title: A physical map of the bovine genome.
abstract: BACKGROUND
  Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project.
  
  
  RESULTS
  A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly.
  
  
  CONCLUSIONS
  Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.
authors: USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA. warren.snelling@ars.usda.gov
authors: Warren M
authors: WM
authors: Snelling
authors: Readman
authors: R
authors: Chiu
authors: Jacqueline E
authors: JE
authors: Schein
authors: Matthew
authors: M
authors: Hobbs
authors: Colette A
authors: CA
authors: Abbey
authors: David L
authors: DL
authors: Adelson
authors: Jan
authors: J
authors: Aerts
authors: Gary L
authors: GL
authors: Bennett
authors: Ian E
authors: IE
authors: Bosdet
authors: Mekki
authors: M
authors: Boussaha
authors: Rudiger
authors: R
authors: Brauning
authors: Alexandre R
authors: AR
authors: Caetano
authors: Marcos M
authors: MM
authors: Costa
authors: Allan M
authors: AM
authors: Crawford
authors: Brian P
authors: BP
authors: Dalrymple
authors: André
authors: A
authors: Eggen
authors: Annelie
authors: A
authors: Everts-van der Wind
authors: Sandrine
authors: S
authors: Floriot
authors: Mathieu
authors: M
authors: Gautier
authors: Clare A
authors: CA
authors: Gill
authors: Ronnie D
authors: RD
authors: Green
authors: Robert
authors: R
authors: Holt
authors: Oliver
authors: O
authors: Jann
authors: Steven Jm
authors: SJ
authors: Jones
authors: Steven M
authors: SM
authors: Kappes
authors: John W
authors: JW
authors: Keele
authors: Pieter J
authors: PJ
authors: de Jong
authors: Denis M
authors: DM
authors: Larkin
authors: Harris A
authors: HA
authors: Lewin
authors: John C
authors: JC
authors: McEwan
authors: Stephanie
authors: S
authors: McKay
authors: Marco A
authors: MA
authors: Marra
authors: Carrie A
authors: CA
authors: Mathewson
authors: Lakshmi K
authors: LK
authors: Matukumalli
authors: Stephen S
authors: SS
authors: Moore
authors: Brenda
authors: B
authors: Murdoch
authors: Frank W
authors: FW
authors: Nicholas
authors: Kazutoyo
authors: K
authors: Osoegawa
authors: Alice
authors: A
authors: Roy
authors: Hanni
authors: H
authors: Salih
authors: Laurent
authors: L
authors: Schibler
authors: Robert D
authors: RD
authors: Schnabel
authors: Licia
authors: L
authors: Silveri
authors: Loren C
authors: LC
authors: Skow
authors: Timothy Pl
authors: TP
authors: Smith
authors: Tad S
authors: TS
authors: Sonstegard
authors: Jeremy F
authors: JF
authors: Taylor
authors: Ross
authors: R
authors: Tellam
authors: Curtis P
authors: CP
authors: Van Tassell
authors: John L
authors: JL
authors: Williams
authors: James E
authors: JE
authors: Womack
authors: Natasja H
authors: NH
authors: Wye
authors: George
authors: G
authors: Yang
authors: Shaying
authors: S
authors: Zhao
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle; D022202:Chromosomes, Artificial, Bacterial / Q000737:chemistry / Q000235:genetics; D033481:Chromosomes, Mammalian / Q000235:genetics*; D015247:Deoxyribonuclease HindIII / Q000737:chemistry; D023061:Gene Order; D005819:Genetic Markers / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010375:Pedigree; D021101:Radiation Hybrid Mapping; D016415:Sequence Alignment
chemical_list: D005819:Genetic Markers; D015247:Deoxyribonuclease HindIII
references: Nature. 2001 Feb 15;409(6822):934-41
references: 11237014
references: BMC Genomics. 2004 Oct 8;5:77
references: 15473903
references: BMC Genomics. 2006;7:283
references: 17087818
references: Genome Res. 2002 Oct;12(10):1599-610
references: 12368253
references: Genome Res. 2002 Apr;12(4):656-64
references: 11932250
references: Nat Rev Genet. 2006 Feb;7(2):85-97
references: 16418744
references: Nature. 2002 Aug 15;418(6899):743-50
references: 12181558
references: Genet Sel Evol. 2004 Mar-Apr;36(2):163-90
references: 15040897
references: Genome Biol. 2007;8(7):R152
references: 17663790
references: Methods Mol Biol. 2004;255:143-56
references: 15020821
references: Genome Res. 1997 Sep;7(9):910-6
references: 9314496
references: Anim Genet. 2007 Apr;38(2):120-5
references: 17302794
references: Mamm Genome. 2002 Aug;13(8):469-74
references: 12226714
references: Genome Res. 2006 Aug;16(8):949-61
references: 16809666
references: Genome Res. 2003 May;13(5):940-53
references: 12727910
references: Bioinformatics. 2004 May 22;20(8):1264-71
references: 14871860
references: Genome Res. 2000 Mar;10(3):350-64
references: 10720576
references: Bioinformatics. 2005 Apr 15;21(8):1703-4
references: 15598829
references: Theor Appl Genet. 2005 Nov;111(8):1514-23
references: 16187118
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D332-8
references: 17090588
references: Nat Genet. 2005 Jul;37(7):727-32
references: 15895083
references: Mamm Genome. 1997 Jan;8(1):21-8
references: 9021143
references: Genome Res. 1997 Nov;7(11):1072-84
references: 9371743
references: Genome Res. 2004 Oct;14(10A):1987-98
references: 15466297
references: Genome Res. 2004 Apr;14(4):766-79
references: 15060021
references: Genetics. 1931 Mar;16(2):97-159
references: 17246615
references: Anim Genet. 2005 Oct;36(5):381-9
references: 16167980
references: Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18526-31
references: 16339895
references: Mamm Genome. 2006 Apr;17(4):346-53
references: 16596456
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Mamm Genome. 2000 Aug;11(8):662-3
references: 10920236
references: Genetics. 1998 Sep;150(1):275-82
references: 9725846
references: Nat Genet. 1999 Jul;22(3):265-70
references: 10391214
references: Genome Res. 2005 Jul;15(7):936-44
references: 15998908
references: Comput Appl Biosci. 1988 Mar;4(1):125-32
references: 2838135
references: Proc Natl Acad Sci U S A. 2005 May 10;102(19):6896-901
references: 15867146
references: Comput Appl Biosci. 1989 Apr;5(2):101-6
references: 2720459
references: Genomics. 2005 Apr;85(4):413-24
references: 15780744
references: Genetics. 2001 Apr;157(4):1819-29
references: 11290733
references: J Anim Sci. 1994 Aug;72(8):2178-200
references: 7982849
references: J Dairy Sci. 2002 Jul;85(7):1863-8
references: 12201537
references: Mamm Genome. 2007 May;18(5):287-99
references: 17588189
references: Theor Appl Genet. 2005 Nov;111(8):1466-88
references: 16215729
references: Genome Res. 2004 Apr;14(4):721-32
references: 15060016
references: Genet Sel Evol. 2004 Jan-Feb;36(1):105-22
references: 14713413
references: Theor Appl Genet. 2006 Aug;113(3):369-82
references: 16799809
references: Genomics. 2005 Oct;86(4):396-404
references: 16026963
references: J Anim Sci. 2000 Aug;78(8):2121-6
references: 10947098
references: Genome Res. 2004 Jul;14(7):1424-37
references: 15231756
references: BMC Genomics. 2005;6:74
references: 15943875
references: Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9300-5
references: 12077321
references: J Comput Biol. 1997 Winter;4(4):517-33
references: 9385543
references: Genome Res. 1997 May;7(5):541-50
references: 9149949
references: Genome Res. 2000 Nov;10(11):1772-87
references: 11076862
references: Genetics. 2003 Jan;163(1):253-66
references: 12586713
references: BMC Bioinformatics. 2006;7:283
references: 16753058
references: Nature. 2001 Feb 15;409(6822):860-921
references: 11237011
references: Comput Appl Biosci. 1997 Oct;13(5):523-35
references: 9367125
references: Genomics. 1995 Sep 20;29(2):413-25
references: 8666390