Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP

Autores
Cappa, Eduardo Pablo; Ratcliffe, Blaise; Chen, Charles; Thomas, Barb R.; Liu, Yang; Klutsch, Jennifer G.; Azcona, Jaime Sebastian; Benowicz, Andy; Sadoway, Shane; Erlilgin, Nadir; El-Kassaby, Yousry A.
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Modeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH: 0.429, and WGR: 0.513) or design (HT: 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918–1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits’ heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Ratchiffe, Blaise. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados Unidos
Fil: Thomas, Barb R. University of Alberta. Department of Renewable Resources; Canadá
Fil: Liu, Yang. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fil: Klutsch, Jennifer G. University of Alberta. Department of Renewable Resources; Canadá
Fil: Sebastian-Azcona, Jaime. University of Alberta. Department of Renewable Resources; Canadá
Fil: Benowicz, Andy. Alberta Agriculture and Forestry. Forest Stewardship and Trade Branch; Canadá
Fil: Sadoway, Shane. Blue Ridge Lumber Inc.; Canadá
Fil: Erbilgin, Nadir. University of Alberta. Department of Renewable Resources; Canadá
Fil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fuente
Heredity 128 (4) : 209-224 (2022)
Materia
Genómica
Evaluación
Árboles Forestales
Genomics
Evaluation
Forest Trees
Capacidad Predictiva
Predictive Ability
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/13180

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oai_identifier_str oai:localhost:20.500.12123/13180
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spelling Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUPCappa, Eduardo PabloRatcliffe, BlaiseChen, CharlesThomas, Barb R.Liu, YangKlutsch, Jennifer G.Azcona, Jaime SebastianBenowicz, AndySadoway, ShaneErlilgin, NadirEl-Kassaby, Yousry A.GenómicaEvaluaciónÁrboles ForestalesGenomicsEvaluationForest TreesCapacidad PredictivaPredictive AbilityModeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH: 0.429, and WGR: 0.513) or design (HT: 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918–1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits’ heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ratchiffe, Blaise. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados UnidosFil: Thomas, Barb R. University of Alberta. Department of Renewable Resources; CanadáFil: Liu, Yang. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Klutsch, Jennifer G. University of Alberta. Department of Renewable Resources; CanadáFil: Sebastian-Azcona, Jaime. University of Alberta. Department of Renewable Resources; CanadáFil: Benowicz, Andy. Alberta Agriculture and Forestry. Forest Stewardship and Trade Branch; CanadáFil: Sadoway, Shane. Blue Ridge Lumber Inc.; CanadáFil: Erbilgin, Nadir. University of Alberta. Department of Renewable Resources; CanadáFil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáSpringer Nature2022-10-21T12:45:19Z2022-10-21T12:45:19Z2022-02-18info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/13180https://www.nature.com/articles/s41437-022-00508-21365-25400018-067Xhttps://doi.org/10.1038/s41437-022-00508-2Heredity 128 (4) : 209-224 (2022)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-09-29T13:45:46Zoai:localhost:20.500.12123/13180instacron: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 13:45:46.507INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
title Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
spellingShingle Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
Cappa, Eduardo Pablo
Genómica
Evaluación
Árboles Forestales
Genomics
Evaluation
Forest Trees
Capacidad Predictiva
Predictive Ability
title_short Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
title_full Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
title_fullStr Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
title_full_unstemmed Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
title_sort Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
dc.creator.none.fl_str_mv Cappa, Eduardo Pablo
Ratcliffe, Blaise
Chen, Charles
Thomas, Barb R.
Liu, Yang
Klutsch, Jennifer G.
Azcona, Jaime Sebastian
Benowicz, Andy
Sadoway, Shane
Erlilgin, Nadir
El-Kassaby, Yousry A.
author Cappa, Eduardo Pablo
author_facet Cappa, Eduardo Pablo
Ratcliffe, Blaise
Chen, Charles
Thomas, Barb R.
Liu, Yang
Klutsch, Jennifer G.
Azcona, Jaime Sebastian
Benowicz, Andy
Sadoway, Shane
Erlilgin, Nadir
El-Kassaby, Yousry A.
author_role author
author2 Ratcliffe, Blaise
Chen, Charles
Thomas, Barb R.
Liu, Yang
Klutsch, Jennifer G.
Azcona, Jaime Sebastian
Benowicz, Andy
Sadoway, Shane
Erlilgin, Nadir
El-Kassaby, Yousry A.
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genómica
Evaluación
Árboles Forestales
Genomics
Evaluation
Forest Trees
Capacidad Predictiva
Predictive Ability
topic Genómica
Evaluación
Árboles Forestales
Genomics
Evaluation
Forest Trees
Capacidad Predictiva
Predictive Ability
dc.description.none.fl_txt_mv Modeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH: 0.429, and WGR: 0.513) or design (HT: 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918–1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits’ heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Ratchiffe, Blaise. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados Unidos
Fil: Thomas, Barb R. University of Alberta. Department of Renewable Resources; Canadá
Fil: Liu, Yang. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fil: Klutsch, Jennifer G. University of Alberta. Department of Renewable Resources; Canadá
Fil: Sebastian-Azcona, Jaime. University of Alberta. Department of Renewable Resources; Canadá
Fil: Benowicz, Andy. Alberta Agriculture and Forestry. Forest Stewardship and Trade Branch; Canadá
Fil: Sadoway, Shane. Blue Ridge Lumber Inc.; Canadá
Fil: Erbilgin, Nadir. University of Alberta. Department of Renewable Resources; Canadá
Fil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
description Modeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH: 0.429, and WGR: 0.513) or design (HT: 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918–1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits’ heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.
publishDate 2022
dc.date.none.fl_str_mv 2022-10-21T12:45:19Z
2022-10-21T12:45:19Z
2022-02-18
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 http://hdl.handle.net/20.500.12123/13180
https://www.nature.com/articles/s41437-022-00508-2
1365-2540
0018-067X
https://doi.org/10.1038/s41437-022-00508-2
url http://hdl.handle.net/20.500.12123/13180
https://www.nature.com/articles/s41437-022-00508-2
https://doi.org/10.1038/s41437-022-00508-2
identifier_str_mv 1365-2540
0018-067X
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 Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv Heredity 128 (4) : 209-224 (2022)
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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