A comprehensive second-generation whole genome radiation hybrid (RH II), cytogenetic and comparative map of the horse genome (2n = 64) has been developed using the 5000rad horse × hamster radiation hybrid panel and fluorescence in situ hybridization (FISH). The map contains 4,103 markers (3,816 RH; 1,144 FISH) assigned to all 31 pairs of autosomes and the X chromosome. The RH maps of individual chromosomes are anchored and oriented using 857 cytogenetic markers. The overall resolution of the map is one marker per 775 kilobase pairs (kb), which represents a more than five-fold improvement over the first-generation map. The RH II incorporates 920 markers shared jointly with the two recently reported meiotic maps. Consequently the two maps were aligned with the RH II maps of individual autosomes and the X chromosome. Additionally, a comparative map of the horse genome was generated by connecting 1,904 loci on the horse map with genome sequences available for eight diverse vertebrates to highlight regions of evolutionarily conserved syntenies, linkages, and chromosomal breakpoints. The integrated map thus obtained presents the most comprehensive information on the physical and comparative organization of the equine genome and will assist future assemblies of whole genome BAC fingerprint maps and the genome sequence. It will also serve as a tool to identify genes governing health, disease and performance traits in horses and assist us in understanding the evolution of the equine genome in relation to other species.

1.
Agarwala R, Applegate DL, Maglott D, Schuler GD, Schäffer AA: A fast and scalable radiation hybrid map construction and integration strategy. Genome Res 10:350–364 (2000).
2.
Applegate DL, Bixby R, Chvátal V, Cook WJ: The Traveling Salesman Problem: A Computational Study (Princeton University Press, New Jersey 2006).
3.
Breen M, Hitte C, Lorentzen TD, Thomas R, Cadieu E, et al: An integrated 4249 marker FISH/RH map of the canine genome. BMC Genomics 5:65 (2004).
4.
Brinkmeyer-Langford C, Raudsepp T, Lee EJ, Goh G, Schäffer AA, et al: A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals. Mamm Genome 16:631–649 (2005).
5.
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al: Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497–3500 (2003).
6.
Chowdhary BP, Raudsepp T: The Horse Genome Derby: racing from map to whole genome sequence. Chromosome Res 16:109–127 (2008).
7.
Chowdhary BP, Raudsepp T, Honeycutt D, Owens EK, Piumi F, et al: Construction of a 5000rad whole-genome radiation hybrid panel in the horse and generation of a comprehensive and comparative map for ECA11. Mamm Genome 13:89–94 (2002).
8.
Chowdhary BP, Raudsepp T, Kata SR, Goh G, Millon LV, et al: The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res 13:742–751 (2003).
9.
Dierks C, Mömke S, Drögemuller C, Leeb T, Chowdhary BP, Distl O: A high-resolution comparative radiation hybrid map of equine chromosome 4q12-q22. Anim Genet 37:513–517 (2006).
10.
Everts-van der Wind A, Kata SR, Band MR, Rebeiz M, Larkin DM, et al: A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Res 14:1424–1437 (2004).
11.
Everts-van der Wind A, Larkin DM, Green CA, Elliott JS, Olmstead CA, et al: A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci USA 102:18526–18531 (2005).
12.
Godard S, Vaiman A, Schibler L, Mariat D, Vaiman D, et al: Cytogenetic localization of 44 new coding sequences in the horse. Mamm Genome 11:1093–1097 (2000).
13.
Goh G, Raudsepp T, Durkin K, Wagner ML, Schäffer AA, et al: High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals. Genomics 89:89–112 (2007).
14.
Gustafson-Seabury A, Raudsepp T, Goh G, Kata SR, Wagner ML, et al: High-resolution RH map of horse chromosome 22 reveals a putative ancestral vertebrate chromosome. Genomics 85:188–200 (2005).
15.
Hamasima N, Suzuki H, Mikawa A, Morozumi T, Plastow G, Mitsuhashi T: Construction of a new porcine whole-genome framework map using a radiation hybrid panel. Anim Genet 34:216–220 (2003).
16.
Itoh T, Watanabe T, Ihara N, Mariani P, Beattie CW, et al: A comprehensive radiation hybrid map of the bovine genome comprising 5593 loci. Genomics 85:413–424 (2005).
17.
Jann OC, Aerts J, Jones M, Hastings N, Law A, et al: A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics 7:283 (2006).
18.
Kehrer-Sawatzki H, Sandig C, Chuzhanova N, Goidts V, Szamalek JM, et al: Breakpoint analysis of the pericentric inversion distinguishing human chromosome 4 from the homologous chromosome in the chimpanzee (Pan troglodytes). Hum Mutat 25:45–55 (2005a).
19.
Kehrer-Sawatzki H, Sandig CA, Goidts V, Hameister H: Breakpoint analysis of the pericentric inversion between chimpanzee chromosome 10 and the homologous chromosome 12 in humans. Cytogenet Genome Res 108:91–97 (2005b).
20.
Kwitek AE, Gullings-Handley J, Yu J, Carlos DC, Orlebeke K, et al: High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Genome Res 14:750–757 (2004).
21.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al: Initial sequencing and analysis of the human genome. Nature 409:860–921 (2001).
22.
Lee EJ, Raudsepp T, Kata SR, Adelson D, Womack JE, et al: A 1.4-Mb interval RH map of horse chromosome 17 provides detailed comparison with human and mouse homologues. Genomics 83:203–215 (2004).
23.
Leeb T, Vogl C, Zhu B, de Jong PJ, Binns MM, et al: A human-horse comparative map based on equine BAC end sequences. Genomics 87:772–776 (2006).
24.
McKay SD, Schnabel RD, Murdoch BM, Aerts J, Gill CA, et al: Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping. Anim Genet 38:120–125 (2007).
25.
Meyers SN, Rogatcheva MB, Larkin DM, Yerle M, Milan D, et al: Piggy-BACing the human genome II. A high-resolution, physically anchored, comparative map of the porcine autosomes. Genomics 86:739–752 (2005).
26.
Milenkovic D, Oustry-Vaiman A, Lear TL, Billault A, Mariat D, et al: Cytogenetic localization of 136 genes in the horse: comparative mapping with the human genome. Mamm Genome 13:524–534 (2002).
27.
Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, et al: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613–617 (2005).
28.
Murphy WJ, Davis B, David VA, Agarwala R, Schäffer AA, et al: A 1.5-Mb resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics 89:189–196 (2007).
29.
Nadeau JH, Sankoff D: Counting on comparative maps. Trends Genet 14:495–501 (1998).
30.
Olivier M, Aggarwal A, Allen J, Almendras AA, Bajorek ES, et al: A high-resolution radiation hybrid map of the human genome draft sequence. Science 291:1298–1302 (2001).
31.
Penedo MCT, Millon LV, Bernoco D, Bailey E, Binns M, et al: International equine gene mapping workshop report: a comprehensive linkage map constructed with data from new markers and by merging four mapping resources. Cytogenet Genome Res 111:5–15 (2005).
32.
Perrocheau M, Boutreux V, Chadi S, Mata X, Decaunes P, et al: Construction of a medium-density horse gene map. Anim Genet 37:145–155 (2006).
33.
Raudsepp T, Frönicke L, Scherthan H, Gustavsson I, Chowdhary BP: Zoo-FISH delineates conserved chromosomal segments in horse and man. Chromosome Res 4:218–225 (1996).
34.
Raudsepp T, Lee EJ, Kata SR, Brinkmeyer C, Mickelson JR, Skow LC, et al: Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping. Proc Natl Acad Sci USA 101:2386–2391 (2004).
35.
Rowe LB, Barter ME, Kelmenson JA, Eppig JT: The comprehensive mouse radiation hybrid map densely cross-referenced to the recombination map: a tool to support the sequence assemblies. Genome Res 13:122–133 (2003).
36.
Schäffer AA, Rice ES, Cook W, Agarwala R: rh_tsp_map 3.0: End-to-end radiation hybrid mapping with improved speed and quality control. Bioinformatics 23:1156–1158 (2007).
37.
Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, et al: The DNA sequence and comparative analysis of human chromosome 5. Nature 431:268–274 (2004).
38.
Schuler GD: Sequence mapping by electronic PCR. Genome Res 7:541–550 (1997).
39.
Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, et al: A physical map of the bovine genome. Genome Biol 8:R165 (2007).
40.
Swinburne J, Gerstenberg C, Breen M, Aldridge V, Lockhart L, et al: First comprehensive low-density horse linkage map based on two 3-generation, full-sibling, cross-bred horse reference families. Genomics 66:123–134 (2000).
41.
Swinburne JE, Boursnell M, Hill G, Pettitt L, Allen T, et al: Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families. Genomics 87:1–29 (2006).
42.
Tozaki T, Swinburne J, Hirota K, Hasegawa T, Ishida N, Tobe T: Improved resolution of the comparative horse-human map: investigating markers with in silico and linkage mapping approaches. Gene 392:181–186 (2007).
43.
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al: The sequence of the human genome. Science 291:1304–1351 (2001).
44.
Wagner ML, Raudsepp T, Goh G, Agarwala R, Schäffer AA, et al: A 1.3-Mb interval map of equine homologs of HSA2. Cytogenet Genome Res 112:227–234 (2006).
45.
Yang F, Fu B, O’Brien PCM, Nie W, Ryder OA, Ferguson-Smith MA: Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules. Chromosome Res 12:65–76 (2004).
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