A physical map of the bovine genome.
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.
Snelling
Warren M
WM
USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA. warren.snelling@ars.usda.gov
Chiu
Readman
R
Schein
Jacqueline E
JE
Hobbs
Matthew
M
Abbey
Colette A
CA
Adelson
David L
DL
Aerts
Jan
J
Bennett
Gary L
GL
Bosdet
Ian E
IE
Boussaha
Mekki
M
Brauning
Rudiger
R
Caetano
Alexandre R
AR
Costa
Marcos M
MM
Crawford
Allan M
AM
Dalrymple
Brian P
BP
Eggen
André
A
Everts-van der Wind
Annelie
A
Floriot
Sandrine
S
Gautier
Mathieu
M
Gill
Clare A
CA
Green
Ronnie D
RD
Holt
Robert
R
Jann
Oliver
O
Jones
Steven Jm
SJ
Kappes
Steven M
SM
Keele
John W
JW
de Jong
Pieter J
PJ
Larkin
Denis M
DM
Lewin
Harris A
HA
McEwan
John C
JC
McKay
Stephanie
S
Marra
Marco A
MA
Mathewson
Carrie A
CA
Matukumalli
Lakshmi K
LK
Moore
Stephen S
SS
Murdoch
Brenda
B
Nicholas
Frank W
FW
Osoegawa
Kazutoyo
K
Roy
Alice
A
Salih
Hanni
H
Schibler
Laurent
L
Schnabel
Robert D
RD
Silveri
Licia
L
Skow
Loren C
LC
Smith
Timothy Pl
TP
Sonstegard
Tad S
TS
Taylor
Jeremy F
JF
Tellam
Ross
R
Van Tassell
Curtis P
CP
Williams
John L
JL
Womack
James E
JE
Wye
Natasja H
NH
Yang
George
G
Zhao
Shaying
S
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
D005819:Genetic Markers; D015247:Deoxyribonuclease HindIII
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