Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa.
Identifieur interne : 002052 ( Main/Exploration ); précédent : 002051; suivant : 002053Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa.
Auteurs : Baohua Xu [République populaire de Chine] ; Jiaxing Tian ; Qingzhang Du ; Chenrui Gong ; Wei Pan ; Deqiang ZhangSource :
- Planta [ 1432-2048 ] ; 2014.
Descripteurs français
- KwdFr :
- ARN messager (génétique), ARN messager (métabolisme), Analyse de profil d'expression de gènes (MeSH), Bois (croissance et développement), Bois (enzymologie), Bois (génétique), Caractère quantitatif héréditaire (MeSH), Données de séquences moléculaires (MeSH), Déséquilibre de liaison (génétique), Glucosyltransferases (composition chimique), Glucosyltransferases (génétique), Gènes de plante (MeSH), Haplotypes (génétique), Locus génétiques (MeSH), Marqueurs génétiques (MeSH), Nucléotides (génétique), Phylogenèse (MeSH), Phénotype (MeSH), Polymorphisme de nucléotide simple (génétique), Populus (croissance et développement), Populus (enzymologie), Populus (génétique), Régulation de l'expression des gènes codant pour des enzymes (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Spécificité d'organe (génétique), Études d'associations génétiques (MeSH).
- MESH :
- composition chimique : Glucosyltransferases.
- croissance et développement : Bois, Populus.
- enzymologie : Bois, Populus.
- génétique : ARN messager, Bois, Déséquilibre de liaison, Glucosyltransferases, Haplotypes, Nucléotides, Polymorphisme de nucléotide simple, Populus, Spécificité d'organe.
- métabolisme : ARN messager.
- Analyse de profil d'expression de gènes, Caractère quantitatif héréditaire, Données de séquences moléculaires, Gènes de plante, Locus génétiques, Marqueurs génétiques, Phylogenèse, Phénotype, Régulation de l'expression des gènes codant pour des enzymes, Régulation de l'expression des gènes végétaux, Études d'associations génétiques.
English descriptors
- KwdEn :
- Gene Expression Profiling (MeSH), Gene Expression Regulation, Enzymologic (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Genetic Association Studies (MeSH), Genetic Loci (MeSH), Genetic Markers (MeSH), Glucosyltransferases (chemistry), Glucosyltransferases (genetics), Haplotypes (genetics), Linkage Disequilibrium (genetics), Molecular Sequence Data (MeSH), Nucleotides (genetics), Organ Specificity (genetics), Phenotype (MeSH), Phylogeny (MeSH), Polymorphism, Single Nucleotide (genetics), Populus (enzymology), Populus (genetics), Populus (growth & development), Quantitative Trait, Heritable (MeSH), RNA, Messenger (genetics), RNA, Messenger (metabolism), Wood (enzymology), Wood (genetics), Wood (growth & development).
- MESH :
- chemical , chemistry : Glucosyltransferases.
- chemical , genetics : Glucosyltransferases, Nucleotides, RNA, Messenger.
- chemical , metabolism : RNA, Messenger.
- chemical : Genetic Markers.
- enzymology : Populus, Wood.
- genetics : Haplotypes, Linkage Disequilibrium, Organ Specificity, Polymorphism, Single Nucleotide, Populus, Wood.
- growth & development : Populus, Wood.
- Gene Expression Profiling, Gene Expression Regulation, Enzymologic, Gene Expression Regulation, Plant, Genes, Plant, Genetic Association Studies, Genetic Loci, Molecular Sequence Data, Phenotype, Phylogeny, Quantitative Trait, Heritable.
Abstract
In plants, the composition and organization of the cell wall determine cell shape, enable cell expansion, and affect the properties of woody tissues. Cellulose synthase (CesA) genes encode the enzymes involved in the synthesis of cellulose which is the major component of plant primary and secondary cell walls. Here, we isolated a full-length PtoCesA3 cDNA from the stem cambium tissue of Populus tomentosa. Tissue-specific expression profiling showed that PtoCesA3 is highly expressed during primary cell wall formation. Estimation of single nucleotide polymorphism (SNP) diversity and linkage disequilibrium (LD) revealed that PtoCesA3 harbors high SNP diversity (π(T) = 0.00995 and θ(w) = 0.0102) and low LD (r(2) ≥ 0.1, within 1,280 bp). Association analysis in a P. tomentosa association population (460 individuals) showed that seven SNPs (false discovery rate Q < 0.10) and five haplotypes (Q < 0.10) were significantly associated with growth and wood properties, explaining 4.09-7.02% of the phenotypic variance. All significant marker-trait associations were validated in at least one of the three smaller subsets (climatic regions) while five associations were repeated in the linkage population. Variation in RNA transcript abundance among genotypic classes of significant loci was also confirmed in the association or linkage populations. Identification of PtoCesA3 and examining its allelic polymorphisms using association studies open an avenue to understand the mechanism of cellulose synthesis in the primary cell wall and its effects on the properties of woody tissues.
DOI: 10.1007/s00425-014-2149-4
PubMed: 25143249
Affiliations:
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Le document en format XML
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génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In plants, the composition and organization of the cell wall determine cell shape, enable cell expansion, and affect the properties of woody tissues. Cellulose synthase (CesA) genes encode the enzymes involved in the synthesis of cellulose which is the major component of plant primary and secondary cell walls. Here, we isolated a full-length PtoCesA3 cDNA from the stem cambium tissue of Populus tomentosa. Tissue-specific expression profiling showed that PtoCesA3 is highly expressed during primary cell wall formation. Estimation of single nucleotide polymorphism (SNP) diversity and linkage disequilibrium (LD) revealed that PtoCesA3 harbors high SNP diversity (π(T) = 0.00995 and θ(w) = 0.0102) and low LD (r(2) ≥ 0.1, within 1,280 bp). Association analysis in a P. tomentosa association population (460 individuals) showed that seven SNPs (false discovery rate Q < 0.10) and five haplotypes (Q < 0.10) were significantly associated with growth and wood properties, explaining 4.09-7.02% of the phenotypic variance. All significant marker-trait associations were validated in at least one of the three smaller subsets (climatic regions) while five associations were repeated in the linkage population. Variation in RNA transcript abundance among genotypic classes of significant loci was also confirmed in the association or linkage populations. Identification of PtoCesA3 and examining its allelic polymorphisms using association studies open an avenue to understand the mechanism of cellulose synthesis in the primary cell wall and its effects on the properties of woody tissues.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25143249</PMID><DateCompleted><Year>2015</Year><Month>11</Month><Day>09</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-2048</ISSN><JournalIssue CitedMedium="Internet"><Volume>240</Volume><Issue>6</Issue><PubDate><Year>2014</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Planta</Title><ISOAbbreviation>Planta</ISOAbbreviation></Journal><ArticleTitle>Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa.</ArticleTitle><Pagination><MedlinePgn>1269-86</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00425-014-2149-4</ELocationID><Abstract><AbstractText>In plants, the composition and organization of the cell wall determine cell shape, enable cell expansion, and affect the properties of woody tissues. Cellulose synthase (CesA) genes encode the enzymes involved in the synthesis of cellulose which is the major component of plant primary and secondary cell walls. Here, we isolated a full-length PtoCesA3 cDNA from the stem cambium tissue of Populus tomentosa. Tissue-specific expression profiling showed that PtoCesA3 is highly expressed during primary cell wall formation. Estimation of single nucleotide polymorphism (SNP) diversity and linkage disequilibrium (LD) revealed that PtoCesA3 harbors high SNP diversity (π(T) = 0.00995 and θ(w) = 0.0102) and low LD (r(2) ≥ 0.1, within 1,280 bp). Association analysis in a P. tomentosa association population (460 individuals) showed that seven SNPs (false discovery rate Q < 0.10) and five haplotypes (Q < 0.10) were significantly associated with growth and wood properties, explaining 4.09-7.02% of the phenotypic variance. All significant marker-trait associations were validated in at least one of the three smaller subsets (climatic regions) while five associations were repeated in the linkage population. Variation in RNA transcript abundance among genotypic classes of significant loci was also confirmed in the association or linkage populations. Identification of PtoCesA3 and examining its allelic polymorphisms using association studies open an avenue to understand the mechanism of cellulose synthesis in the primary cell wall and its effects on the properties of woody tissues.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Baohua</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>Jiaxing</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Qingzhang</ForeName><Initials>Q</Initials></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><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>KF809675</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>2014</Year><Month>08</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Planta</MedlineTA><NlmUniqueID>1250576</NlmUniqueID><ISSNLinking>0032-0935</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009711">Nucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.4.1.-</RegistryNumber><NameOfSubstance UI="D005964">Glucosyltransferases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.4.1.-</RegistryNumber><NameOfSubstance UI="C478648">cellulose synthase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015971" MajorTopicYN="N">Gene Expression Regulation, Enzymologic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</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="D056426" MajorTopicYN="N">Genetic Loci</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005964" MajorTopicYN="N">Glucosyltransferases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009711" MajorTopicYN="N">Nucleotides</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009928" MajorTopicYN="N">Organ Specificity</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></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="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019655" MajorTopicYN="N">Quantitative Trait, Heritable</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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