Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.
Identifieur interne : 001230 ( Main/Exploration ); précédent : 001229; suivant : 001231Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.
Auteurs : Florian Jupe [Royaume-Uni] ; Kamil Witek ; Walter Verweij ; Jadwiga Sliwka ; Leighton Pritchard ; Graham J. Etherington ; Dan Maclean ; Peter J. Cock ; Richard M. Leggett ; Glenn J. Bryan ; Linda Cardle ; Ingo Hein ; Jonathan D G. JonesSource :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2013.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (méthodes), Annotation de séquence moléculaire (méthodes), Cartographie chromosomique (MeSH), Famille multigénique (MeSH), Gènes de plante (MeSH), Immunité des plantes (génétique), Phytophthora infestans (génétique), Polymorphisme de nucléotide simple (génétique), Produits agricoles (génétique), Solanum tuberosum (MeSH).
- MESH :
English descriptors
- KwdEn :
- Chromosome Mapping (MeSH), Crops, Agricultural (genetics), Genes, Plant (MeSH), Molecular Sequence Annotation (methods), Multigene Family (MeSH), Phytophthora infestans (genetics), Plant Immunity (genetics), Polymorphism, Single Nucleotide (genetics), Sequence Analysis, DNA (methods), Solanum tuberosum (MeSH).
- MESH :
Abstract
RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum 'Heinz 1706' extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.
DOI: 10.1111/tpj.12307
PubMed: 23937694
PubMed Central: PMC3935411
Affiliations:
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Jones</name></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Mapping (MeSH)</term><term>Crops, Agricultural (genetics)</term><term>Genes, Plant (MeSH)</term><term>Molecular Sequence Annotation (methods)</term><term>Multigene Family (MeSH)</term><term>Phytophthora infestans (genetics)</term><term>Plant Immunity (genetics)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Solanum tuberosum (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (méthodes)</term><term>Annotation de séquence moléculaire (méthodes)</term><term>Cartographie chromosomique (MeSH)</term><term>Famille multigénique (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Immunité des plantes (génétique)</term><term>Phytophthora infestans (génétique)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Produits agricoles (génétique)</term><term>Solanum tuberosum (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Crops, Agricultural</term><term>Phytophthora infestans</term><term>Plant Immunity</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Immunité des plantes</term><term>Phytophthora infestans</term><term>Polymorphisme de nucléotide simple</term><term>Produits agricoles</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Molecular Sequence Annotation</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Annotation de séquence moléculaire</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Genes, Plant</term><term>Multigene Family</term><term>Solanum tuberosum</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term><term>Famille multigénique</term><term>Gènes de plante</term><term>Solanum tuberosum</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum 'Heinz 1706' extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23937694</PMID><DateCompleted><Year>2014</Year><Month>05</Month><Day>29</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-313X</ISSN><JournalIssue CitedMedium="Internet"><Volume>76</Volume><Issue>3</Issue><PubDate><Year>2013</Year><Month>Nov</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.</ArticleTitle><Pagination><MedlinePgn>530-44</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/tpj.12307</ELocationID><Abstract><AbstractText>RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum 'Heinz 1706' extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.</AbstractText><CopyrightInformation>© 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jupe</LastName><ForeName>Florian</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, Norwich Research Park, NR4 7UH, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Witek</LastName><ForeName>Kamil</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Verweij</LastName><ForeName>Walter</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Sliwka</LastName><ForeName>Jadwiga</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Pritchard</LastName><ForeName>Leighton</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Etherington</LastName><ForeName>Graham J</ForeName><Initials>GJ</Initials></Author><Author ValidYN="Y"><LastName>Maclean</LastName><ForeName>Dan</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Cock</LastName><ForeName>Peter J</ForeName><Initials>PJ</Initials></Author><Author ValidYN="Y"><LastName>Leggett</LastName><ForeName>Richard M</ForeName><Initials>RM</Initials></Author><Author ValidYN="Y"><LastName>Bryan</LastName><ForeName>Glenn J</ForeName><Initials>GJ</Initials></Author><Author ValidYN="Y"><LastName>Cardle</LastName><ForeName>Linda</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Hein</LastName><ForeName>Ingo</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Jones</LastName><ForeName>Jonathan D G</ForeName><Initials>JD</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>BB/C007522/1</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>BB/G02197X/1</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>BB/H019820/1</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant><Grant><GrantID>SCR/929/11</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>10</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant J</MedlineTA><NlmUniqueID>9207397</NlmUniqueID><ISSNLinking>0960-7412</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018556" MajorTopicYN="N">Crops, Agricultural</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D057865" MajorTopicYN="N">Plant Immunity</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011198" MajorTopicYN="N">Solanum tuberosum</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">NB-LRR</Keyword><Keyword MajorTopicYN="N">Solanaceae</Keyword><Keyword MajorTopicYN="N">Solanum berthaultii</Keyword><Keyword MajorTopicYN="N">Solanum lycopersicum</Keyword><Keyword MajorTopicYN="N">Solanum ruiz-ceballosii</Keyword><Keyword MajorTopicYN="N">Solanum tuberosum Group Phureja clone DM1-3 516 R44</Keyword><Keyword MajorTopicYN="N">next-generation sequencing</Keyword><Keyword MajorTopicYN="N">pathogen resistance</Keyword><Keyword MajorTopicYN="N">target enrichment</Keyword><Keyword MajorTopicYN="N">technical advance</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>05</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2013</Year><Month>08</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>08</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>8</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>8</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Bryan</name><name sortKey="Cardle, Linda" sort="Cardle, Linda" uniqKey="Cardle L" first="Linda" last="Cardle">Linda Cardle</name><name sortKey="Cock, Peter J" sort="Cock, Peter J" uniqKey="Cock P" first="Peter J" last="Cock">Peter J. Cock</name><name sortKey="Etherington, Graham J" sort="Etherington, Graham J" uniqKey="Etherington G" first="Graham J" last="Etherington">Graham J. Etherington</name><name sortKey="Hein, Ingo" sort="Hein, Ingo" uniqKey="Hein I" first="Ingo" last="Hein">Ingo Hein</name><name sortKey="Jones, Jonathan D G" sort="Jones, Jonathan D G" uniqKey="Jones J" first="Jonathan D G" last="Jones">Jonathan D G. Jones</name><name sortKey="Leggett, Richard M" sort="Leggett, Richard M" uniqKey="Leggett R" first="Richard M" last="Leggett">Richard M. Leggett</name><name sortKey="Maclean, Dan" sort="Maclean, Dan" uniqKey="Maclean D" first="Dan" last="Maclean">Dan Maclean</name><name sortKey="Pritchard, Leighton" sort="Pritchard, Leighton" uniqKey="Pritchard L" first="Leighton" last="Pritchard">Leighton Pritchard</name><name sortKey="Sliwka, Jadwiga" sort="Sliwka, Jadwiga" uniqKey="Sliwka J" first="Jadwiga" last="Sliwka">Jadwiga Sliwka</name><name sortKey="Verweij, Walter" sort="Verweij, Walter" uniqKey="Verweij W" first="Walter" last="Verweij">Walter Verweij</name><name sortKey="Witek, Kamil" sort="Witek, Kamil" uniqKey="Witek K" first="Kamil" last="Witek">Kamil Witek</name></noCountry><country name="Royaume-Uni"><noRegion><name sortKey="Jupe, Florian" sort="Jupe, Florian" uniqKey="Jupe F" first="Florian" last="Jupe">Florian Jupe</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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