Serveur d'exploration sur le peuplier

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Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides.

Identifieur interne : 001368 ( Main/Exploration ); précédent : 001367; suivant : 001369

Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides.

Auteurs : Annette M. Fahrenkrog [États-Unis] ; Leandro G. Neves [États-Unis] ; Márcio F R. Resende [États-Unis] ; Ana I. Vazquez [États-Unis] ; Gustavo De Los Campos [États-Unis] ; Christopher Dervinis [États-Unis] ; Robert Sykes [États-Unis] ; Mark Davis [États-Unis] ; Ruth Davenport [États-Unis] ; William B. Barbazuk [États-Unis] ; Matias Kirst [États-Unis]

Source :

RBID : pubmed:27596807

Descripteurs français

English descriptors

Abstract

Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. These polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.

DOI: 10.1111/nph.14154
PubMed: 27596807


Affiliations:


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Le document en format XML

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<name sortKey="Kirst, Matias" sort="Kirst, Matias" uniqKey="Kirst M" first="Matias" last="Kirst">Matias Kirst</name>
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<series>
<title level="j">The New phytologist</title>
<idno type="eISSN">1469-8137</idno>
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<date when="2017" type="published">2017</date>
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<keywords scheme="KwdEn" xml:lang="en">
<term>Amino Acid Sequence (MeSH)</term>
<term>Energy Metabolism (genetics)</term>
<term>Genes, Plant (MeSH)</term>
<term>Genetic Loci (MeSH)</term>
<term>Genetic Markers (MeSH)</term>
<term>Genome-Wide Association Study (MeSH)</term>
<term>Plant Proteins (chemistry)</term>
<term>Plant Proteins (genetics)</term>
<term>Polymorphism, Single Nucleotide (genetics)</term>
<term>Populus (genetics)</term>
<term>Quantitative Trait, Heritable (MeSH)</term>
<term>Sequence Analysis, DNA (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Analyse de séquence d'ADN (MeSH)</term>
<term>Caractère quantitatif héréditaire (MeSH)</term>
<term>Gènes de plante (MeSH)</term>
<term>Locus génétiques (MeSH)</term>
<term>Marqueurs génétiques (MeSH)</term>
<term>Métabolisme énergétique (génétique)</term>
<term>Polymorphisme de nucléotide simple (génétique)</term>
<term>Populus (génétique)</term>
<term>Protéines végétales (composition chimique)</term>
<term>Protéines végétales (génétique)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Étude d'association pangénomique (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en">
<term>Plant Proteins</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
<term>Plant Proteins</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en">
<term>Genetic Markers</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr">
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Energy Metabolism</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Métabolisme énergétique</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Populus</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Amino Acid Sequence</term>
<term>Genes, Plant</term>
<term>Genetic Loci</term>
<term>Genome-Wide Association Study</term>
<term>Quantitative Trait, Heritable</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Analyse de séquence d'ADN</term>
<term>Caractère quantitatif héréditaire</term>
<term>Gènes de plante</term>
<term>Locus génétiques</term>
<term>Marqueurs génétiques</term>
<term>Séquence d'acides aminés</term>
<term>Étude d'association pangénomique</term>
</keywords>
</textClass>
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<front>
<div type="abstract" xml:lang="en">Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. These polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.</div>
</front>
</TEI>
<pubmed>
<MedlineCitation Status="MEDLINE" Owner="NLM">
<PMID Version="1">27596807</PMID>
<DateCompleted>
<Year>2018</Year>
<Month>02</Month>
<Day>09</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>213</Volume>
<Issue>2</Issue>
<PubDate>
<Year>2017</Year>
<Month>Jan</Month>
</PubDate>
</JournalIssue>
<Title>The New phytologist</Title>
<ISOAbbreviation>New Phytol</ISOAbbreviation>
</Journal>
<ArticleTitle>Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides.</ArticleTitle>
<Pagination>
<MedlinePgn>799-811</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.14154</ELocationID>
<Abstract>
<AbstractText>Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. These polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.</AbstractText>
<CopyrightInformation>© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Fahrenkrog</LastName>
<ForeName>Annette M</ForeName>
<Initials>AM</Initials>
<AffiliationInfo>
<Affiliation>School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Neves</LastName>
<ForeName>Leandro G</ForeName>
<Initials>LG</Initials>
<AffiliationInfo>
<Affiliation>School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA.</Affiliation>
</AffiliationInfo>
</Author>
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<LastName>Resende</LastName>
<ForeName>Márcio F R</ForeName>
<Initials>MF</Initials>
<Suffix>Jr</Suffix>
<AffiliationInfo>
<Affiliation>School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Genetics and Genomics Graduate Program, University of Florida, PO Box 103610, Gainesville, FL, 32610, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Vazquez</LastName>
<ForeName>Ana I</ForeName>
<Initials>AI</Initials>
<AffiliationInfo>
<Affiliation>Department of Epidemiology and Biostatistics, Michigan State University, 909 Fee Road, East Lansing, MI, 48824, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>de Los Campos</LastName>
<ForeName>Gustavo</ForeName>
<Initials>G</Initials>
<AffiliationInfo>
<Affiliation>Department of Epidemiology and Biostatistics, Michigan State University, 909 Fee Road, East Lansing, MI, 48824, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Statistics Department, Michigan State University, 619 Red Cedar Road, MI, 48824, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Dervinis</LastName>
<ForeName>Christopher</ForeName>
<Initials>C</Initials>
<AffiliationInfo>
<Affiliation>School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Sykes</LastName>
<ForeName>Robert</ForeName>
<Initials>R</Initials>
<AffiliationInfo>
<Affiliation>National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Davis</LastName>
<ForeName>Mark</ForeName>
<Initials>M</Initials>
<AffiliationInfo>
<Affiliation>National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Davenport</LastName>
<ForeName>Ruth</ForeName>
<Initials>R</Initials>
<AffiliationInfo>
<Affiliation>Biology Department, University of Florida, PO Box 118525, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Barbazuk</LastName>
<ForeName>William B</ForeName>
<Initials>WB</Initials>
<AffiliationInfo>
<Affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Biology Department, University of Florida, PO Box 118525, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Kirst</LastName>
<ForeName>Matias</ForeName>
<Initials>M</Initials>
<AffiliationInfo>
<Affiliation>School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, PO Box 110690, Gainesville, FL, 32610, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>University of Florida Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL, 32611, USA.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<DataBankList CompleteYN="Y">
<DataBank>
<DataBankName>GENBANK</DataBankName>
<AccessionNumberList>
<AccessionNumber>SRP066162</AccessionNumber>
</AccessionNumberList>
</DataBank>
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<PublicationType UI="D016428">Journal Article</PublicationType>
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<ArticleDate DateType="Electronic">
<Year>2016</Year>
<Month>09</Month>
<Day>06</Day>
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</Article>
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<Country>England</Country>
<MedlineTA>New Phytol</MedlineTA>
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<ISSNLinking>0028-646X</ISSNLinking>
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<DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName>
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<DescriptorName UI="D004734" MajorTopicYN="N">Energy Metabolism</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName>
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<MeshHeading>
<DescriptorName UI="D056426" MajorTopicYN="N">Genetic Loci</DescriptorName>
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<MeshHeading>
<DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D055106" MajorTopicYN="Y">Genome-Wide Association Study</DescriptorName>
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<MeshHeading>
<DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<MeshHeading>
<DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
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<DescriptorName UI="D019655" MajorTopicYN="Y">Quantitative Trait, Heritable</DescriptorName>
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</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="N">Populus deltoides </Keyword>
<Keyword MajorTopicYN="N">eastern cottonwood</Keyword>
<Keyword MajorTopicYN="N">exome resequencing</Keyword>
<Keyword MajorTopicYN="N">genome-wide association studies (GWAS)</Keyword>
<Keyword MajorTopicYN="N">low-frequency single-nucleotide polymorphisms (SNPs)</Keyword>
<Keyword MajorTopicYN="N">poplar</Keyword>
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</MedlineCitation>
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<Month>05</Month>
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<name sortKey="Davenport, Ruth" sort="Davenport, Ruth" uniqKey="Davenport R" first="Ruth" last="Davenport">Ruth Davenport</name>
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<name sortKey="Kirst, Matias" sort="Kirst, Matias" uniqKey="Kirst M" first="Matias" last="Kirst">Matias Kirst</name>
<name sortKey="Kirst, Matias" sort="Kirst, Matias" uniqKey="Kirst M" first="Matias" last="Kirst">Matias Kirst</name>
<name sortKey="Neves, Leandro G" sort="Neves, Leandro G" uniqKey="Neves L" first="Leandro G" last="Neves">Leandro G. Neves</name>
<name sortKey="Neves, Leandro G" sort="Neves, Leandro G" uniqKey="Neves L" first="Leandro G" last="Neves">Leandro G. Neves</name>
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