PoplarV1, Main, Exploration, bibRecord, 000F69

Defining the genetic components of callus formation: A GWAS approach.

Identifieur interne : 000F69 ( Main/Exploration ); précédent : 000F68; suivant : 000F70

Defining the genetic components of callus formation: A GWAS approach.

Auteurs : Gerald A. Tuskan [États-Unis] ; Ritesh Mewalal [États-Unis] ; Lee E. Gunter [États-Unis] ; Kaitlin J. Palla [États-Unis] ; Kelsey Carter [États-Unis] ; Daniel A. Jacobson [États-Unis] ; Piet C. Jones [États-Unis] ; Benjamin J. Garcia [États-Unis] ; Deborah A. Weighill [États-Unis] ; Philip D. Hyatt [États-Unis] ; Yongil Yang [États-Unis] ; Jin Zhang [États-Unis] ; Nicholas Reis [États-Unis] ; Jin-Gui Chen [États-Unis] ; Wellington Muchero [États-Unis]

Source :

PloS one [ 1932-6203 ] ; 2018.

RBID : pubmed:30118526

Descripteurs français

KwdFr :
- Cal osseux (croissance et développement), Facteurs de transcription (génétique), Phénotype (MeSH), Populus (croissance et développement), Populus (génétique), Régulation de l'expression des gènes végétaux (MeSH), Étude d'association pangénomique (MeSH).
MESH :
- croissance et développement : Cal osseux, Populus.
- génétique : Facteurs de transcription, Populus.
- Phénotype, Régulation de l'expression des gènes végétaux, Étude d'association pangénomique.

English descriptors

KwdEn :
- Bony Callus (growth & development), Gene Expression Regulation, Plant (MeSH), Genome-Wide Association Study (MeSH), Phenotype (MeSH), Populus (genetics), Populus (growth & development), Transcription Factors (genetics).
MESH :
- chemical , genetics : Transcription Factors.
- genetics : Populus.
- growth & development : Bony Callus, Populus.
- Gene Expression Regulation, Plant, Genome-Wide Association Study, Phenotype.

Abstract

A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide-log10 (p) = 4.46 [p = 3.47E-05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showed homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.

DOI: 10.1371/journal.pone.0202519
PubMed: 30118526
PubMed Central: PMC6097687

Affiliations:

États-Unis
Michigan, Oregon, Tennessee

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<author><name sortKey="Yang, Yongil" sort="Yang, Yongil" uniqKey="Yang Y" first="Yongil" last="Yang">Yongil Yang</name>
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<author><name sortKey="Zhang, Jin" sort="Zhang, Jin" uniqKey="Zhang J" first="Jin" last="Zhang">Jin Zhang</name>
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<author><name sortKey="Chen, Jin Gui" sort="Chen, Jin Gui" uniqKey="Chen J" first="Jin-Gui" last="Chen">Jin-Gui Chen</name>
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<author><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name>
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<series><title level="j">PloS one</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bony Callus (growth & development)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genome-Wide Association Study (MeSH)</term>
<term>Phenotype (MeSH)</term>
<term>Populus (genetics)</term>
<term>Populus (growth & development)</term>
<term>Transcription Factors (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Cal osseux (croissance et développement)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Phénotype (MeSH)</term>
<term>Populus (croissance et développement)</term>
<term>Populus (génétique)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Étude d'association pangénomique (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Cal osseux</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>Bony Callus</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Facteurs de transcription</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term>
<term>Genome-Wide Association Study</term>
<term>Phenotype</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Phénotype</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Étude d'association pangénomique</term>
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<front><div type="abstract" xml:lang="en">A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide-log10 (p) = 4.46 [p = 3.47E-05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showed homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30118526</PMID>
<DateCompleted><Year>2019</Year>
<Month>02</Month>
<Day>07</Day>
</DateCompleted>
<DateRevised><Year>2019</Year>
<Month>02</Month>
<Day>15</Day>
</DateRevised>
<Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>13</Volume>
<Issue>8</Issue>
<PubDate><Year>2018</Year>
</PubDate>
</JournalIssue>
<Title>PloS one</Title>
<ISOAbbreviation>PLoS One</ISOAbbreviation>
</Journal>
<ArticleTitle>Defining the genetic components of callus formation: A GWAS approach.</ArticleTitle>
<Pagination><MedlinePgn>e0202519</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0202519</ELocationID>
<Abstract><AbstractText>A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide-log10 (p) = 4.46 [p = 3.47E-05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showed homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tuskan</LastName>
<ForeName>Gerald A</ForeName>
<Initials>GA</Initials>
<AffiliationInfo><Affiliation>Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Mewalal</LastName>
<ForeName>Ritesh</ForeName>
<Initials>R</Initials>
<Identifier Source="ORCID">0000-0002-0153-2434</Identifier>
<AffiliationInfo><Affiliation>Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Gunter</LastName>
<ForeName>Lee E</ForeName>
<Initials>LE</Initials>
<AffiliationInfo><Affiliation>Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Palla</LastName>
<ForeName>Kaitlin J</ForeName>
<Initials>KJ</Initials>
<AffiliationInfo><Affiliation>The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Carter</LastName>
<ForeName>Kelsey</ForeName>
<Initials>K</Initials>
<Identifier Source="ORCID">0000-0001-8327-6413</Identifier>
<AffiliationInfo><Affiliation>School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Jacobson</LastName>
<ForeName>Daniel A</ForeName>
<Initials>DA</Initials>
<AffiliationInfo><Affiliation>Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Jones</LastName>
<ForeName>Piet C</ForeName>
<Initials>PC</Initials>
<AffiliationInfo><Affiliation>The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Garcia</LastName>
<ForeName>Benjamin J</ForeName>
<Initials>BJ</Initials>
<Identifier Source="ORCID">0000-0001-5524-6946</Identifier>
<AffiliationInfo><Affiliation>Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Weighill</LastName>
<ForeName>Deborah A</ForeName>
<Initials>DA</Initials>
<AffiliationInfo><Affiliation>The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hyatt</LastName>
<ForeName>Philip D</ForeName>
<Initials>PD</Initials>
<AffiliationInfo><Affiliation>Computational Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Yang</LastName>
<ForeName>Yongil</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Jin</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Reis</LastName>
<ForeName>Nicholas</ForeName>
<Initials>N</Initials>
<AffiliationInfo><Affiliation>Oak Ridge Associated Universities, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Chen</LastName>
<ForeName>Jin-Gui</ForeName>
<Initials>JG</Initials>
<AffiliationInfo><Affiliation>Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Muchero</LastName>
<ForeName>Wellington</ForeName>
<Initials>W</Initials>
<AffiliationInfo><Affiliation>Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.</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>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2018</Year>
<Month>08</Month>
<Day>17</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>PLoS One</MedlineTA>
<NlmUniqueID>101285081</NlmUniqueID>
<ISSNLinking>1932-6203</ISSNLinking>
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<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance>
</Chemical>
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<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D002146" MajorTopicYN="N">Bony Callus</DescriptorName>
<QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</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="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
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</MeshHeadingList>
<CoiStatement>The authors have declared that no competing interests exist.</CoiStatement>
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<Month>02</Month>
<Day>19</Day>
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<Month>08</Month>
<Day>03</Day>
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<name sortKey="Chen, Jin Gui" sort="Chen, Jin Gui" uniqKey="Chen J" first="Jin-Gui" last="Chen">Jin-Gui Chen</name>
<name sortKey="Garcia, Benjamin J" sort="Garcia, Benjamin J" uniqKey="Garcia B" first="Benjamin J" last="Garcia">Benjamin J. Garcia</name>
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<name sortKey="Jacobson, Daniel A" sort="Jacobson, Daniel A" uniqKey="Jacobson D" first="Daniel A" last="Jacobson">Daniel A. Jacobson</name>
<name sortKey="Jones, Piet C" sort="Jones, Piet C" uniqKey="Jones P" first="Piet C" last="Jones">Piet C. Jones</name>
<name sortKey="Jones, Piet C" sort="Jones, Piet C" uniqKey="Jones P" first="Piet C" last="Jones">Piet C. Jones</name>
<name sortKey="Mewalal, Ritesh" sort="Mewalal, Ritesh" uniqKey="Mewalal R" first="Ritesh" last="Mewalal">Ritesh Mewalal</name>
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<name sortKey="Reis, Nicholas" sort="Reis, Nicholas" uniqKey="Reis N" first="Nicholas" last="Reis">Nicholas Reis</name>
<name sortKey="Weighill, Deborah A" sort="Weighill, Deborah A" uniqKey="Weighill D" first="Deborah A" last="Weighill">Deborah A. Weighill</name>
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<name sortKey="Yang, Yongil" sort="Yang, Yongil" uniqKey="Yang Y" first="Yongil" last="Yang">Yongil Yang</name>
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Defining the genetic components of callus formation: A GWAS approach.

Defining the genetic components of callus formation: A GWAS approach.

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