Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes

Nasiroddin Moghaddar; Andrew Swan; Julius H Van Der Werf

Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes

Nasiroddin Moghaddar
, Andrew Swan
, Julius H Van Der Werf

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

Abstract

High-density (HD) marker genotypes could increase the accuracy of genomic prediction by providing stronger linkage disequilibrium (LD) between markers and quantitative trait loci affecting a trait, especially in populations with a high genetic diversity such as Australian Merino sheep. The aim of this study was to compare the accuracy of genomic prediction for Merino yearling and adult wool traits based on observed and imputed 600K single nucleotide polymorphism (SNP) marker genotypes with the accuracy based on moderate-density (50K) marker genotypes. Genomic best linear unbiased prediction (GBLUP) and a Bayesian approach (BayesR) were used as prediction methods. Results showed a small relative increase in accuracy between 2 to 15% (of the previous accuracy) when using a HD marker set. The results of BayesR were on average similar to GBLUP. Considerably higher (up to 25% relative increase) in prediction accuracy was observed for animals with lower genomic relationship to the reference population.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	Kim Bunter, Tim Byrne, Hans Daetwyler, Susanne Hermesch, Kathryn Kemper, James Kijas, David Nation, Wayne Pitchford, Suzanne Rowe, Matt Shaffer, Alison van Eenennaam
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	165-168
Volume	21
ISBN (Print)	9780646945545
Publication status	Published - 2015
Event	AAABG 2015: 21st Conference of the Association for the Advancement of Animal Breeding and Genetics - Lorne, Australia Duration: 28 Sept 2015 → 30 Sept 2015

Conference

Conference	AAABG 2015: 21st Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Lorne, Australia
Period	28/09/15 → 30/09/15

Keywords

Animal Breeding

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Moghaddar, N., Swan, A., & Van Der Werf, J. H. (2015). Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes. In K. Bunter, T. Byrne, H. Daetwyler, S. Hermesch, K. Kemper, J. Kijas, D. Nation, W. Pitchford, S. Rowe, M. Shaffer, & A. van Eenennaam (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 21, pp. 165-168). Association for the Advancement of Animal Breeding and Genetics (AAABG). http://www.aaabg.org/aaabghome/AAABG21papers/Moghaddar21165.pdf

Moghaddar, Nasiroddin ; Swan, Andrew ; Van Der Werf, Julius H. / Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / Kim Bunter ; Tim Byrne ; Hans Daetwyler ; Susanne Hermesch ; Kathryn Kemper ; James Kijas ; David Nation ; Wayne Pitchford ; Suzanne Rowe ; Matt Shaffer ; Alison van Eenennaam. Vol. 21 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2015. pp. 165-168

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title = "Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes",

abstract = "High-density (HD) marker genotypes could increase the accuracy of genomic prediction by providing stronger linkage disequilibrium (LD) between markers and quantitative trait loci affecting a trait, especially in populations with a high genetic diversity such as Australian Merino sheep. The aim of this study was to compare the accuracy of genomic prediction for Merino yearling and adult wool traits based on observed and imputed 600K single nucleotide polymorphism (SNP) marker genotypes with the accuracy based on moderate-density (50K) marker genotypes. Genomic best linear unbiased prediction (GBLUP) and a Bayesian approach (BayesR) were used as prediction methods. Results showed a small relative increase in accuracy between 2 to 15\% (of the previous accuracy) when using a HD marker set. The results of BayesR were on average similar to GBLUP. Considerably higher (up to 25\% relative increase) in prediction accuracy was observed for animals with lower genomic relationship to the reference population.",

keywords = "Animal Breeding",

author = "Nasiroddin Moghaddar and Andrew Swan and \{Van Der Werf\}, \{Julius H\}",

year = "2015",

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booktitle = "Proceedings of the Association for the Advancement of Animal Breeding and Genetics",

publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

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Moghaddar, N, Swan, A & Van Der Werf, JH 2015, Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes. in K Bunter, T Byrne, H Daetwyler, S Hermesch, K Kemper, J Kijas, D Nation, W Pitchford, S Rowe, M Shaffer & A van Eenennaam (eds), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 21, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 165-168, AAABG 2015: 21st Conference of the Association for the Advancement of Animal Breeding and Genetics, Lorne, Australia, 28/09/15. <http://www.aaabg.org/aaabghome/AAABG21papers/Moghaddar21165.pdf>

Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes. / Moghaddar, Nasiroddin; Swan, Andrew; Van Der Werf, Julius H.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / Kim Bunter; Tim Byrne; Hans Daetwyler; Susanne Hermesch; Kathryn Kemper; James Kijas; David Nation; Wayne Pitchford; Suzanne Rowe; Matt Shaffer; Alison van Eenennaam. Vol. 21 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2015. p. 165-168.

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

TY - GEN

T1 - Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes

AU - Moghaddar, Nasiroddin

AU - Swan, Andrew

AU - Van Der Werf, Julius H

PY - 2015

Y1 - 2015

N2 - High-density (HD) marker genotypes could increase the accuracy of genomic prediction by providing stronger linkage disequilibrium (LD) between markers and quantitative trait loci affecting a trait, especially in populations with a high genetic diversity such as Australian Merino sheep. The aim of this study was to compare the accuracy of genomic prediction for Merino yearling and adult wool traits based on observed and imputed 600K single nucleotide polymorphism (SNP) marker genotypes with the accuracy based on moderate-density (50K) marker genotypes. Genomic best linear unbiased prediction (GBLUP) and a Bayesian approach (BayesR) were used as prediction methods. Results showed a small relative increase in accuracy between 2 to 15% (of the previous accuracy) when using a HD marker set. The results of BayesR were on average similar to GBLUP. Considerably higher (up to 25% relative increase) in prediction accuracy was observed for animals with lower genomic relationship to the reference population.

AB - High-density (HD) marker genotypes could increase the accuracy of genomic prediction by providing stronger linkage disequilibrium (LD) between markers and quantitative trait loci affecting a trait, especially in populations with a high genetic diversity such as Australian Merino sheep. The aim of this study was to compare the accuracy of genomic prediction for Merino yearling and adult wool traits based on observed and imputed 600K single nucleotide polymorphism (SNP) marker genotypes with the accuracy based on moderate-density (50K) marker genotypes. Genomic best linear unbiased prediction (GBLUP) and a Bayesian approach (BayesR) were used as prediction methods. Results showed a small relative increase in accuracy between 2 to 15% (of the previous accuracy) when using a HD marker set. The results of BayesR were on average similar to GBLUP. Considerably higher (up to 25% relative increase) in prediction accuracy was observed for animals with lower genomic relationship to the reference population.

KW - Animal Breeding

UR - http://www.aaabg.org/aaabghome/proceedings21.php

M3 - Conference contribution

SN - 9780646945545

VL - 21

SP - 165

EP - 168

BT - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

A2 - Bunter, Kim

A2 - Byrne, Tim

A2 - Daetwyler, Hans

A2 - Hermesch, Susanne

A2 - Kemper, Kathryn

A2 - Kijas, James

A2 - Nation, David

A2 - Pitchford, Wayne

A2 - Rowe, Suzanne

A2 - Shaffer, Matt

A2 - van Eenennaam, Alison

PB - Association for the Advancement of Animal Breeding and Genetics (AAABG)

CY - Armidale, Australia

T2 - AAABG 2015: 21st Conference of the Association for the Advancement of Animal Breeding and Genetics

Y2 - 28 September 2015 through 30 September 2015

ER -

Moghaddar N, Swan A, Van Der Werf JH. Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes. In Bunter K, Byrne T, Daetwyler H, Hermesch S, Kemper K, Kijas J, Nation D, Pitchford W, Rowe S, Shaffer M, van Eenennaam A, editors, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 21. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2015. p. 165-168

Accuracy of Genomic Prediction for Merino Wool Traits Using High-Density Marker Genotypes

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