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Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa.

Identifieur interne : 001352 ( Main/Exploration ); précédent : 001351; suivant : 001353

Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa.

Auteurs : Daling Zhou [République populaire de Chine] ; Qingzhang Du [République populaire de Chine] ; Jinhui Chen [République populaire de Chine] ; Qingshi Wang [République populaire de Chine] ; Deqiang Zhang [République populaire de Chine]

Source :

RBID : pubmed:28453813

Descripteurs français

English descriptors

Abstract

Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation. Then, 476 and 28 lncRNAs were identified as putative targets and endogenous target mimics (eTMs) of Populus known microRNAs (miRNAs), respectively. Genome re-sequencing of 435 individuals from a natural population of P. tomentosa found 34,015 single nucleotide polymorphisms (SNPs) within 178 lncRNA loci and 522 PTGs. Single-SNP associations analysis detected 2,993 associations with 10 growth and wood-property traits under additive and dominance model. Epistasis analysis identified 17,656 epistatic SNP pairs, providing evidence for potential regulatory interactions between lncRNAs and their PTGs. Furthermore, a reconstructed epistatic network, representing interactions of 8 lncRNAs and 15 PTGs, might enrich regulation roles of genes in the phenylpropanoid pathway. These findings may enhance our understanding of non-coding genes in plants.

DOI: 10.1093/dnares/dsx018
PubMed: 28453813
PubMed Central: PMC5737087


Affiliations:


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Le document en format XML

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<term>Cambium (genetics)</term>
<term>Cambium (growth & development)</term>
<term>Cambium (metabolism)</term>
<term>Epistasis, Genetic (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genetic Association Studies (MeSH)</term>
<term>Polymorphism, Single Nucleotide (MeSH)</term>
<term>Populus (genetics)</term>
<term>Populus (growth & development)</term>
<term>Populus (metabolism)</term>
<term>Quantitative Trait, Heritable (MeSH)</term>
<term>RNA, Long Noncoding (genetics)</term>
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<term>RNA, Plant (physiology)</term>
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<term>Sequence Analysis, RNA (MeSH)</term>
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<term>Xylem (growth & development)</term>
<term>Xylem (metabolism)</term>
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<term>ARN long non codant (génétique)</term>
<term>ARN long non codant (physiologie)</term>
<term>Analyse de séquence d'ADN (MeSH)</term>
<term>Analyse de séquence d'ARN (MeSH)</term>
<term>Cambium (croissance et développement)</term>
<term>Cambium (génétique)</term>
<term>Cambium (métabolisme)</term>
<term>Caractère quantitatif héréditaire (MeSH)</term>
<term>Polymorphisme de nucléotide simple (MeSH)</term>
<term>Populus (croissance et développement)</term>
<term>Populus (génétique)</term>
<term>Populus (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Transcriptome (MeSH)</term>
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<term>Xylème (génétique)</term>
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<term>Épistasie (MeSH)</term>
<term>Études d'associations génétiques (MeSH)</term>
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<term>Sequence Analysis, DNA</term>
<term>Sequence Analysis, RNA</term>
<term>Transcriptome</term>
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<keywords scheme="MESH" xml:lang="fr">
<term>Analyse de séquence d'ADN</term>
<term>Analyse de séquence d'ARN</term>
<term>Caractère quantitatif héréditaire</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Transcriptome</term>
<term>Épistasie</term>
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<front>
<div type="abstract" xml:lang="en">Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation. Then, 476 and 28 lncRNAs were identified as putative targets and endogenous target mimics (eTMs) of Populus known microRNAs (miRNAs), respectively. Genome re-sequencing of 435 individuals from a natural population of P. tomentosa found 34,015 single nucleotide polymorphisms (SNPs) within 178 lncRNA loci and 522 PTGs. Single-SNP associations analysis detected 2,993 associations with 10 growth and wood-property traits under additive and dominance model. Epistasis analysis identified 17,656 epistatic SNP pairs, providing evidence for potential regulatory interactions between lncRNAs and their PTGs. Furthermore, a reconstructed epistatic network, representing interactions of 8 lncRNAs and 15 PTGs, might enrich regulation roles of genes in the phenylpropanoid pathway. These findings may enhance our understanding of non-coding genes in plants.</div>
</front>
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<Year>2017</Year>
<Month>11</Month>
<Day>16</Day>
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<Year>2018</Year>
<Month>11</Month>
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<ISSN IssnType="Electronic">1756-1663</ISSN>
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<Issue>5</Issue>
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<Month>Oct</Month>
<Day>01</Day>
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<Title>DNA research : an international journal for rapid publication of reports on genes and genomes</Title>
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<ArticleTitle>Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa.</ArticleTitle>
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<AbstractText>Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation. Then, 476 and 28 lncRNAs were identified as putative targets and endogenous target mimics (eTMs) of Populus known microRNAs (miRNAs), respectively. Genome re-sequencing of 435 individuals from a natural population of P. tomentosa found 34,015 single nucleotide polymorphisms (SNPs) within 178 lncRNA loci and 522 PTGs. Single-SNP associations analysis detected 2,993 associations with 10 growth and wood-property traits under additive and dominance model. Epistasis analysis identified 17,656 epistatic SNP pairs, providing evidence for potential regulatory interactions between lncRNAs and their PTGs. Furthermore, a reconstructed epistatic network, representing interactions of 8 lncRNAs and 15 PTGs, might enrich regulation roles of genes in the phenylpropanoid pathway. These findings may enhance our understanding of non-coding genes in plants.</AbstractText>
<CopyrightInformation>© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.</CopyrightInformation>
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<LastName>Zhou</LastName>
<ForeName>Daling</ForeName>
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<Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China.</Affiliation>
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<AffiliationInfo>
<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China.</Affiliation>
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<Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China.</Affiliation>
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<DescriptorName UI="D058506" MajorTopicYN="N">Cambium</DescriptorName>
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