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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
item SCHEIN, JACQUELINE
item HOBBS, MATTHEW
item ABBEY, COLETTE
item ADELSON, DAVID
item AERTS, JAN
item Bennett, Gary
item BOSDET, IAN
item BOUSSAHA, MEKKI
item BRAUNING, RUDIGER
item CAETANO, ALEXANDRE
item COSTA, MARCOS
item CRAWFORD, ALLAN
item DALRYMPLE, BRIAN
item EGGEN, ANDRE
item EVERTS-VAN DER WIND, ANNELIE
item FLORIOT, SANDRINE
item GAUTIER, MATHIEU
item GILL, CLARE
item Green, Ronald
item HOLT, ROBERT
item JANN, OLIVER
item JONES, STEVEN
item Kappes, Steven - Steve
item Keele, John
item DE JONG, PIETER
item LARKIN, DENIS
item LEWIN, HARRIS
item MCEWAN, JOHN
item MCKAY, STEPHANIE
item MARRA, MARCO
item MATHEWSON, CARRIE
item MATUKUMALLI, LAKSHMI
item MOORE, STEPHEN
item MURDOCH, BRENDA
item NICHOLAS, FRANK
item OSOEGAWA, KAZUTOYO
item ROY, ALICE
item SALIH, HANNI
item SCHIBLER, LAURENT
item SCHNABEL, ROBERT
item SILVERI, LICIA
item SKOW, LOREN
item Smith, Timothy - Tim
item Sonstegard, Tad
item TAYLOR, JEREMY
item TELLAM, ROSS
item Van Tassell, Curtis - Curt
item WILLIAMS, JOHN
item WOMACK, JAMES
item WYE, NATASJA
item YANG, GEORGE
item ZHAO, SHAYING

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.