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

by Agence Nationale de la Recherche , Daetwyler, Hans D , Klopp, Christophe , Hulsegge, Ina , Hayes, Ben J , Anderson, Charlotte , Stothard, Paul , School of Applied Systems Biology , Milk Levy Fund , Fritz, Sébastien , USDA-ARS , Lund, Mogens S , Eggen, Andre , Rodriguez, Sabrina , Chamberlain, Amanda J , Apisgene , Liao, Xiaoping , Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA) , Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA) , Bouchez, Olivier , Bowman, Phil J , Djari, Anis , Rossignol, Marie-Noelle , Boichard, Didier , Chair of Animal Breeding , Rocha, Dominique , Grohs, Cécile , Esquerre, Diane , Génétique Animale et Biologie Intégrative (GABI) , Capitan, Aurelien , Brøndum, Rasmus F , Veerkamp, Roel F , Fries, Ruedi , Goddard, Mike E , van Binsbergen, Rianne , Guldbrandtsen, Bernt , Pausch, Hubert , Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA) , Laboratoire de Génétique Cellulaire (LGC) , Faculty of Land and Food Resources , Vantassell, Curt P , Coote, David

in 38/43 / 631/208/212 / 631/208/514/1948 / 631/601/1737 / Agriculture / Amino Acid Sequence / Animal Genetics and Genomics / Animal welfare / Animals / Biomedicine / boophilus-microplus resistance / bos-taurus / Breeding of animals / Cancer Research / Cattle / Cattle - genetics / Chromosomes / condensin / dairy-cattle / DNA sequencing / gene / Gene Function / Genetic aspects / Genetic diversity / Genetic improvement / Genome / Genome-Wide Association Study - methods / Genomes / Genomics / Genotype / genotype imputation / Genotypes / holstein calves / Human Genetics / Life Sciences / Male / Methods / Milk / Milk production / milk-yield / mitotic chromosomes / Molecular Sequence Data / Mutation / mutations / Nucleotide sequencing / Polymorphism, Single Nucleotide / Population / Sequence Homology, Amino Acid / Studies

2014

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

2014

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2014

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Journal Article

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

Agence Nationale de la Recherche,

Daetwyler, Hans D,

Klopp, Christophe,

Hulsegge, Ina,

Hayes, Ben J,

Anderson, Charlotte,

Stothard, Paul,

School of Applied Systems Biology,

Milk Levy Fund,

Fritz, Sébastien,

USDA-ARS,

Lund, Mogens S,

Eggen, Andre,

Rodriguez, Sabrina,

Chamberlain, Amanda J,

Apisgene,

Liao, Xiaoping,

Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA),

Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA),

Bouchez, Olivier,

Bowman, Phil J,

Djari, Anis,

Rossignol, Marie-Noelle,

Boichard, Didier,

Chair of Animal Breeding,

Rocha, Dominique,

Grohs, Cécile,

Esquerre, Diane,

Génétique Animale et Biologie Intégrative (GABI),

Capitan, Aurelien,

Brøndum, Rasmus F,

Veerkamp, Roel F,

Fries, Ruedi,

Goddard, Mike E,

van Binsbergen, Rianne,

Guldbrandtsen, Bernt,

Pausch, Hubert,

Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA),

Laboratoire de Génétique Cellulaire (LGC),

Faculty of Land and Food Resources,

Vantassell, Curt P,

Coote, David

2014

Overview

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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Publisher

Nature Publishing Group,CCSD,Nature Publishing Group US

Subject

/ Amino Acid Sequence

/ Animal Genetics and Genomics