A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance.
Identifieur interne : 000813 ( Main/Exploration ); précédent : 000812; suivant : 000814A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance.
Auteurs : Marco Moroldo [France] ; Sophie Paillard ; Raffaella Marconi ; Legeai Fabrice ; Aurelie Canaguier ; Corinne Cruaud ; Veronique De Berardinis ; Cecile Guichard ; Veronique Brunaud ; Isabelle Le Clainche ; Simone Scalabrin ; Raffaele Testolin ; Gabriele Di Gaspero ; Michele Morgante ; Anne-Francoise Adam-BlondonSource :
- BMC plant biology [ 1471-2229 ] ; 2008.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (MeSH), Cartographie physique de chromosome (méthodes), Chromosomes de plante (génétique), Gènes de plante (génétique), Génome végétal (MeSH), Hétérozygote (MeSH), Immunité innée (génétique), Maladies des plantes (génétique), Réaction de polymérisation en chaîne (MeSH), Transduction du signal (génétique), Vitis (génétique).
- MESH :
English descriptors
- KwdEn :
- Chromosomes, Plant (genetics), Genes, Plant (genetics), Genome, Plant (MeSH), Heterozygote (MeSH), Immunity, Innate (genetics), Physical Chromosome Mapping (methods), Plant Diseases (genetics), Polymerase Chain Reaction (MeSH), Sequence Analysis, DNA (MeSH), Signal Transduction (genetics), Vitis (genetics).
- MESH :
Abstract
BACKGROUND
Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed.
RESULTS
The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome.
CONCLUSION
Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.
DOI: 10.1186/1471-2229-8-66
PubMed: 18554400
PubMed Central: PMC2442077
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (genetics)</term><term>Genes, Plant (genetics)</term><term>Genome, Plant (MeSH)</term><term>Heterozygote (MeSH)</term><term>Immunity, Innate (genetics)</term><term>Physical Chromosome Mapping (methods)</term><term>Plant Diseases (genetics)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Signal Transduction (genetics)</term><term>Vitis (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Cartographie physique de chromosome (méthodes)</term><term>Chromosomes de plante (génétique)</term><term>Gènes de plante (génétique)</term><term>Génome végétal (MeSH)</term><term>Hétérozygote (MeSH)</term><term>Immunité innée (génétique)</term><term>Maladies des plantes (génétique)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Transduction du signal (génétique)</term><term>Vitis (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Plant</term><term>Genes, Plant</term><term>Immunity, Innate</term><term>Plant Diseases</term><term>Signal Transduction</term><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chromosomes de plante</term><term>Gènes de plante</term><term>Immunité innée</term><term>Maladies des plantes</term><term>Transduction du signal</term><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Physical Chromosome Mapping</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Cartographie physique de chromosome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Plant</term><term>Heterozygote</term><term>Polymerase Chain Reaction</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Génome végétal</term><term>Hétérozygote</term><term>Réaction de polymérisation en chaîne</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18554400</PMID><DateCompleted><Year>2008</Year><Month>10</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><PubDate><Year>2008</Year><Month>Jun</Month><Day>13</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance.</ArticleTitle><Pagination><MedlinePgn>66</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-8-66</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Moroldo</LastName><ForeName>Marco</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France. moroldo@evry.inra.fr</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paillard</LastName><ForeName>Sophie</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Marconi</LastName><ForeName>Raffaella</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Fabrice</LastName><ForeName>Legeai</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Canaguier</LastName><ForeName>Aurelie</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Cruaud</LastName><ForeName>Corinne</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>De Berardinis</LastName><ForeName>Veronique</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Guichard</LastName><ForeName>Cecile</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Brunaud</LastName><ForeName>Veronique</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Le Clainche</LastName><ForeName>Isabelle</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Scalabrin</LastName><ForeName>Simone</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Testolin</LastName><ForeName>Raffaele</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Di Gaspero</LastName><ForeName>Gabriele</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Morgante</LastName><ForeName>Michele</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Adam-Blondon</LastName><ForeName>Anne-Francoise</ForeName><Initials>AF</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>06</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant Biol</MedlineTA><NlmUniqueID>100967807</NlmUniqueID><ISSNLinking>1471-2229</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006579" MajorTopicYN="N">Heterozygote</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007113" MajorTopicYN="N">Immunity, Innate</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020161" MajorTopicYN="N">Physical Chromosome Mapping</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015398" MajorTopicYN="N">Signal Transduction</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D027843" MajorTopicYN="N">Vitis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2008</Year><Month>02</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2008</Year><Month>06</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>6</Month><Day>17</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>10</Month><Day>3</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>6</Month><Day>17</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId 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first="Veronique" last="Brunaud">Veronique Brunaud</name><name sortKey="Canaguier, Aurelie" sort="Canaguier, Aurelie" uniqKey="Canaguier A" first="Aurelie" last="Canaguier">Aurelie Canaguier</name><name sortKey="Cruaud, Corinne" sort="Cruaud, Corinne" uniqKey="Cruaud C" first="Corinne" last="Cruaud">Corinne Cruaud</name><name sortKey="De Berardinis, Veronique" sort="De Berardinis, Veronique" uniqKey="De Berardinis V" first="Veronique" last="De Berardinis">Veronique De Berardinis</name><name sortKey="Di Gaspero, Gabriele" sort="Di Gaspero, Gabriele" uniqKey="Di Gaspero G" first="Gabriele" last="Di Gaspero">Gabriele Di Gaspero</name><name sortKey="Fabrice, Legeai" sort="Fabrice, Legeai" uniqKey="Fabrice L" first="Legeai" last="Fabrice">Legeai Fabrice</name><name sortKey="Guichard, Cecile" sort="Guichard, Cecile" uniqKey="Guichard C" first="Cecile" last="Guichard">Cecile Guichard</name><name sortKey="Le Clainche, Isabelle" sort="Le Clainche, Isabelle" uniqKey="Le Clainche I" 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|texte= A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance.
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