1000 Bull Genomes Consortium Project

B.J. Hayes, R. Fries, M.S. Lund, D.A. Boichard, P. Stothard, R.F. Veerkamp, C. Tassell, C.L. Anderson, B. Hulsegge, B. Guldbrandtsen, D. Rocha, D. Hinirichs, A. Bagnato, M. Georges, R.J. Spelman, J.M. Reecy, A.L. Archibald, M.E. Goddard, B. Gredler

Research output: Chapter in Book/Report/Conference proceedingConference paper

Abstract

Genomic selection, where selection decisions are based on estimates of breeding value from genome wide-marker effects, has enormous potential to improve genetic gain in dairy and beef cattle. Although successful in dairy cattle, some major challenges remain 1) only a proportion of the genetic variance is captured, particularly for some traits 2) marker effects are rarely consistent across breeds, 3) accuracy of genomic predictions decays rapidly over time. Using full genome sequences rather than DNA markers in genomic selection could address these challenges. However, sequencing all individuals in the very large resource populations required to estimate the typically small effects of mutations on target traits would be prohibitively expensive. An alternative is to sequence key ancestors contributing most of the genetic material of the current population, and to use this reference for imputation of sequence from SNP chip data. The reference set must still be large, in order to capture for example, rare variants which are likely to explain some of the variation in our target traits. Recognising the need for a comprehensive “reference set” of key ancestors by many groups undertaking cattle research and cattle breeding programs, we have initiated the 1000 bull genomes project. The project will assemble whole genome sequences of cattle from institutions around the world, to provide an extended data base for imputation of genetic variants. This will enable the bovine genomics community to impute full genome sequence from SNP genotypes, and then use this data for genomic selection, and rapid discovery of causal mutations. Some preliminary results from the variant detection pipeline will be reported.
Original languageEnglish
Title of host publicationPlant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012
Publication statusPublished - 2012
EventPlant and Animal Genome XX Conference, San Diego, CA, USA -
Duration: 14 Jan 201218 Jan 2012

Conference

ConferencePlant and Animal Genome XX Conference, San Diego, CA, USA
Period14/01/1218/01/12

Fingerprint

bulls
genome
marker-assisted selection
dairy cattle
cattle
ancestry
mutation
cattle breeding
genetic variance
breeding value
beef cattle
genetic improvement
deterioration
breeds
genomics
genetic markers
prediction
genotype

Cite this

Hayes, B. J., Fries, R., Lund, M. S., Boichard, D. A., Stothard, P., Veerkamp, R. F., ... Gredler, B. (2012). 1000 Bull Genomes Consortium Project. In Plant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012 [W139]
Hayes, B.J. ; Fries, R. ; Lund, M.S. ; Boichard, D.A. ; Stothard, P. ; Veerkamp, R.F. ; Tassell, C. ; Anderson, C.L. ; Hulsegge, B. ; Guldbrandtsen, B. ; Rocha, D. ; Hinirichs, D. ; Bagnato, A. ; Georges, M. ; Spelman, R.J. ; Reecy, J.M. ; Archibald, A.L. ; Goddard, M.E. ; Gredler, B. / 1000 Bull Genomes Consortium Project. Plant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012. 2012.
@inproceedings{5fe78588971e47c9af6a2e2de184305c,
title = "1000 Bull Genomes Consortium Project",
abstract = "Genomic selection, where selection decisions are based on estimates of breeding value from genome wide-marker effects, has enormous potential to improve genetic gain in dairy and beef cattle. Although successful in dairy cattle, some major challenges remain 1) only a proportion of the genetic variance is captured, particularly for some traits 2) marker effects are rarely consistent across breeds, 3) accuracy of genomic predictions decays rapidly over time. Using full genome sequences rather than DNA markers in genomic selection could address these challenges. However, sequencing all individuals in the very large resource populations required to estimate the typically small effects of mutations on target traits would be prohibitively expensive. An alternative is to sequence key ancestors contributing most of the genetic material of the current population, and to use this reference for imputation of sequence from SNP chip data. The reference set must still be large, in order to capture for example, rare variants which are likely to explain some of the variation in our target traits. Recognising the need for a comprehensive “reference set” of key ancestors by many groups undertaking cattle research and cattle breeding programs, we have initiated the 1000 bull genomes project. The project will assemble whole genome sequences of cattle from institutions around the world, to provide an extended data base for imputation of genetic variants. This will enable the bovine genomics community to impute full genome sequence from SNP genotypes, and then use this data for genomic selection, and rapid discovery of causal mutations. Some preliminary results from the variant detection pipeline will be reported.",
author = "B.J. Hayes and R. Fries and M.S. Lund and D.A. Boichard and P. Stothard and R.F. Veerkamp and C. Tassell and C.L. Anderson and B. Hulsegge and B. Guldbrandtsen and D. Rocha and D. Hinirichs and A. Bagnato and M. Georges and R.J. Spelman and J.M. Reecy and A.L. Archibald and M.E. Goddard and B. Gredler",
year = "2012",
language = "English",
booktitle = "Plant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012",

}

Hayes, BJ, Fries, R, Lund, MS, Boichard, DA, Stothard, P, Veerkamp, RF, Tassell, C, Anderson, CL, Hulsegge, B, Guldbrandtsen, B, Rocha, D, Hinirichs, D, Bagnato, A, Georges, M, Spelman, RJ, Reecy, JM, Archibald, AL, Goddard, ME & Gredler, B 2012, 1000 Bull Genomes Consortium Project. in Plant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012., W139, Plant and Animal Genome XX Conference, San Diego, CA, USA, 14/01/12.

1000 Bull Genomes Consortium Project. / Hayes, B.J.; Fries, R.; Lund, M.S.; Boichard, D.A.; Stothard, P.; Veerkamp, R.F.; Tassell, C.; Anderson, C.L.; Hulsegge, B.; Guldbrandtsen, B.; Rocha, D.; Hinirichs, D.; Bagnato, A.; Georges, M.; Spelman, R.J.; Reecy, J.M.; Archibald, A.L.; Goddard, M.E.; Gredler, B.

Plant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012. 2012. W139.

Research output: Chapter in Book/Report/Conference proceedingConference paper

TY - GEN

T1 - 1000 Bull Genomes Consortium Project

AU - Hayes, B.J.

AU - Fries, R.

AU - Lund, M.S.

AU - Boichard, D.A.

AU - Stothard, P.

AU - Veerkamp, R.F.

AU - Tassell, C.

AU - Anderson, C.L.

AU - Hulsegge, B.

AU - Guldbrandtsen, B.

AU - Rocha, D.

AU - Hinirichs, D.

AU - Bagnato, A.

AU - Georges, M.

AU - Spelman, R.J.

AU - Reecy, J.M.

AU - Archibald, A.L.

AU - Goddard, M.E.

AU - Gredler, B.

PY - 2012

Y1 - 2012

N2 - Genomic selection, where selection decisions are based on estimates of breeding value from genome wide-marker effects, has enormous potential to improve genetic gain in dairy and beef cattle. Although successful in dairy cattle, some major challenges remain 1) only a proportion of the genetic variance is captured, particularly for some traits 2) marker effects are rarely consistent across breeds, 3) accuracy of genomic predictions decays rapidly over time. Using full genome sequences rather than DNA markers in genomic selection could address these challenges. However, sequencing all individuals in the very large resource populations required to estimate the typically small effects of mutations on target traits would be prohibitively expensive. An alternative is to sequence key ancestors contributing most of the genetic material of the current population, and to use this reference for imputation of sequence from SNP chip data. The reference set must still be large, in order to capture for example, rare variants which are likely to explain some of the variation in our target traits. Recognising the need for a comprehensive “reference set” of key ancestors by many groups undertaking cattle research and cattle breeding programs, we have initiated the 1000 bull genomes project. The project will assemble whole genome sequences of cattle from institutions around the world, to provide an extended data base for imputation of genetic variants. This will enable the bovine genomics community to impute full genome sequence from SNP genotypes, and then use this data for genomic selection, and rapid discovery of causal mutations. Some preliminary results from the variant detection pipeline will be reported.

AB - Genomic selection, where selection decisions are based on estimates of breeding value from genome wide-marker effects, has enormous potential to improve genetic gain in dairy and beef cattle. Although successful in dairy cattle, some major challenges remain 1) only a proportion of the genetic variance is captured, particularly for some traits 2) marker effects are rarely consistent across breeds, 3) accuracy of genomic predictions decays rapidly over time. Using full genome sequences rather than DNA markers in genomic selection could address these challenges. However, sequencing all individuals in the very large resource populations required to estimate the typically small effects of mutations on target traits would be prohibitively expensive. An alternative is to sequence key ancestors contributing most of the genetic material of the current population, and to use this reference for imputation of sequence from SNP chip data. The reference set must still be large, in order to capture for example, rare variants which are likely to explain some of the variation in our target traits. Recognising the need for a comprehensive “reference set” of key ancestors by many groups undertaking cattle research and cattle breeding programs, we have initiated the 1000 bull genomes project. The project will assemble whole genome sequences of cattle from institutions around the world, to provide an extended data base for imputation of genetic variants. This will enable the bovine genomics community to impute full genome sequence from SNP genotypes, and then use this data for genomic selection, and rapid discovery of causal mutations. Some preliminary results from the variant detection pipeline will be reported.

M3 - Conference paper

BT - Plant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012

ER -

Hayes BJ, Fries R, Lund MS, Boichard DA, Stothard P, Veerkamp RF et al. 1000 Bull Genomes Consortium Project. In Plant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012. 2012. W139