Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides.
Identifieur interne : 000016 ( Main/Exploration ); précédent : 000015; suivant : 000017Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides.
Auteurs : Kelly M. Balmant [États-Unis] ; Jerald D. Noble [États-Unis] ; Filipe C Alves [États-Unis] ; Christopher Dervinis [États-Unis] ; Daniel Conde [États-Unis] ; Henry W. Schmidt [États-Unis] ; Ana I. Vazquez [États-Unis] ; William B. Barbazuk [États-Unis] ; Gustavo De Los Campos [États-Unis] ; Marcio F R. Resende [États-Unis] ; Matias Kirst [États-Unis]Source :
- Genome research [ 1549-5469 ] ; 2020.
Abstract
Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in Populus deltoides by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of P. deltoides The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor MYB125 (Potri.003G114100) as a putative trans-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of MYB125 in a diverse population positively correlated with lignin content. Furthermore, overexpression of MYB125 in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that MYB125 is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in P. deltoides.
DOI: 10.1101/gr.261438.120
PubMed: 32817237
PubMed Central: PMC7462072
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Balmant</name><affiliation wicri:level="1"><nlm:affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation></author><author><name sortKey="Noble, Jerald D" sort="Noble, Jerald D" uniqKey="Noble J" first="Jerald D" last="Noble">Jerald D. Noble</name><affiliation wicri:level="1"><nlm:affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation></author><author><name sortKey="C Alves, Filipe" sort="C Alves, Filipe" uniqKey="C Alves F" first="Filipe" last="C Alves">Filipe C Alves</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824</wicri:regionArea><orgName type="university">Université d'État du Michigan</orgName><placeName><settlement type="city">East Lansing</settlement><region type="state">Michigan</region></placeName></affiliation></author><author><name sortKey="Dervinis, Christopher" sort="Dervinis, Christopher" uniqKey="Dervinis C" first="Christopher" last="Dervinis">Christopher Dervinis</name><affiliation wicri:level="1"><nlm:affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation></author><author><name sortKey="Conde, Daniel" sort="Conde, Daniel" uniqKey="Conde D" first="Daniel" last="Conde">Daniel Conde</name><affiliation wicri:level="1"><nlm:affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation></author><author><name sortKey="Schmidt, Henry W" sort="Schmidt, Henry W" uniqKey="Schmidt H" first="Henry W" last="Schmidt">Henry W. Schmidt</name><affiliation wicri:level="1"><nlm:affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation></author><author><name sortKey="Vazquez, Ana I" sort="Vazquez, Ana I" uniqKey="Vazquez A" first="Ana I" last="Vazquez">Ana I. Vazquez</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824</wicri:regionArea><orgName type="university">Université d'État du Michigan</orgName><placeName><settlement type="city">East Lansing</settlement><region type="state">Michigan</region></placeName></affiliation></author><author><name sortKey="Barbazuk, William B" sort="Barbazuk, William B" uniqKey="Barbazuk W" first="William B" last="Barbazuk">William B. Barbazuk</name><affiliation wicri:level="1"><nlm:affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Genetics Institute, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genetics Institute, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation></author><author><name sortKey="Campos, Gustavo De Los" sort="Campos, Gustavo De Los" uniqKey="Campos G" first="Gustavo De Los" last="Campos">Gustavo De Los Campos</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824</wicri:regionArea><orgName type="university">Université d'État du Michigan</orgName><placeName><settlement type="city">East Lansing</settlement><region type="state">Michigan</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Statistics Department, Michigan State University, East Lansing, Michigan 48824, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Statistics Department, Michigan State University, East Lansing, Michigan 48824</wicri:regionArea><orgName type="university">Université d'État du Michigan</orgName><placeName><settlement type="city">East Lansing</settlement><region type="state">Michigan</region></placeName></affiliation></author><author><name sortKey="Resende, Marcio F R" sort="Resende, Marcio F R" uniqKey="Resende M" first="Marcio F R" last="Resende">Marcio F R. Resende</name><affiliation wicri:level="1"><nlm:affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Horticulture Sciences Department, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticulture Sciences Department, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation></author><author><name sortKey="Kirst, Matias" sort="Kirst, Matias" uniqKey="Kirst M" first="Matias" last="Kirst">Matias Kirst</name><affiliation wicri:level="1"><nlm:affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Genetics Institute, University of Florida, Gainesville, Florida 32611, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genetics Institute, University of Florida, Gainesville, Florida 32611</wicri:regionArea><wicri:noRegion>Florida 32611</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genome research</title><idno type="eISSN">1549-5469</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in <i>Populus deltoides</i> by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of <i>P. deltoides</i> The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor <i>MYB125</i> (<i>Potri.003G114100</i>) as a putative <i>trans</i>-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of <i>MYB125</i> in a diverse population positively correlated with lignin content. Furthermore, overexpression of <i>MYB125</i> in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that <i>MYB125</i> is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in <i>P. deltoides</i>.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32817237</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1549-5469</ISSN><JournalIssue CitedMedium="Internet"><Volume>30</Volume><Issue>8</Issue><PubDate><Year>2020</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res</ISOAbbreviation></Journal><ArticleTitle>Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in <i>Populus deltoides</i>.</ArticleTitle><Pagination><MedlinePgn>1131-1143</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1101/gr.261438.120</ELocationID><Abstract><AbstractText>Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in <i>Populus deltoides</i> by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of <i>P. deltoides</i> The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor <i>MYB125</i> (<i>Potri.003G114100</i>) as a putative <i>trans</i>-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of <i>MYB125</i> in a diverse population positively correlated with lignin content. Furthermore, overexpression of <i>MYB125</i> in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that <i>MYB125</i> is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in <i>P. deltoides</i>.</AbstractText><CopyrightInformation>© 2020 Balmant et al.; Published by Cold Spring Harbor Laboratory Press.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Balmant</LastName><ForeName>Kelly M</ForeName><Initials>KM</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Noble</LastName><ForeName>Jerald D</ForeName><Initials>JD</Initials><AffiliationInfo><Affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>C Alves</LastName><ForeName>Filipe</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dervinis</LastName><ForeName>Christopher</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Conde</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmidt</LastName><ForeName>Henry W</ForeName><Initials>HW</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vazquez</LastName><ForeName>Ana I</ForeName><Initials>AI</Initials><AffiliationInfo><Affiliation>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barbazuk</LastName><ForeName>William B</ForeName><Initials>WB</Initials><AffiliationInfo><Affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biology, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Genetics Institute, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Campos</LastName><ForeName>Gustavo de Los</ForeName><Initials>GL</Initials><AffiliationInfo><Affiliation>Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Statistics Department, Michigan State University, East Lansing, Michigan 48824, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Resende</LastName><ForeName>Marcio F R</ForeName><Initials>MFR</Initials><Suffix>Jr</Suffix><AffiliationInfo><Affiliation>Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Horticulture Sciences Department, University of Florida, Gainesville, Florida 32611, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kirst</LastName><ForeName>Matias</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Conservation, University of 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