Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding.
Identifieur interne : 002B31 ( Main/Exploration ); précédent : 002B30; suivant : 002B32Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding.
Auteurs : H. Schroeder [Allemagne] ; A M Hoeltken ; M. FladungSource :
- Plant biology (Stuttgart, Germany) [ 1438-8677 ] ; 2012.
Descripteurs français
- KwdFr :
- ADN des chloroplastes (génétique), ADN intergénique (génétique), Amorces ADN (génétique), Analyse de séquence d'ADN (MeSH), Chloroplastes (génétique), Codage à barres de l'ADN pour la taxonomie (méthodes), Données de séquences moléculaires (MeSH), Gènes chloroplastiques (génétique), Génome de chloroplaste (génétique), Marqueurs génétiques (génétique), Mutation de type INDEL (MeSH), Polymorphisme de nucléotide simple (génétique), Polymorphisme de restriction (génétique), Populus (classification), Populus (génétique), Spécificité d'espèce (MeSH), Sélection (MeSH), Séquence nucléotidique (MeSH).
- MESH :
- génétique : ADN des chloroplastes, ADN intergénique, Amorces ADN, Chloroplastes, Gènes chloroplastiques, Génome de chloroplaste, Marqueurs génétiques, Polymorphisme de nucléotide simple, Polymorphisme de restriction, Populus.
- méthodes : Codage à barres de l'ADN pour la taxonomie.
- Analyse de séquence d'ADN, Données de séquences moléculaires, Mutation de type INDEL, Spécificité d'espèce, Sélection, Séquence nucléotidique.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Breeding (MeSH), Chloroplasts (genetics), DNA Barcoding, Taxonomic (methods), DNA Primers (genetics), DNA, Chloroplast (genetics), DNA, Intergenic (genetics), Genes, Chloroplast (genetics), Genetic Markers (genetics), Genome, Chloroplast (genetics), INDEL Mutation (MeSH), Molecular Sequence Data (MeSH), Polymorphism, Restriction Fragment Length (genetics), Polymorphism, Single Nucleotide (genetics), Populus (classification), Populus (genetics), Sequence Analysis, DNA (MeSH), Species Specificity (MeSH).
- MESH :
- chemical , genetics : DNA Primers, DNA, Chloroplast, DNA, Intergenic, Genetic Markers.
- classification : Populus.
- genetics : Chloroplasts, Genes, Chloroplast, Genome, Chloroplast, Polymorphism, Restriction Fragment Length, Polymorphism, Single Nucleotide, Populus.
- methods : DNA Barcoding, Taxonomic.
- Base Sequence, Breeding, INDEL Mutation, Molecular Sequence Data, Sequence Analysis, DNA, Species Specificity.
Abstract
Within the genus Populus several species belonging to different sections are cross-compatible. Hence, high numbers of interspecies hybrids occur naturally and, additionally, have been artificially produced in huge breeding programmes during the last 100 years. Therefore, determination of a single poplar species, used for the production of 'multi-species hybrids' is often difficult, and represents a great challenge for the use of molecular markers in species identification. Within this study, over 20 chloroplast regions, both intergenic spacers and coding regions, have been tested for their ability to differentiate different poplar species using 23 already published barcoding primer combinations and 17 newly designed primer combinations. About half of the published barcoding primers yielded amplification products, whereas the new primers designed on the basis of the total sequenced cpDNA genome of Populus trichocarpa Torr. & Gray yielded much higher amplification success. Intergenic spacers were found to be more variable than coding regions within the genus Populus. The highest discrimination power of Populus species was found in the combination of two intergenic spacers (trnG-psbK, psbK-psbl) and the coding region rpoC. In barcoding projects, the coding regions matK and rbcL are often recommended, but within the genus Populus they only show moderate variability and are not efficient in species discrimination.
DOI: 10.1111/j.1438-8677.2011.00502.x
PubMed: 21973311
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding.</title><author><name sortKey="Schroeder, H" sort="Schroeder, H" uniqKey="Schroeder H" first="H" last="Schroeder">H. Schroeder</name><affiliation wicri:level="1"><nlm:affiliation>Johann Heinrich von Thünen Institute, Institute for Forest Genetics, Grosshansdorf, Germany. hilke.schroeder@vti.bund.de</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Johann Heinrich von Thünen Institute, Institute for Forest Genetics, Grosshansdorf</wicri:regionArea><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion></affiliation></author><author><name sortKey="Hoeltken, A M" sort="Hoeltken, A M" uniqKey="Hoeltken A" first="A M" last="Hoeltken">A M Hoeltken</name></author><author><name sortKey="Fladung, M" sort="Fladung, M" uniqKey="Fladung M" first="M" last="Fladung">M. Fladung</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:21973311</idno><idno type="pmid">21973311</idno><idno type="doi">10.1111/j.1438-8677.2011.00502.x</idno><idno type="wicri:Area/Main/Corpus">002C67</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002C67</idno><idno type="wicri:Area/Main/Curation">002C67</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002C67</idno><idno type="wicri:Area/Main/Exploration">002C67</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding.</title><author><name sortKey="Schroeder, H" sort="Schroeder, H" uniqKey="Schroeder H" first="H" last="Schroeder">H. Schroeder</name><affiliation wicri:level="1"><nlm:affiliation>Johann Heinrich von Thünen Institute, Institute for Forest Genetics, Grosshansdorf, Germany. hilke.schroeder@vti.bund.de</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Johann Heinrich von Thünen Institute, Institute for Forest Genetics, Grosshansdorf</wicri:regionArea><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion></affiliation></author><author><name sortKey="Hoeltken, A M" sort="Hoeltken, A M" uniqKey="Hoeltken A" first="A M" last="Hoeltken">A M Hoeltken</name></author><author><name sortKey="Fladung, M" sort="Fladung, M" uniqKey="Fladung M" first="M" last="Fladung">M. Fladung</name></author></analytic><series><title level="j">Plant biology (Stuttgart, Germany)</title><idno type="eISSN">1438-8677</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Breeding (MeSH)</term><term>Chloroplasts (genetics)</term><term>DNA Barcoding, Taxonomic (methods)</term><term>DNA Primers (genetics)</term><term>DNA, Chloroplast (genetics)</term><term>DNA, Intergenic (genetics)</term><term>Genes, Chloroplast (genetics)</term><term>Genetic Markers (genetics)</term><term>Genome, Chloroplast (genetics)</term><term>INDEL Mutation (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Polymorphism, Restriction Fragment Length (genetics)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Populus (classification)</term><term>Populus (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Species Specificity (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des chloroplastes (génétique)</term><term>ADN intergénique (génétique)</term><term>Amorces ADN (génétique)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Chloroplastes (génétique)</term><term>Codage à barres de l'ADN pour la taxonomie (méthodes)</term><term>Données de séquences moléculaires (MeSH)</term><term>Gènes chloroplastiques (génétique)</term><term>Génome de chloroplaste (génétique)</term><term>Marqueurs génétiques (génétique)</term><term>Mutation de type INDEL (MeSH)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Polymorphisme de restriction (génétique)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Spécificité d'espèce (MeSH)</term><term>Sélection (MeSH)</term><term>Séquence nucléotidique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Primers</term><term>DNA, Chloroplast</term><term>DNA, Intergenic</term><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chloroplasts</term><term>Genes, Chloroplast</term><term>Genome, Chloroplast</term><term>Polymorphism, Restriction Fragment Length</term><term>Polymorphism, Single Nucleotide</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des chloroplastes</term><term>ADN intergénique</term><term>Amorces ADN</term><term>Chloroplastes</term><term>Gènes chloroplastiques</term><term>Génome de chloroplaste</term><term>Marqueurs génétiques</term><term>Polymorphisme de nucléotide simple</term><term>Polymorphisme de restriction</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>DNA Barcoding, Taxonomic</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Codage à barres de l'ADN pour la taxonomie</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Breeding</term><term>INDEL Mutation</term><term>Molecular Sequence Data</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Mutation de type INDEL</term><term>Spécificité d'espèce</term><term>Sélection</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Within the genus Populus several species belonging to different sections are cross-compatible. Hence, high numbers of interspecies hybrids occur naturally and, additionally, have been artificially produced in huge breeding programmes during the last 100 years. Therefore, determination of a single poplar species, used for the production of 'multi-species hybrids' is often difficult, and represents a great challenge for the use of molecular markers in species identification. Within this study, over 20 chloroplast regions, both intergenic spacers and coding regions, have been tested for their ability to differentiate different poplar species using 23 already published barcoding primer combinations and 17 newly designed primer combinations. About half of the published barcoding primers yielded amplification products, whereas the new primers designed on the basis of the total sequenced cpDNA genome of Populus trichocarpa Torr. & Gray yielded much higher amplification success. Intergenic spacers were found to be more variable than coding regions within the genus Populus. The highest discrimination power of Populus species was found in the combination of two intergenic spacers (trnG-psbK, psbK-psbl) and the coding region rpoC. In barcoding projects, the coding regions matK and rbcL are often recommended, but within the genus Populus they only show moderate variability and are not efficient in species discrimination.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21973311</PMID><DateCompleted><Year>2014</Year><Month>06</Month><Day>30</Day></DateCompleted><DateRevised><Year>2012</Year><Month>02</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1438-8677</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><Issue>2</Issue><PubDate><Year>2012</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Plant biology (Stuttgart, Germany)</Title><ISOAbbreviation>Plant Biol (Stuttg)</ISOAbbreviation></Journal><ArticleTitle>Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding.</ArticleTitle><Pagination><MedlinePgn>374-81</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1438-8677.2011.00502.x</ELocationID><Abstract><AbstractText>Within the genus Populus several species belonging to different sections are cross-compatible. Hence, high numbers of interspecies hybrids occur naturally and, additionally, have been artificially produced in huge breeding programmes during the last 100 years. Therefore, determination of a single poplar species, used for the production of 'multi-species hybrids' is often difficult, and represents a great challenge for the use of molecular markers in species identification. Within this study, over 20 chloroplast regions, both intergenic spacers and coding regions, have been tested for their ability to differentiate different poplar species using 23 already published barcoding primer combinations and 17 newly designed primer combinations. About half of the published barcoding primers yielded amplification products, whereas the new primers designed on the basis of the total sequenced cpDNA genome of Populus trichocarpa Torr. & Gray yielded much higher amplification success. Intergenic spacers were found to be more variable than coding regions within the genus Populus. The highest discrimination power of Populus species was found in the combination of two intergenic spacers (trnG-psbK, psbK-psbl) and the coding region rpoC. In barcoding projects, the coding regions matK and rbcL are often recommended, but within the genus Populus they only show moderate variability and are not efficient in species discrimination.</AbstractText><CopyrightInformation>© 2011 German Botanical Society and The Royal Botanical Society of the Netherlands.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Schroeder</LastName><ForeName>H</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Johann Heinrich von Thünen Institute, Institute for Forest Genetics, Grosshansdorf, Germany. hilke.schroeder@vti.bund.de</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hoeltken</LastName><ForeName>A M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Fladung</LastName><ForeName>M</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>JF429903</AccessionNumber><AccessionNumber>JF429904</AccessionNumber><AccessionNumber>JF429905</AccessionNumber><AccessionNumber>JF429906</AccessionNumber><AccessionNumber>JF429907</AccessionNumber><AccessionNumber>JF429908</AccessionNumber><AccessionNumber>JF429909</AccessionNumber><AccessionNumber>JF429910</AccessionNumber><AccessionNumber>JF429911</AccessionNumber><AccessionNumber>JF429912</AccessionNumber><AccessionNumber>JF429913</AccessionNumber><AccessionNumber>JF429914</AccessionNumber><AccessionNumber>JF429915</AccessionNumber><AccessionNumber>JF429916</AccessionNumber><AccessionNumber>JF429917</AccessionNumber><AccessionNumber>JF429918</AccessionNumber><AccessionNumber>JF429919</AccessionNumber><AccessionNumber>JF429920</AccessionNumber><AccessionNumber>JF429921</AccessionNumber><AccessionNumber>JF429922</AccessionNumber><AccessionNumber>JF429923</AccessionNumber><AccessionNumber>JF429924</AccessionNumber><AccessionNumber>JF429925</AccessionNumber><AccessionNumber>JF429926</AccessionNumber><AccessionNumber>JF429927</AccessionNumber><AccessionNumber>JF429928</AccessionNumber><AccessionNumber>JF429929</AccessionNumber><AccessionNumber>JF429930</AccessionNumber><AccessionNumber>JF429931</AccessionNumber><AccessionNumber>JF429932</AccessionNumber><AccessionNumber>JF429933</AccessionNumber><AccessionNumber>JF429934</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>08</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant Biol (Stuttg)</MedlineTA><NlmUniqueID>101148926</NlmUniqueID><ISSNLinking>1435-8603</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018742">DNA, Chloroplast</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021901">DNA, Intergenic</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001947" MajorTopicYN="N">Breeding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002736" MajorTopicYN="N">Chloroplasts</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058893" MajorTopicYN="N">DNA Barcoding, Taxonomic</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017931" MajorTopicYN="N">DNA Primers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018742" MajorTopicYN="N">DNA, Chloroplast</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D021901" MajorTopicYN="N">DNA, Intergenic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D061125" MajorTopicYN="N">Genes, Chloroplast</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D054628" MajorTopicYN="N">Genome, Chloroplast</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D054643" MajorTopicYN="N">INDEL Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012150" MajorTopicYN="N">Polymorphism, Restriction Fragment Length</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</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="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>10</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>10</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>7</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">21973311</ArticleId><ArticleId IdType="doi">10.1111/j.1438-8677.2011.00502.x</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li></country></list><tree><noCountry><name sortKey="Fladung, M" sort="Fladung, M" uniqKey="Fladung M" first="M" last="Fladung">M. Fladung</name><name sortKey="Hoeltken, A M" sort="Hoeltken, A M" uniqKey="Hoeltken A" first="A M" last="Hoeltken">A M Hoeltken</name></noCountry><country name="Allemagne"><noRegion><name sortKey="Schroeder, H" sort="Schroeder, H" uniqKey="Schroeder H" first="H" last="Schroeder">H. Schroeder</name></noRegion></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 002B31 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002B31 | 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:21973311
|texte= Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:21973311" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |