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Title: A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

Author
item JANN, OLIVER - ROSLIN INSTITUTE
item AERTS, JAN - ROSLIN INSTITUTE
item JONES, MICHELLE - ROSLIN INSTITUTE
item HASTINGS, NICOLA - ROSLIN INSTITUTE
item LAW, ANDY - ROSLIN INSTITUTE
item MCKAY, STEPHANIE - UNIVERSITY OF ALBERTA
item MARQUES, ELISA - UNIVERSITY OF ALBERTA
item PRASAD, APARNA - UNIVERSITY OF ALBERTA
item YU, JODY - UNIVERSITY OF ALBERTA
item MOORE, STEPHEN - UNIVERSITY OF ALBERTA
item FLORITA, SANDRINE - FRANCE
item MAHE, MARIE-FRANCOISE - FRANCE
item EGGEN, ANDRE - FRANCE
item SILVERI, LICIA - FRANCE
item NEGRINI, RICCARDO - ITALY
item MILANESI, ELISABETTA - ITALY
item AJMONE-MARSAN, PAOLO - ITALY
item VAKEBTUBU, AKESSUI - ITALY
item MARCHITELLI, CINZIA - UNIVERSITY OF TUSCIA
item JANITZ, MICHAL - BERLIN, GERMANY
item HERWIG, RALF - BERLIN, GERMANY
item HENNIG, STEFFEN - BERLIN, GERMANY
item SAVARESE, MARLINA - UNIVERSITY OF TUSCIA
item GORNI, CHIARA - ITALY
item Connor, Erin
item Sonstegard, Tad
item Smith, Timothy - Tim
item DROGEMULLER, CORD - U OF VET MED HANNOVER
item WILLIAMS, JOHN - ROSLIN INSTITUTE

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2006
Publication Date: 11/6/2006
Citation: Jann, O.C., Aerts, J., Jones, M., Hastings, N., Law, A., Mckay, S., Marques, E., Prasad, A., Yu, J., Moore, S.S., Florita, S., Mahe, M., Eggen, A., Silveri, L., Negrini, R., Milanesi, E., Ajmone-Marsan, P., Vakebtubu, A., Marchitelli, C., Janitz, M., Herwig, R., Hennig, S., Savarese, M., Gorni, C., Connor, E.E., Sonstegard, T.S., Smith, T.P., Drogemuller, C., Williams, J. 2006. A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics. 7:283-298.

Interpretive Summary: Several approaches can be used to develop maps of a genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative gene orders. The accuracy of the genome maps should be improved if information from different sources were combined to produce integrated maps. The current, publicly available bovine genomic sequence assembly is based on whole genome shotgun sequence data and limited mapping data and it is recognised that this assembly is a draft containing errors. The radiation hybrid maps described here have been contributed to the International sequencing project to aid this process. Sequences of the mapped genes were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in gene order, several cases were observed where the chromosomal assignment of genes differed between maps. Alignment of our BovGen RH map with other published radiation hybrid and genetic maps showed much higher consistency in marker order and chromosome assignment than with the current 6x sequence assembly. This suggests that the bovine assembly would be significantly improved by an integration of the combined map information.

Technical 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 in principle be improved if information from different sources was combined to produce integrated maps. The current, publicly available bovine genomic sequence assembly is based on whole genome shotgun sequence data and limited mapping data and it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improved reliability of ordering of sequence scaffolds on chromosomes. The RH maps described here have been contributed to the International sequencing project to aid this process. Results: Radiation hybrid (RH) maps for the 30 bovine chromosomes are presented. The maps were built using the Roslin 3000-rad RH panel (BovGen RH map) and containing 3966 markers including 2473 new loci in addition to 262 AFLPs that have been reported and 1231 markers published previously 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 bovine maps were aligned with the current 6x bovine assembly and 2898 loci were unambiguously located in the bovine sequence. The order of loci on RH maps 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. Conclusions: Alignment of the BovGen RH map with other published RH and genetic maps showed much higher consistency in marker order and chromosome assignment than with the current 6x sequence assembly. This suggests that the bovine assembly would be significantly improved by an integration of the combined map information.