Genetic interactions among Pto-miR319 family members and their targets influence growth and wood properties in Populus tomentosa.
Identifieur interne : 000322 ( Main/Corpus ); précédent : 000321; suivant : 000323Genetic interactions among Pto-miR319 family members and their targets influence growth and wood properties in Populus tomentosa.
Auteurs : Jingna Si ; Mingyang Quan ; Liang Xiao ; Jianbo Xie ; Qingzhang Du ; Deqiang ZhangSource :
- Molecular genetics and genomics : MGG [ 1617-4623 ] ; 2020.
English descriptors
- KwdEn :
- Alleles (MeSH), Arabidopsis (MeSH), Epistasis, Genetic (genetics), Gene Expression Regulation, Plant (genetics), Genetic Association Studies (MeSH), Linkage Disequilibrium (genetics), MicroRNAs (genetics), Polymorphism, Single Nucleotide (genetics), Populus (genetics), Populus (growth & development), RNA, Messenger (genetics), Wood (genetics).
- MESH :
- chemical , genetics : MicroRNAs, RNA, Messenger.
- genetics : Epistasis, Genetic, Gene Expression Regulation, Plant, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Populus, Wood.
- growth & development : Populus.
- Alleles, Arabidopsis, Genetic Association Studies.
Abstract
MicroRNAs (miRNAs) play crucial roles in all aspects of plant growth and development, but the genetic interactions of miRNAs and their target genes in woody plants are largely unknown. Here, we integrated association genetics and expression profiling to decipher the allelic variations and interactions of the Pto-MIR319 family of miRNAs and 12 putative Pto-miR319 target genes related to wood formation in 435 unrelated individuals of Populus tomentosa Carrière (Chinese white poplar). Expression pattern analysis showed that among all pairings between expressions of pre-miRNA of Pto-MIR319 members and targets, 70.0% showed negative correlation of expression levels (r = - 0.944 to 0.674, P < 0.01) in eight tissues and organs of poplar, suggesting that Pto-miR319 may participate in the regulatory network of wood formation. Single SNP-based association studies identified 137 significant associations (P < 0.01, Q < 0.1), representing 126 unique SNPs from Pto-MIR319 members and their targets, with 10 tree growth traits, revealing that these genetic factors have common roles related to wood formation. Epistasis analysis uncovered 105 significant SNP-SNP associations (P < 0.01) influencing the 10 traits, demonstrating the close genetic interactions between Pto-MIR319 family members and the 12 Pto-miR319 target genes. Notably, one common SNP, in the precursor region of Pto-MIR319e, affected the stability of Pto-MIR319e's secondary structure by altering the stem-loop structure and minimum free energy, contributing to variations in the expression of Pto-MIR319e and Pto-miR319e target genes. This study enriches the understanding of the functions of miR319 family miRNAs in poplar and exemplifies a feasible approach to exploring the genetic effects underlying miRNA-mRNA interactions related to complex traits in trees.
DOI: 10.1007/s00438-020-01667-9
PubMed: 32361785
Links to Exploration step
pubmed:32361785Le document en format XML
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China.</nlm:affiliation></affiliation><affiliation><nlm: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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Quan, Mingyang" sort="Quan, Mingyang" uniqKey="Quan M" first="Mingyang" last="Quan">Mingyang Quan</name><affiliation><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation><affiliation><nlm: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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Xiao, Liang" sort="Xiao, Liang" uniqKey="Xiao L" first="Liang" last="Xiao">Liang Xiao</name><affiliation><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation><affiliation><nlm: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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Xie, Jianbo" sort="Xie, Jianbo" uniqKey="Xie J" first="Jianbo" last="Xie">Jianbo Xie</name><affiliation><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation><affiliation><nlm: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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Du, Qingzhang" sort="Du, Qingzhang" uniqKey="Du Q" first="Qingzhang" last="Du">Qingzhang Du</name><affiliation><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation><affiliation><nlm: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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name><affiliation><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China. DeqiangZhang@bjfu.edu.cn.</nlm:affiliation></affiliation><affiliation><nlm: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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China. DeqiangZhang@bjfu.edu.cn.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China. DeqiangZhang@bjfu.edu.cn.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Molecular genetics and genomics : MGG</title><idno type="eISSN">1617-4623</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term><term>Arabidopsis (MeSH)</term><term>Epistasis, Genetic (genetics)</term><term>Gene Expression Regulation, Plant (genetics)</term><term>Genetic Association Studies (MeSH)</term><term>Linkage Disequilibrium (genetics)</term><term>MicroRNAs (genetics)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term><term>RNA, Messenger (genetics)</term><term>Wood (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Epistasis, Genetic</term><term>Gene Expression Regulation, Plant</term><term>Linkage Disequilibrium</term><term>Polymorphism, Single Nucleotide</term><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Arabidopsis</term><term>Genetic Association Studies</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">MicroRNAs (miRNAs) play crucial roles in all aspects of plant growth and development, but the genetic interactions of miRNAs and their target genes in woody plants are largely unknown. Here, we integrated association genetics and expression profiling to decipher the allelic variations and interactions of the Pto-MIR319 family of miRNAs and 12 putative Pto-miR319 target genes related to wood formation in 435 unrelated individuals of Populus tomentosa Carrière (Chinese white poplar). Expression pattern analysis showed that among all pairings between expressions of pre-miRNA of Pto-MIR319 members and targets, 70.0% showed negative correlation of expression levels (r = - 0.944 to 0.674, P < 0.01) in eight tissues and organs of poplar, suggesting that Pto-miR319 may participate in the regulatory network of wood formation. Single SNP-based association studies identified 137 significant associations (P < 0.01, Q < 0.1), representing 126 unique SNPs from Pto-MIR319 members and their targets, with 10 tree growth traits, revealing that these genetic factors have common roles related to wood formation. Epistasis analysis uncovered 105 significant SNP-SNP associations (P < 0.01) influencing the 10 traits, demonstrating the close genetic interactions between Pto-MIR319 family members and the 12 Pto-miR319 target genes. Notably, one common SNP, in the precursor region of Pto-MIR319e, affected the stability of Pto-MIR319e's secondary structure by altering the stem-loop structure and minimum free energy, contributing to variations in the expression of Pto-MIR319e and Pto-miR319e target genes. This study enriches the understanding of the functions of miR319 family miRNAs in poplar and exemplifies a feasible approach to exploring the genetic effects underlying miRNA-mRNA interactions related to complex traits in trees.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32361785</PMID><DateCompleted><Year>2020</Year><Month>06</Month><Day>25</Day></DateCompleted><DateRevised><Year>2020</Year><Month>06</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1617-4623</ISSN><JournalIssue CitedMedium="Internet"><Volume>295</Volume><Issue>4</Issue><PubDate><Year>2020</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Molecular genetics and genomics : MGG</Title><ISOAbbreviation>Mol Genet Genomics</ISOAbbreviation></Journal><ArticleTitle>Genetic interactions among Pto-miR319 family members and their targets influence growth and wood properties in Populus tomentosa.</ArticleTitle><Pagination><MedlinePgn>855-870</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00438-020-01667-9</ELocationID><Abstract><AbstractText>MicroRNAs (miRNAs) play crucial roles in all aspects of plant growth and development, but the genetic interactions of miRNAs and their target genes in woody plants are largely unknown. Here, we integrated association genetics and expression profiling to decipher the allelic variations and interactions of the Pto-MIR319 family of miRNAs and 12 putative Pto-miR319 target genes related to wood formation in 435 unrelated individuals of Populus tomentosa Carrière (Chinese white poplar). Expression pattern analysis showed that among all pairings between expressions of pre-miRNA of Pto-MIR319 members and targets, 70.0% showed negative correlation of expression levels (r = - 0.944 to 0.674, P < 0.01) in eight tissues and organs of poplar, suggesting that Pto-miR319 may participate in the regulatory network of wood formation. Single SNP-based association studies identified 137 significant associations (P < 0.01, Q < 0.1), representing 126 unique SNPs from Pto-MIR319 members and their targets, with 10 tree growth traits, revealing that these genetic factors have common roles related to wood formation. Epistasis analysis uncovered 105 significant SNP-SNP associations (P < 0.01) influencing the 10 traits, demonstrating the close genetic interactions between Pto-MIR319 family members and the 12 Pto-miR319 target genes. Notably, one common SNP, in the precursor region of Pto-MIR319e, affected the stability of Pto-MIR319e's secondary structure by altering the stem-loop structure and minimum free energy, contributing to variations in the expression of Pto-MIR319e and Pto-miR319e target genes. This study enriches the understanding of the functions of miR319 family miRNAs in poplar and exemplifies a feasible approach to exploring the genetic effects underlying miRNA-mRNA interactions related to complex traits in trees.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Si</LastName><ForeName>Jingna</ForeName><Initials>J</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, P. R. 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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Quan</LastName><ForeName>Mingyang</ForeName><Initials>M</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, P. R. 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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiao</LastName><ForeName>Liang</ForeName><Initials>L</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, P. R. 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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Jianbo</ForeName><Initials>J</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, P. R. 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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Qingzhang</ForeName><Initials>Q</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, P. R. 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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Deqiang</ForeName><Initials>D</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-8849-2366</Identifier><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China. DeqiangZhang@bjfu.edu.cn.</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, No. 35, Qinghua East Road, Beijing, 100083, P. R. China. DeqiangZhang@bjfu.edu.cn.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China. DeqiangZhang@bjfu.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>31670333 and 31401138</GrantID><Agency>the Project of the National Natural Science Foundation of China</Agency><Country></Country></Grant><Grant><GrantID>2018M640084 and 2019T120058</GrantID><Agency>the China Postdoctoral Science Foundation</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>05</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Mol Genet Genomics</MedlineTA><NlmUniqueID>101093320</NlmUniqueID><ISSNLinking>1617-4623</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C000595631">MIRN319 microRNA, Arabidopsis</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</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="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004843" MajorTopicYN="N">Epistasis, Genetic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D056726" MajorTopicYN="Y">Genetic Association Studies</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</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="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Association mapping</Keyword><Keyword MajorTopicYN="N">Epistasis</Keyword><Keyword MajorTopicYN="N">Populus tomentosa</Keyword><Keyword MajorTopicYN="N">Pto-miR319</Keyword><Keyword MajorTopicYN="N">Wood formation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>10</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>5</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>6</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>5</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32361785</ArticleId><ArticleId IdType="doi">10.1007/s00438-020-01667-9</ArticleId><ArticleId IdType="pii">10.1007/s00438-020-01667-9</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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