title: Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle.
abstract: The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls. In the first phase of the 1000 bull genomes project, we sequenced the whole genomes of 234 cattle to an average of 8.3-fold coverage. This sequencing includes data for 129 individuals from the global Holstein-Friesian population, 43 individuals from the Fleckvieh breed and 15 individuals from the Jersey breed. We identified a total of 28.3 million variants, with an average of 1.44 heterozygous sites per kilobase for each individual. We demonstrate the use of this database in identifying a recessive mutation underlying embryonic death and a dominant mutation underlying lethal chrondrodysplasia. We also performed genome-wide association studies for milk production and curly coat, using imputed sequence variants, and identified variants associated with these traits in cattle.
authors.affiliation: 1] Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia. [2] School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia. [3] Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia.
authors.forename: Hans D
authors.initials: HD
authors.lastname: Daetwyler
authors.affiliation: 1] Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France. [2] Union Nationale des Coopératives d'Elevage et d'Insémination Animale, Paris, France.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Capitan
authors.affiliation: Chair of Animal Breeding, Technische Universitaet Muenchen, Freising-Weihenstephan, Germany.
authors.forename: Hubert
authors.initials: H
authors.lastname: Pausch
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Livestock Research, Wageningen, the Netherlands.
authors.forename: Rianne
authors.initials: R
authors.lastname: van Binsbergen
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.
authors.forename: Rasmus F
authors.initials: RF
authors.lastname: Brøndum
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Liao
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Sigenae Bioinformatics Group, UR875, Castanet, France.
authors.forename: Anis
authors.initials: A
authors.lastname: Djari
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
authors.forename: Sabrina C
authors.initials: SC
authors.lastname: Rodriguez
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Grohs
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Get-Plage, UMR 444 Laboratoire de Génétique Cellulaire, Castanet, France.
authors.forename: Diane
authors.initials: D
authors.lastname: Esquerré
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Get-Plage, UMR 444 Laboratoire de Génétique Cellulaire, Castanet, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Bouchez
authors.affiliation: LABOGENA, Jouy-en-Josas, France.
authors.forename: Marie-Noëlle
authors.initials: MN
authors.lastname: Rossignol
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Sigenae Bioinformatics Group, UR875, Castanet, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Rocha
authors.affiliation: Union Nationale des Coopératives d'Elevage et d'Insémination Animale, Paris, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Fritz
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
authors.forename: André
authors.initials: A
authors.lastname: Eggen
authors.affiliation: 1] Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia. [2] Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia.
authors.forename: Phil J
authors.initials: PJ
authors.lastname: Bowman
authors.affiliation: 1] Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia. [2] Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Coote
authors.affiliation: 1] Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia. [2] Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia.
authors.forename: Amanda J
authors.initials: AJ
authors.lastname: Chamberlain
authors.affiliation: Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Anderson
authors.affiliation: US Department of Agriculture, Agricultural Research Service (USDA-ARS), Animal and Natural Resources Institute, Bovine Functional Genomics Laboratory, BARC-East, Beltsville, Maryland, USA.
authors.forename: Curt P
authors.initials: CP
authors.lastname: VanTassell
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Livestock Research, Wageningen, the Netherlands.
authors.forename: Ina
authors.initials: I
authors.lastname: Hulsegge
authors.affiliation: 1] Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia. [2] Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia. [3] Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Mike E
authors.initials: ME
authors.lastname: Goddard
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.
authors.forename: Bernt
authors.initials: B
authors.lastname: Guldbrandtsen
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.
authors.forename: Mogens S
authors.initials: MS
authors.lastname: Lund
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Livestock Research, Wageningen, the Netherlands.
authors.forename: Roel F
authors.initials: RF
authors.lastname: Veerkamp
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
authors.forename: Didier A
authors.initials: DA
authors.lastname: Boichard
authors.affiliation: Chair of Animal Breeding, Technische Universitaet Muenchen, Freising-Weihenstephan, Germany.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Fries
authors.affiliation: 1] Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia. [2] School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia. [3] Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia.
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Hayes
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle / Q000235:genetics*; D016678:Genome; D055106:Genome-Wide Association Study / Q000379:methods; D005838:Genotype; D008297:Male; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017386:Sequence Homology, Amino Acid