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

Hans D  Daetwyler; Aurélien  Capitan; Hubert  Pausch; Paul  Stothard; Rianne  van Binsbergen; Rasmus Froberg Brøndum; Xiaoping Liao; Anis  Djari; Sabrina C  Rodriguez; Cécile  Grohs; Simone  Jung; Diane  Esquerré; Olivier  Bouchez; Nicole S  Gollnick; Marie-Noëlle  Rossignol; Christophe  Klopp; Dominique  Rocha; Sébastien  Fritz; André  Eggen; Phil J  Bowman; David  Coote; Amanda J  Chamberlain; Curt P  VanTassell; Ina  Hulsegge; Mike E  Goddard; Bernt Guldbrandtsen; Mogens Sandø Lund; Roel F  Veerkamp; Didier A  Boichard; Ruedi  Fries; Ben J  Hayes

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

Hans D Daetwyler, Aurélien Capitan, Hubert Pausch, Paul Stothard, Rianne van Binsbergen, Rasmus Froberg Brøndum, Xiaoping Liao, Anis Djari, Sabrina C Rodriguez, Cécile Grohs, Simone Jung, Diane Esquerré, Olivier Bouchez, Nicole S Gollnick, Marie-Noëlle Rossignol, Christophe Klopp, Dominique Rocha, Sébastien Fritz, André Eggen, Phil J BowmanDavid Coote, Amanda J Chamberlain, Curt P VanTassell, Ina Hulsegge, Mike E Goddard, Bernt Guldbrandtsen, Mogens Sandø Lund, Roel F Veerkamp, Didier A Boichard, Ruedi Fries, Ben J Hayes

Center for Quantitative Genetics and Genomics

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

613 Citations (Scopus)

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

Original language	English
Journal	Nature Genetics
Volume	46
Issue	8
Pages (from-to)	858 - 865
Number of pages	7
ISSN	1061-4036
Publication status	Published - 13 Jul 2014

GenSAP : GenSAP - Center for Genomic Selection in Animal and Plants
Lund, M. S. (Project manager), Sørensen, P. (Project manager), Janss, L. (Project manager), Sørensen, A. C. (Project manager), Dybdahl Pedersen, L. (Project coordinator), Jensen, J. (Participant), Christensen, O. F. (Participant), Guldbrandtsen, B. (Participant), Asp, T. (Participant), Bendixen, C. (Participant), Su, G. (Participant), Madsen, P. (Participant), Brøndum, R. F. (Participant), Rasmussen, S. K. (Participant), Nielsen, K. L. (Participant), Goddard, M. (Participant), Meuwissen, T. (Participant), Mackay, T. (Participant), Boichard, D. (Participant), Zhang, Q. (Participant) & Gianola, D. (Participant)
Det Strategiske Forskningsråd, Programkomiteen for Sunhed, fødevarer og velfærd
01/01/2013 → 31/12/2018
Project: Research

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Daetwyler, H. D., Capitan, A., Pausch, H., Stothard, P., van Binsbergen, R., Brøndum, R. F., Liao, X., Djari, A., Rodriguez, S. C., Grohs, C., Jung, S., Esquerré, D., Bouchez, O., Gollnick, N. S., Rossignol, M.-N., Klopp, C., Rocha, D., Fritz, S., Eggen, A., ... Hayes, B. J. (2014). Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics, 46(8), 858 - 865.

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title = "Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle",

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",

author = "Daetwyler, {Hans D} and Aur{\'e}lien Capitan and Hubert Pausch and Paul Stothard and {van Binsbergen}, Rianne and Br{\o}ndum, {Rasmus Froberg} and Xiaoping Liao and Anis Djari and Rodriguez, {Sabrina C} and C{\'e}cile Grohs and Simone Jung and Diane Esquerr{\'e} and Olivier Bouchez and Gollnick, {Nicole S} and Marie-No{\"e}lle Rossignol and Christophe Klopp and Dominique Rocha and S{\'e}bastien Fritz and Andr{\'e} Eggen and Bowman, {Phil J} and David Coote and Chamberlain, {Amanda J} and VanTassell, {Curt P} and Ina Hulsegge and Goddard, {Mike E} and Bernt Guldbrandtsen and Lund, {Mogens Sand{\o}} and Veerkamp, {Roel F} and Boichard, {Didier A} and Ruedi Fries and Hayes, {Ben J}",

note = "Project 12225",

year = "2014",

month = jul,

day = "13",

language = "English",

volume = "46",

pages = "858 -- 865",

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Daetwyler, HD, Capitan, A, Pausch, H, Stothard, P, van Binsbergen, R, Brøndum, RF, Liao, X, Djari, A, Rodriguez, SC, Grohs, C, Jung, S, Esquerré, D, Bouchez, O, Gollnick, NS, Rossignol, M-N, Klopp, C, Rocha, D, Fritz, S, Eggen, A, Bowman, PJ, Coote, D, Chamberlain, AJ, VanTassell, CP, Hulsegge, I, Goddard, ME, Guldbrandtsen, B, Lund, MS, Veerkamp, RF, Boichard, DA, Fries, R & Hayes, BJ 2014, 'Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle', Nature Genetics, vol. 46, no. 8, pp. 858 - 865.

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. / Daetwyler, Hans D ; Capitan, Aurélien ; Pausch, Hubert et al.
In: Nature Genetics, Vol. 46, No. 8, 13.07.2014, p. 858 - 865.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

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T1 - Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

AU - Daetwyler, Hans D

AU - Capitan, Aurélien

AU - Pausch, Hubert

AU - Stothard, Paul

AU - van Binsbergen, Rianne

AU - Brøndum, Rasmus Froberg

AU - Liao, Xiaoping

AU - Djari, Anis

AU - Rodriguez, Sabrina C

AU - Grohs, Cécile

AU - Jung, Simone

AU - Esquerré, Diane

AU - Bouchez, Olivier

AU - Gollnick, Nicole S

AU - Rossignol, Marie-Noëlle

AU - Klopp, Christophe

AU - Rocha, Dominique

AU - Fritz, Sébastien

AU - Eggen, André

AU - Bowman, Phil J

AU - Coote, David

AU - Chamberlain, Amanda J

AU - VanTassell, Curt P

AU - Hulsegge, Ina

AU - Goddard, Mike E

AU - Guldbrandtsen, Bernt

AU - Lund, Mogens Sandø

AU - Veerkamp, Roel F

AU - Boichard, Didier A

AU - Fries, Ruedi

AU - Hayes, Ben J

N1 - Project 12225

PY - 2014/7/13

Y1 - 2014/7/13

N2 - 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

AB - 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

M3 - Journal article

SN - 1061-4036

VL - 46

SP - 858

EP - 865

JO - Nature Genetics

JF - Nature Genetics

IS - 8

ER -

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

Abstract

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GenSAP : GenSAP - Center for Genomic Selection in Animal and Plants

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