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
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/13180
Ver los metadatos del registro completo
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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 |
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INTA Digital (INTA) |
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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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12.559606 |