Mammalian Genome

, Volume 13, Issue 1, pp 5–19

Genetic, physical, and comparative map of the subtelomeric region of mouse Chromosome 4

  • Xia Li
  • Alexander A. Bachmanov
  • Shanru Li
  • Zhenyu Chen
  • Michael G. Tordoff
  • Gary K. Beauchamp
  • Pieter J. de Jong
  • Chenyan Wu
  • Lianchun Chen
  • David B. West
  • David A. Ross
  • Jeffery D. Ohmen
  • Danielle R. Reed
Article

DOI: 10.1007/s0033501-2109-8

Cite this article as:
Li, X., Bachmanov, A.A., Li, S. et al. Mammalian Genome (2002) 13: 5. doi:10.1007/s0033501-2109-8

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.

Copyright information

© Springer-Verlag New York Inc. 2002

Authors and Affiliations

  • Xia Li
    • 1
  • Alexander A. Bachmanov
    • 1
  • Shanru Li
    • 1
  • Zhenyu Chen
    • 1
  • Michael G. Tordoff
    • 1
  • Gary K. Beauchamp
    • 1
  • Pieter J. de Jong
    • 3
  • Chenyan Wu
    • 4
  • Lianchun Chen
    • 4
  • David B. West
    • 4
  • David A. Ross
    • 4
  • Jeffery D. Ohmen
    • 4
  • Danielle R. Reed
  1. 1.Monell Chemical Senses Center, 3500 Market Street, Philadelphia, Pennsylvania 19104, USAUSA
  2. 2.University of Pennsylvania, Philadelphia, Pennsylvania 19104, USAUSA
  3. 3.Children's Hospital Oakland Research Institute, Oakland, California 94609, USAUSA
  4. 4.Pfizer Global Research and Development, Alameda, California 94502, USAUSA