Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits.
Identifieur interne : 000827 ( Main/Exploration ); précédent : 000826; suivant : 000828Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits.
Auteurs : Hari B. Chhetri [États-Unis] ; David Macaya-Sanz [États-Unis] ; David Kainer [États-Unis] ; Ajaya K. Biswal [États-Unis] ; Luke M. Evans [États-Unis] ; Jin-Gui Chen [États-Unis] ; Cassandra Collins [États-Unis] ; Kimberly Hunt [États-Unis] ; Sushree S. Mohanty [États-Unis] ; Todd Rosenstiel [États-Unis] ; David Ryno [États-Unis] ; Kim Winkeler [États-Unis] ; Xiaohan Yang [États-Unis] ; Daniel Jacobson [États-Unis] ; Debra Mohnen [États-Unis] ; Wellington Muchero [États-Unis] ; Steven H. Strauss [États-Unis] ; Timothy J. Tschaplinski [États-Unis] ; Gerald A. Tuskan [États-Unis] ; Stephen P. Difazio [États-Unis]Source :
- The New phytologist [ 1469-8137 ] ; 2019.
Descripteurs français
- KwdFr :
- Analyse en composantes principales (MeSH), Analyse multifactorielle (MeSH), Caractère quantitatif héréditaire (MeSH), Gènes de plante (MeSH), Génotype (MeSH), Géographie (MeSH), Modes de transmission héréditaire (génétique), Polymorphisme de nucléotide simple (génétique), Populus (anatomie et histologie), Populus (génétique), Populus (physiologie), Régulation négative (MeSH), Réseaux de régulation génique (MeSH), Stomates de plante (physiologie), Étude d'association pangénomique (MeSH).
- MESH :
- anatomie et histologie : Populus.
- génétique : Modes de transmission héréditaire, Polymorphisme de nucléotide simple, Populus.
- physiologie : Populus, Stomates de plante.
- Analyse en composantes principales, Analyse multifactorielle, Caractère quantitatif héréditaire, Gènes de plante, Génotype, Géographie, Régulation négative, Réseaux de régulation génique, Étude d'association pangénomique.
English descriptors
- KwdEn :
- Down-Regulation (MeSH), Gene Regulatory Networks (MeSH), Genes, Plant (MeSH), Genome-Wide Association Study (MeSH), Genotype (MeSH), Geography (MeSH), Inheritance Patterns (genetics), Multivariate Analysis (MeSH), Plant Stomata (physiology), Polymorphism, Single Nucleotide (genetics), Populus (anatomy & histology), Populus (genetics), Populus (physiology), Principal Component Analysis (MeSH), Quantitative Trait, Heritable (MeSH).
- MESH :
- anatomy & histology : Populus.
- genetics : Inheritance Patterns, Polymorphism, Single Nucleotide, Populus.
- physiology : Plant Stomata, Populus.
- Down-Regulation, Gene Regulatory Networks, Genes, Plant, Genome-Wide Association Study, Genotype, Geography, Multivariate Analysis, Principal Component Analysis, Quantitative Trait, Heritable.
Abstract
Genome-wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge. We measured 14 morphological and physiological traits and identified single nucleotide polymorphism (SNP)-phenotype associations in a Populus trichocarpa population distributed from California, USA to British Columbia, Canada. We used whole-genome resequencing data of 882 trees with more than 6.78 million SNPs, coupled with multitrait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data. Broad-sense heritability (H2 ) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. In total, 4 and 20 gene models were detected using the single-trait and multitrait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co-expression networks, metabolite analyses, and direct confirmation of gene function through RNAi. Multitrait association identified many more significant associations than single-trait association, potentially revealing pleiotropic effects of individual genes. This approach can be particularly useful for challenging physiological traits such as water-use efficiency or complex traits such as leaf morphology, for which we were able to identify credible candidate genes by combining multitrait association with gene co-expression and co-methylation data.
DOI: 10.1111/nph.15777
PubMed: 30843213
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Mohanty</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation></author><author><name sortKey="Rosenstiel, Todd" sort="Rosenstiel, Todd" uniqKey="Rosenstiel T" first="Todd" last="Rosenstiel">Todd Rosenstiel</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Portland State University, Portland, OR, 97207, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Portland State University, Portland, OR, 97207</wicri:regionArea><wicri:noRegion>97207</wicri:noRegion></affiliation></author><author><name sortKey="Ryno, David" sort="Ryno, David" uniqKey="Ryno D" first="David" last="Ryno">David Ryno</name><affiliation wicri:level="1"><nlm:affiliation>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation></author><author><name sortKey="Winkeler, Kim" sort="Winkeler, Kim" uniqKey="Winkeler K" first="Kim" last="Winkeler">Kim Winkeler</name><affiliation wicri:level="1"><nlm:affiliation>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472</wicri:regionArea><wicri:noRegion>29472</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Jacobson, Daniel" sort="Jacobson, Daniel" uniqKey="Jacobson D" first="Daniel" last="Jacobson">Daniel Jacobson</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Mohnen, Debra" sort="Mohnen, Debra" uniqKey="Mohnen D" first="Debra" last="Mohnen">Debra Mohnen</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation></author><author><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name><affiliation wicri:level="1"><nlm:affiliation>Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331</wicri:regionArea><wicri:noRegion>97331</wicri:noRegion></affiliation></author><author><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506</wicri:regionArea><wicri:noRegion>26506</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30843213</idno><idno type="pmid">30843213</idno><idno type="doi">10.1111/nph.15777</idno><idno type="wicri:Area/Main/Corpus">000A01</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000A01</idno><idno type="wicri:Area/Main/Curation">000A01</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000A01</idno><idno type="wicri:Area/Main/Exploration">000A01</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits.</title><author><name sortKey="Chhetri, Hari B" sort="Chhetri, Hari B" uniqKey="Chhetri H" first="Hari B" last="Chhetri">Hari B. Chhetri</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506</wicri:regionArea><wicri:noRegion>26506</wicri:noRegion></affiliation></author><author><name sortKey="Macaya Sanz, David" sort="Macaya Sanz, David" uniqKey="Macaya Sanz D" first="David" last="Macaya-Sanz">David Macaya-Sanz</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506</wicri:regionArea><wicri:noRegion>26506</wicri:noRegion></affiliation></author><author><name sortKey="Kainer, David" sort="Kainer, David" uniqKey="Kainer D" first="David" last="Kainer">David Kainer</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Biswal, Ajaya K" sort="Biswal, Ajaya K" uniqKey="Biswal A" first="Ajaya K" last="Biswal">Ajaya K. Biswal</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation></author><author><name sortKey="Evans, Luke M" sort="Evans, Luke M" uniqKey="Evans L" first="Luke M" last="Evans">Luke M. Evans</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506</wicri:regionArea><wicri:noRegion>26506</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Jin Gui" sort="Chen, Jin Gui" uniqKey="Chen J" first="Jin-Gui" last="Chen">Jin-Gui Chen</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Collins, Cassandra" sort="Collins, Cassandra" uniqKey="Collins C" first="Cassandra" last="Collins">Cassandra Collins</name><affiliation wicri:level="1"><nlm:affiliation>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472</wicri:regionArea><wicri:noRegion>29472</wicri:noRegion></affiliation></author><author><name sortKey="Hunt, Kimberly" sort="Hunt, Kimberly" uniqKey="Hunt K" first="Kimberly" last="Hunt">Kimberly Hunt</name><affiliation wicri:level="1"><nlm:affiliation>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472</wicri:regionArea><wicri:noRegion>29472</wicri:noRegion></affiliation></author><author><name sortKey="Mohanty, Sushree S" sort="Mohanty, Sushree S" uniqKey="Mohanty S" first="Sushree S" last="Mohanty">Sushree S. Mohanty</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation></author><author><name sortKey="Rosenstiel, Todd" sort="Rosenstiel, Todd" uniqKey="Rosenstiel T" first="Todd" last="Rosenstiel">Todd Rosenstiel</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Portland State University, Portland, OR, 97207, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Portland State University, Portland, OR, 97207</wicri:regionArea><wicri:noRegion>97207</wicri:noRegion></affiliation></author><author><name sortKey="Ryno, David" sort="Ryno, David" uniqKey="Ryno D" first="David" last="Ryno">David Ryno</name><affiliation wicri:level="1"><nlm:affiliation>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation></author><author><name sortKey="Winkeler, Kim" sort="Winkeler, Kim" uniqKey="Winkeler K" first="Kim" last="Winkeler">Kim Winkeler</name><affiliation wicri:level="1"><nlm:affiliation>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472</wicri:regionArea><wicri:noRegion>29472</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Jacobson, Daniel" sort="Jacobson, Daniel" uniqKey="Jacobson D" first="Daniel" last="Jacobson">Daniel Jacobson</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Mohnen, Debra" sort="Mohnen, Debra" uniqKey="Mohnen D" first="Debra" last="Mohnen">Debra Mohnen</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602</wicri:regionArea><wicri:noRegion>30602</wicri:noRegion></affiliation></author><author><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name><affiliation wicri:level="1"><nlm:affiliation>Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331</wicri:regionArea><wicri:noRegion>97331</wicri:noRegion></affiliation></author><author><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation wicri:level="1"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831</wicri:regionArea><wicri:noRegion>37831</wicri:noRegion></affiliation></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV, 26506</wicri:regionArea><wicri:noRegion>26506</wicri:noRegion></affiliation></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Down-Regulation (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Genotype (MeSH)</term><term>Geography (MeSH)</term><term>Inheritance Patterns (genetics)</term><term>Multivariate Analysis (MeSH)</term><term>Plant Stomata (physiology)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Populus (anatomy & histology)</term><term>Populus (genetics)</term><term>Populus (physiology)</term><term>Principal Component Analysis (MeSH)</term><term>Quantitative Trait, Heritable (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse en composantes principales (MeSH)</term><term>Analyse multifactorielle (MeSH)</term><term>Caractère quantitatif héréditaire (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génotype (MeSH)</term><term>Géographie (MeSH)</term><term>Modes de transmission héréditaire (génétique)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Populus (anatomie et histologie)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Régulation négative (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Stomates de plante (physiologie)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="anatomie et histologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="anatomy & histology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Inheritance Patterns</term><term>Polymorphism, Single Nucleotide</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Modes de transmission héréditaire</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Populus</term><term>Stomates de plante</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Plant Stomata</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Down-Regulation</term><term>Gene Regulatory Networks</term><term>Genes, Plant</term><term>Genome-Wide Association Study</term><term>Genotype</term><term>Geography</term><term>Multivariate Analysis</term><term>Principal Component Analysis</term><term>Quantitative Trait, Heritable</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse en composantes principales</term><term>Analyse multifactorielle</term><term>Caractère quantitatif héréditaire</term><term>Gènes de plante</term><term>Génotype</term><term>Géographie</term><term>Régulation négative</term><term>Réseaux de régulation génique</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genome-wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge. We measured 14 morphological and physiological traits and identified single nucleotide polymorphism (SNP)-phenotype associations in a Populus trichocarpa population distributed from California, USA to British Columbia, Canada. We used whole-genome resequencing data of 882 trees with more than 6.78 million SNPs, coupled with multitrait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data. Broad-sense heritability (H<sup>2</sup> ) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. In total, 4 and 20 gene models were detected using the single-trait and multitrait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co-expression networks, metabolite analyses, and direct confirmation of gene function through RNAi. Multitrait association identified many more significant associations than single-trait association, potentially revealing pleiotropic effects of individual genes. This approach can be particularly useful for challenging physiological traits such as water-use efficiency or complex traits such as leaf morphology, for which we were able to identify credible candidate genes by combining multitrait association with gene co-expression and co-methylation data.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30843213</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>11</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>223</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>07</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits.</ArticleTitle><Pagination><MedlinePgn>293-309</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.15777</ELocationID><Abstract><AbstractText>Genome-wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge. We measured 14 morphological and physiological traits and identified single nucleotide polymorphism (SNP)-phenotype associations in a Populus trichocarpa population distributed from California, USA to British Columbia, Canada. We used whole-genome resequencing data of 882 trees with more than 6.78 million SNPs, coupled with multitrait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data. Broad-sense heritability (H<sup>2</sup> ) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. In total, 4 and 20 gene models were detected using the single-trait and multitrait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co-expression networks, metabolite analyses, and direct confirmation of gene function through RNAi. Multitrait association identified many more significant associations than single-trait association, potentially revealing pleiotropic effects of individual genes. This approach can be particularly useful for challenging physiological traits such as water-use efficiency or complex traits such as leaf morphology, for which we were able to identify credible candidate genes by combining multitrait association with gene co-expression and co-methylation data.</AbstractText><CopyrightInformation>No claim to US Government works New Phytologist © 2019 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chhetri</LastName><ForeName>Hari B</ForeName><Initials>HB</Initials><Identifier Source="ORCID">0000-0001-6820-8789</Identifier><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Macaya-Sanz</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kainer</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Biswal</LastName><ForeName>Ajaya K</ForeName><Initials>AK</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Evans</LastName><ForeName>Luke M</ForeName><Initials>LM</Initials><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Jin-Gui</ForeName><Initials>JG</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Collins</LastName><ForeName>Cassandra</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hunt</LastName><ForeName>Kimberly</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mohanty</LastName><ForeName>Sushree S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rosenstiel</LastName><ForeName>Todd</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Biology, Portland State University, Portland, OR, 97207, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ryno</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Winkeler</LastName><ForeName>Kim</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiaohan</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jacobson</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mohnen</LastName><ForeName>Debra</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Muchero</LastName><ForeName>Wellington</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Strauss</LastName><ForeName>Steven H</ForeName><Initials>SH</Initials><AffiliationInfo><Affiliation>Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tschaplinski</LastName><ForeName>Timothy J</ForeName><Initials>TJ</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>DiFazio</LastName><ForeName>Stephen P</ForeName><Initials>SP</Initials><Identifier Source="ORCID">0000-0003-4077-1590</Identifier><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>04</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D015536" MajorTopicYN="N">Down-Regulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="Y">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005843" MajorTopicYN="N">Geography</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040582" MajorTopicYN="N">Inheritance Patterns</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015999" MajorTopicYN="N">Multivariate Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054046" MajorTopicYN="N">Plant Stomata</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000033" MajorTopicYN="N">anatomy & histology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D025341" MajorTopicYN="N">Principal Component Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019655" MajorTopicYN="Y">Quantitative Trait, Heritable</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus
</Keyword><Keyword MajorTopicYN="Y">adaptation</Keyword><Keyword MajorTopicYN="Y">drought tolerance</Keyword><Keyword MajorTopicYN="Y">genome-wide association studies (GWAS)</Keyword><Keyword MajorTopicYN="Y">leaf morphology</Keyword><Keyword MajorTopicYN="Y">pleiotropy</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>12</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>02</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>3</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>3</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30843213</ArticleId><ArticleId IdType="doi">10.1111/nph.15777</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Chhetri, Hari B" sort="Chhetri, Hari B" uniqKey="Chhetri H" first="Hari B" last="Chhetri">Hari B. Chhetri</name></noRegion><name sortKey="Biswal, Ajaya K" sort="Biswal, Ajaya K" uniqKey="Biswal A" first="Ajaya K" last="Biswal">Ajaya K. Biswal</name><name sortKey="Biswal, Ajaya K" sort="Biswal, Ajaya K" uniqKey="Biswal A" first="Ajaya K" last="Biswal">Ajaya K. Biswal</name><name sortKey="Chen, Jin Gui" sort="Chen, Jin Gui" uniqKey="Chen J" first="Jin-Gui" last="Chen">Jin-Gui Chen</name><name sortKey="Collins, Cassandra" sort="Collins, Cassandra" uniqKey="Collins C" first="Cassandra" last="Collins">Cassandra Collins</name><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><name sortKey="Evans, Luke M" sort="Evans, Luke M" uniqKey="Evans L" first="Luke M" last="Evans">Luke M. Evans</name><name sortKey="Hunt, Kimberly" sort="Hunt, Kimberly" uniqKey="Hunt K" first="Kimberly" last="Hunt">Kimberly Hunt</name><name sortKey="Jacobson, Daniel" sort="Jacobson, Daniel" uniqKey="Jacobson D" first="Daniel" last="Jacobson">Daniel Jacobson</name><name sortKey="Kainer, David" sort="Kainer, David" uniqKey="Kainer D" first="David" last="Kainer">David Kainer</name><name sortKey="Macaya Sanz, David" sort="Macaya Sanz, David" uniqKey="Macaya Sanz D" first="David" last="Macaya-Sanz">David Macaya-Sanz</name><name sortKey="Mohanty, Sushree S" sort="Mohanty, Sushree S" uniqKey="Mohanty S" first="Sushree S" last="Mohanty">Sushree S. Mohanty</name><name sortKey="Mohnen, Debra" sort="Mohnen, Debra" uniqKey="Mohnen D" first="Debra" last="Mohnen">Debra Mohnen</name><name sortKey="Mohnen, Debra" sort="Mohnen, Debra" uniqKey="Mohnen D" first="Debra" last="Mohnen">Debra Mohnen</name><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name><name sortKey="Rosenstiel, Todd" sort="Rosenstiel, Todd" uniqKey="Rosenstiel T" first="Todd" last="Rosenstiel">Todd Rosenstiel</name><name sortKey="Ryno, David" sort="Ryno, David" uniqKey="Ryno D" first="David" last="Ryno">David Ryno</name><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><name sortKey="Winkeler, Kim" sort="Winkeler, Kim" uniqKey="Winkeler K" first="Kim" last="Winkeler">Kim Winkeler</name><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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