Transcript abundance patterns of Populus C-repeat binding factor2 orthologs and genetic association of PsCBF2 allelic variation with physiological and biochemical traits in response to abiotic stress.
Identifieur interne : 001A92 ( Main/Exploration ); précédent : 001A91; suivant : 001A93Transcript abundance patterns of Populus C-repeat binding factor2 orthologs and genetic association of PsCBF2 allelic variation with physiological and biochemical traits in response to abiotic stress.
Auteurs : Ying Li [Oman] ; Baohua Xu ; Qingzhang Du ; Deqiang ZhangSource :
- Planta [ 1432-2048 ] ; 2015.
Descripteurs français
- KwdFr :
- ARN messager (génétique), ARN messager (métabolisme), Alignement de séquences (MeSH), Allèles (MeSH), Basse température (MeSH), Caractère quantitatif héréditaire (MeSH), Données de séquences moléculaires (MeSH), Déséquilibre de liaison (MeSH), Génotype (MeSH), Phylogenèse (MeSH), Polymorphisme de nucléotide simple (génétique), Populus (génétique), Populus (physiologie), Protéines végétales (composition chimique), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Spécificité d'espèce (MeSH), Stress physiologique (MeSH), Séquence d'acides aminés (MeSH), Variation génétique (MeSH), Études d'associations génétiques (MeSH).
- MESH :
- composition chimique : Protéines végétales.
- génétique : ARN messager, Polymorphisme de nucléotide simple, Populus, Protéines végétales.
- métabolisme : ARN messager, Protéines végétales.
- physiologie : Populus.
- Alignement de séquences, Allèles, Basse température, Caractère quantitatif héréditaire, Données de séquences moléculaires, Déséquilibre de liaison, Génotype, Phylogenèse, Régulation de l'expression des gènes végétaux, Spécificité d'espèce, Stress physiologique, Séquence d'acides aminés, Variation génétique, Études d'associations génétiques.
English descriptors
- KwdEn :
- Alleles (MeSH), Amino Acid Sequence (MeSH), Cold Temperature (MeSH), Gene Expression Regulation, Plant (MeSH), Genetic Association Studies (MeSH), Genetic Variation (MeSH), Genotype (MeSH), Linkage Disequilibrium (MeSH), Molecular Sequence Data (MeSH), Phylogeny (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Polymorphism, Single Nucleotide (genetics), Populus (genetics), Populus (physiology), Quantitative Trait, Heritable (MeSH), RNA, Messenger (genetics), RNA, Messenger (metabolism), Sequence Alignment (MeSH), Species Specificity (MeSH), Stress, Physiological (MeSH).
- MESH :
- chemical , chemistry : Plant Proteins.
- chemical , genetics : Plant Proteins, RNA, Messenger.
- chemical , metabolism : Plant Proteins, RNA, Messenger.
- genetics : Polymorphism, Single Nucleotide, Populus.
- physiology : Populus.
- Alleles, Amino Acid Sequence, Cold Temperature, Gene Expression Regulation, Plant, Genetic Association Studies, Genetic Variation, Genotype, Linkage Disequilibrium, Molecular Sequence Data, Phylogeny, Quantitative Trait, Heritable, Sequence Alignment, Species Specificity, Stress, Physiological.
Abstract
MAIN CONCLUSION
We conducted a candidate gene-based approach to search for genetic associations between 10 SNPs in PsCBF2 and 10 abiotic stress-related traits. The increasing incidence of abiotic stresses and the limitations of available treatments, particularly in trees, highlight the need to improve our understanding of the mechanisms of stress responses. In Arabidopsis, C-repeat binding factor 2 (CBF2) plays an important role in freezing tolerance and cold acclimation. Here, we isolated orthologs of CBF2 from five Populus species. Expression profiling revealed that the Populus CBF2s were preferentially induced in response to cold, with CBF2 transcript abundances ranging from 5.4- to 62-fold higher than in unstressed controls of the corresponding species. In addition, we used a candidate gene-based approach in Populus simonii Carr. to identify single nucleotide polymorphisms (SNPs) in PsCBF2 associated with physiological and biochemical traits. PsCBF2 showed high nucleotide diversity (π T = 0.00549, θ w = 0.01406) and low average linkage disequilibrium (r (2) = 0.061). Association studies in 528 individuals of an association population showed that nine SNPs (false discovery rate Q < 0.10) and one haplotype (Q < 0.10) were significantly associated with differences in four physiological and biochemical traits (P < 0.005), with each marker explaining 1.31-5.87 % of the total variance in the corresponding trait. PsCBF2 transcript levels differed significantly in abundance among genotypic classes for most of the significant SNPs. Identification of these significant associations will help reveal the molecular basis of physiological differences and provide a starting point for marker-assisted selection for traits involved in stress tolerance in P. simonii.
DOI: 10.1007/s00425-015-2307-3
PubMed: 25916311
Affiliations:
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Le document en format XML
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candidate gene-based approach to search for genetic associations between 10 SNPs in PsCBF2 and 10 abiotic stress-related traits. The increasing incidence of abiotic stresses and the limitations of available treatments, particularly in trees, highlight the need to improve our understanding of the mechanisms of stress responses. In Arabidopsis, C-repeat binding factor 2 (CBF2) plays an important role in freezing tolerance and cold acclimation. Here, we isolated orthologs of CBF2 from five Populus species. Expression profiling revealed that the Populus CBF2s were preferentially induced in response to cold, with CBF2 transcript abundances ranging from 5.4- to 62-fold higher than in unstressed controls of the corresponding species. In addition, we used a candidate gene-based approach in Populus simonii Carr. to identify single nucleotide polymorphisms (SNPs) in PsCBF2 associated with physiological and biochemical traits. PsCBF2 showed high nucleotide diversity (π T = 0.00549, θ w = 0.01406) and low average linkage disequilibrium (r (2) = 0.061). Association studies in 528 individuals of an association population showed that nine SNPs (false discovery rate Q < 0.10) and one haplotype (Q < 0.10) were significantly associated with differences in four physiological and biochemical traits (P < 0.005), with each marker explaining 1.31-5.87 % of the total variance in the corresponding trait. PsCBF2 transcript levels differed significantly in abundance among genotypic classes for most of the significant SNPs. Identification of these significant associations will help reveal the molecular basis of physiological differences and provide a starting point for marker-assisted selection for traits involved in stress tolerance in P. simonii.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25916311</PMID><DateCompleted><Year>2016</Year><Month>04</Month><Day>14</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>242</Volume><Issue>1</Issue><PubDate><Year>2015</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Planta</Title><ISOAbbreviation>Planta</ISOAbbreviation></Journal><ArticleTitle>Transcript abundance patterns of Populus C-repeat binding factor2 orthologs and genetic association of PsCBF2 allelic variation with physiological and biochemical traits in response to abiotic stress.</ArticleTitle><Pagination><MedlinePgn>295-312</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00425-015-2307-3</ELocationID><Abstract><AbstractText Label="MAIN CONCLUSION" NlmCategory="CONCLUSIONS">We conducted a candidate gene-based approach to search for genetic associations between 10 SNPs in PsCBF2 and 10 abiotic stress-related traits. The increasing incidence of abiotic stresses and the limitations of available treatments, particularly in trees, highlight the need to improve our understanding of the mechanisms of stress responses. In Arabidopsis, C-repeat binding factor 2 (CBF2) plays an important role in freezing tolerance and cold acclimation. Here, we isolated orthologs of CBF2 from five Populus species. Expression profiling revealed that the Populus CBF2s were preferentially induced in response to cold, with CBF2 transcript abundances ranging from 5.4- to 62-fold higher than in unstressed controls of the corresponding species. In addition, we used a candidate gene-based approach in Populus simonii Carr. to identify single nucleotide polymorphisms (SNPs) in PsCBF2 associated with physiological and biochemical traits. PsCBF2 showed high nucleotide diversity (π T = 0.00549, θ w = 0.01406) and low average linkage disequilibrium (r (2) = 0.061). Association studies in 528 individuals of an association population showed that nine SNPs (false discovery rate Q < 0.10) and one haplotype (Q < 0.10) were significantly associated with differences in four physiological and biochemical traits (P < 0.005), with each marker explaining 1.31-5.87 % of the total variance in the corresponding trait. PsCBF2 transcript levels differed significantly in abundance among genotypic classes for most of the significant SNPs. Identification of these significant associations will help reveal the molecular basis of physiological differences and provide a starting point for marker-assisted selection for traits involved in stress tolerance in P. simonii.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Ying</ForeName><Initials>Y</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, liying105527@126.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Baohua</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Qingzhang</ForeName><Initials>Q</Initials></Author><Author 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DateType="Electronic"><Year>2015</Year><Month>04</Month><Day>28</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="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</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="D003080" MajorTopicYN="N">Cold Temperature</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056726" MajorTopicYN="Y">Genetic Association Studies</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</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="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</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="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" 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last="Xu">Baohua Xu</name><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></noCountry><country name="Oman"><noRegion><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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