Modeling genotype x environment interaction for genomic selection with unbalanced data from a wheat breeding program.
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.
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 |
format | article |
id | INIAOAI_c11df0547ce14af72852c239946e6b9d |
instacron_str | Instituto Nacional de Investigación Agropecuaria |
institution | Instituto Nacional de Investigación Agropecuaria |
instname_str | Instituto Nacional de Investigación Agropecuaria |
language | eng |
language_invalid_str_mv | en |
network_acronym_str | INIAOAI |
network_name_str | AINFO |
oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/2587 |
publishDate | 2016 |
reponame_str | AINFO |
repository.mail.fl_str_mv | lorrego@inia.org.uy |
repository.name.fl_str_mv | AINFO - Instituto Nacional de Investigación Agropecuaria |
repository_id_str | |
rights_invalid_str_mv | Acceso abierto |
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 |