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Comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )QTL-MAS Workshop

BACKGROUND: Genomic breeding value estimation is the key step in genomic selection. Among many approaches, BLUP methods and Bayesian methods are most commonly used for estimating genomic breeding values. Here, we applied two BLUP methods, TABLUP and GBLUP, and three Bayesian methods, BayesA, BayesB...

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Autores principales: Wang, Chong-Long, Ma, Pei-Pei, Zhang, Zhe, Ding, Xiang-Dong, Liu, Jian-Feng, Fu, Wei-Xuan, Weng, Zi-Qing, Zhang, Qin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3363155/
https://www.ncbi.nlm.nih.gov/pubmed/22640547
http://dx.doi.org/10.1186/1753-6561-6-S2-S13
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author Wang, Chong-Long
Ma, Pei-Pei
Zhang, Zhe
Ding, Xiang-Dong
Liu, Jian-Feng
Fu, Wei-Xuan
Weng, Zi-Qing
Zhang, Qin
author_facet Wang, Chong-Long
Ma, Pei-Pei
Zhang, Zhe
Ding, Xiang-Dong
Liu, Jian-Feng
Fu, Wei-Xuan
Weng, Zi-Qing
Zhang, Qin
author_sort Wang, Chong-Long
collection PubMed
description BACKGROUND: Genomic breeding value estimation is the key step in genomic selection. Among many approaches, BLUP methods and Bayesian methods are most commonly used for estimating genomic breeding values. Here, we applied two BLUP methods, TABLUP and GBLUP, and three Bayesian methods, BayesA, BayesB and BayesCπ, to the common dataset provided by the 15(th )QTL-MAS Workshop to evaluate and compare their predictive performances. RESULTS: For the 1000 progenies without phenotypic values, the correlations between GEBVs by different methods ranged from 0.812 (GBLUP and BayesCπ) to 0.997 (TABLUP and BayesB). The accuracies of GEBVs (measured as correlations between true breeding values (TBVs) and GEBVs) were from 0.774 (GBLUP) to 0.938 (BayesCπ) and the biases of GEBVs (measure as regressions of TBVs on GEBVs) were from 1.033 (TABLUP) to 1.648 (GBLUP). The three Bayesian methods and TABLUP had similar accuracy and bias. CONCLUSIONS: BayesA, BayesB, BayesCπ and TABLUP performed similarly and satisfactorily and remarkably outperformed GBLUP for genomic breeding value estimation in this dataset. TABLUP is a promising method for genomic breeding value estimation because of its easy computation of reliabilities of GEBVs and its easy extension to real life conditions such as multiple traits and consideration of individuals without genotypes.
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spelling pubmed-33631552012-06-01 Comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )QTL-MAS Workshop Wang, Chong-Long Ma, Pei-Pei Zhang, Zhe Ding, Xiang-Dong Liu, Jian-Feng Fu, Wei-Xuan Weng, Zi-Qing Zhang, Qin BMC Proc Proceedings BACKGROUND: Genomic breeding value estimation is the key step in genomic selection. Among many approaches, BLUP methods and Bayesian methods are most commonly used for estimating genomic breeding values. Here, we applied two BLUP methods, TABLUP and GBLUP, and three Bayesian methods, BayesA, BayesB and BayesCπ, to the common dataset provided by the 15(th )QTL-MAS Workshop to evaluate and compare their predictive performances. RESULTS: For the 1000 progenies without phenotypic values, the correlations between GEBVs by different methods ranged from 0.812 (GBLUP and BayesCπ) to 0.997 (TABLUP and BayesB). The accuracies of GEBVs (measured as correlations between true breeding values (TBVs) and GEBVs) were from 0.774 (GBLUP) to 0.938 (BayesCπ) and the biases of GEBVs (measure as regressions of TBVs on GEBVs) were from 1.033 (TABLUP) to 1.648 (GBLUP). The three Bayesian methods and TABLUP had similar accuracy and bias. CONCLUSIONS: BayesA, BayesB, BayesCπ and TABLUP performed similarly and satisfactorily and remarkably outperformed GBLUP for genomic breeding value estimation in this dataset. TABLUP is a promising method for genomic breeding value estimation because of its easy computation of reliabilities of GEBVs and its easy extension to real life conditions such as multiple traits and consideration of individuals without genotypes. BioMed Central 2012-05-21 /pmc/articles/PMC3363155/ /pubmed/22640547 http://dx.doi.org/10.1186/1753-6561-6-S2-S13 Text en Copyright ©2012 Wang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Wang, Chong-Long
Ma, Pei-Pei
Zhang, Zhe
Ding, Xiang-Dong
Liu, Jian-Feng
Fu, Wei-Xuan
Weng, Zi-Qing
Zhang, Qin
Comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )QTL-MAS Workshop
title Comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )QTL-MAS Workshop
title_full Comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )QTL-MAS Workshop
title_fullStr Comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )QTL-MAS Workshop
title_full_unstemmed Comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )QTL-MAS Workshop
title_short Comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )QTL-MAS Workshop
title_sort comparison of five methods for genomic breeding value estimation for the common dataset of the 15(th )qtl-mas workshop
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3363155/
https://www.ncbi.nlm.nih.gov/pubmed/22640547
http://dx.doi.org/10.1186/1753-6561-6-S2-S13
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