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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #211273
Title: A physical map of the bovine genome

Author
item Snelling, Warren
item CHIU, READMAN - GENOME SCIENCES CENTRE
item SCHEIN, JACQUELINE - GENOME SCIENCES CENTRE
item HOBBS, MATTHEW - UNIV SYDNEY, AUSTRALIA
item ABBEY, COLETTE - TEXAS A&M-COLLEGE STATION
item ADELSON, DAVID - TEXAS A&M-COLLEGE STATION
item AERTS, JAN - ROSLIN INSTITUTE-UK
item Bennett, Gary
item BOSDET, IAN - GENOME SCIENCES CENTRE
item BOUSSAHA, MEKKI - INRA, FRANCE
item BRAUNING, RUDIGER - AGRESEARCH, NEW ZEALAND
item CAETANO, ALEXANDRE - EMBRAPA, BRAZIL
item COSTA, MARCOS - EMBRAPA, BRAZIL
item CRAWFORD, ALLAN - AGRESEARCH, NEW ZEALAND
item DALRYMPLE, BRIAN - CSIRO, AUSTRALIA
item EGGEN, ANDRE - INRA, FRANCE
item EVERTS-VAN DER WIND, ANNELIE - UNIV ILLINOIS-URBANA
item FLORIOT, SANDRINE - INRA, FRANCE
item GAUTIER, MATHIEU - INRA, FRANCE
item GILL, CLARE - TEXAS A&M-COLLEGE STATION
item Green, Ronald
item HOLT, ROBERT - GENOME SCI CENTRE-CANADA
item JANN, OLIVER - ROSLIN INSTITUTE-UK
item JONES, STEVEN - GENOME SCI CENTRE-CANADA
item Kappes, Steven - Steve
item Keele, John
item DE JONG, PIETER - CHILDREN'S HOSPITAL-CALIF
item LARKIN, DENIS - UNIV ILLINOIS-URBANA
item LEWIN, HARRIS - INST GENOMIC BIOL, URBANA
item MCEWAN, JOHN - AGRESEARCH, NEW ZEALAND
item MCKAY, STEPHANIE - UNIV ALBERTA, CANADA
item MARRA, MARCO - GENOME SCI CENTRE-CANADA
item MATHEWSON, CARRIE - GENOME SCI CENTRE-CANADA
item MATUKUMALLI, LAKSHMI - GEORGE MASON UNIVERSITY
item MOORE, STEPHEN - UNIV ALBERTA, CANADA
item MURDOCH, BRENDA - UNIV ALBERTA, CANADA
item NICHOLAS, FRANK - UNIV SYDNEY, AUSTRALIA
item OSOEGAWA, KAZUTOYO - CHILDREN'S HOSPITAL-CALIF
item ROY, ALICE - GENOSCOPE, FRANCE
item SALIH, HANNI - TEXAS A&M-COLLEGE STATION
item SCHIBLER, LAURENT - INRA, FRANCE
item SCHNABEL, ROBERT - UNIV MISSOURI, COLUMBIA
item SILVERI, LICIA - UNIV CATTOLICA, ITALY
item SKOW, LOREN - TEXAS A&M-COLLEGE STATION
item Smith, Timothy - Tim
item Sonstegard, Tad
item TAYLOR, JEREMY - UNIV MISSOURI, COLUMBIA
item TELLAM, ROSS - CSIRO, AUSTRALIA
item Van Tassell, Curtis - Curt
item WILLIAMS, JOHN - ROSLIN INST, SCOTLAND
item WOMACK, JAMES - TEXAS A&M-COLLEGE STATION
item WYE, NATASJA - GENOME SCI CENTRE-CANADA
item YANG, GEORGE - GENOME SCI CENTRE-CANADA
item ZHAO, SHAYING - INST GENOMIC RES-MARYLAND

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/14/2007
Publication Date: 8/14/2007
Citation: Snelling, W.M., Chiu, R., Schein, J.E., Hobbs, M., Abbey, C.A., Adelson, D.L., Aerts, J., Bennett, G.L., Bosdet, I.E., Boussaha, M., Brauning, R., Caetano, A.R., Costa, M.M., Crawford, A.M., Dalrymple, B.P., Eggen, A., Everts-Van Der Wind, A., Floriot, S., Gautier, M., Gill, C.A., Green, R.D., Holt, R., Jann, O., Jones, S.J., Kappes, S.M., Keele, J.W., De Jong, P.J., Larkin, D.M., Lewin, H.A., Mcewan, J.C., Mckay, S., Marra, M.A., Mathewson, C.A., Matukumalli, L.K., Moore, S.S., Murdoch, B., Nicholas, F.W., Osoegawa, K., Roy, A., Salih, H., Schibler, L., Schnabel, R.D., Silveri, L., Skow, L.C., Smith, T.P., Sonstegard, T.S., Taylor, J.F., Tellam, R., Van Tassell, C.P., Williams, J.L., Womack, J.E., Wye, N.H., Yang, G., Zhao, S. 2007. A physical map of the bovine genome. Genome Biology. 8:R165 (17 pp).

Interpretive Summary: A resource describing the cattle genome was created by integrating several sources of information. A moderate resolution composite map of DNA markers was developed by combining data from five independent maps. A high-resolution physical (bacterial artificial chromosome, or BAC) map was created using fingerprints of each BAC clone and partial sequence of clones aligned with the human genome. The maps were integrated with a draft assembly of the complete bovine sequence. The maps can assist with refining the sequence assembly, and will be useful to help identify variations in DNA that affect meat and milk production.

Technical Abstract: Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences (BES) assisted with BAC map ordering and assembly. A minimally overlapping set of clones, used as sequencing templates in the bovine sequencing project, was selected from the BAC map. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map, ordered with maximum likelihood procedures and projected onto common scales. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. The integrated maps are accessible from http://www.bovinegenome.org. Conclusions Together, the BAC and composite maps provide a guide for ordering and orienting genome sequence. In addition to contributing to a high quality genome assembly, the maps are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.