SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis.
Identifieur interne : 000B36 ( Main/Exploration ); précédent : 000B35; suivant : 000B37SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis.
Auteurs : Zachariah R. Hansen [États-Unis] ; Brian J. Knaus ; Javier F. Tabima ; Caroline M. Press ; Howard S. Judelson ; Niklaus J. Grünwald ; Christine D. Smart [États-Unis]Source :
- Plant disease [ 0191-2917 ] ; 2016.
Abstract
Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic differences can exist between lineages. Whole P. infestans genomes were aligned and single nucleotide polymorphisms (SNPs) identified as targets for the development of clonal-lineage-specific molecular diagnostic tools. Informative SNPs were used to develop high-resolution melt (HRM) assays and locked nucleic acid (LNA) probes to differentiate lineage US-23, the predominant lineage in the Eastern United States for the past several years, from three other U.S. lineages. Three different primer pairs targeting one to three SNPs were capable of separating lineage US-23 from lineages US-8, US-11, and US-24 using HRM analysis. A fourth HRM primer pair targeted a highly variable genomic region containing nine polymorphisms within 63 bp. These primers separated US-23, US-11, and US-8 plus US-24 into three separate groups following HRM analysis but did not separate US-8 from US-24. Additionally, two LNA probes were designed to target a portion of the P. infestans genome containing two SNPs diagnostic for US-23. A single multiplex quantitative polymerase chain reaction assay containing both differentially labeled LNA probes differentiated individuals belonging to lineage US-23 from those belonging to US-8, US-11, and US-24.
DOI: 10.1094/PDIS-11-15-1247-RE
PubMed: 30686206
Affiliations:
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Hansen</name><affiliation wicri:level="4"><nlm:affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, NYSAES, Geneva, NY, 14456.</nlm:affiliation><orgName type="university">Université Cornell</orgName><country>États-Unis</country><placeName><settlement type="city">Ithaca (New York)</settlement><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Knaus, Brian J" sort="Knaus, Brian J" uniqKey="Knaus B" first="Brian J" last="Knaus">Brian J. Knaus</name><affiliation><nlm:affiliation>Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, (USDA-ARS) Corvallis, OR, 97331.</nlm:affiliation><wicri:noCountry code="subField">97331</wicri:noCountry></affiliation></author><author><name sortKey="Tabima, Javier F" sort="Tabima, Javier F" uniqKey="Tabima J" first="Javier F" last="Tabima">Javier F. Tabima</name><affiliation><nlm:affiliation>Botany and Plant Pathology, Oregon State University, Corvallis, 97331.</nlm:affiliation><wicri:noCountry code="subField">97331</wicri:noCountry></affiliation></author><author><name sortKey="Press, Caroline M" sort="Press, Caroline M" uniqKey="Press C" first="Caroline M" last="Press">Caroline M. Press</name><affiliation><nlm:affiliation>Horticultural Crops Research Laboratory, USDA-ARS.</nlm:affiliation><wicri:noCountry code="subField">USDA-ARS</wicri:noCountry></affiliation></author><author><name sortKey="Judelson, Howard S" sort="Judelson, Howard S" uniqKey="Judelson H" first="Howard S" last="Judelson">Howard S. Judelson</name><affiliation><nlm:affiliation>Department of Plant Pathology and Microbiology, University of California, Riverside, 92521.</nlm:affiliation><wicri:noCountry code="subField">92521</wicri:noCountry></affiliation></author><author><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. Grünwald</name><affiliation><nlm:affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University; Horticultural Crops Research Laboratory, USDA-ARS; and Botany and Plant Pathology, Oregon State University.</nlm:affiliation><wicri:noCountry code="subField">Oregon State University</wicri:noCountry></affiliation></author><author><name sortKey="Smart, Christine D" sort="Smart, Christine D" uniqKey="Smart C" first="Christine D" last="Smart">Christine D. Smart</name><affiliation wicri:level="4"><nlm:affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University.</nlm:affiliation><country>États-Unis</country><placeName><settlement type="city">Ithaca (New York)</settlement><region type="state">État de New York</region></placeName><orgName type="university">Université Cornell</orgName></affiliation></author></analytic><series><title level="j">Plant disease</title><idno type="ISSN">0191-2917</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic differences can exist between lineages. Whole P. infestans genomes were aligned and single nucleotide polymorphisms (SNPs) identified as targets for the development of clonal-lineage-specific molecular diagnostic tools. Informative SNPs were used to develop high-resolution melt (HRM) assays and locked nucleic acid (LNA) probes to differentiate lineage US-23, the predominant lineage in the Eastern United States for the past several years, from three other U.S. lineages. Three different primer pairs targeting one to three SNPs were capable of separating lineage US-23 from lineages US-8, US-11, and US-24 using HRM analysis. A fourth HRM primer pair targeted a highly variable genomic region containing nine polymorphisms within 63 bp. These primers separated US-23, US-11, and US-8 plus US-24 into three separate groups following HRM analysis but did not separate US-8 from US-24. Additionally, two LNA probes were designed to target a portion of the P. infestans genome containing two SNPs diagnostic for US-23. A single multiplex quantitative polymerase chain reaction assay containing both differentially labeled LNA probes differentiated individuals belonging to lineage US-23 from those belonging to US-8, US-11, and US-24.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">30686206</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0191-2917</ISSN><JournalIssue CitedMedium="Print"><Volume>100</Volume><Issue>7</Issue><PubDate><Year>2016</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Plant disease</Title><ISOAbbreviation>Plant Dis</ISOAbbreviation></Journal><ArticleTitle>SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis.</ArticleTitle><Pagination><MedlinePgn>1297-1306</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PDIS-11-15-1247-RE</ELocationID><Abstract><AbstractText>Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic differences can exist between lineages. Whole P. infestans genomes were aligned and single nucleotide polymorphisms (SNPs) identified as targets for the development of clonal-lineage-specific molecular diagnostic tools. Informative SNPs were used to develop high-resolution melt (HRM) assays and locked nucleic acid (LNA) probes to differentiate lineage US-23, the predominant lineage in the Eastern United States for the past several years, from three other U.S. lineages. Three different primer pairs targeting one to three SNPs were capable of separating lineage US-23 from lineages US-8, US-11, and US-24 using HRM analysis. A fourth HRM primer pair targeted a highly variable genomic region containing nine polymorphisms within 63 bp. These primers separated US-23, US-11, and US-8 plus US-24 into three separate groups following HRM analysis but did not separate US-8 from US-24. Additionally, two LNA probes were designed to target a portion of the P. infestans genome containing two SNPs diagnostic for US-23. A single multiplex quantitative polymerase chain reaction assay containing both differentially labeled LNA probes differentiated individuals belonging to lineage US-23 from those belonging to US-8, US-11, and US-24.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hansen</LastName><ForeName>Zachariah R</ForeName><Initials>ZR</Initials><AffiliationInfo><Affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, NYSAES, Geneva, NY, 14456.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Knaus</LastName><ForeName>Brian J</ForeName><Initials>BJ</Initials><AffiliationInfo><Affiliation>Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service, (USDA-ARS) Corvallis, OR, 97331.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tabima</LastName><ForeName>Javier F</ForeName><Initials>JF</Initials><AffiliationInfo><Affiliation>Botany and Plant Pathology, Oregon State University, Corvallis, 97331.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Press</LastName><ForeName>Caroline M</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Horticultural Crops Research Laboratory, USDA-ARS.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Judelson</LastName><ForeName>Howard S</ForeName><Initials>HS</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology and Microbiology, University of California, Riverside, 92521.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grünwald</LastName><ForeName>Niklaus J</ForeName><Initials>NJ</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-1656-7602</Identifier><AffiliationInfo><Affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University; Horticultural Crops Research Laboratory, USDA-ARS; and Botany and Plant Pathology, Oregon State University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smart</LastName><ForeName>Christine D</ForeName><Initials>CD</Initials><AffiliationInfo><Affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>03</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Dis</MedlineTA><NlmUniqueID>9882809</NlmUniqueID><ISSNLinking>0191-2917</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>1</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>7</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>7</Month><Day>1</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30686206</ArticleId><ArticleId IdType="doi">10.1094/PDIS-11-15-1247-RE</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>État de New York</li></region><settlement><li>Ithaca (New York)</li></settlement><orgName><li>Université Cornell</li></orgName></list><tree><noCountry><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. Grünwald</name><name sortKey="Judelson, Howard S" sort="Judelson, Howard S" uniqKey="Judelson H" first="Howard S" last="Judelson">Howard S. Judelson</name><name sortKey="Knaus, Brian J" sort="Knaus, Brian J" uniqKey="Knaus B" first="Brian J" last="Knaus">Brian J. Knaus</name><name sortKey="Press, Caroline M" sort="Press, Caroline M" uniqKey="Press C" first="Caroline M" last="Press">Caroline M. Press</name><name sortKey="Tabima, Javier F" sort="Tabima, Javier F" uniqKey="Tabima J" first="Javier F" last="Tabima">Javier F. Tabima</name></noCountry><country name="États-Unis"><region name="État de New York"><name sortKey="Hansen, Zachariah R" sort="Hansen, Zachariah R" uniqKey="Hansen Z" first="Zachariah R" last="Hansen">Zachariah R. Hansen</name></region><name sortKey="Smart, Christine D" sort="Smart, Christine D" uniqKey="Smart C" first="Christine D" last="Smart">Christine D. Smart</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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