Contact Reflectance Spectroscopy for Rapid, Accurate, and Nondestructive Phytophthora infestans Clonal Lineage Discrimination.
Identifieur interne : 000262 ( Main/Exploration ); précédent : 000261; suivant : 000263Contact Reflectance Spectroscopy for Rapid, Accurate, and Nondestructive Phytophthora infestans Clonal Lineage Discrimination.
Auteurs : Kaitlin M. Gold [États-Unis] ; Philip A. Townsend [États-Unis] ; Eric R. Larson [États-Unis] ; Ittai Herrmann [Israël] ; Amanda J. Gevens [États-Unis]Source :
- Phytopathology [ 0031-949X ] ; 2020.
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Abstract
Populations of Phytophthora infestans, the oomycete causal agent of potato late blight in the United States, are predominantly asexual, and isolates are characterized by clonal lineage or asexual descendants of a single genotype. Current tools for clonal lineage identification are time consuming and require laboratory equipment. We previously found that foliar spectroscopy can be used for high-accuracy pre- and postsymptomatic detection of P. infestans infections caused by clonal lineages US-08 and US-23. In this work, we found subtle but distinct differences in spectral responses of potato foliage infected by these clonal lineages in both growth-chamber time-course experiments (12- to 24-h intervals over 5 days) and naturally infected samples from commercial production fields. In both settings, we measured continuous visible to shortwave infrared reflectance (400 to 2,500 nm) on leaves using a portable spectrometer with contact probe. We consistently discriminated between infections caused by the two clonal lineages across all stages of disease progression using partial least squares (PLS) discriminant analysis, with total accuracies ranging from 88 to 98%. Three-class random forest differentiation between control, US-08, and US-23 yielded total discrimination accuracy ranging from 68 to 76%. Differences were greatest during presymptomatic infection stages and progressed toward uniformity as symptoms advanced. Using PLS-regression trait models, we found that total phenolics, sugar, and leaf mass per area were different between lineages. Shortwave infrared wavelengths (>1,100 nm) were important for clonal lineage differentiation. This work provides a foundation for future use of hyperspectral sensing as a nondestructive tool for pathovar differentiation.
DOI: 10.1094/PHYTO-08-19-0294-R
PubMed: 31880984
Affiliations:
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Gold</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Townsend, Philip A" sort="Townsend, Philip A" uniqKey="Townsend P" first="Philip A" last="Townsend">Philip A. Townsend</name><affiliation wicri:level="2"><nlm:affiliation>Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Larson, Eric R" sort="Larson, Eric R" uniqKey="Larson E" first="Eric R" last="Larson">Eric R. Larson</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Herrmann, Ittai" sort="Herrmann, Ittai" uniqKey="Herrmann I" first="Ittai" last="Herrmann">Ittai Herrmann</name><affiliation wicri:level="1"><nlm:affiliation>The Robert H. Smith Institute for Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel.</nlm:affiliation><country xml:lang="fr">Israël</country><wicri:regionArea>The Robert H. Smith Institute for Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. 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Gevens</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></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><keywords scheme="KwdEn" xml:lang="en"><term>Genotype (MeSH)</term><term>Phytophthora infestans (MeSH)</term><term>Plant Diseases (MeSH)</term><term>Solanum tuberosum (MeSH)</term><term>Spectrum Analysis (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse spectrale (MeSH)</term><term>Génotype (MeSH)</term><term>Maladies des plantes (MeSH)</term><term>Phytophthora infestans (MeSH)</term><term>Solanum tuberosum (MeSH)</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genotype</term><term>Phytophthora infestans</term><term>Plant Diseases</term><term>Solanum tuberosum</term><term>Spectrum Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse spectrale</term><term>Génotype</term><term>Maladies des plantes</term><term>Phytophthora infestans</term><term>Solanum tuberosum</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populations of <i>Phytophthora infestans</i>, the oomycete causal agent of potato late blight in the United States, are predominantly asexual, and isolates are characterized by clonal lineage or asexual descendants of a single genotype. Current tools for clonal lineage identification are time consuming and require laboratory equipment. We previously found that foliar spectroscopy can be used for high-accuracy pre- and postsymptomatic detection of <i>P. infestans</i> infections caused by clonal lineages US-08 and US-23. In this work, we found subtle but distinct differences in spectral responses of potato foliage infected by these clonal lineages in both growth-chamber time-course experiments (12- to 24-h intervals over 5 days) and naturally infected samples from commercial production fields. In both settings, we measured continuous visible to shortwave infrared reflectance (400 to 2,500 nm) on leaves using a portable spectrometer with contact probe. We consistently discriminated between infections caused by the two clonal lineages across all stages of disease progression using partial least squares (PLS) discriminant analysis, with total accuracies ranging from 88 to 98%. Three-class random forest differentiation between control, US-08, and US-23 yielded total discrimination accuracy ranging from 68 to 76%. Differences were greatest during presymptomatic infection stages and progressed toward uniformity as symptoms advanced. Using PLS-regression trait models, we found that total phenolics, sugar, and leaf mass per area were different between lineages. Shortwave infrared wavelengths (>1,100 nm) were important for clonal lineage differentiation. This work provides a foundation for future use of hyperspectral sensing as a nondestructive tool for pathovar differentiation.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM"><PMID Version="1">31880984</PMID><DateCompleted><Year>2020</Year><Month>04</Month><Day>07</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-949X</ISSN><JournalIssue CitedMedium="Print"><Volume>110</Volume><Issue>4</Issue><PubDate><Year>2020</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Phytopathology</Title><ISOAbbreviation>Phytopathology</ISOAbbreviation></Journal><ArticleTitle>Contact Reflectance Spectroscopy for Rapid, Accurate, and Nondestructive <i>Phytophthora infestans</i> Clonal Lineage Discrimination.</ArticleTitle><Pagination><MedlinePgn>851-862</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PHYTO-08-19-0294-R</ELocationID><Abstract><AbstractText>Populations of <i>Phytophthora infestans</i>, the oomycete causal agent of potato late blight in the United States, are predominantly asexual, and isolates are characterized by clonal lineage or asexual descendants of a single genotype. Current tools for clonal lineage identification are time consuming and require laboratory equipment. We previously found that foliar spectroscopy can be used for high-accuracy pre- and postsymptomatic detection of <i>P. infestans</i> infections caused by clonal lineages US-08 and US-23. In this work, we found subtle but distinct differences in spectral responses of potato foliage infected by these clonal lineages in both growth-chamber time-course experiments (12- to 24-h intervals over 5 days) and naturally infected samples from commercial production fields. In both settings, we measured continuous visible to shortwave infrared reflectance (400 to 2,500 nm) on leaves using a portable spectrometer with contact probe. We consistently discriminated between infections caused by the two clonal lineages across all stages of disease progression using partial least squares (PLS) discriminant analysis, with total accuracies ranging from 88 to 98%. Three-class random forest differentiation between control, US-08, and US-23 yielded total discrimination accuracy ranging from 68 to 76%. Differences were greatest during presymptomatic infection stages and progressed toward uniformity as symptoms advanced. Using PLS-regression trait models, we found that total phenolics, sugar, and leaf mass per area were different between lineages. Shortwave infrared wavelengths (>1,100 nm) were important for clonal lineage differentiation. This work provides a foundation for future use of hyperspectral sensing as a nondestructive tool for pathovar differentiation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gold</LastName><ForeName>Kaitlin M</ForeName><Initials>KM</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-0306-9244</Identifier><AffiliationInfo><Affiliation>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Townsend</LastName><ForeName>Philip A</ForeName><Initials>PA</Initials><AffiliationInfo><Affiliation>Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Larson</LastName><ForeName>Eric R</ForeName><Initials>ER</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Herrmann</LastName><ForeName>Ittai</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>The Robert H. Smith Institute for Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gevens</LastName><ForeName>Amanda J</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phytopathology</MedlineTA><NlmUniqueID>9427222</NlmUniqueID><ISSNLinking>0031-949X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="Y">Phytophthora infestans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011198" MajorTopicYN="Y">Solanum tuberosum</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013057" MajorTopicYN="N">Spectrum Analysis</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">analytical and theoretical plant pathology</Keyword><Keyword MajorTopicYN="N">ecology and epidemiology</Keyword><Keyword MajorTopicYN="N">techniques</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>12</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>12</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31880984</ArticleId><ArticleId IdType="doi">10.1094/PHYTO-08-19-0294-R</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Israël</li><li>États-Unis</li></country><region><li>Wisconsin</li></region></list><tree><country name="États-Unis"><region name="Wisconsin"><name sortKey="Gold, Kaitlin M" sort="Gold, Kaitlin M" uniqKey="Gold K" first="Kaitlin M" last="Gold">Kaitlin M. Gold</name></region><name sortKey="Gevens, Amanda J" sort="Gevens, Amanda J" uniqKey="Gevens A" first="Amanda J" last="Gevens">Amanda J. Gevens</name><name sortKey="Larson, Eric R" sort="Larson, Eric R" uniqKey="Larson E" first="Eric R" last="Larson">Eric R. Larson</name><name sortKey="Townsend, Philip A" sort="Townsend, Philip A" uniqKey="Townsend P" first="Philip A" last="Townsend">Philip A. Townsend</name></country><country name="Israël"><noRegion><name sortKey="Herrmann, Ittai" sort="Herrmann, Ittai" uniqKey="Herrmann I" first="Ittai" last="Herrmann">Ittai Herrmann</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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