A computational framework for mapping the timing of vegetative phase change.
Identifieur interne : 001876 ( Main/Corpus ); précédent : 001875; suivant : 001877A computational framework for mapping the timing of vegetative phase change.
Auteurs : Meng Xu ; Libo Jiang ; Sheng Zhu ; Chunguo Zhou ; Meixia Ye ; Ke Mao ; Lidan Sun ; Xiaohua Su ; Huixin Pan ; Shougong Zhang ; Minren Huang ; Rongling WuSource :
- The New phytologist [ 1469-8137 ] ; 2016.
English descriptors
- KwdEn :
- Chromosome Segregation (genetics), Computer Simulation (MeSH), Crosses, Genetic (MeSH), Inheritance Patterns (genetics), Models, Theoretical (MeSH), Plant Development (genetics), Plant Stems (growth & development), Polymorphism, Single Nucleotide (genetics), Populus (genetics), Populus (growth & development), Quantitative Trait Loci (genetics), Rain (MeSH), Temperature (MeSH), Time Factors (MeSH).
- MESH :
- genetics : Chromosome Segregation, Inheritance Patterns, Plant Development, Polymorphism, Single Nucleotide, Populus, Quantitative Trait Loci.
- growth & development : Plant Stems, Populus.
- Computer Simulation, Crosses, Genetic, Models, Theoretical, Rain, Temperature, Time Factors.
Abstract
Phase change plays a prominent role in determining the form of growth and development. Although considerable attention has been focused on identifying the regulatory control mechanisms of phase change, a detailed understanding of the genetic architecture of this phenomenon is still lacking. We address this issue by deriving a computational model. The model is founded on the framework of functional mapping aimed at characterizing the interplay between quantitative trait loci (QTLs) and development through biologically meaningful mathematical equations. A multiphasic growth equation was implemented into functional mapping, which, via a series of hypothesis tests, allows the quantification of how QTLs regulate the timing and pattern of vegetative phase transition between independently regulated, temporally coordinated processes. The model was applied to analyze stem radial growth data of an interspecific hybrid family derived from two Populus species during the first 24 yr of ontogeny. Several key QTLs related to phase change have been characterized, most of which were observed to be in the adjacent regions of candidate genes. The identification of phase transition QTLs, whose expression is regulated by endogenous and environmental signals, may enhance our understanding of the evolution of development in changing environments.
DOI: 10.1111/nph.13907
PubMed: 26958803
Links to Exploration step
pubmed:26958803Le document en format XML
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Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Chunguo" sort="Zhou, Chunguo" uniqKey="Zhou C" first="Chunguo" last="Zhou">Chunguo Zhou</name><affiliation><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Meixia" sort="Ye, Meixia" uniqKey="Ye M" first="Meixia" last="Ye">Meixia Ye</name><affiliation><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Mao, Ke" sort="Mao, Ke" uniqKey="Mao K" first="Ke" last="Mao">Ke Mao</name><affiliation><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Lidan" sort="Sun, Lidan" uniqKey="Sun L" first="Lidan" last="Sun">Lidan Sun</name><affiliation><nlm:affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Su, Xiaohua" sort="Su, Xiaohua" uniqKey="Su X" first="Xiaohua" last="Su">Xiaohua Su</name><affiliation><nlm:affiliation>Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100094, China.</nlm:affiliation></affiliation></author><author><name sortKey="Pan, Huixin" sort="Pan, Huixin" uniqKey="Pan H" first="Huixin" last="Pan">Huixin Pan</name><affiliation><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Shougong" sort="Zhang, Shougong" uniqKey="Zhang S" first="Shougong" last="Zhang">Shougong Zhang</name><affiliation><nlm:affiliation>Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100094, China.</nlm:affiliation></affiliation></author><author><name sortKey="Huang, Minren" sort="Huang, Minren" uniqKey="Huang M" first="Minren" last="Huang">Minren Huang</name><affiliation><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><affiliation><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:26958803</idno><idno type="pmid">26958803</idno><idno type="doi">10.1111/nph.13907</idno><idno type="wicri:Area/Main/Corpus">001876</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001876</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A computational framework for mapping the timing of vegetative phase change.</title><author><name sortKey="Xu, Meng" sort="Xu, Meng" uniqKey="Xu M" first="Meng" last="Xu">Meng Xu</name><affiliation><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Jiang, Libo" sort="Jiang, Libo" uniqKey="Jiang L" first="Libo" last="Jiang">Libo Jiang</name><affiliation><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhu, Sheng" sort="Zhu, Sheng" uniqKey="Zhu S" first="Sheng" last="Zhu">Sheng Zhu</name><affiliation><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Chunguo" sort="Zhou, Chunguo" uniqKey="Zhou C" first="Chunguo" last="Zhou">Chunguo Zhou</name><affiliation><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Meixia" sort="Ye, Meixia" uniqKey="Ye M" first="Meixia" last="Ye">Meixia Ye</name><affiliation><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Mao, Ke" sort="Mao, Ke" uniqKey="Mao K" first="Ke" last="Mao">Ke Mao</name><affiliation><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Lidan" sort="Sun, Lidan" uniqKey="Sun L" first="Lidan" last="Sun">Lidan Sun</name><affiliation><nlm:affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Su, Xiaohua" sort="Su, Xiaohua" uniqKey="Su X" first="Xiaohua" last="Su">Xiaohua Su</name><affiliation><nlm:affiliation>Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100094, China.</nlm:affiliation></affiliation></author><author><name sortKey="Pan, Huixin" sort="Pan, Huixin" uniqKey="Pan H" first="Huixin" last="Pan">Huixin Pan</name><affiliation><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Shougong" sort="Zhang, Shougong" uniqKey="Zhang S" first="Shougong" last="Zhang">Shougong Zhang</name><affiliation><nlm:affiliation>Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100094, China.</nlm:affiliation></affiliation></author><author><name sortKey="Huang, Minren" sort="Huang, Minren" uniqKey="Huang M" first="Minren" last="Huang">Minren Huang</name><affiliation><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><affiliation><nlm:affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Segregation (genetics)</term><term>Computer Simulation (MeSH)</term><term>Crosses, Genetic (MeSH)</term><term>Inheritance Patterns (genetics)</term><term>Models, Theoretical (MeSH)</term><term>Plant Development (genetics)</term><term>Plant Stems (growth & development)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term><term>Quantitative Trait Loci (genetics)</term><term>Rain (MeSH)</term><term>Temperature (MeSH)</term><term>Time Factors (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosome Segregation</term><term>Inheritance Patterns</term><term>Plant Development</term><term>Polymorphism, Single Nucleotide</term><term>Populus</term><term>Quantitative Trait Loci</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Plant Stems</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Crosses, Genetic</term><term>Models, Theoretical</term><term>Rain</term><term>Temperature</term><term>Time Factors</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Phase change plays a prominent role in determining the form of growth and development. Although considerable attention has been focused on identifying the regulatory control mechanisms of phase change, a detailed understanding of the genetic architecture of this phenomenon is still lacking. We address this issue by deriving a computational model. The model is founded on the framework of functional mapping aimed at characterizing the interplay between quantitative trait loci (QTLs) and development through biologically meaningful mathematical equations. A multiphasic growth equation was implemented into functional mapping, which, via a series of hypothesis tests, allows the quantification of how QTLs regulate the timing and pattern of vegetative phase transition between independently regulated, temporally coordinated processes. The model was applied to analyze stem radial growth data of an interspecific hybrid family derived from two Populus species during the first 24 yr of ontogeny. Several key QTLs related to phase change have been characterized, most of which were observed to be in the adjacent regions of candidate genes. The identification of phase transition QTLs, whose expression is regulated by endogenous and environmental signals, may enhance our understanding of the evolution of development in changing environments.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26958803</PMID><DateCompleted><Year>2018</Year><Month>01</Month><Day>31</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>211</Volume><Issue>2</Issue><PubDate><Year>2016</Year><Month>07</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>A computational framework for mapping the timing of vegetative phase change.</ArticleTitle><Pagination><MedlinePgn>750-60</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.13907</ELocationID><Abstract><AbstractText>Phase change plays a prominent role in determining the form of growth and development. Although considerable attention has been focused on identifying the regulatory control mechanisms of phase change, a detailed understanding of the genetic architecture of this phenomenon is still lacking. We address this issue by deriving a computational model. The model is founded on the framework of functional mapping aimed at characterizing the interplay between quantitative trait loci (QTLs) and development through biologically meaningful mathematical equations. A multiphasic growth equation was implemented into functional mapping, which, via a series of hypothesis tests, allows the quantification of how QTLs regulate the timing and pattern of vegetative phase transition between independently regulated, temporally coordinated processes. The model was applied to analyze stem radial growth data of an interspecific hybrid family derived from two Populus species during the first 24 yr of ontogeny. Several key QTLs related to phase change have been characterized, most of which were observed to be in the adjacent regions of candidate genes. The identification of phase transition QTLs, whose expression is regulated by endogenous and environmental signals, may enhance our understanding of the evolution of development in changing environments.</AbstractText><CopyrightInformation>© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Meng</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Libo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Sheng</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Chunguo</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Meixia</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mao</LastName><ForeName>Ke</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Lidan</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Xiaohua</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100094, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pan</LastName><ForeName>Huixin</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Shougong</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100094, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Minren</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Rongling</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.</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>03</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020090" MajorTopicYN="N">Chromosome Segregation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003433" MajorTopicYN="N">Crosses, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040582" MajorTopicYN="N">Inheritance Patterns</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008962" MajorTopicYN="Y">Models, Theoretical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063245" MajorTopicYN="Y">Plant Development</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018547" MajorTopicYN="N">Plant Stems</DescriptorName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</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="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D040641" MajorTopicYN="N">Quantitative Trait Loci</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011891" MajorTopicYN="N">Rain</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013696" MajorTopicYN="N">Temperature</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013997" MajorTopicYN="N">Time Factors</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus</Keyword><Keyword MajorTopicYN="Y">functional mapping</Keyword><Keyword MajorTopicYN="Y">growth equation</Keyword><Keyword MajorTopicYN="Y">phase change</Keyword><Keyword MajorTopicYN="Y">quantitative trait loci (QTLs)</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>12</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>01</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>3</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>3</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>2</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26958803</ArticleId><ArticleId IdType="doi">10.1111/nph.13907</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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