Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data.
Identifieur interne : 000A31 ( Main/Exploration ); précédent : 000A30; suivant : 000A32Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data.
Auteurs : Marie-Claude Gagnon [Canada] ; Nicolas Feau [Canada] ; Angela L. Dale [Canada] ; Braham Dhillon ; Richard C. Hamelin [Canada] ; Clive M. Brasier [Royaume-Uni] ; Niklaus J. Grünwald [États-Unis] ; Stephan C. Brière [Canada] ; Guillaume J. Bilodeau [Canada]Source :
- Plant disease [ 0191-2917 ] ; 2017.
Abstract
Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.
DOI: 10.1094/PDIS-11-16-1586-RE
PubMed: 30678572
Affiliations:
- Canada, Royaume-Uni, États-Unis
- Colombie-Britannique , Oregon, Québec
- Québec (ville), Vancouver
- Université Laval, Université de la Colombie-Britannique
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Dale</name><affiliation wicri:level="4"><nlm:affiliation>Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Dhillon, Braham" sort="Dhillon, Braham" uniqKey="Dhillon B" first="Braham" last="Dhillon">Braham Dhillon</name><affiliation><nlm:affiliation>UBC and Department of Plant Pathology, University of Arkansas, Fayetteville.</nlm:affiliation><wicri:noCountry code="subField">Fayetteville</wicri:noCountry></affiliation></author><author><name sortKey="Hamelin, Richard C" sort="Hamelin, Richard C" uniqKey="Hamelin R" first="Richard C" last="Hamelin">Richard C. Hamelin</name><affiliation wicri:level="4"><nlm:affiliation>UBC and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>UBC and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC</wicri:regionArea><orgName type="university">Université Laval</orgName><placeName><settlement type="city">Québec (ville)</settlement><region type="state">Québec</region></placeName></affiliation></author><author><name sortKey="Brasier, Clive M" sort="Brasier, Clive M" uniqKey="Brasier C" first="Clive M" last="Brasier">Clive M. Brasier</name><affiliation wicri:level="1"><nlm:affiliation>Forest Research (FR), Farnham, SRY, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Forest Research (FR), Farnham, SRY</wicri:regionArea><wicri:noRegion>SRY</wicri:noRegion></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 wicri:level="2"><nlm:affiliation>Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Oregon</region></placeName><wicri:cityArea>Horticultural Crops Research Laboratory, USDA-ARS, Corvallis</wicri:cityArea></affiliation></author><author><name sortKey="Briere, Stephan C" sort="Briere, Stephan C" uniqKey="Briere S" first="Stephan C" last="Brière">Stephan C. Brière</name><affiliation wicri:level="1"><nlm:affiliation>CFIA, Ottawa, ON, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>CFIA, Ottawa, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Bilodeau, Guillaume J" sort="Bilodeau, Guillaume J" uniqKey="Bilodeau G" first="Guillaume J" last="Bilodeau">Guillaume J. Bilodeau</name><affiliation wicri:level="1"><nlm:affiliation>CFIA, Ottawa, ON, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>CFIA, Ottawa, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author></analytic><series><title level="j">Plant disease</title><idno type="ISSN">0191-2917</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">30678572</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>101</Volume><Issue>5</Issue><PubDate><Year>2017</Year><Month>May</Month></PubDate></JournalIssue><Title>Plant disease</Title><ISOAbbreviation>Plant Dis</ISOAbbreviation></Journal><ArticleTitle>Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data.</ArticleTitle><Pagination><MedlinePgn>666-673</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PDIS-11-16-1586-RE</ELocationID><Abstract><AbstractText>Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gagnon</LastName><ForeName>Marie-Claude</ForeName><Initials>MC</Initials><AffiliationInfo><Affiliation>Canadian Food Inspection Agency (CFIA), Ottawa, ON, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feau</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dale</LastName><ForeName>Angela L</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dhillon</LastName><ForeName>Braham</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>UBC and Department of Plant Pathology, University of Arkansas, Fayetteville.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hamelin</LastName><ForeName>Richard C</ForeName><Initials>RC</Initials><AffiliationInfo><Affiliation>UBC and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brasier</LastName><ForeName>Clive M</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Forest Research (FR), Farnham, SRY, United Kingdom.</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>Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brière</LastName><ForeName>Stephan C</ForeName><Initials>SC</Initials><AffiliationInfo><Affiliation>CFIA, Ottawa, ON, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bilodeau</LastName><ForeName>Guillaume J</ForeName><Initials>GJ</Initials><AffiliationInfo><Affiliation>CFIA, Ottawa, ON, Canada.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>03</Month><Day>16</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>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>5</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>5</Month><Day>1</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30678572</ArticleId><ArticleId IdType="doi">10.1094/PDIS-11-16-1586-RE</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Colombie-Britannique </li><li>Oregon</li><li>Québec</li></region><settlement><li>Québec (ville)</li><li>Vancouver</li></settlement><orgName><li>Université Laval</li><li>Université de la Colombie-Britannique</li></orgName></list><tree><noCountry><name sortKey="Dhillon, Braham" sort="Dhillon, Braham" uniqKey="Dhillon B" first="Braham" last="Dhillon">Braham Dhillon</name></noCountry><country name="Canada"><noRegion><name sortKey="Gagnon, Marie Claude" sort="Gagnon, Marie Claude" uniqKey="Gagnon M" first="Marie-Claude" last="Gagnon">Marie-Claude Gagnon</name></noRegion><name sortKey="Bilodeau, Guillaume J" sort="Bilodeau, Guillaume J" uniqKey="Bilodeau G" first="Guillaume J" last="Bilodeau">Guillaume J. Bilodeau</name><name sortKey="Briere, Stephan C" sort="Briere, Stephan C" uniqKey="Briere S" first="Stephan C" last="Brière">Stephan C. Brière</name><name sortKey="Dale, Angela L" sort="Dale, Angela L" uniqKey="Dale A" first="Angela L" last="Dale">Angela L. Dale</name><name sortKey="Feau, Nicolas" sort="Feau, Nicolas" uniqKey="Feau N" first="Nicolas" last="Feau">Nicolas Feau</name><name sortKey="Hamelin, Richard C" sort="Hamelin, Richard C" uniqKey="Hamelin R" first="Richard C" last="Hamelin">Richard C. Hamelin</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Brasier, Clive M" sort="Brasier, Clive M" uniqKey="Brasier C" first="Clive M" last="Brasier">Clive M. Brasier</name></noRegion></country><country name="États-Unis"><region name="Oregon"><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. 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