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Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus.

Identifieur interne : 001919 ( Main/Exploration ); précédent : 001918; suivant : 001920

Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus.

Auteurs : B. Chen [République populaire de Chine] ; Q. Du [République populaire de Chine] ; J. Chen [République populaire de Chine] ; X. Yang [République populaire de Chine] ; J. Tian [République populaire de Chine] ; B. Li [République populaire de Chine, États-Unis] ; D. Zhang [République populaire de Chine]

Source :

RBID : pubmed:27118153

Descripteurs français

English descriptors

Abstract

MicroRNAs (miRNAs) have important roles in the regulation of genes; however, for trees few studies have explored the potential impact of the interactions between miRNAs and their target genes. Here, we performed transcript profiling and association genetics (single-SNP, haplotype-based and multi-SNP associations) to study the genetic regulatory relationship of Pto-miR257 and its 12 target genes in 435 individuals of a natural population of Populus tomentosa. Expression profiling of Pto-miR257 and its targets showed a negative relationship between their expression levels. Of the 61 single-nucleotide polymorphisms (SNPs) detected in Pto-miR257, 6 in the pre-mature region strongly affected its secondary stability and 1 in the mature region could alter its target spectrum. Among the 1029 SNPs in the targets, 3 were located in target sites that could change the binding affinity of Pto-miR257. Single-SNP association analysis revealed that SNPs in Pto-miR257 and target genes associated with both growth and wood property traits, in agreement with haplotype-based identifications. Multi-SNP association found that 10 targets shared at least one common trait with Pto-miR257, with phenotypic variance from 0.5 to 8.5%, suggesting a possible internal genetic interaction between them. Epistasis analysis showed significant epistatic interactions among Pto-miR257 and its targets. Therefore, our study demonstrated Pto-miR257 and its 12 targets had roles in wood formation and revealed the genetic interaction network between the miRNA and its targets under additive, dominant and epistatic models. Thus, association genetics can be used to decipher the interactions between miRNAs and their target genes and to help understand the genetic architecture of complex traits.

DOI: 10.1038/hdy.2016.26
PubMed: 27118153
PubMed Central: PMC4949725


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Le document en format XML

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<term>Epistasis, Genetic (MeSH)</term>
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<term>Genes, Plant (MeSH)</term>
<term>Haplotypes (MeSH)</term>
<term>MicroRNAs (genetics)</term>
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<term>Polymorphism, Single Nucleotide (MeSH)</term>
<term>Populus (genetics)</term>
<term>Populus (growth & development)</term>
<term>RNA, Plant (genetics)</term>
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<term>ARN des plantes (génétique)</term>
<term>Bois (croissance et développement)</term>
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<term>Haplotypes (MeSH)</term>
<term>Modèles génétiques (MeSH)</term>
<term>Polymorphisme de nucléotide simple (MeSH)</term>
<term>Populus (croissance et développement)</term>
<term>Populus (génétique)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>microARN (génétique)</term>
<term>Épistasie (MeSH)</term>
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<term>MicroRNAs</term>
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<term>Bois</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="growth & development" xml:lang="en">
<term>Populus</term>
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<term>Gene Expression Regulation, Plant</term>
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<term>Haplotypes</term>
<term>Models, Genetic</term>
<term>Polymorphism, Single Nucleotide</term>
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<term>Modèles génétiques</term>
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<front>
<div type="abstract" xml:lang="en">MicroRNAs (miRNAs) have important roles in the regulation of genes; however, for trees few studies have explored the potential impact of the interactions between miRNAs and their target genes. Here, we performed transcript profiling and association genetics (single-SNP, haplotype-based and multi-SNP associations) to study the genetic regulatory relationship of Pto-miR257 and its 12 target genes in 435 individuals of a natural population of Populus tomentosa. Expression profiling of Pto-miR257 and its targets showed a negative relationship between their expression levels. Of the 61 single-nucleotide polymorphisms (SNPs) detected in Pto-miR257, 6 in the pre-mature region strongly affected its secondary stability and 1 in the mature region could alter its target spectrum. Among the 1029 SNPs in the targets, 3 were located in target sites that could change the binding affinity of Pto-miR257. Single-SNP association analysis revealed that SNPs in Pto-miR257 and target genes associated with both growth and wood property traits, in agreement with haplotype-based identifications. Multi-SNP association found that 10 targets shared at least one common trait with Pto-miR257, with phenotypic variance from 0.5 to 8.5%, suggesting a possible internal genetic interaction between them. Epistasis analysis showed significant epistatic interactions among Pto-miR257 and its targets. Therefore, our study demonstrated Pto-miR257 and its 12 targets had roles in wood formation and revealed the genetic interaction network between the miRNA and its targets under additive, dominant and epistatic models. Thus, association genetics can be used to decipher the interactions between miRNAs and their target genes and to help understand the genetic architecture of complex traits.</div>
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<Title>Heredity</Title>
<ISOAbbreviation>Heredity (Edinb)</ISOAbbreviation>
</Journal>
<ArticleTitle>Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus.</ArticleTitle>
<Pagination>
<MedlinePgn>73-83</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1038/hdy.2016.26</ELocationID>
<Abstract>
<AbstractText>MicroRNAs (miRNAs) have important roles in the regulation of genes; however, for trees few studies have explored the potential impact of the interactions between miRNAs and their target genes. Here, we performed transcript profiling and association genetics (single-SNP, haplotype-based and multi-SNP associations) to study the genetic regulatory relationship of Pto-miR257 and its 12 target genes in 435 individuals of a natural population of Populus tomentosa. Expression profiling of Pto-miR257 and its targets showed a negative relationship between their expression levels. Of the 61 single-nucleotide polymorphisms (SNPs) detected in Pto-miR257, 6 in the pre-mature region strongly affected its secondary stability and 1 in the mature region could alter its target spectrum. Among the 1029 SNPs in the targets, 3 were located in target sites that could change the binding affinity of Pto-miR257. Single-SNP association analysis revealed that SNPs in Pto-miR257 and target genes associated with both growth and wood property traits, in agreement with haplotype-based identifications. Multi-SNP association found that 10 targets shared at least one common trait with Pto-miR257, with phenotypic variance from 0.5 to 8.5%, suggesting a possible internal genetic interaction between them. Epistasis analysis showed significant epistatic interactions among Pto-miR257 and its targets. Therefore, our study demonstrated Pto-miR257 and its 12 targets had roles in wood formation and revealed the genetic interaction network between the miRNA and its targets under additive, dominant and epistatic models. Thus, association genetics can be used to decipher the interactions between miRNAs and their target genes and to help understand the genetic architecture of complex traits.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Chen</LastName>
<ForeName>B</ForeName>
<Initials>B</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Du</LastName>
<ForeName>Q</ForeName>
<Initials>Q</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Chen</LastName>
<ForeName>J</ForeName>
<Initials>J</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Yang</LastName>
<ForeName>X</ForeName>
<Initials>X</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Tian</LastName>
<ForeName>J</ForeName>
<Initials>J</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Li</LastName>
<ForeName>B</ForeName>
<Initials>B</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Department of Forestry, North Carolina State University, Raleigh, NC, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Zhang</LastName>
<ForeName>D</ForeName>
<Initials>D</Initials>
<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.</Affiliation>
</AffiliationInfo>
</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>2016</Year>
<Month>04</Month>
<Day>27</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>England</Country>
<MedlineTA>Heredity (Edinb)</MedlineTA>
<NlmUniqueID>0373007</NlmUniqueID>
<ISSNLinking>0018-067X</ISSNLinking>
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<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D004843" MajorTopicYN="Y">Epistasis, Genetic</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="D006239" MajorTopicYN="N">Haplotypes</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName>
</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="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName>
<QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName>
</MeshHeading>
</MeshHeadingList>
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<Year>2015</Year>
<Month>12</Month>
<Day>23</Day>
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<Year>2016</Year>
<Month>03</Month>
<Day>02</Day>
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<PubMedPubDate PubStatus="entrez">
<Year>2016</Year>
<Month>4</Month>
<Day>28</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<Year>2016</Year>
<Month>4</Month>
<Day>28</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<Year>2017</Year>
<Month>6</Month>
<Day>24</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<li>Pékin</li>
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<name sortKey="Chen, J" sort="Chen, J" uniqKey="Chen J" first="J" last="Chen">J. Chen</name>
<name sortKey="Chen, J" sort="Chen, J" uniqKey="Chen J" first="J" last="Chen">J. Chen</name>
<name sortKey="Du, Q" sort="Du, Q" uniqKey="Du Q" first="Q" last="Du">Q. Du</name>
<name sortKey="Du, Q" sort="Du, Q" uniqKey="Du Q" first="Q" last="Du">Q. Du</name>
<name sortKey="Li, B" sort="Li, B" uniqKey="Li B" first="B" last="Li">B. Li</name>
<name sortKey="Li, B" sort="Li, B" uniqKey="Li B" first="B" last="Li">B. Li</name>
<name sortKey="Tian, J" sort="Tian, J" uniqKey="Tian J" first="J" last="Tian">J. Tian</name>
<name sortKey="Tian, J" sort="Tian, J" uniqKey="Tian J" first="J" last="Tian">J. Tian</name>
<name sortKey="Yang, X" sort="Yang, X" uniqKey="Yang X" first="X" last="Yang">X. Yang</name>
<name sortKey="Yang, X" sort="Yang, X" uniqKey="Yang X" first="X" last="Yang">X. Yang</name>
<name sortKey="Zhang, D" sort="Zhang, D" uniqKey="Zhang D" first="D" last="Zhang">D. Zhang</name>
<name sortKey="Zhang, D" sort="Zhang, D" uniqKey="Zhang D" first="D" last="Zhang">D. Zhang</name>
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