Genomic selection using a fast EM algorythm. 2. Analysis of simulated data

R.K. Shepherd; T.H.E. Meuwissen; J.A. Woolliams

Genomic selection using a fast EM algorythm. 2. Analysis of simulated data

R.K. Shepherd, T.H.E. Meuwissen, J.A. Woolliams

Royal (Dick) School of Veterinary Studies

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

The paper reports on a fast EM algorithm for genomic selection by mapping QTL in genome-wide dense SNP marker data. The algorithm called emBayesB was used to analyse a 6000 SNP dataset simulated for the QTLMAS XII workshop. True breeding value was accurately predicted by GEBV with a correlation of 0.85 in the validation data, while the regression coefficient of 0.97 indicated unbiased predictions of breeding value. The results were similar to Bayesian MCMC estimates but were calculated in a fraction of the time. emBayesB was also able to accurately map the location of individual QTL which explain more than 1% of the total genetic variation.

Original language	Undefined/Unknown
Title of host publication	Proceedings of the 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, South Australia, 28 September - 1 October 2009
Place of Publication	Adelaide
Publisher	Association for the Advancement of Animal Breeding and Genetics
Pages	84-87
Number of pages	4
Publication status	Published - 2009
Event	Association for the Advancement of Animal Breeding and Genetics - Barossa Valley, Australia Duration: 28 Sep 2009 → 1 Oct 2009

Conference

Conference	Association for the Advancement of Animal Breeding and Genetics
Country	Australia
City	Barossa Valley
Period	28/09/09 → 1/10/09

Access to Document

http://www.aaabg.org/proceedings18/index.html

Cite this

Shepherd, R. K., Meuwissen, T. H. E., & Woolliams, J. A. (2009). Genomic selection using a fast EM algorythm. 2. Analysis of simulated data. In Proceedings of the 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, South Australia, 28 September - 1 October 2009 (pp. 84-87). Association for the Advancement of Animal Breeding and Genetics. http://www.aaabg.org/proceedings18/index.html

Shepherd, R.K. ; Meuwissen, T.H.E. ; Woolliams, J.A. / Genomic selection using a fast EM algorythm. 2. Analysis of simulated data. Proceedings of the 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, South Australia, 28 September - 1 October 2009. Adelaide : Association for the Advancement of Animal Breeding and Genetics, 2009. pp. 84-87

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abstract = "The paper reports on a fast EM algorithm for genomic selection by mapping QTL in genome-wide dense SNP marker data. The algorithm called emBayesB was used to analyse a 6000 SNP dataset simulated for the QTLMAS XII workshop. True breeding value was accurately predicted by GEBV with a correlation of 0.85 in the validation data, while the regression coefficient of 0.97 indicated unbiased predictions of breeding value. The results were similar to Bayesian MCMC estimates but were calculated in a fraction of the time. emBayesB was also able to accurately map the location of individual QTL which explain more than 1% of the total genetic variation.",

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Shepherd, RK, Meuwissen, THE & Woolliams, JA 2009, Genomic selection using a fast EM algorythm. 2. Analysis of simulated data. in Proceedings of the 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, South Australia, 28 September - 1 October 2009. Association for the Advancement of Animal Breeding and Genetics, Adelaide, pp. 84-87, Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, Australia, 28/09/09. <http://www.aaabg.org/proceedings18/index.html>

Genomic selection using a fast EM algorythm. 2. Analysis of simulated data. / Shepherd, R.K.; Meuwissen, T.H.E.; Woolliams, J.A.

Proceedings of the 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, South Australia, 28 September - 1 October 2009. Adelaide : Association for the Advancement of Animal Breeding and Genetics, 2009. p. 84-87.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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N2 - The paper reports on a fast EM algorithm for genomic selection by mapping QTL in genome-wide dense SNP marker data. The algorithm called emBayesB was used to analyse a 6000 SNP dataset simulated for the QTLMAS XII workshop. True breeding value was accurately predicted by GEBV with a correlation of 0.85 in the validation data, while the regression coefficient of 0.97 indicated unbiased predictions of breeding value. The results were similar to Bayesian MCMC estimates but were calculated in a fraction of the time. emBayesB was also able to accurately map the location of individual QTL which explain more than 1% of the total genetic variation.

AB - The paper reports on a fast EM algorithm for genomic selection by mapping QTL in genome-wide dense SNP marker data. The algorithm called emBayesB was used to analyse a 6000 SNP dataset simulated for the QTLMAS XII workshop. True breeding value was accurately predicted by GEBV with a correlation of 0.85 in the validation data, while the regression coefficient of 0.97 indicated unbiased predictions of breeding value. The results were similar to Bayesian MCMC estimates but were calculated in a fraction of the time. emBayesB was also able to accurately map the location of individual QTL which explain more than 1% of the total genetic variation.

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Shepherd RK, Meuwissen THE, Woolliams JA. Genomic selection using a fast EM algorythm. 2. Analysis of simulated data. In Proceedings of the 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, South Australia, 28 September - 1 October 2009. Adelaide: Association for the Advancement of Animal Breeding and Genetics. 2009. p. 84-87