PCR amplification of SNP loci from crude DNA for large-scale genotyping of oomycetes.
Identifieur interne : 000F51 ( Main/Exploration ); précédent : 000F50; suivant : 000F52PCR amplification of SNP loci from crude DNA for large-scale genotyping of oomycetes.
Auteurs : Jian Hu [États-Unis] ; Rebecca Lyon [États-Unis] ; Yuxin Zhou [États-Unis] ; Kurt Lamour [États-Unis]Source :
- Mycologia [ 0027-5514 ]
Descripteurs français
- KwdFr :
- MESH :
- génétique : ADN, Oomycetes.
- isolement et purification : Oomycetes.
- microbiologie : Maladies des plantes.
- Génotype, Polymorphisme de nucléotide simple, Réaction de polymérisation en chaîne.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA.
- genetics : Oomycetes.
- isolation & purification : Oomycetes.
- microbiology : Plant Diseases.
- Genotype, Polymerase Chain Reaction, Polymorphism, Single Nucleotide.
Abstract
Similar to other eukaryotes, single nucleotide polymorphism (SNP) markers are abundant in many oomycete plant pathogen genomes. High resolution DNA melting analysis (HR-DMA) is a cost-effective method for SNP genotyping, but like many SNP marker technologies, is limited by the amount and quality of template DNA. We describe PCR preamplification of Phytophthora and Peronospora SNP loci from crude DNA extracted from a small amount of mycelium and/or infected plant tissue to produce sufficient template to genotype at least 10 000 SNPs. The approach is fast, inexpensive, requires minimal biological material and should be useful for many organisms in a variety of contexts.
DOI: 10.3852/13-218
PubMed: 24871597
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville</wicri:cityArea></affiliation></author><author><name sortKey="Zhou, Yuxin" sort="Zhou, Yuxin" uniqKey="Zhou Y" first="Yuxin" last="Zhou">Yuxin Zhou</name><affiliation wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville</wicri:cityArea></affiliation></author><author><name sortKey="Lamour, Kurt" sort="Lamour, Kurt" uniqKey="Lamour K" first="Kurt" last="Lamour">Kurt Lamour</name><affiliation wicri:level="1"><nlm:affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996 klamour@utk.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville</wicri:regionArea><wicri:noRegion>Knoxville</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014 May-Jun</date><idno type="RBID">pubmed:24871597</idno><idno type="pmid">24871597</idno><idno type="doi">10.3852/13-218</idno><idno type="wicri:Area/Main/Corpus">001056</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001056</idno><idno type="wicri:Area/Main/Curation">001056</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">001056</idno><idno 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Lyon</name><affiliation wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville</wicri:cityArea></affiliation></author><author><name sortKey="Zhou, Yuxin" sort="Zhou, Yuxin" uniqKey="Zhou Y" first="Yuxin" last="Zhou">Yuxin Zhou</name><affiliation wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville</wicri:cityArea></affiliation></author><author><name sortKey="Lamour, Kurt" sort="Lamour, Kurt" uniqKey="Lamour K" first="Kurt" last="Lamour">Kurt Lamour</name><affiliation wicri:level="1"><nlm:affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996 klamour@utk.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville</wicri:regionArea><wicri:noRegion>Knoxville</wicri:noRegion></affiliation></author></analytic><series><title level="j">Mycologia</title><idno type="ISSN">0027-5514</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA (genetics)</term><term>Genotype (MeSH)</term><term>Oomycetes (genetics)</term><term>Oomycetes (isolation & purification)</term><term>Plant Diseases (microbiology)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (génétique)</term><term>Génotype (MeSH)</term><term>Maladies des plantes (microbiologie)</term><term>Oomycetes (génétique)</term><term>Oomycetes (isolement et purification)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Réaction de polymérisation en chaîne (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Oomycetes</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>Oomycetes</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Oomycetes</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Oomycetes</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genotype</term><term>Polymerase Chain Reaction</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génotype</term><term>Polymorphisme de nucléotide simple</term><term>Réaction de polymérisation en chaîne</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Similar to other eukaryotes, single nucleotide polymorphism (SNP) markers are abundant in many oomycete plant pathogen genomes. High resolution DNA melting analysis (HR-DMA) is a cost-effective method for SNP genotyping, but like many SNP marker technologies, is limited by the amount and quality of template DNA. We describe PCR preamplification of Phytophthora and Peronospora SNP loci from crude DNA extracted from a small amount of mycelium and/or infected plant tissue to produce sufficient template to genotype at least 10 000 SNPs. The approach is fast, inexpensive, requires minimal biological material and should be useful for many organisms in a variety of contexts. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24871597</PMID><DateCompleted><Year>2014</Year><Month>09</Month><Day>04</Day></DateCompleted><DateRevised><Year>2014</Year><Month>06</Month><Day>06</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0027-5514</ISSN><JournalIssue CitedMedium="Print"><Volume>106</Volume><Issue>3</Issue><PubDate><MedlineDate>2014 May-Jun</MedlineDate></PubDate></JournalIssue><Title>Mycologia</Title><ISOAbbreviation>Mycologia</ISOAbbreviation></Journal><ArticleTitle>PCR amplification of SNP loci from crude DNA for large-scale genotyping of oomycetes.</ArticleTitle><Pagination><MedlinePgn>607-9</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3852/13-218</ELocationID><Abstract><AbstractText>Similar to other eukaryotes, single nucleotide polymorphism (SNP) markers are abundant in many oomycete plant pathogen genomes. High resolution DNA melting analysis (HR-DMA) is a cost-effective method for SNP genotyping, but like many SNP marker technologies, is limited by the amount and quality of template DNA. We describe PCR preamplification of Phytophthora and Peronospora SNP loci from crude DNA extracted from a small amount of mycelium and/or infected plant tissue to produce sufficient template to genotype at least 10 000 SNPs. The approach is fast, inexpensive, requires minimal biological material and should be useful for many organisms in a variety of contexts. </AbstractText><CopyrightInformation>© 2014 by The Mycological Society of America.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Jian</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, China Agricultural University, Beijing, and Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lyon</LastName><ForeName>Rebecca</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Yuxin</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lamour</LastName><ForeName>Kurt</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee 37996 klamour@utk.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>05</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mycologia</MedlineTA><NlmUniqueID>0400764</NlmUniqueID><ISSNLinking>0027-5514</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009868" MajorTopicYN="N">Oomycetes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Peronospora</Keyword><Keyword MajorTopicYN="N">Phytophthora</Keyword><Keyword MajorTopicYN="N">SNP genotyping</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>5</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>5</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>9</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24871597</ArticleId><ArticleId IdType="pii">13-218</ArticleId><ArticleId IdType="doi">10.3852/13-218</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Tennessee</li></region></list><tree><country name="États-Unis"><region name="Tennessee"><name sortKey="Hu, Jian" sort="Hu, Jian" uniqKey="Hu J" first="Jian" last="Hu">Jian Hu</name></region><name sortKey="Lamour, Kurt" sort="Lamour, Kurt" uniqKey="Lamour K" first="Kurt" last="Lamour">Kurt Lamour</name><name sortKey="Lyon, Rebecca" sort="Lyon, Rebecca" uniqKey="Lyon R" first="Rebecca" last="Lyon">Rebecca Lyon</name><name sortKey="Zhou, Yuxin" sort="Zhou, Yuxin" uniqKey="Zhou Y" first="Yuxin" last="Zhou">Yuxin Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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