Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus

Autores
Cappa, Eduardo Pablo; El Kassaby, Yousry A.; Garcia, Martin Nahuel; Acuña, Cintia Vanesa; Borralho, Nuno M.; Grattapaglia, Dario; Marcucci Poltri, Susana Noemi
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model (UMM) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S∶G ratio), a key wood property trait. The two DArT markers associated with S∶G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus.
Instituto de Recursos Biológicos
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canada
Fil: Garcia, Martin Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Acuña, Cintia Vanesa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Borralho, Nuno M. Universidade Técnica de Lisboa. Instituto Superior de Agronomia. Centro de Estudos Florestais; Portugal
Fil: Grattapaglia, Dario. Universidade Católica de Brasília; Brasil. EMBRAPA; Brasil
Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fuente
PLoS ONE 8 (11) : e81267. (November 2013)
Materia
Eucalyptus
Estructura de la Población
Genomas
Genotipos
Interacción Genotipo Ambiente
Modelos
Population Structure
Genomes
Genotypes
Genotype Environment Interaction
Models
Eucalyptus Globulus
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
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oai_identifier_str oai:localhost:20.500.12123/4760
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network_name_str INTA Digital (INTA)
spelling Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulusCappa, Eduardo PabloEl Kassaby, Yousry A.Garcia, Martin NahuelAcuña, Cintia VanesaBorralho, Nuno M.Grattapaglia, DarioMarcucci Poltri, Susana NoemiEucalyptusEstructura de la PoblaciónGenomasGenotiposInteracción Genotipo AmbienteModelosPopulation StructureGenomesGenotypesGenotype Environment InteractionModelsEucalyptus GlobulusThe promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model (UMM) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S∶G ratio), a key wood property trait. The two DArT markers associated with S∶G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus.Instituto de Recursos BiológicosFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadaFil: Garcia, Martin Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Acuña, Cintia Vanesa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Borralho, Nuno M. Universidade Técnica de Lisboa. Instituto Superior de Agronomia. Centro de Estudos Florestais; PortugalFil: Grattapaglia, Dario. Universidade Católica de Brasília; Brasil. EMBRAPA; BrasilFil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaPlos One2019-03-27T14:56:41Z2019-03-27T14:56:41Z2013-11-25info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081267http://hdl.handle.net/20.500.12123/47601932-6203https://doi.org/10.1371/journal.pone.0081267PLoS ONE 8 (11) : e81267. (November 2013)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-10-16T09:29:29Zoai:localhost:20.500.12123/4760instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:29:29.557INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
title Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
spellingShingle Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
Cappa, Eduardo Pablo
Eucalyptus
Estructura de la Población
Genomas
Genotipos
Interacción Genotipo Ambiente
Modelos
Population Structure
Genomes
Genotypes
Genotype Environment Interaction
Models
Eucalyptus Globulus
title_short Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
title_full Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
title_fullStr Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
title_full_unstemmed Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
title_sort Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
dc.creator.none.fl_str_mv Cappa, Eduardo Pablo
El Kassaby, Yousry A.
Garcia, Martin Nahuel
Acuña, Cintia Vanesa
Borralho, Nuno M.
Grattapaglia, Dario
Marcucci Poltri, Susana Noemi
author Cappa, Eduardo Pablo
author_facet Cappa, Eduardo Pablo
El Kassaby, Yousry A.
Garcia, Martin Nahuel
Acuña, Cintia Vanesa
Borralho, Nuno M.
Grattapaglia, Dario
Marcucci Poltri, Susana Noemi
author_role author
author2 El Kassaby, Yousry A.
Garcia, Martin Nahuel
Acuña, Cintia Vanesa
Borralho, Nuno M.
Grattapaglia, Dario
Marcucci Poltri, Susana Noemi
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Eucalyptus
Estructura de la Población
Genomas
Genotipos
Interacción Genotipo Ambiente
Modelos
Population Structure
Genomes
Genotypes
Genotype Environment Interaction
Models
Eucalyptus Globulus
topic Eucalyptus
Estructura de la Población
Genomas
Genotipos
Interacción Genotipo Ambiente
Modelos
Population Structure
Genomes
Genotypes
Genotype Environment Interaction
Models
Eucalyptus Globulus
dc.description.none.fl_txt_mv The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model (UMM) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S∶G ratio), a key wood property trait. The two DArT markers associated with S∶G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus.
Instituto de Recursos Biológicos
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canada
Fil: Garcia, Martin Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Acuña, Cintia Vanesa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Borralho, Nuno M. Universidade Técnica de Lisboa. Instituto Superior de Agronomia. Centro de Estudos Florestais; Portugal
Fil: Grattapaglia, Dario. Universidade Católica de Brasília; Brasil. EMBRAPA; Brasil
Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
description The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model (UMM) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S∶G ratio), a key wood property trait. The two DArT markers associated with S∶G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly heterozygous forest trees, and provides additional insights into the nature of complex quantitative traits in Eucalyptus.
publishDate 2013
dc.date.none.fl_str_mv 2013-11-25
2019-03-27T14:56:41Z
2019-03-27T14:56:41Z
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://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081267
http://hdl.handle.net/20.500.12123/4760
1932-6203
https://doi.org/10.1371/journal.pone.0081267
url https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081267
http://hdl.handle.net/20.500.12123/4760
https://doi.org/10.1371/journal.pone.0081267
identifier_str_mv 1932-6203
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
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Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Plos One
publisher.none.fl_str_mv Plos One
dc.source.none.fl_str_mv PLoS ONE 8 (11) : e81267. (November 2013)
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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