1000 Bull Genomes Consortium Project Benjamin Hayes, Ruedi Fries, Mogens Sando Lund, Didier Boichard, Paul Stothard, Roel F. Veerkamp, Curt van Tassell, Charlotte Anderson, Ina Hulsegge, Bernt Guldbrandtsen, et al. To cite this version: Benjamin Hayes, Ruedi Fries, Mogens Sando Lund, Didier Boichard, Paul Stothard, et al.. 1000 Bull Genomes Consortium Project. Plant and Animal Meeting, Jan 2012, San Diego, United States. hal-01001345 HAL Id: hal-01001345 https://hal.archives-ouvertes.fr/hal-01001345 Submitted on 3 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. PAG meeting, January 14-18 2012 W139 : 1000 Bull Genomes Consortium Project Benjamin Hayes , Department of Primary Industries (Victoria), Melbourne, Victoria, Australia Ruedi Fries , Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, 85354 Freising, Germany Mogens Sando Lund , Aarhus University, Faculty of Science and Technology, Department of Genetics and Biotechnology, Tjele, Denmark, Tjele, Denmark Didier A. Boichard , INRA, Jouy en Josas, France Paul Stothard , Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada Roel F. Veerkamp , Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen, Netherlands Curt Van Tassell , Bovine Functional Genomics Laboratory, Agricultural Research Service, USDA, Beltsville, MD, USA Charlotte Anderson , Biosciences Research Division, Department of Primary Industries, Bundoora, Victoria 3083, Australia Ina Hulsegge , Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, PO Box 65, NL-8200 AB Lelystad, the Netherlands Bernt Guldbrandtsen , Aarhus University Dominique Rocha , INRA UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France Dirk Hinirichs , Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, D-24098 Kiel, Germany Alessandro Bagnato , Università degli Studi di Milano, Milano, Italy Michel Georges , University of Liege/Unit of Animal Genomics, Liege(Sart Tilman), Belgium Richard Spelman , Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand James Reecy , Iowa State University, Ames, IA Alan L. Archibald , Roslin Institute,University of Edinburgh Roslin, United Kingdom Mike Goddard , Biosciences Research Division, Department of Primary Industries, Bundoora, Victoria 3083, Australia Birgit Gredler , Qualitas AG, Switzerland Genomic selection, where selection decisions are based on estimates of breeding value from genome wide-marker effects, has enormous potential to improve genetic gain in dairy and beef cattle. Although successful in dairy cattle, some major challenges remain 1) only a proportion of the genetic variance is captured, particularly for some traits 2) marker effects are rarely consistent across breeds, 3) accuracy of genomic predictions decays rapidly over time. Using full genome sequences rather than DNA markers in genomic selection could address these challenges. However, sequencing all individuals in the very large resource populations required to estimate the typically small effects of mutations on target traits would be prohibitively expensive. An alternative is to sequence key ancestors contributing most of the genetic material of the current population, and to use this reference for imputation of sequence from SNP chip data. The reference set must still be large, in order to capture for example, rare variants which are likely to explain some of the variation in our target traits. Recognising the need for a comprehensive “reference set” of key ancestors by many groups undertaking cattle research and cattle breeding programs, we have initiated the 1000 bull genomes project. The project will assemble whole genome sequences of cattle from institutions around the world, to provide an extended data base for imputation of genetic variants. This will enable the bovine genomics community to impute full genome sequence from SNP genotypes, and then use this data for genomic selection, and rapid discovery of causal mutations. Some preliminary results from the variant detection pipeline will be reported. .