About the Authors

Amaury Vaysse

Contributed equally to this work with: Amaury Vaysse, Abhirami Ratnakumar

Affiliation Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, Rennes, France

Abhirami Ratnakumar

Contributed equally to this work with: Amaury Vaysse, Abhirami Ratnakumar

Affiliation Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

Thomas Derrien

Affiliation Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, Rennes, France

Erik Axelsson

Affiliation Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

Gerli Rosengren Pielberg

Affiliation Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

Snaevar Sigurdsson

Affiliation Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

Tove Fall

Affiliation Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden

Eija H. Seppälä

Affiliation Department of Veterinary Biosciences, Research Programs Unit, Molecular Medicine, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland

Mark S. T. Hansen

Affiliation Illumina, San Diego, California, United States of America

Cindy T. Lawley

Affiliation Illumina, San Diego, California, United States of America

Elinor K. Karlsson

Affiliations Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America

The LUPA Consortium
Danika Bannasch

Affiliation Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America

Carles Vilà

Affiliation Department of Integrative Ecology, Doñana Biological Station (CSIC), Seville, Spain

Hannes Lohi

Affiliation Department of Veterinary Biosciences, Research Programs Unit, Molecular Medicine, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland

Francis Galibert

Affiliation Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, Rennes, France

Merete Fredholm

Affiliation Faculty of Life Sciences, Division of Genetics and Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, Frederiksberg, Denmark

Jens Häggström

Affiliation Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden

Åke Hedhammar

Affiliation Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden

Catherine André

Affiliation Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, Rennes, France

Kerstin Lindblad-Toh

Affiliations Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

Christophe Hitte

Affiliation Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, Rennes, France

Matthew T. Webster

matthew.webster@imbim.uu.se

Affiliation Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: KL-T CH MTW. Performed the experiments: GRP SS MSTH CTL. Analyzed the data: AV (di, FDR analysis), AR (phasing and imputation, Si, XP-EHH, shared haplotype analysis), TD (browser display), EA (coalescent simulations), KL-T (input on all analyses), CH (GO analysis), MTW (SNP discovery analysis, HD array design, dataset construction, breed relationships, across-breed GWAS, FST, chromosome 10 resequencing, FDR analysis). Contributed reagents/materials/analysis tools: TF EKK EHS DB CV HL FG MF JH ÅH CA KL-T. Wrote the paper: AV AR KL-T CH MTW.