A 4,103 marker integrated physical and comparative map of the horse genome

Cytogenetic and Genome Research

Volumn 122, Issue 1, 2008, Pages 28-36

  Raudsepp, T ^a   Gustafson Seabury, A ^a   Durkin, K ^a   Wagner, M L ^b   Goh, G ^a   Seabury, C M ^a   Brinkmeyer Langford, C ^a   Lee, E J ^a   Agarwala, R ^c   Stallknecht Rice, E ^c   Schaffer A A ^c   Skow, L C ^a   Tozaki, T ^d   Yasue, H ^e   Penedo, M C T ^f   Lyons, L A ^f   Khazanehdari, K A ^g   Binns, M M ^h   MacLeod, J N ⁱ   Distl, O ^j   Guerin G ^k   Leeb, T ^l   Mickelson, J R ^b   Chowdhary, B P ^a   more..

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d LABORATORY OF RACING CHEMISTRY   (Japan)

^e NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g CENTRAL VETERINARY RESEARCH LABORATORY   (United Arab Emirates)

^h ROYAL VETERINARY COLLEGE   (United Kingdom)

ⁱ UNIVERSITY OF KENTUCKY   (United States)

^j UNIVERSITY OF VETERINARY MEDICINE HANNOVER   (Germany)

^k CEMAGREF   (France)

^l UNIVERSITY OF BERN   (Switzerland)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; BASE PAIRING; CHROMOSOME BREAKAGE; COMPARATIVE GENE MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; CYTOGENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LOCUS; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC LINKAGE; GENOME; GENOME ANALYSIS; HORSE; MARKER GENE; MEIOSIS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SYNTENY; VERTEBRATE; X CHROMOSOME;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CYTOGENETICS; GENETIC MARKERS; HORSES; IN SITU HYBRIDIZATION, FLUORESCENCE; LOD SCORE; PHYSICAL CHROMOSOME MAPPING; RADIATION HYBRID MAPPING; SPECIES SPECIFICITY;

CRICETINAE; EQUIDAE; VERTEBRATA;

EID: 54249144448     PISSN: 14248581     EISSN: None     Source Type: Journal    
DOI: 10.1159/000151313     Document Type: Article

References (45)

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 5000 rad 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).