Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).
Identifieur interne : 003181 ( Main/Exploration ); précédent : 003180; suivant : 003182Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).
Auteurs : Matthew S. Olson [États-Unis] ; Amanda L. Robertson ; Naoki Takebayashi ; Salim Silim ; William R. Schroeder ; Peter TiffinSource :
- The New phytologist [ 1469-8137 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
- Wicri :
- geographic : Canada.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Nucleotides.
- geographic : Canada.
- genetics : Genetic Loci, Genome, Plant, Linkage Disequilibrium, Populus.
- Diploidy, Genetic Variation, Geography, Polymorphism, Genetic.
Abstract
*Current perceptions that poplars have high levels of nucleotide variation, large effective population sizes, and rapid decay of linkage disequilibrium are based primarily on studies from one poplar species, Populus tremula. *We analysed 590 gene fragments (average length 565 bp) from each of 15 individuals from different populations from throughout the range of Populus balsamifera. *Nucleotide diversity (theta(total) = 0.0028, pi = 0.0027) was low compared with other trees and model agricultural systems. Patterns of nucleotide diversity and site frequency spectra were consistent with purifying selection on replacement and intron sites. When averaged across all loci we found no evidence for decay of linkage disequilibrium across 750 bp, consistent with the low estimates of the scaled recombination parameter, rho = 0.0092. *Compared with P. tremula, a well studied congener with a similar distribution, P. balsamifera has low diversity and low effective recombination, both of which indicate a lower effective population size in P. balsamifera. Patterns of diversity and linkage indicate that there is considerable variation in population genomic patterns among poplar species and unlike P. tremula, association mapping techniques in balsam poplar should consider sampling single nucleotide polymorphisms (SNPs) at well-spaced intervals.
DOI: 10.1111/j.1469-8137.2009.03174.x
PubMed: 20122131
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).</title><author><name sortKey="Olson, Matthew S" sort="Olson, Matthew S" uniqKey="Olson M" first="Matthew S" last="Olson">Matthew S. Olson</name><affiliation wicri:level="2"><nlm:affiliation>Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, AK 99775, USA. msolson@alaska.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, AK 99775</wicri:regionArea><placeName><region type="state">Alaska</region></placeName></affiliation></author><author><name sortKey="Robertson, Amanda L" sort="Robertson, Amanda L" uniqKey="Robertson A" first="Amanda L" last="Robertson">Amanda L. Robertson</name></author><author><name sortKey="Takebayashi, Naoki" sort="Takebayashi, Naoki" uniqKey="Takebayashi N" first="Naoki" last="Takebayashi">Naoki Takebayashi</name></author><author><name sortKey="Silim, Salim" sort="Silim, Salim" uniqKey="Silim S" first="Salim" last="Silim">Salim Silim</name></author><author><name sortKey="Schroeder, William R" sort="Schroeder, William R" uniqKey="Schroeder W" first="William R" last="Schroeder">William R. Schroeder</name></author><author><name sortKey="Tiffin, Peter" sort="Tiffin, Peter" uniqKey="Tiffin P" first="Peter" last="Tiffin">Peter Tiffin</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:20122131</idno><idno type="pmid">20122131</idno><idno type="doi">10.1111/j.1469-8137.2009.03174.x</idno><idno type="wicri:Area/Main/Corpus">003315</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003315</idno><idno type="wicri:Area/Main/Curation">003315</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003315</idno><idno type="wicri:Area/Main/Exploration">003315</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).</title><author><name sortKey="Olson, Matthew S" sort="Olson, Matthew S" uniqKey="Olson M" first="Matthew S" last="Olson">Matthew S. Olson</name><affiliation wicri:level="2"><nlm:affiliation>Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, AK 99775, USA. msolson@alaska.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, AK 99775</wicri:regionArea><placeName><region type="state">Alaska</region></placeName></affiliation></author><author><name sortKey="Robertson, Amanda L" sort="Robertson, Amanda L" uniqKey="Robertson A" first="Amanda L" last="Robertson">Amanda L. Robertson</name></author><author><name sortKey="Takebayashi, Naoki" sort="Takebayashi, Naoki" uniqKey="Takebayashi N" first="Naoki" last="Takebayashi">Naoki Takebayashi</name></author><author><name sortKey="Silim, Salim" sort="Silim, Salim" uniqKey="Silim S" first="Salim" last="Silim">Salim Silim</name></author><author><name sortKey="Schroeder, William R" sort="Schroeder, William R" uniqKey="Schroeder W" first="William R" last="Schroeder">William R. Schroeder</name></author><author><name sortKey="Tiffin, Peter" sort="Tiffin, Peter" uniqKey="Tiffin P" first="Peter" last="Tiffin">Peter Tiffin</name></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Canada (MeSH)</term><term>Diploidy (MeSH)</term><term>Genetic Loci (genetics)</term><term>Genetic Variation (MeSH)</term><term>Genome, Plant (genetics)</term><term>Geography (MeSH)</term><term>Linkage Disequilibrium (genetics)</term><term>Nucleotides (genetics)</term><term>Polymorphism, Genetic (MeSH)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Canada (MeSH)</term><term>Diploïdie (MeSH)</term><term>Déséquilibre de liaison (génétique)</term><term>Génome végétal (génétique)</term><term>Géographie (MeSH)</term><term>Locus génétiques (génétique)</term><term>Nucléotides (génétique)</term><term>Polymorphisme génétique (MeSH)</term><term>Populus (génétique)</term><term>Variation génétique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Nucleotides</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Canada</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genetic Loci</term><term>Genome, Plant</term><term>Linkage Disequilibrium</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Déséquilibre de liaison</term><term>Génome végétal</term><term>Locus génétiques</term><term>Nucléotides</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Diploidy</term><term>Genetic Variation</term><term>Geography</term><term>Polymorphism, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Canada</term><term>Diploïdie</term><term>Géographie</term><term>Polymorphisme génétique</term><term>Variation génétique</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Canada</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">*Current perceptions that poplars have high levels of nucleotide variation, large effective population sizes, and rapid decay of linkage disequilibrium are based primarily on studies from one poplar species, Populus tremula. *We analysed 590 gene fragments (average length 565 bp) from each of 15 individuals from different populations from throughout the range of Populus balsamifera. *Nucleotide diversity (theta(total) = 0.0028, pi = 0.0027) was low compared with other trees and model agricultural systems. Patterns of nucleotide diversity and site frequency spectra were consistent with purifying selection on replacement and intron sites. When averaged across all loci we found no evidence for decay of linkage disequilibrium across 750 bp, consistent with the low estimates of the scaled recombination parameter, rho = 0.0092. *Compared with P. tremula, a well studied congener with a similar distribution, P. balsamifera has low diversity and low effective recombination, both of which indicate a lower effective population size in P. balsamifera. Patterns of diversity and linkage indicate that there is considerable variation in population genomic patterns among poplar species and unlike P. tremula, association mapping techniques in balsam poplar should consider sampling single nucleotide polymorphisms (SNPs) at well-spaced intervals.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20122131</PMID><DateCompleted><Year>2010</Year><Month>07</Month><Day>15</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>186</Volume><Issue>2</Issue><PubDate><Year>2010</Year><Month>Apr</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).</ArticleTitle><Pagination><MedlinePgn>526-36</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1469-8137.2009.03174.x</ELocationID><Abstract><AbstractText>*Current perceptions that poplars have high levels of nucleotide variation, large effective population sizes, and rapid decay of linkage disequilibrium are based primarily on studies from one poplar species, Populus tremula. *We analysed 590 gene fragments (average length 565 bp) from each of 15 individuals from different populations from throughout the range of Populus balsamifera. *Nucleotide diversity (theta(total) = 0.0028, pi = 0.0027) was low compared with other trees and model agricultural systems. Patterns of nucleotide diversity and site frequency spectra were consistent with purifying selection on replacement and intron sites. When averaged across all loci we found no evidence for decay of linkage disequilibrium across 750 bp, consistent with the low estimates of the scaled recombination parameter, rho = 0.0092. *Compared with P. tremula, a well studied congener with a similar distribution, P. balsamifera has low diversity and low effective recombination, both of which indicate a lower effective population size in P. balsamifera. Patterns of diversity and linkage indicate that there is considerable variation in population genomic patterns among poplar species and unlike P. tremula, association mapping techniques in balsam poplar should consider sampling single nucleotide polymorphisms (SNPs) at well-spaced intervals.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Olson</LastName><ForeName>Matthew S</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, AK 99775, USA. msolson@alaska.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Robertson</LastName><ForeName>Amanda L</ForeName><Initials>AL</Initials></Author><Author ValidYN="Y"><LastName>Takebayashi</LastName><ForeName>Naoki</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Silim</LastName><ForeName>Salim</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Schroeder</LastName><ForeName>William R</ForeName><Initials>WR</Initials></Author><Author ValidYN="Y"><LastName>Tiffin</LastName><ForeName>Peter</ForeName><Initials>P</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>01</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009711">Nucleotides</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002170" MajorTopicYN="N" Type="Geographic">Canada</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004171" MajorTopicYN="N">Diploidy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056426" MajorTopicYN="N">Genetic Loci</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005843" MajorTopicYN="N">Geography</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009711" MajorTopicYN="N">Nucleotides</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="N">Polymorphism, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>2</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>2</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2010</Year><Month>7</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">20122131</ArticleId><ArticleId IdType="pii">NPH3174</ArticleId><ArticleId IdType="doi">10.1111/j.1469-8137.2009.03174.x</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Alaska</li></region></list><tree><noCountry><name sortKey="Robertson, Amanda L" sort="Robertson, Amanda L" uniqKey="Robertson A" first="Amanda L" last="Robertson">Amanda L. Robertson</name><name sortKey="Schroeder, William R" sort="Schroeder, William R" uniqKey="Schroeder W" first="William R" last="Schroeder">William R. Schroeder</name><name sortKey="Silim, Salim" sort="Silim, Salim" uniqKey="Silim S" first="Salim" last="Silim">Salim Silim</name><name sortKey="Takebayashi, Naoki" sort="Takebayashi, Naoki" uniqKey="Takebayashi N" first="Naoki" last="Takebayashi">Naoki Takebayashi</name><name sortKey="Tiffin, Peter" sort="Tiffin, Peter" uniqKey="Tiffin P" first="Peter" last="Tiffin">Peter Tiffin</name></noCountry><country name="États-Unis"><region name="Alaska"><name sortKey="Olson, Matthew S" sort="Olson, Matthew S" uniqKey="Olson M" first="Matthew S" last="Olson">Matthew S. Olson</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003181 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003181 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:20122131
|texte= Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:20122131" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |