Association of allelic variation in PtoXET16A with growth and wood properties in Populus tomentosa.
Identifieur interne : 002357 ( Main/Exploration ); précédent : 002356; suivant : 002358Association of allelic variation in PtoXET16A with growth and wood properties in Populus tomentosa.
Auteurs : Bowen Wang [République populaire de Chine] ; Deqiang Zhang [République populaire de Chine]Source :
- International journal of molecular sciences [ 1422-0067 ] ; 2014.
Descripteurs français
- KwdFr :
- Allèles (MeSH), Bois (cytologie), Domaine catalytique (MeSH), Données de séquences moléculaires (MeSH), Déséquilibre de liaison (MeSH), Exons (MeSH), Glycosyltransferase (biosynthèse), Glycosyltransferase (génétique), Gènes de plante (MeSH), Génotype (MeSH), Haplotypes (génétique), Introns (MeSH), Isoformes de protéines (génétique), Paroi cellulaire (composition chimique), Paroi cellulaire (ultrastructure), Phylogenèse (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (croissance et développement), Populus (génétique), Protéines végétales (biosynthèse), Protéines végétales (génétique), Régulation de l'expression des gènes végétaux (MeSH), Spécificité d'organe (MeSH), Séquence d'acides aminés (MeSH), Séquence nucléotidique (MeSH), Transcription génétique (MeSH), Variation génétique (MeSH), Études d'associations génétiques (MeSH).
- MESH :
- biosynthèse : Glycosyltransferase, Protéines végétales.
- composition chimique : Paroi cellulaire.
- croissance et développement : Populus.
- cytologie : Bois.
- génétique : Glycosyltransferase, Haplotypes, Isoformes de protéines, Populus, Protéines végétales.
- ultrastructure : Allèles, Domaine catalytique, Données de séquences moléculaires, Déséquilibre de liaison, Exons, Gènes de plante, Génotype, Introns, Paroi cellulaire, Phylogenèse, Polymorphisme de nucléotide simple, Régulation de l'expression des gènes végétaux, Spécificité d'organe, Séquence d'acides aminés, Séquence nucléotidique, Transcription génétique, Variation génétique, Études d'associations génétiques.
English descriptors
- KwdEn :
- Alleles (MeSH), Amino Acid Sequence (MeSH), Base Sequence (MeSH), Catalytic Domain (MeSH), Cell Wall (chemistry), Cell Wall (ultrastructure), Exons (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Genetic Association Studies (MeSH), Genetic Variation (MeSH), Genotype (MeSH), Glycosyltransferases (biosynthesis), Glycosyltransferases (genetics), Haplotypes (genetics), Introns (MeSH), Linkage Disequilibrium (MeSH), Molecular Sequence Data (MeSH), Organ Specificity (MeSH), Phylogeny (MeSH), Plant Proteins (biosynthesis), Plant Proteins (genetics), Polymorphism, Single Nucleotide (MeSH), Populus (genetics), Populus (growth & development), Protein Isoforms (genetics), Transcription, Genetic (MeSH), Wood (cytology).
- MESH :
- chemical , biosynthesis : Glycosyltransferases, Plant Proteins.
- chemistry : Cell Wall.
- cytology : Wood.
- chemical , genetics : Glycosyltransferases, Haplotypes, Plant Proteins, Populus, Protein Isoforms.
- growth & development : Populus.
- ultrastructure : Cell Wall.
- Alleles, Amino Acid Sequence, Base Sequence, Catalytic Domain, Exons, Gene Expression Regulation, Plant, Genes, Plant, Genetic Association Studies, Genetic Variation, Genotype, Introns, Linkage Disequilibrium, Molecular Sequence Data, Organ Specificity, Phylogeny, Polymorphism, Single Nucleotide, Transcription, Genetic.
Abstract
Xyloglucan endo-transglycosylases (XETs) modify the xyloglucan-cellulose framework of plant cell walls and, thus, affect cell wall expansion and strength. Dissecting the mechanism by which natural variation in XETs affects wood properties can inform breeding efforts to improve wood quality and yield traits. To this end, we isolated a full-length PtoXET16A cDNA clone from Populus tomentosa. Real-time PCR analysis showed that PtoXET16A was maximally expressed in the root, followed by phloem, cambium, and developing xylem, suggesting that PtoXET16A plays important roles in the development of vascular tissues. Nucleotide diversity and linkage disequilibrium analysis revealed that PtoXET16A has high single nucleotide polymorphism (SNP) diversity (π = 0.01266 and θ(w) = 0.01392) and low linkage disequilibrium (r² ≥ 0.1, within 900 bp). SNP- and haplotype-based association analyses of 426 individuals from a natural population indicated that nine SNPs (including two non-synonymous markers and one splicing variant) (p ≤ 0.05, false discovery rate Q ≤ 0.01), and nine haplotypes (p ≤ 0.05) were significantly associated with growth and wood properties, each explaining from 3.40%-10.95% of phenotypic variance. This work shows that examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of wood formation. Moreover, the SNP markers identified in this study can potentially be applied for marker-assisted selection to improve growth and wood-property traits in Populus.
DOI: 10.3390/ijms150916949
PubMed: 25250912
PubMed Central: PMC4200824
Affiliations:
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Le document en format XML
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génétique</term><term>Variation génétique</term><term>Études d'associations génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Xyloglucan endo-transglycosylases (XETs) modify the xyloglucan-cellulose framework of plant cell walls and, thus, affect cell wall expansion and strength. Dissecting the mechanism by which natural variation in XETs affects wood properties can inform breeding efforts to improve wood quality and yield traits. To this end, we isolated a full-length PtoXET16A cDNA clone from Populus tomentosa. Real-time PCR analysis showed that PtoXET16A was maximally expressed in the root, followed by phloem, cambium, and developing xylem, suggesting that PtoXET16A plays important roles in the development of vascular tissues. Nucleotide diversity and linkage disequilibrium analysis revealed that PtoXET16A has high single nucleotide polymorphism (SNP) diversity (π = 0.01266 and θ(w) = 0.01392) and low linkage disequilibrium (r² ≥ 0.1, within 900 bp). SNP- and haplotype-based association analyses of 426 individuals from a natural population indicated that nine SNPs (including two non-synonymous markers and one splicing variant) (p ≤ 0.05, false discovery rate Q ≤ 0.01), and nine haplotypes (p ≤ 0.05) were significantly associated with growth and wood properties, each explaining from 3.40%-10.95% of phenotypic variance. This work shows that examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of wood formation. Moreover, the SNP markers identified in this study can potentially be applied for marker-assisted selection to improve growth and wood-property traits in Populus.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25250912</PMID><DateCompleted><Year>2015</Year><Month>06</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1422-0067</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>9</Issue><PubDate><Year>2014</Year><Month>Sep</Month><Day>23</Day></PubDate></JournalIssue><Title>International journal of molecular sciences</Title><ISOAbbreviation>Int J Mol Sci</ISOAbbreviation></Journal><ArticleTitle>Association of allelic variation in PtoXET16A with growth and wood properties in Populus tomentosa.</ArticleTitle><Pagination><MedlinePgn>16949-74</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms150916949</ELocationID><Abstract><AbstractText>Xyloglucan endo-transglycosylases (XETs) modify the xyloglucan-cellulose framework of plant cell walls and, thus, affect cell wall expansion and strength. Dissecting the mechanism by which natural variation in XETs affects wood properties can inform breeding efforts to improve wood quality and yield traits. To this end, we isolated a full-length PtoXET16A cDNA clone from Populus tomentosa. Real-time PCR analysis showed that PtoXET16A was maximally expressed in the root, followed by phloem, cambium, and developing xylem, suggesting that PtoXET16A plays important roles in the development of vascular tissues. Nucleotide diversity and linkage disequilibrium analysis revealed that PtoXET16A has high single nucleotide polymorphism (SNP) diversity (π = 0.01266 and θ(w) = 0.01392) and low linkage disequilibrium (r² ≥ 0.1, within 900 bp). SNP- and haplotype-based association analyses of 426 individuals from a natural population indicated that nine SNPs (including two non-synonymous markers and one splicing variant) (p ≤ 0.05, false discovery rate Q ≤ 0.01), and nine haplotypes (p ≤ 0.05) were significantly associated with growth and wood properties, each explaining from 3.40%-10.95% of phenotypic variance. This work shows that examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of wood formation. Moreover, the SNP markers identified in this study can potentially be applied for marker-assisted selection to improve growth and wood-property traits in Populus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Bowen</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. 15210908561@yeah.net.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Deqiang</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. deqiangzhang@bjfu.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>KM267530</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><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>09</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Int J Mol Sci</MedlineTA><NlmUniqueID>101092791</NlmUniqueID><ISSNLinking>1422-0067</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020033">Protein Isoforms</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.4.-</RegistryNumber><NameOfSubstance UI="D016695">Glycosyltransferases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.4.1.207</RegistryNumber><NameOfSubstance UI="C473049">xyloglucan - xyloglucosyltransferase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000483" MajorTopicYN="N">Alleles</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020134" MajorTopicYN="N">Catalytic Domain</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000648" MajorTopicYN="N">ultrastructure</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005091" MajorTopicYN="N">Exons</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="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016695" MajorTopicYN="N">Glycosyltransferases</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</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="D007438" MajorTopicYN="N">Introns</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009928" MajorTopicYN="N">Organ Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020033" MajorTopicYN="N">Protein Isoforms</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000166" MajorTopicYN="N">cytology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>08</Month><Day>16</Day></PubMedPubDate><PubMedPubDate 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last="Wang">Bowen Wang</name></noRegion><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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