Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus
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 heritab...
| Main Authors: | , , , , , , |
|---|---|
| Format: | info:ar-repo/semantics/artículo |
| Language: | Inglés |
| Published: |
Plos One
2019
|
| Subjects: | |
| Online Access: | 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 |
| _version_ | 1855035379456933888 |
|---|---|
| author | Cappa, Eduardo Pablo El Kassaby, Yousry A. Garcia, Martin Nahuel Acuña, Cintia Vanesa Borralho, Nuno M. Grattapaglia, Dario Marcucci Poltri, Susana Noemi |
| author_browse | Acuña, Cintia Vanesa Borralho, Nuno M. Cappa, Eduardo Pablo El Kassaby, Yousry A. Garcia, Martin Nahuel Grattapaglia, Dario Marcucci Poltri, Susana Noemi |
| 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_sort | Cappa, Eduardo Pablo |
| collection | INTA Digital |
| 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. |
| format | info:ar-repo/semantics/artículo |
| id | INTA4760 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Plos One |
| publisherStr | Plos One |
| record_format | dspace |
| spelling | INTA47602019-03-27T14:58:16Z 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 El Kassaby, Yousry A. Garcia, Martin Nahuel Acuña, Cintia Vanesa Borralho, Nuno M. Grattapaglia, Dario Marcucci Poltri, Susana Noemi Eucalyptus Estructura de la Población Genomas Genotipos Interacción Genotipo Ambiente Modelos Population Structure Genomes Genotypes Genotype Environment Interaction Models Eucalyptus Globulus 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 2019-03-27T14:56:41Z 2019-03-27T14:56:41Z 2013-11-25 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Plos One PLoS ONE 8 (11) : e81267. (November 2013) |
| spellingShingle | Eucalyptus Estructura de la Población Genomas Genotipos Interacción Genotipo Ambiente Modelos Population Structure Genomes Genotypes Genotype Environment Interaction Models Eucalyptus Globulus Cappa, Eduardo Pablo El Kassaby, Yousry A. Garcia, Martin Nahuel Acuña, Cintia Vanesa Borralho, Nuno M. Grattapaglia, Dario Marcucci Poltri, Susana Noemi 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 |
| 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_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_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 |
| topic | Eucalyptus Estructura de la Población Genomas Genotipos Interacción Genotipo Ambiente Modelos Population Structure Genomes Genotypes Genotype Environment Interaction Models Eucalyptus Globulus |
| 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 |
| work_keys_str_mv | AT cappaeduardopablo impactsofpopulationstructureandanalyticalmodelsingenomewideassociationstudiesofcomplextraitsinforesttreesacasestudyineucalyptusglobulus AT elkassabyyousrya impactsofpopulationstructureandanalyticalmodelsingenomewideassociationstudiesofcomplextraitsinforesttreesacasestudyineucalyptusglobulus AT garciamartinnahuel impactsofpopulationstructureandanalyticalmodelsingenomewideassociationstudiesofcomplextraitsinforesttreesacasestudyineucalyptusglobulus AT acunacintiavanesa impactsofpopulationstructureandanalyticalmodelsingenomewideassociationstudiesofcomplextraitsinforesttreesacasestudyineucalyptusglobulus AT borralhonunom impactsofpopulationstructureandanalyticalmodelsingenomewideassociationstudiesofcomplextraitsinforesttreesacasestudyineucalyptusglobulus AT grattapagliadario impactsofpopulationstructureandanalyticalmodelsingenomewideassociationstudiesofcomplextraitsinforesttreesacasestudyineucalyptusglobulus AT marcuccipoltrisusananoemi impactsofpopulationstructureandanalyticalmodelsingenomewideassociationstudiesofcomplextraitsinforesttreesacasestudyineucalyptusglobulus |