A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Jann, Oliver C ^a   Aerts, Jan ^a   Jones, Michelle ^a   Hastings, Nicola ^a   Law, Andy ^a   McKay, Stephanie ^b   Marques, Elisa ^b   Prasad, Aparna ^b   Yu, Jody ^b   Moore, Stephen ^b   Floriot, Sandrine ^c   Mahé, Marie Françoise ^c   Eggen, André ^c   Silveri, Licia ^c,d   Negrini, Riccardo ^d   Milanesi, Elisabetta ^d   Ajmone Marsan, Paolo ^d   Valentini, Alessio ^e   Marchitelli, Cinzia ^e   Savarese, Maria C ^e   Janitz, Michal ^f   Herwig, Ralf ^f   Hennig, Steffen ^g   Gorni, Chiara ^d,h   Connor, Erin E ⁱ   Sonstegard, Tad S ⁱ   Smith, Timothy ^j   Drögemüller, Cord ^k   Williams, John L ^a,h   more..

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF ALBERTA   (Canada)

^c CEMAGREF   (France)

^d UNIVERSITÀ CATTOLICA DEL SACRO CUORE   (Italy)

^e UNIVERSITY OF TUSCIA   (Italy)

^f MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^g German Genome Resource Center RZPD   (Germany)

^h PARCO TECNOLOGICO PADANO   (Italy)

ⁱ AGRICULTURAL RESEARCH SERVICE   (United States)

^j U S MEAT ANIMAL RESEARCH CENTER   (United States)

^k UNIVERSITY OF VETERINARY MEDICINE HANNOVER   (Germany)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; CATTLE; CHROMOSOMAL LOCALIZATION; CHROMOSOME ANALYSIS; CHROMOSOME MAP; CONTROLLED STUDY; GENE ASSIGNMENT; GENE LOCUS; GENE SEQUENCE; GENETIC DIFFERENCE; GENETIC IDENTIFICATION; GENETIC LINKAGE; MARKER CHROMOSOME; NONHUMAN; NUCLEOTIDE SEQUENCE; RADIATION HYBRID MAPPING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

ANIMALS; CATTLE; CHROMOSOMES; CHROMOSOMES, ARTIFICIAL, BACTERIAL; EXPRESSED SEQUENCE TAGS; GENETIC LINKAGE; GENETIC MARKERS; GENOME; MICROSATELLITE REPEATS; RADIATION HYBRID MAPPING; SEQUENCE ANALYSIS, DNA;

BOS TAURUS;

EID: 33751190094     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-283     Document Type: Article

References (45)

1. Barendse W, Vaiman D, Kemp SJ, Sugimoto Y, Armitage SM, Williams JL, Sun HS, Eggen A, Agaba M, Aleyasin SA, Band M, Bishop MD, Buitkamp J, Byrne K, Collins F, Cooper L, Coppettiers W, Denys B, Drinkwater RD, Easterday K, Elduque C, Ennis S, Erhardt G, Ferretti L, Flavin N, Gao Q, Georges M, Gurung R, Harlizius B, Hawkins G, Hetzel J, Hirano T, Hulme D, Jorgensen C, Kessler M, Kirkpatrick BW, Konfortov B, Kostia S, Kuhn C, Lenstra JA, Leveziel H, Lewin H, Leyhe B, Lil L, Martin Burriel I, McGraw RA, Miller JR, Moody DE, Moore SS, Nakane S, Nijman IJ, Olsaker I, Pomp D, Rando A, Ron M, Shalom A, Teale AJ, Thieven U, Urquhart BGD, Vage DI, Van de Weghe A, Varvio S, Velmala R, Vilkki J, Weikard R, Woodside C, Womack JE: A medium-density genetic linkage map of the bovine genome. Mamm Genome 1997, 8:21-28. Erratum in: Mamm Genome 1997, 8:798.
2. Kappes SM, Keele JW, Stone RT, McGraw RA, Sonstegard TS, Smith TP, Lopez-Corrales NL, Beattie CW: A second-generation linkage map of the bovine genome. Genome Res 1997, 7:235-249.
3. Ihara N, Takasuga A, Mizoshita K, Takeda H, Sugimoto M, Mizoguchi Y, Hirano T, Itoh T, Watanabe T, Reed KM, Snelling WM, Kappes SM, Beattie CW, Bennett GL, Sugimoto Y: A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Res 2004, 14:1987-1998.
4. Womack JE, Johnson JS, Owens EK, Rexroad CE 3rd, Schlapfer J, Yang YP: A whole-genome radiation hybrid panel for bovine gene mapping. Mamm Genome 1997, 8:854-856.
5. Rexroad CE, Schlapfer JS, Yang Y, Harlizius B, Womack JE: A radiation hybrid map of bovine chromosome one. Anim Genet 1999, 30:325-332.
6. Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J, Windish R, Steining C, Mahyuddin P, Womack JE, Lewin HA: An ordered comparative map of the cattle and human genomes. Genome Res 2000, 10:1359-1368.
7. Williams JL, Eggen A, Ferretti L, Farr CJ, Gautier M, Amati G, Ball G, Caramorr T, Critcher R, Costa S, Hextall P, Hills D, Jeulin A, Kiguwa SL, Ross O, Smith AL, Saunier K, Urquhart B, Waddington D: A bovine whole-genome radiation hybrid panel and outline map. Mammalian Genome 2002, 13:469-474.
8. Itoh T, Watanabe T, Ihara N, Mariani P, Beattie CW, Sugimoto Y, Takasuga A: A comprehensive radiation hybrid map of the bovine genome comprising 5593 loci. Genomics 2005, 85:413-424.
9. Amaral ME, Kata SR, Womack JE: A radiation hybrid map of bovine X chromosome (BTAX). Mamm Genome 2002, 13:268-271.
10. Goldammer T, Kata SR, Brunner RM, Dorroch U, Sanftleben H, Schwerin M, Womack JE: A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice. Proc Natl Acad Sci USA 2002, 99:2106-2111.
11. Gautier M, Hayes H, Eggen A: An extensive and comprehensive radiation hybrid map of bovine Chromosome 15: comparison with human Chromosome 11. Mamm Genome 2002, 13:316-319.
12. Gautier M, Hayes H, Bonsdorff T, Eggen A: Development of a comprehensive comparative radiation hybrid map of bovine chromosome 7 (BTA 7) versus human chromosomes 1 (HSA 1), 5 (HSA 5) and 19 (HSA 19). Cytogenet Genome Res 2003, 102:25-31.
13. Larkin DM, Everts-van der Wind A, Rebeiz M, Schweitzer PA, Bachman S, Green C, Wright CL, Campos EJ, Benson LD, Edwards J, Liu L, Osoegawa K, Womack JE, de Jong PJ, Lewin HA: A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res 2003, 13:1966-1972.
14. Everts-van der Wind A, Kata SR, Band MR, Rebeiz M, Larkin DM, Everts RE, Green CA, Liu L, Natarajan S, Goldammer T, Lee JH, McKay S, Womack JE, Lewin HA: A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Res 2004, 14:1424-1437.
15. Everts-van der Wind A, Larkin DM, Green CA, Elliott JS, Olmstead CA, Chiu R, Schein JE, Marra MA, Womack JE, Lewin HA: A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci USA 2005, 102:18526-18531.
16. Coulson A, Waterston R, Kiff J, Sulston J, Kohara Y: Genome linking with yeast artificial chromosomes. Nature 1988, 335:184-186.
17. Olson MV, Dutchik JE, Graham MY, Brodeur GM, Helms C, Frank M, MacCollin M, Scheinman R, Frank T: Random-clone strategy for genomic restriction mapping in yeast. Proc Natl Acad Sci USA 1986, 83:7826-7830.
18. Cao Y, Kang HL, Xu X, Wang M, Dho SH, Huh JR, Lee BJ, Kalush F, Bocskai D, Ding Y, Tesmer JG, Lee J, Moon E, Jurecic V, Baldini A, Weier HU, Doggett NA, Simon MI, Adams MD, Kim UJ: A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2. Genome Res 1999, 9:763-774.
19. Hoskins RA, Nelson CR, Berman BP, Laverty TR, George RA, Ciesiolka L, Naeemuddin M, Arenson AD, Durbin J, David RG, Tabor PE, Bailey MR, DeShazo DR, Catanese J, Mammoser A, Osoegawa K, de Jong PJ, Celniker SE, Gibbs RA, Rubin GM, Scherer SE: A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science 287:2271-2274. 2000, Mar 24, Erratum in: Science 2000, 288:1751.
20. McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, HumphR SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, et al. International Human Genome Mapping Consortium: A physical map of the human genome. Nature 2001, 409:934-941.
21. Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, GR C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR: A physical map of the mouse genome. Nature 2002, 418:743-750.
22. Eggen A, Gautier M, Billaut A, Petit E, Hayes H, Laurent P, Urban C, Pfister-Genskow M, Eilertsen K, Bishop MD: Construction and characterization of a bovine BAC library with four genome-equivalent coverage. Genet Sel Evol 2001, 33:543-548.
23. CHORI-240 Bovine BAC Library [http://bacpac.chori.org/bovine240.htm]
24. Snelling WM, Gautier M, Keele JW, Smith TP, Stone RT, Harhay GP, Bennett GL, Ihara N, Takasuga A, Takeda H, Sugimoto Y, Eggen A: Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. BMC Genomics 2004, 5:77.
25. Weikard R, Goldammer T, Laurent P, Womack JE, Kuehn C: A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits. BMC Genomics 2006, 7:53.
26. Gorni C, Williams JL, Heuven HCM, Negrini R, Valentini A, van Eijk MJT, Waddington D, Zevenbergen M, Ajmone Marsan P, Peleman JD: Application of AFLP® technology to radiation hybrid mapping. Chromosome Research 2004, 12:285-297.
27. ArkDB Public database browser [http://www.thearkdb.org]
28. Ranz JM, Casals F, Ruiz A: How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila. Genome Res 2001, 11:230-239.
29. Fiedorek FT Jr, Kay ES: Mapping of the focal adhesion kinase (Fadk) gene to mouse chromosome 15 and human chromosome 8. Mamm Genome 1995, 6:123-6.
30. Inazawa J, Sasaki H, Nagura K, Kakazu N, Abe T, Sasaki T: Precise localization of the human gene encoding cell adhesion kinase beta (CAK beta/PYK2) to chromosome 8 at p21.1 by fluorescence in situ hybridization. Hum Genet 1996, 98:508-510.
31. Goedert M, Marsh S, Carter N: Localization of the human kinesin light chain gene (KNS2) to chromosome 14q32.3 by fluorescence in situ hybridization. Genomics 1996, 32:173-175.
32. Polyprimers [http://www.unitus.it/SAG/primers.zip]
33. SantaLucia J Jr, Allawi HT, Seneviratne PA: Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 1996, 35:3555-3562.
34. Slonim D, Kruglyak L, Stein L, Lander E: Building human genome maps with radiation hybrids. J of Computational Biology 1997, 4:487-504.
35. Schiex T, Gaspin C: Carthagene: constructing and joining maximum likelihood genetic maps. Proceedings of ISMB'97, Halkidiki, Greece Porto Carras 1997:258-267.
36. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
37. Wheelan SJ, Church DM, Ostell JM: Spidey: a tool for mRNA-togenomic alignments. Genome Res 2001, 11:1952-1957.
38. GMOD Generic Software Components for Model Organism Databases [http://www.gmod.org/cmap/]
39. Sonstegard TS, Abel Ponce de Leon F, Beattie CW, Kappes SM: A chromosome-specific microdissected library increases marker density on bovine chromosome 1. Genome Res 1997, 7:76-80.
40. Dietz AB, Womack JE, Swarbrick PA, Crawford AM: Assignment of five polymorphic ovine microsatellites to bovine syntenic groups. Anim Genet 1993, 24:433-436.
41. Yokoyama H, Baraona E, Lieber CS: Molecular cloning and chromosomal localization of the ADH7 gene encoding human class IV (sigma) ADH. Genomics 1996, 31:243-245.
42. Xu YL, Xue JL, Qiu XF, Qi M, Xu Y: Regional assignment of human alcohol dehydrogenase (ADH) gene to 4pter - 4q21. Sci Sin [B] 1987, 30:720-726.
43. Tsukahara M, Yoshida A: Chromosomal assignment of the alcohol dehydrogenase cluster locus to human chromosome 4q21-23 by in situ hybridization. Genomics 1989, 4:218-220.
44. Couch FJ, Abel KJ, Brody LC, Boehnke M, Collins FS, Weber BL: Localization of the gene for ATP citrate lyase (ACLY) distal to gastrin(GAS) and proximal to D17S856 on chromosome 17q12-q21. Genomics 1994, 21:444-446.
45. De Marchis L, Cropp C, Sheng ZM, Bargo S, Callahan R: Candidate target genes for loss of heterozygosity on human chromosome 17q21. Br J Cancer 2004, 90:2384-2389. Erratum in: Br J Cancer 2004, 91:1001.