Projecting results of zoned multi-environment trials to new locations using environmental covariates with random coefficient models: accuracy and precision
Key message We propose the utilisation of environmental covariates in random coefficient models to predict the genotype performances in new locations. Multi-environment trials (MET) are conducted to assess the performance of a set of genotypes in a target population of environments. From a grower’s...
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description | Key message
We propose the utilisation of environmental covariates in random coefficient models to predict the genotype performances in new locations.
Multi-environment trials (MET) are conducted to assess the performance of a set of genotypes in a target population of environments. From a grower’s perspective, MET results must provide high accuracy and precision for predictions of genotype performance in new locations, i.e. the grower’s locations, which hardly ever coincide with the locations at which the trials were conducted. Linear mixed modelling can provide predictions for new locations. Moreover, the precision of the predictions is of primary concern and should be assessed. Besides, the precision can be improved when auxiliary information is available to characterize the targeted locations. Thus, in this study, we demonstrate the benefit of using environmental information (covariates) for predicting genotype performance in some new locations for Swedish winter wheat official trials. Swedish MET locations can be stratified into zones, allowing borrowing information between zones when best linear unbiased prediction (BLUP) is used. To account for correlations between zones, as well as for intercepts and slopes for the regression on covariates, we fitted random coefficient (RC) models. The results showed that the RC model with appropriate covariate scaling and model for covariate terms improved the precision of predictions of genotypic performance for new locations. The prediction accuracy of the RC model was competitive compared to the model without covariates. The RC model reduced the standard errors of predictions for individual genotypes and standard errors of predictions of genotype differences in new locations by 30–38% and 12–40%, respectively. |
doi_str_mv | 10.1007/s00122-021-03786-2 |
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We propose the utilisation of environmental covariates in random coefficient models to predict the genotype performances in new locations.
Multi-environment trials (MET) are conducted to assess the performance of a set of genotypes in a target population of environments. From a grower’s perspective, MET results must provide high accuracy and precision for predictions of genotype performance in new locations, i.e. the grower’s locations, which hardly ever coincide with the locations at which the trials were conducted. Linear mixed modelling can provide predictions for new locations. Moreover, the precision of the predictions is of primary concern and should be assessed. Besides, the precision can be improved when auxiliary information is available to characterize the targeted locations. Thus, in this study, we demonstrate the benefit of using environmental information (covariates) for predicting genotype performance in some new locations for Swedish winter wheat official trials. Swedish MET locations can be stratified into zones, allowing borrowing information between zones when best linear unbiased prediction (BLUP) is used. To account for correlations between zones, as well as for intercepts and slopes for the regression on covariates, we fitted random coefficient (RC) models. The results showed that the RC model with appropriate covariate scaling and model for covariate terms improved the precision of predictions of genotypic performance for new locations. The prediction accuracy of the RC model was competitive compared to the model without covariates. The RC model reduced the standard errors of predictions for individual genotypes and standard errors of predictions of genotype differences in new locations by 30–38% and 12–40%, respectively.</description><identifier>ISSN: 0040-5752</identifier><identifier>ISSN: 1432-2242</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-021-03786-2</identifier><identifier>PMID: 33830294</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Accuracy ; Agricultural estimating and reporting ; Agricultural land ; Agricultural research ; Agriculture ; Biochemistry ; Biomedical and Life Sciences ; Biotechnology ; Environmental aspects ; Environmental Sciences ; Gene-Environment Interaction ; Genetic aspects ; Genetics, Population ; Genome, Plant ; Genotype ; Genotype & phenotype ; Genotypes ; Life Sciences ; Methods ; Miljövetenskap ; Models, Genetic ; Original ; Original Article ; Phenotype ; Plant Biochemistry ; Plant breeding ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Predictions ; Regression analysis ; Statistical models ; Triticum - genetics ; Triticum - growth & development</subject><ispartof>Theoretical and applied genetics, 2021-05, Vol.134 (5), p.1513-1530</ispartof><rights>The Author(s) 2021</rights><rights>COPYRIGHT 2021 Springer</rights><rights>The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c614t-bdf675d934292f3798d191d691c6ffd0014afb4080477ecfdbb6a61e6d1ab1e13</citedby><cites>FETCH-LOGICAL-c614t-bdf675d934292f3798d191d691c6ffd0014afb4080477ecfdbb6a61e6d1ab1e13</cites><orcidid>0000-0001-8917-3781 ; 0000-0002-5796-0710 ; 0000-0001-7813-2992</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00122-021-03786-2$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00122-021-03786-2$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,552,780,784,885,27922,27923,41486,42555,51317</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33830294$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://res.slu.se/id/publ/111752$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Buntaran, Harimurti</creatorcontrib><creatorcontrib>Forkman, Johannes</creatorcontrib><creatorcontrib>Piepho, Hans-Peter</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><title>Projecting results of zoned multi-environment trials to new locations using environmental covariates with random coefficient models: accuracy and precision</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><addtitle>Theor Appl Genet</addtitle><description>Key message
We propose the utilisation of environmental covariates in random coefficient models to predict the genotype performances in new locations.
Multi-environment trials (MET) are conducted to assess the performance of a set of genotypes in a target population of environments. From a grower’s perspective, MET results must provide high accuracy and precision for predictions of genotype performance in new locations, i.e. the grower’s locations, which hardly ever coincide with the locations at which the trials were conducted. Linear mixed modelling can provide predictions for new locations. Moreover, the precision of the predictions is of primary concern and should be assessed. Besides, the precision can be improved when auxiliary information is available to characterize the targeted locations. Thus, in this study, we demonstrate the benefit of using environmental information (covariates) for predicting genotype performance in some new locations for Swedish winter wheat official trials. Swedish MET locations can be stratified into zones, allowing borrowing information between zones when best linear unbiased prediction (BLUP) is used. To account for correlations between zones, as well as for intercepts and slopes for the regression on covariates, we fitted random coefficient (RC) models. The results showed that the RC model with appropriate covariate scaling and model for covariate terms improved the precision of predictions of genotypic performance for new locations. The prediction accuracy of the RC model was competitive compared to the model without covariates. The RC model reduced the standard errors of predictions for individual genotypes and standard errors of predictions of genotype differences in new locations by 30–38% and 12–40%, respectively.</description><subject>Accuracy</subject><subject>Agricultural estimating and reporting</subject><subject>Agricultural land</subject><subject>Agricultural research</subject><subject>Agriculture</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Environmental aspects</subject><subject>Environmental Sciences</subject><subject>Gene-Environment Interaction</subject><subject>Genetic aspects</subject><subject>Genetics, Population</subject><subject>Genome, Plant</subject><subject>Genotype</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Life Sciences</subject><subject>Methods</subject><subject>Miljövetenskap</subject><subject>Models, Genetic</subject><subject>Original</subject><subject>Original Article</subject><subject>Phenotype</subject><subject>Plant Biochemistry</subject><subject>Plant breeding</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Predictions</subject><subject>Regression analysis</subject><subject>Statistical models</subject><subject>Triticum - 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genetics</topic><topic>Triticum - growth & development</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Buntaran, Harimurti</creatorcontrib><creatorcontrib>Forkman, Johannes</creatorcontrib><creatorcontrib>Piepho, Hans-Peter</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Freely available online</collection><collection>SwePub Articles full text</collection><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Buntaran, Harimurti</au><au>Forkman, Johannes</au><au>Piepho, Hans-Peter</au><aucorp>Sveriges lantbruksuniversitet</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Projecting results of zoned multi-environment trials to new locations using environmental covariates with random coefficient models: accuracy and precision</atitle><jtitle>Theoretical and applied genetics</jtitle><stitle>Theor Appl Genet</stitle><addtitle>Theor Appl Genet</addtitle><date>2021-05-01</date><risdate>2021</risdate><volume>134</volume><issue>5</issue><spage>1513</spage><epage>1530</epage><pages>1513-1530</pages><issn>0040-5752</issn><issn>1432-2242</issn><eissn>1432-2242</eissn><abstract>Key message
We propose the utilisation of environmental covariates in random coefficient models to predict the genotype performances in new locations.
Multi-environment trials (MET) are conducted to assess the performance of a set of genotypes in a target population of environments. From a grower’s perspective, MET results must provide high accuracy and precision for predictions of genotype performance in new locations, i.e. the grower’s locations, which hardly ever coincide with the locations at which the trials were conducted. Linear mixed modelling can provide predictions for new locations. Moreover, the precision of the predictions is of primary concern and should be assessed. Besides, the precision can be improved when auxiliary information is available to characterize the targeted locations. Thus, in this study, we demonstrate the benefit of using environmental information (covariates) for predicting genotype performance in some new locations for Swedish winter wheat official trials. Swedish MET locations can be stratified into zones, allowing borrowing information between zones when best linear unbiased prediction (BLUP) is used. To account for correlations between zones, as well as for intercepts and slopes for the regression on covariates, we fitted random coefficient (RC) models. The results showed that the RC model with appropriate covariate scaling and model for covariate terms improved the precision of predictions of genotypic performance for new locations. The prediction accuracy of the RC model was competitive compared to the model without covariates. The RC model reduced the standard errors of predictions for individual genotypes and standard errors of predictions of genotype differences in new locations by 30–38% and 12–40%, respectively.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>33830294</pmid><doi>10.1007/s00122-021-03786-2</doi><tpages>18</tpages><orcidid>https://orcid.org/0000-0001-8917-3781</orcidid><orcidid>https://orcid.org/0000-0002-5796-0710</orcidid><orcidid>https://orcid.org/0000-0001-7813-2992</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Accuracy Agricultural estimating and reporting Agricultural land Agricultural research Agriculture Biochemistry Biomedical and Life Sciences Biotechnology Environmental aspects Environmental Sciences Gene-Environment Interaction Genetic aspects Genetics, Population Genome, Plant Genotype Genotype & phenotype Genotypes Life Sciences Methods Miljövetenskap Models, Genetic Original Original Article Phenotype Plant Biochemistry Plant breeding Plant Breeding/Biotechnology Plant Genetics and Genomics Predictions Regression analysis Statistical models Triticum - genetics Triticum - growth & development |
title | Projecting results of zoned multi-environment trials to new locations using environmental covariates with random coefficient models: accuracy and precision |
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