title: A second generation radiation hybrid map to aid the assembly of the bovine genome sequence.
abstract: 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.
authors.affiliation: Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK. Oliver.Jann@bbsrc.ac.uk
authors.forename: Oliver C
authors.initials: OC
authors.lastname: Jann
authors.forename: Jan
authors.initials: J
authors.lastname: Aerts
authors.forename: Michelle
authors.initials: M
authors.lastname: Jones
authors.forename: Nicola
authors.initials: N
authors.lastname: Hastings
authors.forename: Andy
authors.initials: A
authors.lastname: Law
authors.forename: Stephanie
authors.initials: S
authors.lastname: McKay
authors.forename: Elisa
authors.initials: E
authors.lastname: Marques
authors.forename: Aparna
authors.initials: A
authors.lastname: Prasad
authors.forename: Jody
authors.initials: J
authors.lastname: Yu
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Moore
authors.forename: Sandrine
authors.initials: S
authors.lastname: Floriot
authors.forename: Marie-Françoise
authors.initials: MF
authors.lastname: Mahé
authors.forename: André
authors.initials: A
authors.lastname: Eggen
authors.forename: Licia
authors.initials: L
authors.lastname: Silveri
authors.forename: Riccardo
authors.initials: R
authors.lastname: Negrini
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Milanesi
authors.forename: Paolo
authors.initials: P
authors.lastname: Ajmone-Marsan
authors.forename: Alessio
authors.initials: A
authors.lastname: Valentini
authors.forename: Cinzia
authors.initials: C
authors.lastname: Marchitelli
authors.forename: Maria C
authors.initials: MC
authors.lastname: Savarese
authors.forename: Michal
authors.initials: M
authors.lastname: Janitz
authors.forename: Ralf
authors.initials: R
authors.lastname: Herwig
authors.forename: Steffen
authors.initials: S
authors.lastname: Hennig
authors.forename: Chiara
authors.initials: C
authors.lastname: Gorni
authors.forename: Erin E
authors.initials: EE
authors.lastname: Connor
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.forename: Timothy
authors.initials: T
authors.lastname: Smith
authors.forename: Cord
authors.initials: C
authors.lastname: Drögemüller
authors.forename: John L
authors.initials: JL
authors.lastname: Williams
mesh_terms: 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
chemical_list: D005819:Genetic Markers