Genome-Wide Association Study in New York Phytophthora capsici Isolates Reveals Loci Involved in Mating Type and Mefenoxam Sensitivity.
Identifieur interne : 000185 ( Main/Exploration ); précédent : 000184; suivant : 000186Genome-Wide Association Study in New York Phytophthora capsici Isolates Reveals Loci Involved in Mating Type and Mefenoxam Sensitivity.
Auteurs : Gregory Vogel [États-Unis] ; Michael A. Gore [États-Unis] ; Christine D. Smart [États-Unis]Source :
- Phytopathology [ 0031-949X ] ; 2020.
Abstract
Phytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) state and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam sensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam sensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA polymerase I, the hypothesized target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.
DOI: 10.1094/PHYTO-04-20-0112-FI
PubMed: 32539639
Affiliations:
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Gore</name><affiliation wicri:level="2"><nlm:affiliation>Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca</wicri:cityArea></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="2"><nlm:affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva</wicri:cityArea></affiliation></author></analytic><series><title level="j">Phytopathology</title><idno type="ISSN">0031-949X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Phytophthora capsici</i> is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) state and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single nucleotide polymorphism (SNP) genotyped 252 <i>P. capsici</i> isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam sensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of F<sub>ST</sub> between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam sensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA polymerase I, the hypothesized target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of <i>P. capsici</i> and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32539639</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-949X</ISSN><JournalIssue CitedMedium="Print"><PubDate><Year>2020</Year><Month>Oct</Month><Day>14</Day></PubDate></JournalIssue><Title>Phytopathology</Title><ISOAbbreviation>Phytopathology</ISOAbbreviation></Journal><ArticleTitle>Genome-Wide Association Study in New York <i>Phytophthora capsici</i> Isolates Reveals Loci Involved in Mating Type and Mefenoxam Sensitivity.</ArticleTitle><Pagination><MedlinePgn>PHYTO04200112FI</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PHYTO-04-20-0112-FI</ELocationID><Abstract><AbstractText><i>Phytophthora capsici</i> is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) state and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single nucleotide polymorphism (SNP) genotyped 252 <i>P. capsici</i> isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam sensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of F<sub>ST</sub> between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam sensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA polymerase I, the hypothesized target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of <i>P. capsici</i> and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vogel</LastName><ForeName>Gregory</ForeName><Initials>G</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-7935-2727</Identifier><AffiliationInfo><Affiliation>Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gore</LastName><ForeName>Michael A</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853.</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, Geneva, NY 14456.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phytopathology</MedlineTA><NlmUniqueID>9427222</NlmUniqueID><ISSNLinking>0031-949X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">ecology and epidemiology</Keyword><Keyword MajorTopicYN="N">genetics and resistance</Keyword><Keyword MajorTopicYN="N">population biology</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>6</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>6</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32539639</ArticleId><ArticleId IdType="doi">10.1094/PHYTO-04-20-0112-FI</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>État de New York</li></region></list><tree><country name="États-Unis"><region name="État de New York"><name sortKey="Vogel, Gregory" sort="Vogel, Gregory" uniqKey="Vogel G" first="Gregory" last="Vogel">Gregory Vogel</name></region><name sortKey="Gore, Michael A" sort="Gore, Michael A" uniqKey="Gore M" first="Michael A" last="Gore">Michael A. Gore</name><name sortKey="Smart, Christine D" sort="Smart, Christine D" uniqKey="Smart C" first="Christine D" last="Smart">Christine D. Smart</name><name sortKey="Vogel, Gregory" sort="Vogel, Gregory" uniqKey="Vogel G" first="Gregory" last="Vogel">Gregory Vogel</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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