Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP
- Autores
- Cappa, Eduardo Pablo; de Lima, Bruno Marco; Silva-Junior, Orzenil B. da; García, Carla C.; Mansfield, Shawn D.; Grattapaglia, Dario
- Año de publicación
- 2019
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Genomic Best Linear Unbiased Prediction (GBLUP) in tree breeding typically only uses information from genotyped trees. However, information from phenotyped but non-genotyped trees can also be highly valuable. The single-step GBLUP approach(ssGBLUP) allows genomic prediction to takeinto account both genotyped and nongenotyped trees simultaneously in a single evaluation. In this study, we investigated the advantage, in terms of breeding value accuracy and bias, of including phenotypic observation from non-genotyped trees in a standard tree GBLUP evaluation. We compared the efficiency of the conventional pedigree-based (ABLUP), GBLUP and ssGBLUP approaches to evaluate eight growth and wood quality traits in a Eucalyptus hybrid population, genotyped with 33,398 single nucleotide polymorphisms (SNPs) using the EucHIP60k. Theoretical accuracies, predictive ability and bias were calculated by ten-fold cross validation on all traits. The use of additional phenotypic information from non-genotyped trees by means of ssGBLUP provided higher predictive ability (from 37% to 75%) and lower prediction bias (from 21% to 73%) for the genetic component of non-phenotyped but genotyped trees when compared to GBLUP. The increase (decrease) in the prediction accuracy (bias) became stronger as trait heritability decreased. We concluded that ssGBLUP is a promising breeding tool to improve accuracies and bias over classical GBLUP for genomic evaluation in Eucalyptus breeding practice.
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: de Lima, Bruno Marco. FIBRIA S.A. Technology Center; Brasil
Fil: Silva-Junior, Orzenil B. da. EMBRAPA Recursos Genéticos e Biotecnologia; Brasil. Universidade Católica de Brasilia. Programa de Ciencias Genéticas y Biotecnología; Brasil
Fil: García, Carla C. International Paper of Brazil; Brasil
Fil: Mansfield, Shawn D. University of British Columbia. Faculty of Forestry. Department of Wood Science; Canadá
Fil: Grattapaglia, Dario. EMBRAPA Recursos Genéticos e Biotecnologia; Brasil. Universidade Católica de Brasilia. Programa de Ciencias Genéticas y Biotecnología; Brasil - Fuente
- Plant Science 284 : 9-15 (July 2019)
- Materia
-
Eucalyptus
Evaluación
Información Fenotípico
Genomic Features
Evaluation
Phenotypic Information
Genetics
Genética
Accuracy Bias
Sesgo de Precisión
Características Genómicas - Nivel de accesibilidad
- acceso restringido
- Condiciones de uso
- Repositorio
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/6227
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Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUPCappa, Eduardo Pablode Lima, Bruno MarcoSilva-Junior, Orzenil B. daGarcía, Carla C.Mansfield, Shawn D.Grattapaglia, DarioEucalyptusEvaluaciónInformación FenotípicoGenomic FeaturesEvaluationPhenotypic InformationGeneticsGenéticaAccuracy BiasSesgo de PrecisiónCaracterísticas GenómicasGenomic Best Linear Unbiased Prediction (GBLUP) in tree breeding typically only uses information from genotyped trees. However, information from phenotyped but non-genotyped trees can also be highly valuable. The single-step GBLUP approach(ssGBLUP) allows genomic prediction to takeinto account both genotyped and nongenotyped trees simultaneously in a single evaluation. In this study, we investigated the advantage, in terms of breeding value accuracy and bias, of including phenotypic observation from non-genotyped trees in a standard tree GBLUP evaluation. We compared the efficiency of the conventional pedigree-based (ABLUP), GBLUP and ssGBLUP approaches to evaluate eight growth and wood quality traits in a Eucalyptus hybrid population, genotyped with 33,398 single nucleotide polymorphisms (SNPs) using the EucHIP60k. Theoretical accuracies, predictive ability and bias were calculated by ten-fold cross validation on all traits. The use of additional phenotypic information from non-genotyped trees by means of ssGBLUP provided higher predictive ability (from 37% to 75%) and lower prediction bias (from 21% to 73%) for the genetic component of non-phenotyped but genotyped trees when compared to GBLUP. The increase (decrease) in the prediction accuracy (bias) became stronger as trait heritability decreased. We concluded that ssGBLUP is a promising breeding tool to improve accuracies and bias over classical GBLUP for genomic evaluation in Eucalyptus breeding practice.Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: de Lima, Bruno Marco. FIBRIA S.A. Technology Center; BrasilFil: Silva-Junior, Orzenil B. da. EMBRAPA Recursos Genéticos e Biotecnologia; Brasil. Universidade Católica de Brasilia. Programa de Ciencias Genéticas y Biotecnología; BrasilFil: García, Carla C. International Paper of Brazil; BrasilFil: Mansfield, Shawn D. University of British Columbia. Faculty of Forestry. Department of Wood Science; CanadáFil: Grattapaglia, Dario. EMBRAPA Recursos Genéticos e Biotecnologia; Brasil. Universidade Católica de Brasilia. Programa de Ciencias Genéticas y Biotecnología; BrasilElsevier2019-10-29T13:54:32Z2019-10-29T13:54:32Z2019-03-28info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://www.sciencedirect.com/science/article/pii/S0168945218314134http://hdl.handle.net/20.500.12123/62270168-9452https://doi.org/10.1016/j.plantsci.2019.03.017Plant Science 284 : 9-15 (July 2019)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-09-29T13:44:48Zoai:localhost:20.500.12123/6227instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:44:49.162INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse |
dc.title.none.fl_str_mv |
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP |
title |
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP |
spellingShingle |
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP Cappa, Eduardo Pablo Eucalyptus Evaluación Información Fenotípico Genomic Features Evaluation Phenotypic Information Genetics Genética Accuracy Bias Sesgo de Precisión Características Genómicas |
title_short |
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP |
title_full |
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP |
title_fullStr |
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP |
title_full_unstemmed |
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP |
title_sort |
Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP |
dc.creator.none.fl_str_mv |
Cappa, Eduardo Pablo de Lima, Bruno Marco Silva-Junior, Orzenil B. da García, Carla C. Mansfield, Shawn D. Grattapaglia, Dario |
author |
Cappa, Eduardo Pablo |
author_facet |
Cappa, Eduardo Pablo de Lima, Bruno Marco Silva-Junior, Orzenil B. da García, Carla C. Mansfield, Shawn D. Grattapaglia, Dario |
author_role |
author |
author2 |
de Lima, Bruno Marco Silva-Junior, Orzenil B. da García, Carla C. Mansfield, Shawn D. Grattapaglia, Dario |
author2_role |
author author author author author |
dc.subject.none.fl_str_mv |
Eucalyptus Evaluación Información Fenotípico Genomic Features Evaluation Phenotypic Information Genetics Genética Accuracy Bias Sesgo de Precisión Características Genómicas |
topic |
Eucalyptus Evaluación Información Fenotípico Genomic Features Evaluation Phenotypic Information Genetics Genética Accuracy Bias Sesgo de Precisión Características Genómicas |
dc.description.none.fl_txt_mv |
Genomic Best Linear Unbiased Prediction (GBLUP) in tree breeding typically only uses information from genotyped trees. However, information from phenotyped but non-genotyped trees can also be highly valuable. The single-step GBLUP approach(ssGBLUP) allows genomic prediction to takeinto account both genotyped and nongenotyped trees simultaneously in a single evaluation. In this study, we investigated the advantage, in terms of breeding value accuracy and bias, of including phenotypic observation from non-genotyped trees in a standard tree GBLUP evaluation. We compared the efficiency of the conventional pedigree-based (ABLUP), GBLUP and ssGBLUP approaches to evaluate eight growth and wood quality traits in a Eucalyptus hybrid population, genotyped with 33,398 single nucleotide polymorphisms (SNPs) using the EucHIP60k. Theoretical accuracies, predictive ability and bias were calculated by ten-fold cross validation on all traits. The use of additional phenotypic information from non-genotyped trees by means of ssGBLUP provided higher predictive ability (from 37% to 75%) and lower prediction bias (from 21% to 73%) for the genetic component of non-phenotyped but genotyped trees when compared to GBLUP. The increase (decrease) in the prediction accuracy (bias) became stronger as trait heritability decreased. We concluded that ssGBLUP is a promising breeding tool to improve accuracies and bias over classical GBLUP for genomic evaluation in Eucalyptus breeding practice. Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: de Lima, Bruno Marco. FIBRIA S.A. Technology Center; Brasil Fil: Silva-Junior, Orzenil B. da. EMBRAPA Recursos Genéticos e Biotecnologia; Brasil. Universidade Católica de Brasilia. Programa de Ciencias Genéticas y Biotecnología; Brasil Fil: García, Carla C. International Paper of Brazil; Brasil Fil: Mansfield, Shawn D. University of British Columbia. Faculty of Forestry. Department of Wood Science; Canadá Fil: Grattapaglia, Dario. EMBRAPA Recursos Genéticos e Biotecnologia; Brasil. Universidade Católica de Brasilia. Programa de Ciencias Genéticas y Biotecnología; Brasil |
description |
Genomic Best Linear Unbiased Prediction (GBLUP) in tree breeding typically only uses information from genotyped trees. However, information from phenotyped but non-genotyped trees can also be highly valuable. The single-step GBLUP approach(ssGBLUP) allows genomic prediction to takeinto account both genotyped and nongenotyped trees simultaneously in a single evaluation. In this study, we investigated the advantage, in terms of breeding value accuracy and bias, of including phenotypic observation from non-genotyped trees in a standard tree GBLUP evaluation. We compared the efficiency of the conventional pedigree-based (ABLUP), GBLUP and ssGBLUP approaches to evaluate eight growth and wood quality traits in a Eucalyptus hybrid population, genotyped with 33,398 single nucleotide polymorphisms (SNPs) using the EucHIP60k. Theoretical accuracies, predictive ability and bias were calculated by ten-fold cross validation on all traits. The use of additional phenotypic information from non-genotyped trees by means of ssGBLUP provided higher predictive ability (from 37% to 75%) and lower prediction bias (from 21% to 73%) for the genetic component of non-phenotyped but genotyped trees when compared to GBLUP. The increase (decrease) in the prediction accuracy (bias) became stronger as trait heritability decreased. We concluded that ssGBLUP is a promising breeding tool to improve accuracies and bias over classical GBLUP for genomic evaluation in Eucalyptus breeding practice. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-29T13:54:32Z 2019-10-29T13:54:32Z 2019-03-28 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
https://www.sciencedirect.com/science/article/pii/S0168945218314134 http://hdl.handle.net/20.500.12123/6227 0168-9452 https://doi.org/10.1016/j.plantsci.2019.03.017 |
url |
https://www.sciencedirect.com/science/article/pii/S0168945218314134 http://hdl.handle.net/20.500.12123/6227 https://doi.org/10.1016/j.plantsci.2019.03.017 |
identifier_str_mv |
0168-9452 |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/restrictedAccess |
eu_rights_str_mv |
restrictedAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier |
publisher.none.fl_str_mv |
Elsevier |
dc.source.none.fl_str_mv |
Plant Science 284 : 9-15 (July 2019) reponame:INTA Digital (INTA) instname:Instituto Nacional de Tecnología Agropecuaria |
reponame_str |
INTA Digital (INTA) |
collection |
INTA Digital (INTA) |
instname_str |
Instituto Nacional de Tecnología Agropecuaria |
repository.name.fl_str_mv |
INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria |
repository.mail.fl_str_mv |
tripaldi.nicolas@inta.gob.ar |
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1844619139170172928 |
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12.559606 |