Physical and Radiation Hybrid Mapping of Canine Chromosome 12, in a Region Corresponding to Human Chromosome 6p12–q12 Robin Li,* Juliette H. Faraco,* Ling Lin,* Xiaoyan Lin,* Linda Hinton,* William Rogers,* Jennifer K. Lowe,² , ‡ Elaine A. Ostrander,‡ and Emmanuel Mignot * ,1 * Stanford Center for Narcolepsy Research, 1201 Welch Road, Room P-114, Stanford, California 94305-5485; ² Molecular and Cellular Biology Program, University of Washington, Seattle, Box 357275, Seattle, Washington 98195; and ‡Human Biology Division and Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., D4-100, Seattle, Washington 98109-1024 Received October 11, 2000; accepted December 27, 2000 The positional cloning of the hypocretin receptor 2, the gene for autosomal recessive canine narcolepsy, has led to the development of a physical map spanning a large portion of canine chromosome 12 (CFA12), in a region corresponding to human chromosome 6p12– q13. More than 40 expressed sequence tags (ESTs) were used in homology search experiments, together with chromosome walking, to build both physical and radiation hybrid maps of the CFA12 13–21 region. The resulting map of bacterial artificial chromosome ends, ESTs, and microsatellite markers represents the long- est continuous high-density map of the dog genome reported to date. These data further establish the dog as a system for studying disease genes of interest to human populations and highlight feasible approaches for positional cloning of disease genes in organisms where genomic resources are limited. © 2001 Academic Press INTRODUCTION Mapping human disease susceptibility genes is gen- erally a laborious and expensive task, largely reflecting inherent limitations in the structure of human families such as small size, long generation time, and with a few isolated exceptions, the outbred nature of the spe- cies. Mapping may be further complicated by the fact that for many common diseases, such as cancer, diabe- tes, and heart disease, a high frequency of phenocopies exists in the population, which confounds linkage re- sults and complicates analyses. We and others have proposed, therefore, that map- ping of disease genes is best performed in an animal model where large families can be generated, directed matings are possible, multiple generations are easily collected, and because of the shorter life span, clinical symptoms often manifest in relatively short periods of time (Ostrander et al., 2000; Ostrander and Kruglyak, 2000; Patterson et al., 1982; Galibert et al., 1998). In this regard the domestic dog offers unique opportuni- ties. There are over 50 million dogs in the United States alone (Troutman, 1988). This population pro- vides a large reservoir of naturally occurring disease mutations, most of which are not currently studied at the molecular level. The segmentation of the species into over 300 genetically isolated populations, called breeds, favors genetic analysis of both wildtype and pathological traits (Ostrander et al., 2000). Until recently, our ability to use the canine system for disease gene mapping has been retarded by a lack of available genomic infrastructure for the dog. This situation is changing rapidly. Both meiotic linkage and radiation hybrid (RH) maps of the dog have been de- veloped (Mellersh et al., 1997; Priat et al., 1998; Neff et al., 1999; Werner et al., 1999). The most recent pub- lished version of the map, which integrates the meiotic linkage and RH maps, has 724 unique markers, of which 600 are ordered on the RH map and 341 are on the meiotic linkage map (Mellersh et al., 2000). The RH map places a marker, on average, every 24.3 cR 5000 (2.4 Mb) and provides theoretical coverage of the complete 2700-cM canine genome. A total of 218 genes have thus far been ordered on the 600-marker RH map and have proven valuable for orienting the canine genome to the corresponding parts of the human genome. Our knowl- edge of the relationship between the human and the dog genomes has been further enhanced by the appli- cation of whole-chromosome paint probes, produced from degenerate oligonucleotide-primed PCR amplifi- cation of flow-sorted human and dog chromosomes (Breen et al., 1999; Yang et al., 1999a). Using one set of such paints, 68 evolutionarily conserved segments have been identified between the dog and the human genomes (Breen et al., 1999). All canine chromosome arms are now assigned to human chromosome regions with the specific results confirmed by reciprocal paint- ing studies (Breen et al., 1999; Yang et al., 1999a). The ability to correlate a critical region of linkage, defined 1 To whom correspondence should be addressed. Telephone: (650) 725-6516. Fax: (650) 498-7761. E-mail: mignot@Leland.stanford.edu. Genomics 73, 299 –315 (2001) doi:10.1006/geno.2000.6487, available online at http://www.idealibrary.com on 299 0888-7543/01 $35.00 Copyright © 2001 by Academic Press All rights of reproduction in any form reserved.