Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
Hans D Daetwyler
(1, 2, 3)
,
Aurelien Capitan
(4, 5)
,
Hubert Pausch
(6)
,
Paul Stothard
(7)
,
Rianne van Binsbergen
(8)
,
Rasmus F Brøndum
(9)
,
Xiaoping Liao
(7)
,
Anis Djari
(10)
,
Sabrina Rodriguez
(4)
,
Cécile Grohs
(4)
,
Diane Esquerre
(11)
,
Olivier Bouchez
(11)
,
Marie-Noelle Rossignol
(12)
,
Christophe C. Klopp
(10)
,
Dominique Rocha
(4)
,
Sébastien Fritz
(5)
,
Andre Eggen
(4)
,
Phil J Bowman
(1, 3)
,
David Coote
(1, 3)
,
Amanda J Chamberlain
(1, 3)
,
Charlotte Anderson
(1)
,
Curt P Vantassell
(13)
,
Ina Hulsegge
(8)
,
Mike E Goddard
(1, 3, 14)
,
Bernt Guldbrandtsen
(9)
,
Mogens S Lund
(9)
,
Roel F Veerkamp
(8)
,
Didier Boichard
(4)
,
Ruedi Fries
(6)
,
Ben J Hayes
(1, 2, 3)
1
Biosciences Research Division
2 School of Applied Systems Biology
3 Dairy Futures Cooperative Research Centre
4 GABI - Génétique Animale et Biologie Intégrative
5 UNCEIA - Union nationale des coopératives d’élevage et d’insémination animale
6 Chair of Animal Breeding
7 Department of Agricultural, Food and Nutritional Science
8 Animal Breeding and Genomics Centre
9 Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics
10 UBIA - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)
11 LGC - Laboratoire de Génétique Cellulaire
12 LABOGENA - Laboratoire d'Analyse Génétique pour les Espèces Animales
13 Animal and Natural Resources Institute, Bovine Functional Genomics Laboratory, BARC-East
14 Faculty of Land and Food Resources
2 School of Applied Systems Biology
3 Dairy Futures Cooperative Research Centre
4 GABI - Génétique Animale et Biologie Intégrative
5 UNCEIA - Union nationale des coopératives d’élevage et d’insémination animale
6 Chair of Animal Breeding
7 Department of Agricultural, Food and Nutritional Science
8 Animal Breeding and Genomics Centre
9 Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics
10 UBIA - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)
11 LGC - Laboratoire de Génétique Cellulaire
12 LABOGENA - Laboratoire d'Analyse Génétique pour les Espèces Animales
13 Animal and Natural Resources Institute, Bovine Functional Genomics Laboratory, BARC-East
14 Faculty of Land and Food Resources
Anis Djari
- Fonction : Auteur
- PersonId : 974345
- ORCID : 0000-0002-9093-440X
Sabrina Rodriguez
- Fonction : Auteur
- PersonId : 1205148
- IdHAL : sabrina-legoueix
Cécile Grohs
- Fonction : Auteur
- PersonId : 744404
- IdHAL : cecile-grohs
- ORCID : 0000-0002-3563-8966
Diane Esquerre
- Fonction : Auteur
- PersonId : 1203847
- ORCID : 0000-0001-6646-1932
Olivier Bouchez
- Fonction : Auteur
- PersonId : 1151095
- IdHAL : obouchez
- ORCID : 0000-0002-7255-0058
Christophe C. Klopp
- Fonction : Auteur
- PersonId : 735911
- IdHAL : 0000-0001-7126-5477
- ORCID : 0000-0001-7126-5477
Dominique Rocha
- Fonction : Auteur
- PersonId : 744969
- IdHAL : dominique-rocha
- ORCID : 0000-0003-4998-9641
- IdRef : 183665732
Sébastien Fritz
- Fonction : Auteur
- PersonId : 766840
- ORCID : 0000-0002-3378-1048
Bernt Guldbrandtsen
- Fonction : Auteur
- PersonId : 769945
- ORCID : 0000-0003-1764-135X
Didier Boichard
- Fonction : Auteur
- PersonId : 744221
- IdHAL : didier-boichard
- ORCID : 0000-0003-0361-2961
- IdRef : 132520087
Résumé
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.