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Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa
To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed mo...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509168/ https://www.ncbi.nlm.nih.gov/pubmed/33013968 http://dx.doi.org/10.3389/fpls.2020.545748 |
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author | Chhetri, Hari B. Furches, Anna Macaya-Sanz, David Walker, Alejandro R. Kainer, David Jones, Piet Harman-Ware, Anne E. Tschaplinski, Timothy J. Jacobson, Daniel Tuskan, Gerald A. DiFazio, Stephen P. |
author_facet | Chhetri, Hari B. Furches, Anna Macaya-Sanz, David Walker, Alejandro R. Kainer, David Jones, Piet Harman-Ware, Anne E. Tschaplinski, Timothy J. Jacobson, Daniel Tuskan, Gerald A. DiFazio, Stephen P. |
author_sort | Chhetri, Hari B. |
collection | PubMed |
description | To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production. |
format | Online Article Text |
id | pubmed-7509168 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75091682020-10-02 Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa Chhetri, Hari B. Furches, Anna Macaya-Sanz, David Walker, Alejandro R. Kainer, David Jones, Piet Harman-Ware, Anne E. Tschaplinski, Timothy J. Jacobson, Daniel Tuskan, Gerald A. DiFazio, Stephen P. Front Plant Sci Plant Science To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production. Frontiers Media S.A. 2020-09-09 /pmc/articles/PMC7509168/ /pubmed/33013968 http://dx.doi.org/10.3389/fpls.2020.545748 Text en Copyright © 2020 Chhetri, Furches, Macaya-Sanz, Walker, Kainer, Jones, Harman-Ware, Tschaplinski, Jacobson, Tuskan and DiFazio http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Chhetri, Hari B. Furches, Anna Macaya-Sanz, David Walker, Alejandro R. Kainer, David Jones, Piet Harman-Ware, Anne E. Tschaplinski, Timothy J. Jacobson, Daniel Tuskan, Gerald A. DiFazio, Stephen P. Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa |
title | Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa |
title_full | Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa |
title_fullStr | Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa |
title_full_unstemmed | Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa |
title_short | Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa |
title_sort | genome-wide association study of wood anatomical and morphological traits in populus trichocarpa |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509168/ https://www.ncbi.nlm.nih.gov/pubmed/33013968 http://dx.doi.org/10.3389/fpls.2020.545748 |
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