Application of multi-trait Bayesian decision theory for parental genomic selection
In all breeding programs, the decision about which individuals to select and intermate to form the next selection cycle is crucial. The improvement of genetic stocks requires considering multiple traits simultaneously, given that economic value and net genetic merits depend on many traits; therefore, with the advance of computational and statistical tools and genomic selection (GS), researchers are focusing on multi-trait selection. Selection of the best individuals is difficult, especially in traits that are antagonistically correlated, where improvement in one trait might imply a reduction in other(s). There are approaches that facilitate multi-trait selection, and recently a Bayesian decision theory (BDT) has been proposed. Parental selection using BDT has the potential to be effective in multi-trait selection given that it summarizes all relevant quantitative genetic concepts such as heritability, response to selection and the structure of dependence between traits (correlation). In this study, we applied BDT to provide a treatment for the complexity of multi-trait parental selection using three multivariate loss functions (LF), Kullback–Leibler (KL), Energy Score, and Multivariate Asymmetric Loss (MALF), to select the best-performing parents for the next breeding cycle in two extensive real wheat data sets. Results show that the high ranking lines in genomic estimated breeding value (GEBV) for certain traits did not always have low values for the posterior expected loss (PEL). For both data sets, the KL LF gave similar importance to all traits including grain yield. In contrast, the Energy Score and MALF gave a better performance in three of four traits that were different than grain yield. The BDT approach should help breeders to decide based not only on the GEBV per se of the parent to be selected, but also on the level of uncertainty according to the Bayesian paradigm.
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Genetics Society of America
2021
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Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Loss Function, Multi-Trait Selection, Parental Selection, Genomic Selection, Wheat Multi-Trait Data, Genomic Prediction, MARKER-ASSISTED SELECTION, WHEAT, DATA, GENOMICS, BAYESIAN THEORY, |
Online Access: | https://hdl.handle.net/10883/21328 |
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dig-cimmyt-10883-213282023-10-19T17:35:41Z Application of multi-trait Bayesian decision theory for parental genomic selection Villar-Hernandez, B.d.J. Pérez-Elizalde, S. Martini, J.W.R. Toledo, F.H. Perez-Rodriguez, P. Krause, M. García-Calvillo, I.D. Covarrubias-Pazaran, G. Crossa, J. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Loss Function Multi-Trait Selection Parental Selection Genomic Selection Wheat Multi-Trait Data Genomic Prediction MARKER-ASSISTED SELECTION WHEAT DATA GENOMICS BAYESIAN THEORY In all breeding programs, the decision about which individuals to select and intermate to form the next selection cycle is crucial. The improvement of genetic stocks requires considering multiple traits simultaneously, given that economic value and net genetic merits depend on many traits; therefore, with the advance of computational and statistical tools and genomic selection (GS), researchers are focusing on multi-trait selection. Selection of the best individuals is difficult, especially in traits that are antagonistically correlated, where improvement in one trait might imply a reduction in other(s). There are approaches that facilitate multi-trait selection, and recently a Bayesian decision theory (BDT) has been proposed. Parental selection using BDT has the potential to be effective in multi-trait selection given that it summarizes all relevant quantitative genetic concepts such as heritability, response to selection and the structure of dependence between traits (correlation). In this study, we applied BDT to provide a treatment for the complexity of multi-trait parental selection using three multivariate loss functions (LF), Kullback–Leibler (KL), Energy Score, and Multivariate Asymmetric Loss (MALF), to select the best-performing parents for the next breeding cycle in two extensive real wheat data sets. Results show that the high ranking lines in genomic estimated breeding value (GEBV) for certain traits did not always have low values for the posterior expected loss (PEL). For both data sets, the KL LF gave similar importance to all traits including grain yield. In contrast, the Energy Score and MALF gave a better performance in three of four traits that were different than grain yield. The BDT approach should help breeders to decide based not only on the GEBV per se of the parent to be selected, but also on the level of uncertainty according to the Bayesian paradigm. 2021-03-30T00:10:14Z 2021-03-30T00:10:14Z 2021 Article Published Version https://hdl.handle.net/10883/21328 10.1093/g3journal/jkab012 English http://hdl.handle.net/11529/10548420 CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose Open Access Bethesda, MD (USA) Genetics Society of America 2 11 2160-1836 G3: Genes, Genomes, Genetics jkab012 |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Loss Function Multi-Trait Selection Parental Selection Genomic Selection Wheat Multi-Trait Data Genomic Prediction MARKER-ASSISTED SELECTION WHEAT DATA GENOMICS BAYESIAN THEORY AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Loss Function Multi-Trait Selection Parental Selection Genomic Selection Wheat Multi-Trait Data Genomic Prediction MARKER-ASSISTED SELECTION WHEAT DATA GENOMICS BAYESIAN THEORY |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Loss Function Multi-Trait Selection Parental Selection Genomic Selection Wheat Multi-Trait Data Genomic Prediction MARKER-ASSISTED SELECTION WHEAT DATA GENOMICS BAYESIAN THEORY AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Loss Function Multi-Trait Selection Parental Selection Genomic Selection Wheat Multi-Trait Data Genomic Prediction MARKER-ASSISTED SELECTION WHEAT DATA GENOMICS BAYESIAN THEORY Villar-Hernandez, B.d.J. Pérez-Elizalde, S. Martini, J.W.R. Toledo, F.H. Perez-Rodriguez, P. Krause, M. García-Calvillo, I.D. Covarrubias-Pazaran, G. Crossa, J. Application of multi-trait Bayesian decision theory for parental genomic selection |
description |
In all breeding programs, the decision about which individuals to select and intermate to form the next selection cycle is crucial. The improvement of genetic stocks requires considering multiple traits simultaneously, given that economic value and net genetic merits depend on many traits; therefore, with the advance of computational and statistical tools and genomic selection (GS), researchers are focusing on multi-trait selection. Selection of the best individuals is difficult, especially in traits that are antagonistically correlated, where improvement in one trait might imply a reduction in other(s). There are approaches that facilitate multi-trait selection, and recently a Bayesian decision theory (BDT) has been proposed. Parental selection using BDT has the potential to be effective in multi-trait selection given that it summarizes all relevant quantitative genetic concepts such as heritability, response to selection and the structure of dependence between traits (correlation). In this study, we applied BDT to provide a treatment for the complexity of multi-trait parental selection using three multivariate loss functions (LF), Kullback–Leibler (KL), Energy Score, and Multivariate Asymmetric Loss (MALF), to select the best-performing parents for the next breeding cycle in two extensive real wheat data sets. Results show that the high ranking lines in genomic estimated breeding value (GEBV) for certain traits did not always have low values for the posterior expected loss (PEL). For both data sets, the KL LF gave similar importance to all traits including grain yield. In contrast, the Energy Score and MALF gave a better performance in three of four traits that were different than grain yield. The BDT approach should help breeders to decide based not only on the GEBV per se of the parent to be selected, but also on the level of uncertainty according to the Bayesian paradigm. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Loss Function Multi-Trait Selection Parental Selection Genomic Selection Wheat Multi-Trait Data Genomic Prediction MARKER-ASSISTED SELECTION WHEAT DATA GENOMICS BAYESIAN THEORY |
author |
Villar-Hernandez, B.d.J. Pérez-Elizalde, S. Martini, J.W.R. Toledo, F.H. Perez-Rodriguez, P. Krause, M. García-Calvillo, I.D. Covarrubias-Pazaran, G. Crossa, J. |
author_facet |
Villar-Hernandez, B.d.J. Pérez-Elizalde, S. Martini, J.W.R. Toledo, F.H. Perez-Rodriguez, P. Krause, M. García-Calvillo, I.D. Covarrubias-Pazaran, G. Crossa, J. |
author_sort |
Villar-Hernandez, B.d.J. |
title |
Application of multi-trait Bayesian decision theory for parental genomic selection |
title_short |
Application of multi-trait Bayesian decision theory for parental genomic selection |
title_full |
Application of multi-trait Bayesian decision theory for parental genomic selection |
title_fullStr |
Application of multi-trait Bayesian decision theory for parental genomic selection |
title_full_unstemmed |
Application of multi-trait Bayesian decision theory for parental genomic selection |
title_sort |
application of multi-trait bayesian decision theory for parental genomic selection |
publisher |
Genetics Society of America |
publishDate |
2021 |
url |
https://hdl.handle.net/10883/21328 |
work_keys_str_mv |
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