hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean.
Identifieur interne : 000345 ( Main/Exploration ); précédent : 000344; suivant : 000346hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean.
Auteurs : Austin G. Mccoy [États-Unis] ; Zachary Noel [États-Unis] ; Adam H. Sparks [Australie] ; Martin Chilvers [États-Unis]Source :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- méthodes : Parasitologie.
- parasitologie : Soja.
- Logiciel, Phytophthora.
English descriptors
- KwdEn :
- MESH :
- methods : Parasitology.
- parasitology : Soybeans.
- Phytophthora, Software.
Abstract
Phytophthora sojae is a significant pathogen of soybean worldwide. Pathotype surveys for Phytophthora sojae are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for P. sojae or other gene-for-gene pathosystem studies.
DOI: 10.1094/MPMI-07-19-0180-A
PubMed: 31415224
Affiliations:
Links toward previous steps (curation, corpus...)
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Sparks</name><affiliation wicri:level="1"><nlm:affiliation>University of Southern Queensland, Centre for Crop Health, Toowoomba, Qld 4350, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>University of Southern Queensland, Centre for Crop Health, Toowoomba, Qld 4350</wicri:regionArea><wicri:noRegion>Qld 4350</wicri:noRegion></affiliation></author><author><name sortKey="Chilvers, Martin" sort="Chilvers, Martin" uniqKey="Chilvers M" first="Martin" last="Chilvers">Martin Chilvers</name><affiliation wicri:level="4"><nlm:affiliation>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824</wicri:regionArea><placeName><region type="state">Michigan</region><settlement type="city">East Lansing</settlement></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University.</nlm:affiliation><country>États-Unis</country><placeName><settlement type="city">East Lansing</settlement><region type="state">Michigan</region></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation></author></analytic><series><title level="j">Molecular plant-microbe interactions : MPMI</title><idno type="ISSN">0894-0282</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Parasitology (methods)</term><term>Phytophthora (MeSH)</term><term>Software (MeSH)</term><term>Soybeans (parasitology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Logiciel (MeSH)</term><term>Parasitologie (méthodes)</term><term>Phytophthora (MeSH)</term><term>Soja (parasitologie)</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Parasitology</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Parasitologie</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Soja</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Soybeans</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Phytophthora</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Logiciel</term><term>Phytophthora</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Phytophthora sojae</i> is a significant pathogen of soybean worldwide. Pathotype surveys for <i>Phytophthora sojae</i> are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for <i>P. sojae</i> or other gene-for-gene pathosystem studies.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">31415224</PMID><DateCompleted><Year>2019</Year><Month>11</Month><Day>21</Day></DateCompleted><DateRevised><Year>2019</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>32</Volume><Issue>12</Issue><PubDate><Year>2019</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>hagis, an R Package Resource for Pathotype Analysis of <i>Phytophthora sojae</i> Populations Causing Stem and Root Rot of Soybean.</ArticleTitle><Pagination><MedlinePgn>1574-1576</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/MPMI-07-19-0180-A</ELocationID><Abstract><AbstractText><i>Phytophthora sojae</i> is a significant pathogen of soybean worldwide. Pathotype surveys for <i>Phytophthora sojae</i> are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for <i>P. sojae</i> or other gene-for-gene pathosystem studies.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>McCoy</LastName><ForeName>Austin G</ForeName><Initials>AG</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-2483-4184</Identifier><AffiliationInfo><Affiliation>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Noel</LastName><ForeName>Zachary</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sparks</LastName><ForeName>Adam H</ForeName><Initials>AH</Initials><AffiliationInfo><Affiliation>University of Southern Queensland, Centre for Crop Health, Toowoomba, Qld 4350, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chilvers</LastName><ForeName>Martin</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>10</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Plant Microbe Interact</MedlineTA><NlmUniqueID>9107902</NlmUniqueID><ISSNLinking>0894-0282</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D010274" MajorTopicYN="Y">Parasitology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="Y">Phytophthora</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013025" MajorTopicYN="N">Soybeans</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora diseases</Keyword><Keyword MajorTopicYN="N">avirulence factors</Keyword><Keyword MajorTopicYN="N">fungal effectors</Keyword><Keyword MajorTopicYN="N">oomycete effectors</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>8</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>11</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>8</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31415224</ArticleId><ArticleId IdType="doi">10.1094/MPMI-07-19-0180-A</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Australie</li><li>États-Unis</li></country><region><li>Michigan</li></region><settlement><li>East Lansing</li></settlement><orgName><li>Université d'État du Michigan</li></orgName></list><tree><country name="États-Unis"><region name="Michigan"><name sortKey="Mccoy, Austin G" sort="Mccoy, Austin G" uniqKey="Mccoy A" first="Austin G" last="Mccoy">Austin G. Mccoy</name></region><name sortKey="Chilvers, Martin" sort="Chilvers, Martin" uniqKey="Chilvers M" first="Martin" last="Chilvers">Martin Chilvers</name><name sortKey="Chilvers, Martin" sort="Chilvers, Martin" uniqKey="Chilvers M" first="Martin" last="Chilvers">Martin Chilvers</name><name sortKey="Noel, Zachary" sort="Noel, Zachary" uniqKey="Noel Z" first="Zachary" last="Noel">Zachary Noel</name><name sortKey="Noel, Zachary" sort="Noel, Zachary" uniqKey="Noel Z" first="Zachary" last="Noel">Zachary Noel</name></country><country name="Australie"><noRegion><name sortKey="Sparks, Adam H" sort="Sparks, Adam H" uniqKey="Sparks A" first="Adam H" last="Sparks">Adam H. Sparks</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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