Development and application of microsatellites in candidate genes related to wood properties in the Chinese white poplar (Populus tomentosa Carr.).
Identifieur interne : 002737 ( Main/Exploration ); précédent : 002736; suivant : 002738Development and application of microsatellites in candidate genes related to wood properties in the Chinese white poplar (Populus tomentosa Carr.).
Auteurs : Qingzhang Du [République populaire de Chine] ; Chenrui Gong ; Wei Pan ; Deqiang ZhangSource :
- DNA research : an international journal for rapid publication of reports on genes and genomes [ 1756-1663 ] ; 2013.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), ADN des plantes (isolement et purification), Allèles (MeSH), Analyse de séquence d'ADN (MeSH), Cartographie chromosomique (MeSH), Génome végétal (MeSH), Génotype (MeSH), Liaison génétique (MeSH), Locus génétiques (MeSH), Marqueurs génétiques (MeSH), Phylogenèse (MeSH), Phénotype (MeSH), Polymorphisme génétique (MeSH), Populus (génétique), Répétitions microsatellites (MeSH), Spécificité d'espèce (MeSH).
- MESH :
- génétique : ADN des plantes, Populus.
- isolement et purification : ADN des plantes.
- Allèles, Analyse de séquence d'ADN, Cartographie chromosomique, Génome végétal, Génotype, Liaison génétique, Locus génétiques, Marqueurs génétiques, Phylogenèse, Phénotype, Polymorphisme génétique, Répétitions microsatellites, Spécificité d'espèce.
English descriptors
- KwdEn :
- Alleles (MeSH), Chromosome Mapping (MeSH), DNA, Plant (genetics), DNA, Plant (isolation & purification), Genetic Linkage (MeSH), Genetic Loci (MeSH), Genetic Markers (MeSH), Genome, Plant (MeSH), Genotype (MeSH), Microsatellite Repeats (MeSH), Phenotype (MeSH), Phylogeny (MeSH), Polymorphism, Genetic (MeSH), Populus (genetics), Sequence Analysis, DNA (MeSH), Species Specificity (MeSH).
- MESH :
- chemical , genetics : DNA, Plant.
- chemical , isolation & purification : DNA, Plant.
- genetics : Populus.
- Alleles, Chromosome Mapping, Genetic Linkage, Genetic Loci, Genetic Markers, Genome, Plant, Genotype, Microsatellite Repeats, Phenotype, Phylogeny, Polymorphism, Genetic, Sequence Analysis, DNA, Species Specificity.
Abstract
Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2-7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.
DOI: 10.1093/dnares/dss031
PubMed: 23213110
PubMed Central: PMC3576656
Affiliations:
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Gong</name></author><author><name sortKey="Pan, Wei" sort="Pan, Wei" uniqKey="Pan W" first="Wei" last="Pan">Wei Pan</name></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23213110</idno><idno type="pmid">23213110</idno><idno type="doi">10.1093/dnares/dss031</idno><idno type="pmc">PMC3576656</idno><idno type="wicri:Area/Main/Corpus">002780</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002780</idno><idno type="wicri:Area/Main/Curation">002780</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002780</idno><idno type="wicri:Area/Main/Exploration">002780</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Development and application of microsatellites in candidate genes related to wood properties in the Chinese white poplar (Populus tomentosa Carr.).</title><author><name sortKey="Du, Qingzhang" sort="Du, Qingzhang" uniqKey="Du Q" first="Qingzhang" last="Du">Qingzhang Du</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Gong, Chenrui" sort="Gong, Chenrui" uniqKey="Gong C" first="Chenrui" last="Gong">Chenrui Gong</name></author><author><name sortKey="Pan, Wei" sort="Pan, Wei" uniqKey="Pan W" first="Wei" last="Pan">Wei Pan</name></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></author></analytic><series><title level="j">DNA research : an international journal for rapid publication of reports on genes and genomes</title><idno type="eISSN">1756-1663</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>Chromosome Mapping (MeSH)</term><term>DNA, Plant (genetics)</term><term>DNA, Plant (isolation & purification)</term><term>Genetic Linkage (MeSH)</term><term>Genetic Loci (MeSH)</term><term>Genetic Markers (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genotype (MeSH)</term><term>Microsatellite Repeats (MeSH)</term><term>Phenotype (MeSH)</term><term>Phylogeny (MeSH)</term><term>Polymorphism, Genetic (MeSH)</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 plantes (génétique)</term><term>ADN des plantes (isolement et purification)</term><term>Allèles (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Cartographie chromosomique (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génotype (MeSH)</term><term>Liaison génétique (MeSH)</term><term>Locus génétiques (MeSH)</term><term>Marqueurs génétiques (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Phénotype (MeSH)</term><term>Polymorphisme génétique (MeSH)</term><term>Populus (génétique)</term><term>Répétitions microsatellites (MeSH)</term><term>Spécificité d'espèce (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" 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>Alleles</term><term>Chromosome Mapping</term><term>Genetic Linkage</term><term>Genetic Loci</term><term>Genetic Markers</term><term>Genome, Plant</term><term>Genotype</term><term>Microsatellite Repeats</term><term>Phenotype</term><term>Phylogeny</term><term>Polymorphism, Genetic</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Analyse de séquence d'ADN</term><term>Cartographie chromosomique</term><term>Génome végétal</term><term>Génotype</term><term>Liaison génétique</term><term>Locus génétiques</term><term>Marqueurs génétiques</term><term>Phylogenèse</term><term>Phénotype</term><term>Polymorphisme génétique</term><term>Répétitions microsatellites</term><term>Spécificité d'espèce</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2-7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23213110</PMID><DateCompleted><Year>2013</Year><Month>08</Month><Day>13</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1756-1663</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>1</Issue><PubDate><Year>2013</Year><Month>Feb</Month></PubDate></JournalIssue><Title>DNA research : an international journal for rapid publication of reports on genes and genomes</Title><ISOAbbreviation>DNA Res</ISOAbbreviation></Journal><ArticleTitle>Development and application of microsatellites in candidate genes related to wood properties in the Chinese white poplar (Populus tomentosa Carr.).</ArticleTitle><Pagination><MedlinePgn>31-44</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/dnares/dss031</ELocationID><Abstract><AbstractText>Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2-7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Qingzhang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gong</LastName><ForeName>Chenrui</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Pan</LastName><ForeName>Wei</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Deqiang</ForeName><Initials>D</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>2012</Year><Month>12</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>DNA Res</MedlineTA><NlmUniqueID>9423827</NlmUniqueID><ISSNLinking>1340-2838</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000483" 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first="Deqiang" last="Zhang">Deqiang Zhang</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Du, Qingzhang" sort="Du, Qingzhang" uniqKey="Du Q" first="Qingzhang" last="Du">Qingzhang Du</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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