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Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]

Identifying genetic loci associated with yield stability has helped plant breeders and geneticists begin to understand the role and influence of genotype by environment (GxE) interactions in soybean [Glycine max (L.) Merr.] productivity, as well as other crops. Quantifying a genotype’s range of perf...

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Autores principales: Happ, Mary M., Graef, George L., Wang, Haichuan, Howard, Reka, Posadas, Luis, Hyten, David L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044453/
https://www.ncbi.nlm.nih.gov/pubmed/33868333
http://dx.doi.org/10.3389/fpls.2021.630175
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author Happ, Mary M.
Graef, George L.
Wang, Haichuan
Howard, Reka
Posadas, Luis
Hyten, David L.
author_facet Happ, Mary M.
Graef, George L.
Wang, Haichuan
Howard, Reka
Posadas, Luis
Hyten, David L.
author_sort Happ, Mary M.
collection PubMed
description Identifying genetic loci associated with yield stability has helped plant breeders and geneticists begin to understand the role and influence of genotype by environment (GxE) interactions in soybean [Glycine max (L.) Merr.] productivity, as well as other crops. Quantifying a genotype’s range of performance across testing locations has been developed over decades with dozens of methodologies available. This includes directly modeling GxE interactions as part of an overall model for yield, as well as methods which generate overall yield “stability” values from multi-environment trial data. Correspondence between these methods as it pertains to the outcomes of genome wide association studies (GWAS) has not been well defined. In this study, the GWAS results for yield and yield stability were compared in 213 soybean lines across 11 environments to determine their utility and potential intersection. Both univariate and multivariate conventional stability estimates were considered alongside a mixed model for yield that fit marker by environment interactions as a random effect. One-hundred and six total QTL were discovered across all mapping results, however, genetic loci that were significant in the mixed model for grain yield that fit marker by environment interactions were completely distinct from those that were significant when mapping using traditional stability measures as a phenotype. Furthermore, 73.21% of QTL discovered in the mixed model were determined to cause a crossover interaction effect which cause genotype rank changes between environments. Overall, the QTL discovered via explicitly mapping GxE interactions also explained more yield variance that those QTL associated with differences in traditional stability estimates making their theoretical impact on selection greater. A lack of intersecting results between mapping approaches highlights the importance of examining stability in multiple contexts when attempting to manipulate GxE interactions in soybean.
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spelling pubmed-80444532021-04-15 Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.] Happ, Mary M. Graef, George L. Wang, Haichuan Howard, Reka Posadas, Luis Hyten, David L. Front Plant Sci Plant Science Identifying genetic loci associated with yield stability has helped plant breeders and geneticists begin to understand the role and influence of genotype by environment (GxE) interactions in soybean [Glycine max (L.) Merr.] productivity, as well as other crops. Quantifying a genotype’s range of performance across testing locations has been developed over decades with dozens of methodologies available. This includes directly modeling GxE interactions as part of an overall model for yield, as well as methods which generate overall yield “stability” values from multi-environment trial data. Correspondence between these methods as it pertains to the outcomes of genome wide association studies (GWAS) has not been well defined. In this study, the GWAS results for yield and yield stability were compared in 213 soybean lines across 11 environments to determine their utility and potential intersection. Both univariate and multivariate conventional stability estimates were considered alongside a mixed model for yield that fit marker by environment interactions as a random effect. One-hundred and six total QTL were discovered across all mapping results, however, genetic loci that were significant in the mixed model for grain yield that fit marker by environment interactions were completely distinct from those that were significant when mapping using traditional stability measures as a phenotype. Furthermore, 73.21% of QTL discovered in the mixed model were determined to cause a crossover interaction effect which cause genotype rank changes between environments. Overall, the QTL discovered via explicitly mapping GxE interactions also explained more yield variance that those QTL associated with differences in traditional stability estimates making their theoretical impact on selection greater. A lack of intersecting results between mapping approaches highlights the importance of examining stability in multiple contexts when attempting to manipulate GxE interactions in soybean. Frontiers Media S.A. 2021-03-31 /pmc/articles/PMC8044453/ /pubmed/33868333 http://dx.doi.org/10.3389/fpls.2021.630175 Text en Copyright © 2021 Happ, Graef, Wang, Howard, Posadas and Hyten. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Happ, Mary M.
Graef, George L.
Wang, Haichuan
Howard, Reka
Posadas, Luis
Hyten, David L.
Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]
title Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]
title_full Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]
title_fullStr Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]
title_full_unstemmed Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]
title_short Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]
title_sort comparing a mixed model approach to traditional stability estimators for mapping genotype by environment interactions and yield stability in soybean [glycine max (l.) merr.]
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044453/
https://www.ncbi.nlm.nih.gov/pubmed/33868333
http://dx.doi.org/10.3389/fpls.2021.630175
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