PoplarV1, Main, Corpus, bibRecord, 000A92

Hardwood Tree Genomics: Unlocking Woody Plant Biology.

Identifieur interne : 000A92 ( Main/Corpus ); précédent : 000A91; suivant : 000A93

Hardwood Tree Genomics: Unlocking Woody Plant Biology.

Auteurs : Gerald A. Tuskan ; Andrew T. Groover ; Jeremy Schmutz ; Stephen Paul Difazio ; Alexander Myburg ; Dario Grattapaglia ; Lawrence B. Smart ; Tongming Yin ; Jean-Marc Aury ; Antoine Kremer ; Thibault Leroy ; Gregoire Le Provost ; Christophe Plomion ; John E. Carlson ; Jennifer Randall ; Jared Westbrook ; Jane Grimwood ; Wellington Muchero ; Daniel Jacobson ; Joshua K. Michener

Source :

Frontiers in plant science [ 1664-462X ] ; 2018.

RBID : pubmed:30619389

Abstract

Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

DOI: 10.3389/fpls.2018.01799
PubMed: 30619389
PubMed Central: PMC6304363

Links to Exploration step

pubmed:30619389

Le document en format XML

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<author><name sortKey="Carlson, John E" sort="Carlson, John E" uniqKey="Carlson J" first="John E" last="Carlson">John E. Carlson</name>
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</affiliation>
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<author><name sortKey="Randall, Jennifer" sort="Randall, Jennifer" uniqKey="Randall J" first="Jennifer" last="Randall">Jennifer Randall</name>
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</affiliation>
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<author><name sortKey="Westbrook, Jared" sort="Westbrook, Jared" uniqKey="Westbrook J" first="Jared" last="Westbrook">Jared Westbrook</name>
<affiliation><nlm:affiliation>The American Chestnut Foundation, Asheville, NC, United States.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Grimwood, Jane" sort="Grimwood, Jane" uniqKey="Grimwood J" first="Jane" last="Grimwood">Jane Grimwood</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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</affiliation>
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<author><name sortKey="Jacobson, Daniel" sort="Jacobson, Daniel" uniqKey="Jacobson D" first="Daniel" last="Jacobson">Daniel Jacobson</name>
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<author><name sortKey="Michener, Joshua K" sort="Michener, Joshua K" uniqKey="Michener J" first="Joshua K" last="Michener">Joshua K. Michener</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Hardwood Tree Genomics: Unlocking Woody Plant Biology.</title>
<author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name>
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</affiliation>
<affiliation><nlm:affiliation>Joint Genome Institute, Walnut Creek, CA, United States.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Difazio, Stephen Paul" sort="Difazio, Stephen Paul" uniqKey="Difazio S" first="Stephen Paul" last="Difazio">Stephen Paul Difazio</name>
<affiliation><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, United States.</nlm:affiliation>
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<author><name sortKey="Myburg, Alexander" sort="Myburg, Alexander" uniqKey="Myburg A" first="Alexander" last="Myburg">Alexander Myburg</name>
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</affiliation>
</author>
<author><name sortKey="Grattapaglia, Dario" sort="Grattapaglia, Dario" uniqKey="Grattapaglia D" first="Dario" last="Grattapaglia">Dario Grattapaglia</name>
<affiliation><nlm:affiliation>Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.</nlm:affiliation>
</affiliation>
<affiliation><nlm:affiliation>Universidade Católica de Brasília, Brasília, Brazil.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Smart, Lawrence B" sort="Smart, Lawrence B" uniqKey="Smart L" first="Lawrence B" last="Smart">Lawrence B. Smart</name>
<affiliation><nlm:affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name>
<affiliation><nlm:affiliation>The Key Laboratory for Poplar Improvement of Jiangsu Province, Nanjing Forestry University, Nanjing, China.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Aury, Jean Marc" sort="Aury, Jean Marc" uniqKey="Aury J" first="Jean-Marc" last="Aury">Jean-Marc Aury</name>
<affiliation><nlm:affiliation>Commissariat à l'Energie Atomique, Genoscope, Institut de Biologie François-Jacob, Evry, France.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Kremer, Antoine" sort="Kremer, Antoine" uniqKey="Kremer A" first="Antoine" last="Kremer">Antoine Kremer</name>
<affiliation><nlm:affiliation>BIOGECO, INRA, Université de Bordeaux, Cestas, France.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Leroy, Thibault" sort="Leroy, Thibault" uniqKey="Leroy T" first="Thibault" last="Leroy">Thibault Leroy</name>
<affiliation><nlm:affiliation>BIOGECO, INRA, Université de Bordeaux, Cestas, France.</nlm:affiliation>
</affiliation>
<affiliation><nlm:affiliation>ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Le Provost, Gregoire" sort="Le Provost, Gregoire" uniqKey="Le Provost G" first="Gregoire" last="Le Provost">Gregoire Le Provost</name>
<affiliation><nlm:affiliation>BIOGECO, INRA, Université de Bordeaux, Cestas, France.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Plomion, Christophe" sort="Plomion, Christophe" uniqKey="Plomion C" first="Christophe" last="Plomion">Christophe Plomion</name>
<affiliation><nlm:affiliation>BIOGECO, INRA, Université de Bordeaux, Cestas, France.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Carlson, John E" sort="Carlson, John E" uniqKey="Carlson J" first="John E" last="Carlson">John E. Carlson</name>
<affiliation><nlm:affiliation>Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, United States.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Randall, Jennifer" sort="Randall, Jennifer" uniqKey="Randall J" first="Jennifer" last="Randall">Jennifer Randall</name>
<affiliation><nlm:affiliation>Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Westbrook, Jared" sort="Westbrook, Jared" uniqKey="Westbrook J" first="Jared" last="Westbrook">Jared Westbrook</name>
<affiliation><nlm:affiliation>The American Chestnut Foundation, Asheville, NC, United States.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Grimwood, Jane" sort="Grimwood, Jane" uniqKey="Grimwood J" first="Jane" last="Grimwood">Jane Grimwood</name>
<affiliation><nlm:affiliation>HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name>
<affiliation><nlm:affiliation>Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Jacobson, Daniel" sort="Jacobson, Daniel" uniqKey="Jacobson D" first="Daniel" last="Jacobson">Daniel Jacobson</name>
<affiliation><nlm:affiliation>Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Michener, Joshua K" sort="Michener, Joshua K" uniqKey="Michener J" first="Joshua K" last="Michener">Joshua K. Michener</name>
<affiliation><nlm:affiliation>Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.</nlm:affiliation>
</affiliation>
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<series><title level="j">Frontiers in plant science</title>
<idno type="ISSN">1664-462X</idno>
<imprint><date when="2018" type="published">2018</date>
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<front><div type="abstract" xml:lang="en">Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of <i>Populus</i>
 and <i>Eucalyptus</i>
, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">30619389</PMID>
<DateRevised><Year>2020</Year>
<Month>10</Month>
<Day>01</Day>
</DateRevised>
<Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN>
<JournalIssue CitedMedium="Print"><Volume>9</Volume>
<PubDate><Year>2018</Year>
</PubDate>
</JournalIssue>
<Title>Frontiers in plant science</Title>
<ISOAbbreviation>Front Plant Sci</ISOAbbreviation>
</Journal>
<ArticleTitle>Hardwood Tree Genomics: Unlocking Woody Plant Biology.</ArticleTitle>
<Pagination><MedlinePgn>1799</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2018.01799</ELocationID>
<Abstract><AbstractText>Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of <i>Populus</i>
 and <i>Eucalyptus</i>
, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tuskan</LastName>
<ForeName>Gerald A</ForeName>
<Initials>GA</Initials>
<AffiliationInfo><Affiliation>Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Groover</LastName>
<ForeName>Andrew T</ForeName>
<Initials>AT</Initials>
<AffiliationInfo><Affiliation>Pacific Southwest Research Station, USDA Forest Service, Davis, CA, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Schmutz</LastName>
<ForeName>Jeremy</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Joint Genome Institute, Walnut Creek, CA, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>DiFazio</LastName>
<ForeName>Stephen Paul</ForeName>
<Initials>SP</Initials>
<AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Myburg</LastName>
<ForeName>Alexander</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Grattapaglia</LastName>
<ForeName>Dario</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Universidade Católica de Brasília, Brasília, Brazil.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Smart</LastName>
<ForeName>Lawrence B</ForeName>
<Initials>LB</Initials>
<AffiliationInfo><Affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Yin</LastName>
<ForeName>Tongming</ForeName>
<Initials>T</Initials>
<AffiliationInfo><Affiliation>The Key Laboratory for Poplar Improvement of Jiangsu Province, Nanjing Forestry University, Nanjing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Aury</LastName>
<ForeName>Jean-Marc</ForeName>
<Initials>JM</Initials>
<AffiliationInfo><Affiliation>Commissariat à l'Energie Atomique, Genoscope, Institut de Biologie François-Jacob, Evry, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Kremer</LastName>
<ForeName>Antoine</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>BIOGECO, INRA, Université de Bordeaux, Cestas, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Leroy</LastName>
<ForeName>Thibault</ForeName>
<Initials>T</Initials>
<AffiliationInfo><Affiliation>BIOGECO, INRA, Université de Bordeaux, Cestas, France.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Le Provost</LastName>
<ForeName>Gregoire</ForeName>
<Initials>G</Initials>
<AffiliationInfo><Affiliation>BIOGECO, INRA, Université de Bordeaux, Cestas, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Plomion</LastName>
<ForeName>Christophe</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>BIOGECO, INRA, Université de Bordeaux, Cestas, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Carlson</LastName>
<ForeName>John E</ForeName>
<Initials>JE</Initials>
<AffiliationInfo><Affiliation>Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Randall</LastName>
<ForeName>Jennifer</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Westbrook</LastName>
<ForeName>Jared</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>The American Chestnut Foundation, Asheville, NC, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Grimwood</LastName>
<ForeName>Jane</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Muchero</LastName>
<ForeName>Wellington</ForeName>
<Initials>W</Initials>
<AffiliationInfo><Affiliation>Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Jacobson</LastName>
<ForeName>Daniel</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Michener</LastName>
<ForeName>Joshua K</ForeName>
<Initials>JK</Initials>
<AffiliationInfo><Affiliation>Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.</Affiliation>
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Hardwood Tree Genomics: Unlocking Woody Plant Biology.

Hardwood Tree Genomics: Unlocking Woody Plant Biology.

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