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Nat Genet. 2014 Aug;46(8):858-65. doi: 10.1038/ng.3034. Epub 2014 Jul 13.

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle.

Author information

1
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.
2
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.
3
Chair of Animal Breeding, Technische Universitaet Muenchen, Freising-Weihenstephan, Germany.
4
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
5
Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Livestock Research, Wageningen, the Netherlands.
6
Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.
7
Institut National de la Recherche Agronomique (INRA), Sigenae Bioinformatics Group, UR875, Castanet, France.
8
Institut National de la Recherche Agronomique (INRA), UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
9
Institut National de la Recherche Agronomique (INRA), Get-Plage, UMR 444 Laboratoire de Génétique Cellulaire, Castanet, France.
10
LABOGENA, Jouy-en-Josas, France.
11
Union Nationale des Coopératives d'Elevage et d'Insémination Animale, Paris, France.
12
1] Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia. [2] Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia.
13
Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia.
14
US Department of Agriculture, Agricultural Research Service (USDA-ARS), Animal and Natural Resources Institute, Bovine Functional Genomics Laboratory, BARC-East, Beltsville, Maryland, USA.
15
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.

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.

PMID:
25017103
DOI:
10.1038/ng.3034
[Indexed for MEDLINE]

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