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Genomic prediction from whole genome sequence in livestock: the 1000 bull genomes project

Thursday, August 21, 2014: 2:30 PM
Bayshore Grand Ballroom E-F (The Westin Bayshore)
Ben J Hayes , Department of Environment and Primary Industries, Bundoora, Australia
Iona M MacLeod , University of Melbourne, Melbourne, Australia
Hans D Daetwyler , CRC for Sheep Industry Innovation, Armidale, Australia
Bowman J Phil , Department of Environment and Primary Industries, Bundoora, Australia
Amanda J Chamberlain , The Department of Environment and Primary Industries, Bundoora, Australia
Christy Vander Jagt , The Department of Environment and Primary Industries, Bundoora, Australia
Aurélien Capitan , UNCEIA, Paris, France
Hubert Pausch , Chair of Animal Breeding, Technische Universitaet Muenchen, Freising, Germany
Paul Stothard , University of Alberta, Edmonton, AB, Canada
Xiaoping Liao , University of Alberta, Edmonton, AB, Canada
Chris Schrooten , CRV, Arnhem, Netherlands
Erik Mullaart , CRV BV, Arnhem, Netherlands
Ruedi Fries , Chair of Animal Breeding, Technische Universitaet Muenchen, Freising, Germany
Bernt Guldbrandtsen , Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
Mogens Sandø Lund , Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
Didier Boichard , INRA, UMR1313 GABI, Jouy-en-Josas, France
Roel F. Veerkamp , Animal Breeding and Genomics Centre, Wageningen University, Wageningen, Netherlands
Curt P VanTassell , Bovine Functional Genomics Laboratory ARS-USDA, Beltsville, MD
Birgit Gredler , Qualitas AG, Zug, Switzerland
Tom Druet , University of Liège, Liège, Belgium
Alessandro Bagnato , Università degli Studi di Milano, Milano, Italy
Johanna Vilkki , MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
Dirk-Jan de Koning , Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
Enrico Santus , ANARB, Italian Brown Cattle Breeders' Association, Bussolengo (VR), Italy
Michael E. Goddard , Department of Primary Industries, Melbourne, Australia
Recorded Presentation (flv)
Abstract Text: Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds.  The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls, for imputing sequence variant genotypes into reference sets for genomic prediction.  Run 3.0 included 429 sequences, with 31.8 million variants detected.   BayesRC, a new method for genomic prediction, addresses some challenges associated with using the sequence data, and takes advantage of biological information.  In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data.  We could demonstrate the method identified causal mutations in some cases.  Further improvements will come from more accurate imputation of sequence variant genotypes and improved biological information.

Keywords: Genomic prediction, whole genome sequence, biological information

See more of: Symposium: Methods and Tools - Genome Sequencing
See more of: Methods and Tools: Genome sequencing
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