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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 lo...

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Autores principales: 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
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636650/
https://www.ncbi.nlm.nih.gov/pubmed/17087818
http://dx.doi.org/10.1186/1471-2164-7-283
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author 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
author_facet 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
author_sort Jann, Oliver C
collection PubMed
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. 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 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. CONCLUSION: 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.
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spelling pubmed-16366502006-11-16 A second generation radiation hybrid map to aid the assembly of the bovine genome sequence 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 BMC Genomics Research Article 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. 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 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. CONCLUSION: 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. BioMed Central 2006-11-06 /pmc/articles/PMC1636650/ /pubmed/17087818 http://dx.doi.org/10.1186/1471-2164-7-283 Text en Copyright © 2006 Jann et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
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
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
title A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
title_full A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
title_fullStr A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
title_full_unstemmed A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
title_short A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
title_sort second generation radiation hybrid map to aid the assembly of the bovine genome sequence
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636650/
https://www.ncbi.nlm.nih.gov/pubmed/17087818
http://dx.doi.org/10.1186/1471-2164-7-283
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