Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms.
Identifieur interne : 002671 ( Main/Exploration ); précédent : 002670; suivant : 002672Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms.
Auteurs : Ilga Porth [Canada] ; Jaroslav Klapšte ; Oleksandr Skyba ; Jan Hannemann ; Athena D. Mckown ; Robert D. Guy ; Stephen P. Difazio ; Wellington Muchero ; Priya Ranjan ; Gerald A. Tuskan ; Michael C. Friedmann ; Juergen Ehlting ; Quentin C B. Cronk ; Yousry A. El-Kassaby ; Carl J. Douglas ; Shawn D. MansfieldSource :
- The New phytologist [ 1469-8137 ] ; 2013.
Descripteurs français
- KwdFr :
- Allèles (MeSH), Bois (croissance et développement), Bois (métabolisme), Bois (ultrastructure), Gènes de plante (MeSH), Génome végétal (MeSH), Génotype (MeSH), Paroi cellulaire (MeSH), Phénotype (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (croissance et développement), Populus (génétique), Populus (métabolisme), Populus (ultrastructure), Études d'associations génétiques (MeSH).
- MESH :
- croissance et développement : Bois, Populus.
- génétique : Populus.
- métabolisme : Bois, Populus.
- ultrastructure : Allèles, Bois, Gènes de plante, Génome végétal, Génotype, Paroi cellulaire, Phénotype, Polymorphisme de nucléotide simple, Populus, Études d'associations génétiques.
English descriptors
- KwdEn :
- Alleles (MeSH), Cell Wall (MeSH), Genes, Plant (MeSH), Genetic Association Studies (MeSH), Genome, Plant (MeSH), Genotype (MeSH), Phenotype (MeSH), Polymorphism, Single Nucleotide (MeSH), Populus (genetics), Populus (growth & development), Populus (metabolism), Populus (ultrastructure), Wood (growth & development), Wood (metabolism), Wood (ultrastructure).
- MESH :
- genetics : Populus.
- growth & development : Populus, Wood.
- metabolism : Populus, Wood.
- ultrastructure : Populus, Wood.
- Alleles, Cell Wall, Genes, Plant, Genetic Association Studies, Genome, Plant, Genotype, Phenotype, Polymorphism, Single Nucleotide.
Abstract
Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29,233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genome-wide associations. The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, individually explaining 3-7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.
DOI: 10.1111/nph.12422
PubMed: 23889164
Affiliations:
Links toward previous steps (curation, corpus...)
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Mckown</name></author><author><name sortKey="Guy, Robert D" sort="Guy, Robert D" uniqKey="Guy R" first="Robert D" last="Guy">Robert D. Guy</name></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name></author><author><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name></author><author><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name></author><author><name sortKey="Friedmann, Michael C" sort="Friedmann, Michael C" uniqKey="Friedmann M" first="Michael C" last="Friedmann">Michael C. Friedmann</name></author><author><name sortKey="Ehlting, Juergen" sort="Ehlting, Juergen" uniqKey="Ehlting J" first="Juergen" last="Ehlting">Juergen Ehlting</name></author><author><name sortKey="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. Cronk</name></author><author><name sortKey="El Kassaby, Yousry A" sort="El Kassaby, Yousry A" uniqKey="El Kassaby Y" first="Yousry A" last="El-Kassaby">Yousry A. El-Kassaby</name></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name></author><author><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term><term>Cell Wall (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genetic Association Studies (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genotype (MeSH)</term><term>Phenotype (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term><term>Populus (metabolism)</term><term>Populus (ultrastructure)</term><term>Wood (growth & development)</term><term>Wood (metabolism)</term><term>Wood (ultrastructure)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Allèles (MeSH)</term><term>Bois (croissance et développement)</term><term>Bois (métabolisme)</term><term>Bois (ultrastructure)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génotype (MeSH)</term><term>Paroi cellulaire (MeSH)</term><term>Phénotype (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (croissance et développement)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Populus (ultrastructure)</term><term>Études d'associations génétiques (MeSH)</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Bois</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Bois</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="ultrastructure" xml:lang="en"><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Cell Wall</term><term>Genes, Plant</term><term>Genetic Association Studies</term><term>Genome, Plant</term><term>Genotype</term><term>Phenotype</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" qualifier="ultrastructure" xml:lang="fr"><term>Allèles</term><term>Bois</term><term>Gènes de plante</term><term>Génome végétal</term><term>Génotype</term><term>Paroi cellulaire</term><term>Phénotype</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term><term>Études d'associations génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29,233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genome-wide associations. The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, individually explaining 3-7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23889164</PMID><DateCompleted><Year>2014</Year><Month>04</Month><Day>29</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>200</Volume><Issue>3</Issue><PubDate><Year>2013</Year><Month>Nov</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms.</ArticleTitle><Pagination><MedlinePgn>710-26</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.12422</ELocationID><Abstract><AbstractText>Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29,233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genome-wide associations. The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, individually explaining 3-7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.</AbstractText><CopyrightInformation>© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Porth</LastName><ForeName>Ilga</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Klapšte</LastName><ForeName>Jaroslav</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Skyba</LastName><ForeName>Oleksandr</ForeName><Initials>O</Initials></Author><Author ValidYN="Y"><LastName>Hannemann</LastName><ForeName>Jan</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>McKown</LastName><ForeName>Athena D</ForeName><Initials>AD</Initials></Author><Author ValidYN="Y"><LastName>Guy</LastName><ForeName>Robert D</ForeName><Initials>RD</Initials></Author><Author ValidYN="Y"><LastName>DiFazio</LastName><ForeName>Stephen P</ForeName><Initials>SP</Initials></Author><Author ValidYN="Y"><LastName>Muchero</LastName><ForeName>Wellington</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Ranjan</LastName><ForeName>Priya</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials></Author><Author ValidYN="Y"><LastName>Friedmann</LastName><ForeName>Michael C</ForeName><Initials>MC</Initials></Author><Author ValidYN="Y"><LastName>Ehlting</LastName><ForeName>Juergen</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Cronk</LastName><ForeName>Quentin C B</ForeName><Initials>QC</Initials></Author><Author ValidYN="Y"><LastName>El-Kassaby</LastName><ForeName>Yousry A</ForeName><Initials>YA</Initials></Author><Author ValidYN="Y"><LastName>Douglas</LastName><ForeName>Carl J</ForeName><Initials>CJ</Initials></Author><Author ValidYN="Y"><LastName>Mansfield</LastName><ForeName>Shawn D</ForeName><Initials>SD</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>07</Month><Day>26</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="D000483" MajorTopicYN="N">Alleles</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056726" MajorTopicYN="N">Genetic Association Studies</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="Y">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="Y">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000648" MajorTopicYN="N">ultrastructure</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="Y">Wood</DescriptorName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000648" MajorTopicYN="N">ultrastructure</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus</Keyword><Keyword MajorTopicYN="N">association genetics</Keyword><Keyword MajorTopicYN="N">cellulose</Keyword><Keyword MajorTopicYN="N">lignin</Keyword><Keyword MajorTopicYN="N">single nucleotide polymorphism (SNP)</Keyword><Keyword MajorTopicYN="N">wood traits</Keyword><Keyword MajorTopicYN="N">wood ultrastructure</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>03</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>06</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>7</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>7</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>4</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23889164</ArticleId><ArticleId IdType="doi">10.1111/nph.12422</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country><region><li>Colombie-Britannique </li></region><settlement><li>Vancouver</li></settlement><orgName><li>Université de la Colombie-Britannique</li></orgName></list><tree><noCountry><name sortKey="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. Cronk</name><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name><name sortKey="Ehlting, Juergen" sort="Ehlting, Juergen" uniqKey="Ehlting J" first="Juergen" last="Ehlting">Juergen Ehlting</name><name sortKey="El Kassaby, Yousry A" sort="El Kassaby, Yousry A" uniqKey="El Kassaby Y" first="Yousry A" last="El-Kassaby">Yousry A. El-Kassaby</name><name sortKey="Friedmann, Michael C" sort="Friedmann, Michael C" uniqKey="Friedmann M" first="Michael C" last="Friedmann">Michael C. Friedmann</name><name sortKey="Guy, Robert D" sort="Guy, Robert D" uniqKey="Guy R" first="Robert D" last="Guy">Robert D. Guy</name><name sortKey="Hannemann, Jan" sort="Hannemann, Jan" uniqKey="Hannemann J" first="Jan" last="Hannemann">Jan Hannemann</name><name sortKey="Klapste, Jaroslav" sort="Klapste, Jaroslav" uniqKey="Klapste J" first="Jaroslav" last="Klapšte">Jaroslav Klapšte</name><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name><name sortKey="Mckown, Athena D" sort="Mckown, Athena D" uniqKey="Mckown A" first="Athena D" last="Mckown">Athena D. Mckown</name><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name><name sortKey="Skyba, Oleksandr" sort="Skyba, Oleksandr" uniqKey="Skyba O" first="Oleksandr" last="Skyba">Oleksandr Skyba</name><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name></noCountry><country name="Canada"><region name="Colombie-Britannique "><name sortKey="Porth, Ilga" sort="Porth, Ilga" uniqKey="Porth I" first="Ilga" last="Porth">Ilga Porth</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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