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.

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H.P. and R.F. acknowledge funding from the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr 'Synbreed—Synergistic Plant and Animal Breeding' (grant 0315527B). We acknowledge the Bavarian State Research Center and Vereinigte Informationssysteme Tierhaltung (VIT) Verden for providing phenotype data. Swissgenetics is acknowledged for providing the DNA material for a Swiss Simmental bull. P.S. and X.L. acknowledge funding from the Genome Canada project entitled 'Whole-Genome Sequence Selection Through Genome-Wide Imputation in Beef Cattle' and acknowledge WestGrid and Compute/Calcul Canada for providing computing resources. D.A.B., A.C., S.F. and D.R. acknowledge the Agence Nationale de la Recherche and Apisgene for funding the Cartoseq project (ANR-10-GENM-0018). T. Simon (EVOLUTION), S. Legrain and P. Laurent (INRA) are acknowledged for providing samples from bulldog calves and information. J.-M. Vacelet (GEN'IAtest), G. Fayolle (UMOTEST) and D. Peinturier (Jura Bétail) are acknowledged for providing samples and phenotypic information for curly coat in Montbeliarde cattle. A. Baur (UNCEIA) and A. Barbat (INRA) are acknowledged for providing haplotype and fertility information for the HH3 study. We would like to thank E. Mullaart (CRV) for providing sequences for ten of the bulls used in this project. B.G., R.F.B. and M.S.L. acknowledge support from grant 3405-10-0137 from the Green Development and Demonstration Programme of the Danish Ministry of Food, Agriculture and Fisheries, the Milk Levy Fund, grant 12-132452 (GenSAP) from the Strategic Research Council and Viking Genetics. C.P.V. acknowledges funding from USDA-ARS project 1245-31000-104-00D and USDA-National Institute of Food and Agriculture (NIFA) competitive grant 2009-65205-05635 from the Animal Genome Program. B.J.H., H.D.D., A.J.C., P.J.B. and M.E.G. acknowledge funding from the Dairy Futures Cooperative Research Centre, Dairy Australia and the Cooperative Research Centre for Beef Genetic Technologies.

Author information


  1. Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia.

    • Hans D Daetwyler
    • , Phil J Bowman
    • , David Coote
    • , Amanda J Chamberlain
    • , Charlotte Anderson
    • , Mike E Goddard
    •  & Ben J Hayes
  2. School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.

    • Hans D Daetwyler
    •  & Ben J Hayes
  3. Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia.

    • Hans D Daetwyler
    • , Phil J Bowman
    • , David Coote
    • , Amanda J Chamberlain
    • , Mike E Goddard
    •  & Ben J Hayes
  4. Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.

    • Aurélien Capitan
    • , Sabrina C Rodriguez
    • , Cécile Grohs
    • , Dominique Rocha
    • , André Eggen
    •  & Didier A Boichard
  5. Union Nationale des Coopératives d'Elevage et d'Insémination Animale, Paris, France.

    • Aurélien Capitan
    •  & Sébastien Fritz
  6. Chair of Animal Breeding, Technische Universitaet Muenchen, Freising-Weihenstephan, Germany.

    • Hubert Pausch
    •  & Ruedi Fries
  7. Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.

    • Paul Stothard
    •  & Xiaoping Liao
  8. Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Livestock Research, Wageningen, the Netherlands.

    • Rianne van Binsbergen
    • , Ina Hulsegge
    •  & Roel F Veerkamp
  9. Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.

    • Rasmus F Brøndum
    • , Bernt Guldbrandtsen
    •  & Mogens S Lund
  10. Institut National de la Recherche Agronomique (INRA), Sigenae Bioinformatics Group, UR875, Castanet, France.

    • Anis Djari
    •  & Christophe Klopp
  11. Institut National de la Recherche Agronomique (INRA), Get-Plage, UMR 444 Laboratoire de Génétique Cellulaire, Castanet, France.

    • Diane Esquerré
    •  & Olivier Bouchez
  12. LABOGENA, Jouy-en-Josas, France.

    • Marie-Noëlle Rossignol
  13. US Department of Agriculture, Agricultural Research Service (USDA-ARS), Animal and Natural Resources Institute, Bovine Functional Genomics Laboratory, BARC-East, Beltsville, Maryland, USA.

    • Curt P VanTassell
  14. Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia.

    • Mike E Goddard


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B.J.H., D.A.B., R.F.V., M.S.L., B.G., M.E.G., R.F., D.R. and C.P.V. designed the study. A.C., H.P., H.D.D., R.v.B., R.F.B. and S.F. performed statistical analyses. P.S. and X.L. performed variant annotation. A.J.C., P.S., X.L., C.A., P.J.B., D.C., I.H. and H.D.D. performed quality control analyses and prepared data. H.D.D., D.C. and P.J.B. designed and developed software to process sequences. A.D., A.E., S.C.R., C.G., D.E., M.-N.R., C.K. and O.B. contributed genotype and phenotype data. H.D.D., R.F., H.P., A.C., D.A.B., R.F.V., B.G., M.S.L., C.P.V., P.S. and B.J.H. contributed to writing the manuscript.

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The authors declare no competing financial interests.

Corresponding author

Correspondence to Ben J Hayes.

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