doi:10.1111/j.1365-2052.2005.01401.x Construction of a medium-density horse gene map M. Perrocheau*, V. Boutreux*, S. Chadi*, X. Mata*, P. Decaunes*, T. Raudsepp † , K. Durkin † , D. Incarnato ‡ , L. Iannuzzi ‡ , T. L. Lear § , K. Hirota ¶ , T. Hasegawa ** , B. Zhu †† , P. de Jong †† , E. P. Cribiu*, B. P. Chowdhary † and G. Gue ´ rin* *De ´ partement de Ge ´ ne ´ tique animale, Laboratoire de Ge ´ ne ´ tique biochimique et de Cytoge ´ ne ´ tique, Centre de Recherches de Jouy, INRA, 78350, Jouy-en-Josas, France. † Department of Veterinary Anatomy & Public Health, College of Veterinary Medicine, Texas A&M University, College Station TX-77843, USA. ‡ Laboratory of Animal Cytogenetics and Gene Mapping, National Research Council (CNR), ISPAAM, Naples, Italy. § Department of Veterinary Science, M.H. Gluck Equine Research Center, University of Kentucky Lexington, KY 40546-0099, USA. ¶ Department of Molecular Genetics, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi 320-0851, Japan. **Laboratory of Molecular and Cellular Biology Equine Research Institute Japan Racing Association, 321-4 Tokami-Cho, Utsunomiya, Tochigi 320-0856, Japan. †† BACPAC Resources, Children’s Hospital Oakland Research Institute, Oakland, 747 52nd St, CA 947609 USA Summary A medium-density map of the horse genome (Equus caballus) was constructed using genes evenly distributed over the human genome. Three hundred and twenty-three exonic primer pairs were used to screen the INRA and the CHORI-241 equine BAC libraries by polymerase chain reaction and by filter hybridization respectively. Two hundred and thirty-seven BACs containing equine gene orthologues, confirmed by sequencing, were isolated. The BACs were localized to horse chromosomes by fluorescent in situ hybridization (FISH). Overall, 165 genes were assigned to the equine genomic map by radiation hybrid (RH) (using an equine RH 5000 panel) and/or by FISH mapping. A comparison of localizations of 713 genes mapped on the horse genome and on the human genome revealed 59 homologous seg- ments and 131 conserved segments. Two of these homologies (ECA27/HSA8 and ECA12p/ HSA11p) had not been previously identified. An enhanced resolution of conserved and rearranged chromosomal segments presented in this study provides clarification of chro- mosome evolution history. Keywords comparative mapping, gene mapping, horse. Introduction Genome mapping in domestic animals is used to reveal the structure and evolution of the genome and to identify markers for genes of interest that might be used in selection. Construction of genetic linkage maps for the horse (Equus caballus) was initiated using anonymous microsatellite markers (Gue ´rin et al. 2003; Penedo et al. 2005), but these maps did not allow for interspecific comparisons except for a few microsatellite-flanking sequences (Farber & Medrano 2004). A major step towards comparative mapping oc- curred with chromosome painting of human chromosomes on the equine karyotype (Raudsepp et al. 1996). Further refinement of the horse–human comparative map occurred through the localization of genes using somatic cell hybrids (SCH) and by radiation hybrid (RH) and cytogenetic (FISH) mapping (Shiue et al. 1999; Milenkovic et al. 2002; Chowdhary et al. 2003). A likely comparative evolution of chromosomes in mammals from a common ancestor was first described by Chowdhary et al. (1998), who used chromosome painting data from eight species belonging to five different orders. Comparisons across species have also been performed with genes mapped to specific locations (Milenkovic et al. 2002; Chowdhary et al. 2003; Gustafson-Seabury et al. 2005). Dense gene maps covering the entire horse genome are still needed, but once available, these will allow for a general comparison of genomes (Murphy et al. 2005). Specific algo- rithms for studying mammalian chromosome evolution are Address for correspondence G. Gue ´ rin, Laboratoire de Ge ´ ne ´ tique biochimique et de Cytoge ´ ne ´ tique, De ´ partement de Ge ´ ne ´ tique animale, INRA, Centre de Recherches de Jouy, 78350, Jouy-en-Josas, France. Email: gerard.guerin@jouy.inra.fr Accepted for publication 29 October 2005 Ó 2006 The Authors, Journal compilation Ó 2006 International Society for Animal Genetics, Animal Genetics, 37, 145–155 145