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; ... (2006). A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics, 7, p. 283. London: BioMed Central 10.1186/1471-2164-7-283

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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. 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 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics

UniBE Contributor:

Drögemüller, Cord

ISSN:

1471-2164

Publisher:

BioMed Central

Language:

English

Submitter:

Factscience Import

Date Deposited:

04 Oct 2013 14:45

Last Modified:

04 Sep 2015 08:35

Publisher DOI:

10.1186/1471-2164-7-283

PubMed ID:

17087818

Web of Science ID:

000242045100001

BORIS DOI:

10.7892/boris.18469

URI:

https://boris.unibe.ch/id/eprint/18469 (FactScience: 612)

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