Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.

LADO, B. - GONZÁLEZ BARRIOS, P. - QUINCKE, M. - SILVA, P. - GUTIÉRREZ, L.

Resumen:

ABSTRACT.Genomic selection (GS) has successfully been used in plant breeding to improve selection efficiency and reduce breeding time and cost. However, there is not a clear strategy on how to incorporate genotype ? environment interaction (GEI) to GS models. Increased prediction accuracy could be achieved using mixed models to exploit GEI by borrowing information from other environments. The objective of this work was to compare strategies to exploit GEI in GS using mixed models. Specifically, we compared strategies topredict new genotypes by borrowing information from other environments modeling the correlation matrix across environments and to design sets of environments aiming for low GEI to predict genomic performance in new environments. We evaluated 1477 advanced wheat (Triticum aestivum L.) lines for yield in 35 location?year combinations genotyped with genotyping-bysequencing (GBS). Mixed models were used to obtain either overall or by-environment predictions for different sets of environments. Overall accuracy was high (0.5). Borrowing information from relatives evaluated in multiple environments and modeling the correlation matrix across environments was the best strategy to predict newgenotypes. On the other hand, the best strategy for predicting the performance of genotypes in new environments was either to predict across locations for single years or to predict within defined mega-environments (MEs) for any year or location. In summary, higher predictive ability was obtained by characterizing and by modeling GEI in the GS context.© 2016. Crop Science Society of America, Inc.


Detalles Bibliográficos
2016
WHEAT
GENOMIC SELECTION
TRIGO
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=55260&biblioteca=vazio&busca=55260&qFacets=55260
Acceso abierto
_version_ 1805580527912091648
author LADO, B.
author2 GONZÁLEZ BARRIOS, P.
QUINCKE, M.
SILVA, P.
GUTIÉRREZ, L.
author2_role author
author
author
author
author_facet LADO, B.
GONZÁLEZ BARRIOS, P.
QUINCKE, M.
SILVA, P.
GUTIÉRREZ, L.
author_role author
bitstream.checksum.fl_str_mv 193701523dd7a969782ae76f6698c42c
bitstream.checksumAlgorithm.fl_str_mv MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2587/1/sword-2022-12-16T17%3a46%3a52.original.xml
collection AINFO
dc.creator.none.fl_str_mv LADO, B.
GONZÁLEZ BARRIOS, P.
QUINCKE, M.
SILVA, P.
GUTIÉRREZ, L.
dc.date.accessioned.none.fl_str_mv 2022-12-16T20:46:52Z
dc.date.available.none.fl_str_mv 2022-12-16T20:46:52Z
dc.date.issued.none.fl_str_mv 2016
dc.date.updated.none.fl_str_mv 2022-12-16T20:46:52Z
dc.description.abstract.none.fl_txt_mv ABSTRACT.Genomic selection (GS) has successfully been used in plant breeding to improve selection efficiency and reduce breeding time and cost. However, there is not a clear strategy on how to incorporate genotype ? environment interaction (GEI) to GS models. Increased prediction accuracy could be achieved using mixed models to exploit GEI by borrowing information from other environments. The objective of this work was to compare strategies to exploit GEI in GS using mixed models. Specifically, we compared strategies topredict new genotypes by borrowing information from other environments modeling the correlation matrix across environments and to design sets of environments aiming for low GEI to predict genomic performance in new environments. We evaluated 1477 advanced wheat (Triticum aestivum L.) lines for yield in 35 location?year combinations genotyped with genotyping-bysequencing (GBS). Mixed models were used to obtain either overall or by-environment predictions for different sets of environments. Overall accuracy was high (0.5). Borrowing information from relatives evaluated in multiple environments and modeling the correlation matrix across environments was the best strategy to predict newgenotypes. On the other hand, the best strategy for predicting the performance of genotypes in new environments was either to predict across locations for single years or to predict within defined mega-environments (MEs) for any year or location. In summary, higher predictive ability was obtained by characterizing and by modeling GEI in the GS context.© 2016. Crop Science Society of America, Inc.
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=55260&biblioteca=vazio&busca=55260&qFacets=55260
dc.language.iso.none.fl_str_mv en
eng
dc.rights.es.fl_str_mv Acceso abierto
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.source.none.fl_str_mv reponame:AINFO
instname:Instituto Nacional de Investigación Agropecuaria
instacron:Instituto Nacional de Investigación Agropecuaria
dc.subject.none.fl_str_mv WHEAT
GENOMIC SELECTION
TRIGO
dc.title.none.fl_str_mv Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
dc.type.none.fl_str_mv Article
PublishedVersion
info:eu-repo/semantics/article
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description ABSTRACT.Genomic selection (GS) has successfully been used in plant breeding to improve selection efficiency and reduce breeding time and cost. However, there is not a clear strategy on how to incorporate genotype ? environment interaction (GEI) to GS models. Increased prediction accuracy could be achieved using mixed models to exploit GEI by borrowing information from other environments. The objective of this work was to compare strategies to exploit GEI in GS using mixed models. Specifically, we compared strategies topredict new genotypes by borrowing information from other environments modeling the correlation matrix across environments and to design sets of environments aiming for low GEI to predict genomic performance in new environments. We evaluated 1477 advanced wheat (Triticum aestivum L.) lines for yield in 35 location?year combinations genotyped with genotyping-bysequencing (GBS). Mixed models were used to obtain either overall or by-environment predictions for different sets of environments. Overall accuracy was high (0.5). Borrowing information from relatives evaluated in multiple environments and modeling the correlation matrix across environments was the best strategy to predict newgenotypes. On the other hand, the best strategy for predicting the performance of genotypes in new environments was either to predict across locations for single years or to predict within defined mega-environments (MEs) for any year or location. In summary, higher predictive ability was obtained by characterizing and by modeling GEI in the GS context.© 2016. Crop Science Society of America, Inc.
eu_rights_str_mv openAccess
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repository.name.fl_str_mv AINFO - Instituto Nacional de Investigación Agropecuaria
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spelling 2022-12-16T20:46:52Z2022-12-16T20:46:52Z20162022-12-16T20:46:52Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=55260&biblioteca=vazio&busca=55260&qFacets=55260ABSTRACT.Genomic selection (GS) has successfully been used in plant breeding to improve selection efficiency and reduce breeding time and cost. However, there is not a clear strategy on how to incorporate genotype ? environment interaction (GEI) to GS models. Increased prediction accuracy could be achieved using mixed models to exploit GEI by borrowing information from other environments. The objective of this work was to compare strategies to exploit GEI in GS using mixed models. Specifically, we compared strategies topredict new genotypes by borrowing information from other environments modeling the correlation matrix across environments and to design sets of environments aiming for low GEI to predict genomic performance in new environments. We evaluated 1477 advanced wheat (Triticum aestivum L.) lines for yield in 35 location?year combinations genotyped with genotyping-bysequencing (GBS). Mixed models were used to obtain either overall or by-environment predictions for different sets of environments. Overall accuracy was high (0.5). Borrowing information from relatives evaluated in multiple environments and modeling the correlation matrix across environments was the best strategy to predict newgenotypes. On the other hand, the best strategy for predicting the performance of genotypes in new environments was either to predict across locations for single years or to predict within defined mega-environments (MEs) for any year or location. In summary, higher predictive ability was obtained by characterizing and by modeling GEI in the GS context.© 2016. Crop Science Society of America, Inc.https://hdl.handle.net/20.500.12381/2587enenginfo:eu-repo/semantics/openAccessAcceso abiertoWHEATGENOMIC SELECTIONTRIGOModeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaLADO, B.GONZÁLEZ BARRIOS, P.QUINCKE, M.SILVA, P.GUTIÉRREZ, L.SWORDsword-2022-12-16T17:46:52.original.xmlOriginal SWORD entry documentapplication/octet-stream2688https://redi.anii.org.uy/jspui/bitstream/20.500.12381/2587/1/sword-2022-12-16T17%3a46%3a52.original.xml193701523dd7a969782ae76f6698c42cMD5120.500.12381/25872022-12-16 17:46:53.24oai:redi.anii.org.uy:20.500.12381/2587Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-12-16T20:46:53AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
LADO, B.
WHEAT
GENOMIC SELECTION
TRIGO
status_str publishedVersion
title Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
title_full Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
title_fullStr Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
title_full_unstemmed Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
title_short Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
title_sort Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
topic WHEAT
GENOMIC SELECTION
TRIGO
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=55260&biblioteca=vazio&busca=55260&qFacets=55260