A second generation radiation hybrid map to aid the assembly of the bovine genome sequence.
BACKGROUND
Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6x coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process.


RESULTS
An RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6x bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map.


CONCLUSIONS
Alignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.
Jann
Oliver C
OC
Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK. Oliver.Jann@bbsrc.ac.uk
Aerts
Jan
J
Jones
Michelle
M
Hastings
Nicola
N
Law
Andy
A
McKay
Stephanie
S
Marques
Elisa
E
Prasad
Aparna
A
Yu
Jody
J
Moore
Stephen S
SS
Floriot
Sandrine
S
Mahé
Marie-Françoise
MF
Eggen
André
A
Silveri
Licia
L
Negrini
Riccardo
R
Milanesi
Elisabetta
E
Ajmone-Marsan
Paolo
P
Valentini
Alessio
A
Marchitelli
Cinzia
C
Savarese
Maria C
MC
Janitz
Michal
M
Herwig
Ralf
R
Hennig
Steffen
S
Gorni
Chiara
C
Connor
Erin E
EE
Sonstegard
Tad S
TS
Smith
Timothy
T
Drögemüller
Cord
C
Williams
John L
JL
D000818:Animals; D002417:Cattle; D002875:Chromosomes / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D005819:Genetic Markers; D016678:Genome; D018895:Microsatellite Repeats; D021101:Radiation Hybrid Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA
D005819:Genetic Markers