Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study.
Identifieur interne : 002778 ( Main/Exploration ); précédent : 002777; suivant : 002779Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study.
Auteurs : Bartel Vanholme [Belgique] ; Igor Cesarino ; Geert Goeminne ; Hoon Kim ; Fabio Marroni ; Rebecca Van Acker ; Ruben Vanholme ; Kris Morreel ; Bart Ivens ; Sara Pinosio ; Michele Morgante ; John Ralph ; Catherine Bastien ; Wout BoerjanSource :
- The New phytologist [ 1469-8137 ] ; 2013.
Descripteurs français
- KwdFr :
- Acide shikimique (analogues et dérivés), Acide shikimique (métabolisme), Acyltransferases (génétique), Allèles (MeSH), Analyse de séquence d'ADN (méthodes), Données de séquences moléculaires (MeSH), Homozygote (MeSH), Lignine (composition chimique), Lignine (génétique), Lignine (métabolisme), Mutation (MeSH), Paroi cellulaire (composition chimique), Paroi cellulaire (génétique), Populus (composition chimique), Populus (génétique), Spectroscopie par résonance magnétique (MeSH), Sélection (méthodes).
- MESH :
- analogues et dérivés : Acide shikimique.
- composition chimique : Lignine, Paroi cellulaire, Populus.
- génétique : Acyltransferases, Lignine, Paroi cellulaire, Populus.
- métabolisme : Acide shikimique, Lignine.
- méthodes : Analyse de séquence d'ADN, Sélection.
- Allèles, Données de séquences moléculaires, Homozygote, Mutation, Spectroscopie par résonance magnétique.
English descriptors
- KwdEn :
- Acyltransferases (genetics), Alleles (MeSH), Breeding (methods), Cell Wall (chemistry), Cell Wall (genetics), Homozygote (MeSH), Lignin (chemistry), Lignin (genetics), Lignin (metabolism), Magnetic Resonance Spectroscopy (MeSH), Molecular Sequence Data (MeSH), Mutation (MeSH), Populus (chemistry), Populus (genetics), Sequence Analysis, DNA (methods), Shikimic Acid (analogs & derivatives), Shikimic Acid (metabolism).
- MESH :
- chemical , analogs & derivatives : Shikimic Acid.
- chemical , chemistry : Lignin.
- chemical , genetics : Acyltransferases, Lignin.
- chemistry : Cell Wall, Populus.
- genetics : Cell Wall, Populus.
- chemical , metabolism : Lignin, Shikimic Acid.
- methods : Breeding, Sequence Analysis, DNA.
- Alleles, Homozygote, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Mutation.
Abstract
Next-generation (NG) sequencing in a natural population of Populus nigra revealed a mutant with a premature stop codon in the gene encoding hydroxycinnamoyl-CoA : shikimate hydroxycinnamoyl transferase1 (HCT1), an essential enzyme in lignin biosynthesis. The lignin composition of P. nigra trees homozygous for the defective allele was compared with that of heterozygous trees and trees without the defective allele. The lignin was characterized by phenolic profiling, lignin oligomer sequencing, thioacidolysis and NMR. In addition, HCT1 was heterologously expressed for activity assays and crosses were made to introduce the mutation in different genetic backgrounds. HCT1 converts p-coumaroyl-CoA into p-coumaroyl shikimate. The mutant allele, PnHCT1-Δ73, encodes a truncated protein, and trees homozygous for this recessive allele have a modified lignin composition characterized by a 17-fold increase in p-hydroxyphenyl units. Using the lignin pathway as proof of concept, we illustrated that the capture of rare defective alleles is a straightforward approach to initiate reverse genetics and accelerate tree breeding. The proposed breeding strategy, called 'breeding with rare defective alleles' (BRDA), should be widely applicable, independent of the target gene or the species.
DOI: 10.1111/nph.12179
PubMed: 23432219
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Igor" uniqKey="Cesarino I" first="Igor" last="Cesarino">Igor Cesarino</name></author><author><name sortKey="Goeminne, Geert" sort="Goeminne, Geert" uniqKey="Goeminne G" first="Geert" last="Goeminne">Geert Goeminne</name></author><author><name sortKey="Kim, Hoon" sort="Kim, Hoon" uniqKey="Kim H" first="Hoon" last="Kim">Hoon Kim</name></author><author><name sortKey="Marroni, Fabio" sort="Marroni, Fabio" uniqKey="Marroni F" first="Fabio" last="Marroni">Fabio Marroni</name></author><author><name sortKey="Van Acker, Rebecca" sort="Van Acker, Rebecca" uniqKey="Van Acker R" first="Rebecca" last="Van Acker">Rebecca Van Acker</name></author><author><name sortKey="Vanholme, Ruben" sort="Vanholme, Ruben" uniqKey="Vanholme R" first="Ruben" last="Vanholme">Ruben Vanholme</name></author><author><name sortKey="Morreel, Kris" sort="Morreel, Kris" uniqKey="Morreel K" first="Kris" last="Morreel">Kris Morreel</name></author><author><name sortKey="Ivens, Bart" sort="Ivens, Bart" uniqKey="Ivens B" first="Bart" last="Ivens">Bart Ivens</name></author><author><name sortKey="Pinosio, Sara" sort="Pinosio, Sara" uniqKey="Pinosio S" first="Sara" last="Pinosio">Sara Pinosio</name></author><author><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name></author><author><name sortKey="Ralph, John" sort="Ralph, John" uniqKey="Ralph J" first="John" last="Ralph">John Ralph</name></author><author><name sortKey="Bastien, Catherine" sort="Bastien, Catherine" uniqKey="Bastien C" first="Catherine" last="Bastien">Catherine Bastien</name></author><author><name sortKey="Boerjan, Wout" sort="Boerjan, Wout" uniqKey="Boerjan W" first="Wout" last="Boerjan">Wout Boerjan</name></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Acyltransferases (genetics)</term><term>Alleles (MeSH)</term><term>Breeding (methods)</term><term>Cell Wall (chemistry)</term><term>Cell Wall (genetics)</term><term>Homozygote (MeSH)</term><term>Lignin (chemistry)</term><term>Lignin (genetics)</term><term>Lignin (metabolism)</term><term>Magnetic Resonance Spectroscopy (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Mutation (MeSH)</term><term>Populus (chemistry)</term><term>Populus (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Shikimic Acid (analogs & derivatives)</term><term>Shikimic Acid (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Acide shikimique (analogues et dérivés)</term><term>Acide shikimique (métabolisme)</term><term>Acyltransferases (génétique)</term><term>Allèles (MeSH)</term><term>Analyse de séquence d'ADN (méthodes)</term><term>Données de séquences moléculaires (MeSH)</term><term>Homozygote (MeSH)</term><term>Lignine (composition chimique)</term><term>Lignine (génétique)</term><term>Lignine (métabolisme)</term><term>Mutation (MeSH)</term><term>Paroi cellulaire (composition chimique)</term><term>Paroi cellulaire (génétique)</term><term>Populus (composition chimique)</term><term>Populus (génétique)</term><term>Spectroscopie par résonance magnétique (MeSH)</term><term>Sélection (méthodes)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analogs & derivatives" xml:lang="en"><term>Shikimic Acid</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Lignin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Acyltransferases</term><term>Lignin</term></keywords><keywords scheme="MESH" qualifier="analogues et dérivés" xml:lang="fr"><term>Acide shikimique</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Cell Wall</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Lignine</term><term>Paroi cellulaire</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Wall</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Acyltransferases</term><term>Lignine</term><term>Paroi cellulaire</term><term>Populus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Lignin</term><term>Shikimic Acid</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Breeding</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Acide shikimique</term><term>Lignine</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Sélection</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Homozygote</term><term>Magnetic Resonance Spectroscopy</term><term>Molecular Sequence Data</term><term>Mutation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Données de séquences moléculaires</term><term>Homozygote</term><term>Mutation</term><term>Spectroscopie par résonance magnétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Next-generation (NG) sequencing in a natural population of Populus nigra revealed a mutant with a premature stop codon in the gene encoding hydroxycinnamoyl-CoA : shikimate hydroxycinnamoyl transferase1 (HCT1), an essential enzyme in lignin biosynthesis. The lignin composition of P. nigra trees homozygous for the defective allele was compared with that of heterozygous trees and trees without the defective allele. The lignin was characterized by phenolic profiling, lignin oligomer sequencing, thioacidolysis and NMR. In addition, HCT1 was heterologously expressed for activity assays and crosses were made to introduce the mutation in different genetic backgrounds. HCT1 converts p-coumaroyl-CoA into p-coumaroyl shikimate. The mutant allele, PnHCT1-Δ73, encodes a truncated protein, and trees homozygous for this recessive allele have a modified lignin composition characterized by a 17-fold increase in p-hydroxyphenyl units. Using the lignin pathway as proof of concept, we illustrated that the capture of rare defective alleles is a straightforward approach to initiate reverse genetics and accelerate tree breeding. The proposed breeding strategy, called 'breeding with rare defective alleles' (BRDA), should be widely applicable, independent of the target gene or the species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23432219</PMID><DateCompleted><Year>2013</Year><Month>11</Month><Day>25</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>198</Volume><Issue>3</Issue><PubDate><Year>2013</Year><Month>May</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study.</ArticleTitle><Pagination><MedlinePgn>765-76</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.12179</ELocationID><Abstract><AbstractText>Next-generation (NG) sequencing in a natural population of Populus nigra revealed a mutant with a premature stop codon in the gene encoding hydroxycinnamoyl-CoA : shikimate hydroxycinnamoyl transferase1 (HCT1), an essential enzyme in lignin biosynthesis. The lignin composition of P. nigra trees homozygous for the defective allele was compared with that of heterozygous trees and trees without the defective allele. The lignin was characterized by phenolic profiling, lignin oligomer sequencing, thioacidolysis and NMR. In addition, HCT1 was heterologously expressed for activity assays and crosses were made to introduce the mutation in different genetic backgrounds. HCT1 converts p-coumaroyl-CoA into p-coumaroyl shikimate. The mutant allele, PnHCT1-Δ73, encodes a truncated protein, and trees homozygous for this recessive allele have a modified lignin composition characterized by a 17-fold increase in p-hydroxyphenyl units. Using the lignin pathway as proof of concept, we illustrated that the capture of rare defective alleles is a straightforward approach to initiate reverse genetics and accelerate tree breeding. The proposed breeding strategy, called 'breeding with rare defective alleles' (BRDA), should be widely applicable, independent of the target gene or the species.</AbstractText><CopyrightInformation>© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vanholme</LastName><ForeName>Bartel</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052, Gent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cesarino</LastName><ForeName>Igor</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Goeminne</LastName><ForeName>Geert</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Hoon</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Marroni</LastName><ForeName>Fabio</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Van Acker</LastName><ForeName>Rebecca</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Vanholme</LastName><ForeName>Ruben</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Morreel</LastName><ForeName>Kris</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Ivens</LastName><ForeName>Bart</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Pinosio</LastName><ForeName>Sara</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Morgante</LastName><ForeName>Michele</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Ralph</LastName><ForeName>John</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Bastien</LastName><ForeName>Catherine</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Boerjan</LastName><ForeName>Wout</ForeName><Initials>W</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>JF693234</AccessionNumber></AccessionNumberList></DataBank></DataBankList><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>2013</Year><Month>02</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C548291">4-coumaroylshikimic acid</NameOfSubstance></Chemical><Chemical><RegistryNumber>29MS2WI2NU</RegistryNumber><NameOfSubstance UI="D012765">Shikimic Acid</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.3.-</RegistryNumber><NameOfSubstance UI="D000217">Acyltransferases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>New Phytol. 2013 May;198(3):635-7</RefSource><PMID Version="1">23577594</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000217" MajorTopicYN="N">Acyltransferases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000483" MajorTopicYN="N">Alleles</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001947" MajorTopicYN="N">Breeding</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006720" MajorTopicYN="N">Homozygote</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009682" MajorTopicYN="N">Magnetic Resonance Spectroscopy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="Y">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012765" MajorTopicYN="N">Shikimic Acid</DescriptorName><QualifierName UI="Q000031" MajorTopicYN="N">analogs & derivatives</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>11</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>01</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>2</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>2</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>12</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23432219</ArticleId><ArticleId IdType="doi">10.1111/nph.12179</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Belgique</li></country></list><tree><noCountry><name sortKey="Bastien, Catherine" sort="Bastien, Catherine" uniqKey="Bastien C" first="Catherine" last="Bastien">Catherine Bastien</name><name sortKey="Boerjan, Wout" sort="Boerjan, Wout" uniqKey="Boerjan W" first="Wout" last="Boerjan">Wout Boerjan</name><name sortKey="Cesarino, Igor" sort="Cesarino, Igor" uniqKey="Cesarino I" first="Igor" last="Cesarino">Igor Cesarino</name><name sortKey="Goeminne, Geert" sort="Goeminne, Geert" uniqKey="Goeminne G" first="Geert" last="Goeminne">Geert Goeminne</name><name sortKey="Ivens, Bart" sort="Ivens, Bart" uniqKey="Ivens B" first="Bart" last="Ivens">Bart Ivens</name><name sortKey="Kim, Hoon" sort="Kim, Hoon" uniqKey="Kim H" first="Hoon" last="Kim">Hoon Kim</name><name sortKey="Marroni, Fabio" sort="Marroni, Fabio" uniqKey="Marroni F" first="Fabio" last="Marroni">Fabio Marroni</name><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name><name sortKey="Morreel, Kris" sort="Morreel, Kris" uniqKey="Morreel K" first="Kris" last="Morreel">Kris Morreel</name><name sortKey="Pinosio, Sara" sort="Pinosio, Sara" uniqKey="Pinosio S" first="Sara" last="Pinosio">Sara Pinosio</name><name sortKey="Ralph, John" sort="Ralph, John" uniqKey="Ralph J" first="John" last="Ralph">John Ralph</name><name sortKey="Van Acker, Rebecca" sort="Van Acker, Rebecca" uniqKey="Van Acker R" first="Rebecca" last="Van Acker">Rebecca Van Acker</name><name sortKey="Vanholme, Ruben" sort="Vanholme, Ruben" uniqKey="Vanholme R" first="Ruben" last="Vanholme">Ruben Vanholme</name></noCountry><country name="Belgique"><noRegion><name sortKey="Vanholme, Bartel" sort="Vanholme, Bartel" uniqKey="Vanholme B" first="Bartel" last="Vanholme">Bartel Vanholme</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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