MPI für molekulare Genetik / Department of Vertebrate Genomics |
|A second generation radiation hybrid map to aid the assembly of the bovine genome sequence|
|Authors:||Jann, Oliver C.; Aerts, Jan; Jones, Michelle; Hastings, Nicola; Law, Andy; McKay, Stephanie; Marques, Elisa; Prasad, Aparna; Yu, Jody; Moore, Stephen S.; Floriot, Sandrine; Mahé, Marie-Françoise; Eggen, André; Silveri, Licia; Negrini, Riccardo; Milanesi, Elisabetta; Ajmone-Marsan, Paolo; Valentini, Alessio; Marchitelli, Cinzia; Savarese, Maria C.; Janitz, Michal; Herwig, Ralf; Hennig, Steffen; Gorni, Chiara; Connor, Erin E.; Sonstegard, Tad S.; Smith, Timothy; Drögemüller, Cord; Williams, John L.|
|Date of Publication (YYYY-MM-DD):||2006-11-06|
|Title of Journal:||BMC Genomics|
|Copyright:||© 1999-2007 BioMed Central Ltd|
|Review Status:||not specified|
|Abstract / Description:||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 6× 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.
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 6× 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.
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 6× sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.
|External Publication Status:||published|
|Communicated by:||Hans Lehrach|
|Affiliations:||MPI für molekulare Genetik|
|External Affiliations:||Division of Genetics & Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh, EH25 9PS, UK;
University of Alberta, Edmonton, AB, T6G 2P5, Canada;
Laboratoire de Génétique Biochimique et Cytogénétique, INRA-CRJ, 78350 Jouy-en-Josas, France;
Istituto di Zootecnica, Università Cattolica del S. Cuore via E. Parmense 84, 29100 Piacenza, Italy;
Department of Animal Productions, University of Tuscia, Viterbo, Italy;
RZPD German Resource Center for Genome Research, 14059 Berlin, Germany;
Parco Tecnologico Padano, via Einstein, Polo Universitario, Lodi 26900, Italy;
USDA-ARS, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705, USA;
USDA-ARS U.S. Meat Animal Research Center P.O. Box 166 Clay Center, NE 68933-0166, USA;
Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany
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