References
-
- Belknap JK, Crabbe JC, Plomin R, McClearn GE, Sampson KE, et al. Single-locus control of saccharin intake in BXD/Ty recombinant inbred (RI) mice: some methodological implications for RI strain analysis. Behav Genet. 1992;22:81–100. - PubMed
Publication types
MeSH terms
Substances
Associated data
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
- Actions
Grants and funding
- R01AA11028/AA/NIAAA NIH HHS/United States
- R01DC00882/DC/NIDCD NIH HHS/United States
- R03 DC003509-04/DC/NIDCD NIH HHS/United States
- R01DC04188/DC/NIDCD NIH HHS/United States
- R03 DC003854-02/DC/NIDCD NIH HHS/United States
- R01 DK058797/DK/NIDDK NIH HHS/United States
- R01 DK55853/DK/NIDDK NIH HHS/United States
- R01 AA011028/AA/NIAAA NIH HHS/United States
- R01 AA011028-08/AA/NIAAA NIH HHS/United States
- R01 DC000882/DC/NIDCD NIH HHS/United States
- R01 DC000882-24/DC/NIDCD NIH HHS/United States
- R01 DK058797-07/DK/NIDDK NIH HHS/United States
- R03DC03509/DC/NIDCD NIH HHS/United States
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases
Research Materials
Miscellaneous