Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.
Identifieur interne : 003C91 ( Main/Exploration ); précédent : 003C90; suivant : 003C92Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.
Auteurs : Erin J. Gilchrist [Canada] ; George W. Haughn ; Cheng C. Ying ; Sarah P. Otto ; Jun Zhuang ; Dorothy Cheung ; Björn Hamberger ; Fariba Aboutorabi ; Tatyana Kalynyak ; Lee Johnson ; Joerg Bohlmann ; Brian E. Ellis ; Carl J. Douglas ; Quentin C B. CronkSource :
- Molecular ecology [ 0962-1083 ] ; 2006.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), ADN des plantes (isolement et purification), Canada (MeSH), Cartographie chromosomique (MeSH), Déséquilibre de liaison (MeSH), Gènes de plante (MeSH), Génétique des populations (MeSH), Géographie (MeSH), Phylogenèse (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (classification), Populus (génétique), Variation génétique (MeSH), Écosystème (MeSH), États-Unis (MeSH).
- MESH :
- génétique : ADN des plantes, Populus.
- isolement et purification : ADN des plantes.
- Canada, Cartographie chromosomique, Déséquilibre de liaison, Gènes de plante, Génétique des populations, Géographie, Phylogenèse, Polymorphisme de nucléotide simple, Variation génétique, Écosystème, États-Unis.
- Wicri :
- geographic : Canada, États-Unis.
English descriptors
- KwdEn :
- Canada (MeSH), Chromosome Mapping (MeSH), DNA, Plant (genetics), DNA, Plant (isolation & purification), Ecosystem (MeSH), Genes, Plant (MeSH), Genetic Variation (MeSH), Genetics, Population (MeSH), Geography (MeSH), Linkage Disequilibrium (MeSH), Phylogeny (MeSH), Polymorphism, Single Nucleotide (MeSH), Populus (classification), Populus (genetics), United States (MeSH).
- MESH :
- chemical , genetics : DNA, Plant.
- chemical , isolation & purification : DNA, Plant.
- geographic : Canada, United States.
- classification : Populus.
- genetics : Populus.
- Chromosome Mapping, Ecosystem, Genes, Plant, Genetic Variation, Genetics, Population, Geography, Linkage Disequilibrium, Phylogeny, Polymorphism, Single Nucleotide.
Abstract
Abstract Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucleotide diversity, measured as (Total), was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.
DOI: 10.1111/j.1365-294X.2006.02885.x
PubMed: 16626459
Affiliations:
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Haughn</name></author><author><name sortKey="Ying, Cheng C" sort="Ying, Cheng C" uniqKey="Ying C" first="Cheng C" last="Ying">Cheng C. Ying</name></author><author><name sortKey="Otto, Sarah P" sort="Otto, Sarah P" uniqKey="Otto S" first="Sarah P" last="Otto">Sarah P. Otto</name></author><author><name sortKey="Zhuang, Jun" sort="Zhuang, Jun" uniqKey="Zhuang J" first="Jun" last="Zhuang">Jun Zhuang</name></author><author><name sortKey="Cheung, Dorothy" sort="Cheung, Dorothy" uniqKey="Cheung D" first="Dorothy" last="Cheung">Dorothy Cheung</name></author><author><name sortKey="Hamberger, Bjorn" sort="Hamberger, Bjorn" uniqKey="Hamberger B" first="Björn" last="Hamberger">Björn Hamberger</name></author><author><name sortKey="Aboutorabi, Fariba" sort="Aboutorabi, Fariba" uniqKey="Aboutorabi F" first="Fariba" last="Aboutorabi">Fariba Aboutorabi</name></author><author><name sortKey="Kalynyak, Tatyana" sort="Kalynyak, Tatyana" uniqKey="Kalynyak T" first="Tatyana" last="Kalynyak">Tatyana Kalynyak</name></author><author><name sortKey="Johnson, Lee" sort="Johnson, Lee" uniqKey="Johnson L" first="Lee" last="Johnson">Lee Johnson</name></author><author><name sortKey="Bohlmann, Joerg" sort="Bohlmann, Joerg" uniqKey="Bohlmann J" first="Joerg" last="Bohlmann">Joerg Bohlmann</name></author><author><name sortKey="Ellis, Brian E" sort="Ellis, Brian E" uniqKey="Ellis B" first="Brian E" last="Ellis">Brian E. Ellis</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="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. Cronk</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16626459</idno><idno type="pmid">16626459</idno><idno type="doi">10.1111/j.1365-294X.2006.02885.x</idno><idno type="wicri:Area/Main/Corpus">003E24</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003E24</idno><idno type="wicri:Area/Main/Curation">003E24</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003E24</idno><idno type="wicri:Area/Main/Exploration">003E24</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.</title><author><name sortKey="Gilchrist, Erin J" sort="Gilchrist, Erin J" uniqKey="Gilchrist E" first="Erin J" last="Gilchrist">Erin J. Gilchrist</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, Vancouver, BC</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Haughn, George W" sort="Haughn, George W" uniqKey="Haughn G" first="George W" last="Haughn">George W. Haughn</name></author><author><name sortKey="Ying, Cheng C" sort="Ying, Cheng C" uniqKey="Ying C" first="Cheng C" last="Ying">Cheng C. Ying</name></author><author><name sortKey="Otto, Sarah P" sort="Otto, Sarah P" uniqKey="Otto S" first="Sarah P" last="Otto">Sarah P. Otto</name></author><author><name sortKey="Zhuang, Jun" sort="Zhuang, Jun" uniqKey="Zhuang J" first="Jun" last="Zhuang">Jun Zhuang</name></author><author><name sortKey="Cheung, Dorothy" sort="Cheung, Dorothy" uniqKey="Cheung D" first="Dorothy" last="Cheung">Dorothy Cheung</name></author><author><name sortKey="Hamberger, Bjorn" sort="Hamberger, Bjorn" uniqKey="Hamberger B" first="Björn" last="Hamberger">Björn Hamberger</name></author><author><name sortKey="Aboutorabi, Fariba" sort="Aboutorabi, Fariba" uniqKey="Aboutorabi F" first="Fariba" last="Aboutorabi">Fariba Aboutorabi</name></author><author><name sortKey="Kalynyak, Tatyana" sort="Kalynyak, Tatyana" uniqKey="Kalynyak T" first="Tatyana" last="Kalynyak">Tatyana Kalynyak</name></author><author><name sortKey="Johnson, Lee" sort="Johnson, Lee" uniqKey="Johnson L" first="Lee" last="Johnson">Lee Johnson</name></author><author><name sortKey="Bohlmann, Joerg" sort="Bohlmann, Joerg" uniqKey="Bohlmann J" first="Joerg" last="Bohlmann">Joerg Bohlmann</name></author><author><name sortKey="Ellis, Brian E" sort="Ellis, Brian E" uniqKey="Ellis B" first="Brian E" last="Ellis">Brian E. Ellis</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="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. Cronk</name></author></analytic><series><title level="j">Molecular ecology</title><idno type="ISSN">0962-1083</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Canada (MeSH)</term><term>Chromosome Mapping (MeSH)</term><term>DNA, Plant (genetics)</term><term>DNA, Plant (isolation & purification)</term><term>Ecosystem (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genetics, Population (MeSH)</term><term>Geography (MeSH)</term><term>Linkage Disequilibrium (MeSH)</term><term>Phylogeny (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term><term>United States (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>ADN des plantes (isolement et purification)</term><term>Canada (MeSH)</term><term>Cartographie chromosomique (MeSH)</term><term>Déséquilibre de liaison (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génétique des populations (MeSH)</term><term>Géographie (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Variation génétique (MeSH)</term><term>Écosystème (MeSH)</term><term>États-Unis (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Canada</term><term>United States</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ADN des plantes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Ecosystem</term><term>Genes, Plant</term><term>Genetic Variation</term><term>Genetics, Population</term><term>Geography</term><term>Linkage Disequilibrium</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Canada</term><term>Cartographie chromosomique</term><term>Déséquilibre de liaison</term><term>Gènes de plante</term><term>Génétique des populations</term><term>Géographie</term><term>Phylogenèse</term><term>Polymorphisme de nucléotide simple</term><term>Variation génétique</term><term>Écosystème</term><term>États-Unis</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Canada</term><term>États-Unis</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucleotide diversity, measured as (Total), was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16626459</PMID><DateCompleted><Year>2006</Year><Month>06</Month><Day>23</Day></DateCompleted><DateRevised><Year>2008</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0962-1083</ISSN><JournalIssue CitedMedium="Print"><Volume>15</Volume><Issue>5</Issue><PubDate><Year>2006</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol Ecol</ISOAbbreviation></Journal><ArticleTitle>Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>1367-78</MedlinePgn></Pagination><Abstract><AbstractText>Abstract Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucleotide diversity, measured as (Total), was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gilchrist</LastName><ForeName>Erin J</ForeName><Initials>EJ</Initials><AffiliationInfo><Affiliation>Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Haughn</LastName><ForeName>George W</ForeName><Initials>GW</Initials></Author><Author ValidYN="Y"><LastName>Ying</LastName><ForeName>Cheng C</ForeName><Initials>CC</Initials></Author><Author ValidYN="Y"><LastName>Otto</LastName><ForeName>Sarah P</ForeName><Initials>SP</Initials></Author><Author ValidYN="Y"><LastName>Zhuang</LastName><ForeName>Jun</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Cheung</LastName><ForeName>Dorothy</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Hamberger</LastName><ForeName>Björn</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Aboutorabi</LastName><ForeName>Fariba</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Kalynyak</LastName><ForeName>Tatyana</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Johnson</LastName><ForeName>Lee</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Bohlmann</LastName><ForeName>Joerg</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Ellis</LastName><ForeName>Brian E</ForeName><Initials>BE</Initials></Author><Author ValidYN="Y"><LastName>Douglas</LastName><ForeName>Carl J</ForeName><Initials>CJ</Initials></Author><Author ValidYN="Y"><LastName>Cronk</LastName><ForeName>Quentin C B</ForeName><Initials>QC</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></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol</MedlineTA><NlmUniqueID>9214478</NlmUniqueID><ISSNLinking>0962-1083</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002170" MajorTopicYN="N" Type="Geographic">Canada</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017753" MajorTopicYN="N">Ecosystem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="N">Genetics, Population</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005843" MajorTopicYN="N">Geography</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014481" MajorTopicYN="N" Type="Geographic">United States</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>4</Month><Day>22</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>6</Month><Day>24</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>4</Month><Day>22</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16626459</ArticleId><ArticleId IdType="pii">MEC2885</ArticleId><ArticleId IdType="doi">10.1111/j.1365-294X.2006.02885.x</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="Aboutorabi, Fariba" sort="Aboutorabi, Fariba" uniqKey="Aboutorabi F" first="Fariba" last="Aboutorabi">Fariba Aboutorabi</name><name sortKey="Bohlmann, Joerg" sort="Bohlmann, Joerg" uniqKey="Bohlmann J" first="Joerg" last="Bohlmann">Joerg Bohlmann</name><name sortKey="Cheung, Dorothy" sort="Cheung, Dorothy" uniqKey="Cheung D" first="Dorothy" last="Cheung">Dorothy Cheung</name><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="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name><name sortKey="Ellis, Brian E" sort="Ellis, Brian E" uniqKey="Ellis B" first="Brian E" last="Ellis">Brian E. Ellis</name><name sortKey="Hamberger, Bjorn" sort="Hamberger, Bjorn" uniqKey="Hamberger B" first="Björn" last="Hamberger">Björn Hamberger</name><name sortKey="Haughn, George W" sort="Haughn, George W" uniqKey="Haughn G" first="George W" last="Haughn">George W. Haughn</name><name sortKey="Johnson, Lee" sort="Johnson, Lee" uniqKey="Johnson L" first="Lee" last="Johnson">Lee Johnson</name><name sortKey="Kalynyak, Tatyana" sort="Kalynyak, Tatyana" uniqKey="Kalynyak T" first="Tatyana" last="Kalynyak">Tatyana Kalynyak</name><name sortKey="Otto, Sarah P" sort="Otto, Sarah P" uniqKey="Otto S" first="Sarah P" last="Otto">Sarah P. Otto</name><name sortKey="Ying, Cheng C" sort="Ying, Cheng C" uniqKey="Ying C" first="Cheng C" last="Ying">Cheng C. Ying</name><name sortKey="Zhuang, Jun" sort="Zhuang, Jun" uniqKey="Zhuang J" first="Jun" last="Zhuang">Jun Zhuang</name></noCountry><country name="Canada"><region name="Colombie-Britannique "><name sortKey="Gilchrist, Erin J" sort="Gilchrist, Erin J" uniqKey="Gilchrist E" first="Erin J" last="Gilchrist">Erin J. Gilchrist</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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