Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
2014
Daetwyler, Hans D | Capitan, Aurelien | Pausch, Hubert | Stothard, Paul | van Binsbergen, Rianne | Brøndum, Rasmus F | Liao, Xiaoping | Djari, Anis | Rodriguez, Sabrina | Grohs, Cécile | Esquerre, Diane | Bouchez, Olivier | Rossignol, Marie-Noelle | Klopp, Christophe | Rocha, Dominique | Fritz, Sébastien | Eggen, Andre | Bowman, Phil J | Coote, David | Chamberlain, Amanda J | Anderson, Charlotte | Vantassell, Curt P | Hulsegge, Ina | Goddard, Mike E | Guldbrandtsen, Bernt | Lund, Mogens S | Veerkamp, Roel F | Boichard, Didier | Fries, Ruedi | Hayes, Ben J | Biosciences Research Division ; Department of Environment and Primary Industries | School of Applied Systems Biology ; La Trobe University [Melbourne] | Dairy Futures Cooperative Research Centre | Génétique Animale et Biologie Intégrative (GABI) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA) | Chair of Animal Breeding ; Technische Universität Munchen - Technical University Munich - Université Technique de Munich (TUM) | Department of Agricultural, Food and Nutritional Science ; University of Alberta | Animal Breeding and Genomics Centre ; Wageningen University and Research [Wageningen] (WUR) | Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics ; Aarhus University [Aarhus] | Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA) ; Institut National de la Recherche Agronomique (INRA) | Laboratoire de Génétique Cellulaire (LGC) ; Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT) | Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA) ; Institut National de la Recherche Agronomique (INRA) | Animal and Natural Resources Institute, Bovine Functional Genomics Laboratory, BARC-East ; United States Department of Agriculture | Faculty of Land and Food Resources ; University of Melbourne | German Federal Ministry of Education and Research (BMBF) [0315527B]; Genome Canada project entitled 'Whole-Genome Sequence Selection Through Genome-Wide Imputation in Beef Cattle'; Agence Nationale de la Recherche; Apisgene [ANR-10-GENM-0018]; Green Development and Demonstration Programme of the Danish Ministry of Food, Agriculture and Fisheries [3405-10-0137]; Milk Levy Fund; Strategic Research Council and Viking Genetics [12-132452 (GenSAP)]; USDA-ARS [1245-31000-104-00D]; USDA-National Institute of Food and Agriculture (NIFA) competitive grant from the Animal Genome Program [2009-65205-05635]; Dairy Futures Cooperative Research Centre, Dairy Australia; Cooperative Research Centre for Beef Genetic Technologies | ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
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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