Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici.
Identifieur interne : 000288 ( Main/Exploration ); précédent : 000287; suivant : 000289Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici.
Auteurs : Gabriela K. Orquera-Tornakian [États-Unis] ; Patricia Garrido [Équateur] ; Brent Kronmiller [États-Unis] ; Robert Hunger [États-Unis] ; Brett M. Tyler [États-Unis] ; Carla D. Garzon [États-Unis] ; Stephen M. Marek [États-Unis]Source :
- Journal of microbiological methods [ 1872-8359 ] ; 2017.
Descripteurs français
- KwdFr :
- Banque de gènes (MeSH), Basidiomycota (classification), Basidiomycota (croissance et développement), Basidiomycota (génétique), Basidiomycota (pathogénicité), Génome fongique (MeSH), Iowa (MeSH), Marqueurs génétiques (MeSH), Polymorphisme génétique (MeSH), Réaction de polymérisation en chaîne (méthodes), Répétitions microsatellites (MeSH), Typage moléculaire (MeSH), Variation génétique (MeSH), Étiquettes de séquences exprimées (MeSH).
- MESH :
- croissance et développement : Basidiomycota.
- génétique : Basidiomycota.
- méthodes : Réaction de polymérisation en chaîne.
- pathogénicité : Basidiomycota.
- Banque de gènes, Basidiomycota, Génome fongique, Iowa, Marqueurs génétiques, Polymorphisme génétique, Répétitions microsatellites, Typage moléculaire, Variation génétique, Étiquettes de séquences exprimées.
English descriptors
- KwdEn :
- Basidiomycota (classification), Basidiomycota (genetics), Basidiomycota (growth & development), Basidiomycota (pathogenicity), Expressed Sequence Tags (MeSH), Gene Library (MeSH), Genetic Markers (MeSH), Genetic Variation (MeSH), Genome, Fungal (MeSH), Iowa (MeSH), Microsatellite Repeats (MeSH), Molecular Typing (MeSH), Polymerase Chain Reaction (methods), Polymorphism, Genetic (MeSH).
- MESH :
- chemical : Genetic Markers.
- classification : Basidiomycota.
- genetics : Basidiomycota.
- growth & development : Basidiomycota.
- methods : Polymerase Chain Reaction.
- pathogenicity : Basidiomycota.
- Expressed Sequence Tags, Gene Library, Genetic Variation, Genome, Fungal, Iowa, Microsatellite Repeats, Molecular Typing, Polymorphism, Genetic.
Abstract
Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P. novopanici. This study reports the development and characterization of novel simple sequence repeat (SSR) markers from a Puccinia emaculata s.l. microsatellite-enriched library and expressed sequence tags (ESTs). Microsatellites were evaluated for polymorphisms on P. emaculata s.l. urediniospores collected in Iowa (IA), Mississippi (MS), Oklahoma (OK), South Dakota (SD) and Virginia (VA). Puccinia novopanici single spore whole genome amplifications were used as templates to validate the SSR reactions protocol and to assess a preliminary population genetics statistics of the pathogen. Eighteen microsatellite markers were polymorphic (average PIC=0.72) on individual urediniospores, with an average of 8.3 alleles per locus (range 3 to 17). Of the 49 SSRs loci initially identified in P. emaculata s.l., 18 were transferable to P. striiformis f. sp. tritici, 23 to P. triticina, 20 to P. sorghi and 31 to P. andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species.
DOI: 10.1016/j.mimet.2017.04.011
PubMed: 28457942
Affiliations:
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Le document en format XML
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Orquera-Tornakian</name><affiliation wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States. Electronic address: orquera@okstate.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078</wicri:regionArea><placeName><region type="state">Oklahoma</region></placeName></affiliation></author><author><name sortKey="Garrido, Patricia" sort="Garrido, Patricia" uniqKey="Garrido P" first="Patricia" last="Garrido">Patricia Garrido</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad Tecnológica Equinoccial, EC171029 Quito, Ecuador.</nlm:affiliation><country xml:lang="fr">Équateur</country><wicri:regionArea>Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad Tecnológica Equinoccial, EC171029 Quito</wicri:regionArea><wicri:noRegion>EC171029 Quito</wicri:noRegion></affiliation></author><author><name sortKey="Kronmiller, Brent" sort="Kronmiller, Brent" uniqKey="Kronmiller B" first="Brent" last="Kronmiller">Brent Kronmiller</name><affiliation wicri:level="2"><nlm:affiliation>Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Hunger, Robert" sort="Hunger, Robert" uniqKey="Hunger R" first="Robert" last="Hunger">Robert Hunger</name><affiliation wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078</wicri:regionArea><placeName><region type="state">Oklahoma</region></placeName></affiliation></author><author><name sortKey="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. 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Marek</name><affiliation wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078</wicri:regionArea><placeName><region type="state">Oklahoma</region></placeName></affiliation></author></analytic><series><title level="j">Journal of microbiological methods</title><idno type="eISSN">1872-8359</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Basidiomycota (classification)</term><term>Basidiomycota (genetics)</term><term>Basidiomycota (growth & development)</term><term>Basidiomycota (pathogenicity)</term><term>Expressed Sequence Tags (MeSH)</term><term>Gene Library (MeSH)</term><term>Genetic Markers (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Fungal (MeSH)</term><term>Iowa (MeSH)</term><term>Microsatellite Repeats (MeSH)</term><term>Molecular Typing (MeSH)</term><term>Polymerase Chain Reaction (methods)</term><term>Polymorphism, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Banque de gènes (MeSH)</term><term>Basidiomycota (classification)</term><term>Basidiomycota (croissance et développement)</term><term>Basidiomycota (génétique)</term><term>Basidiomycota (pathogénicité)</term><term>Génome fongique (MeSH)</term><term>Iowa (MeSH)</term><term>Marqueurs génétiques (MeSH)</term><term>Polymorphisme génétique (MeSH)</term><term>Réaction de polymérisation en chaîne (méthodes)</term><term>Répétitions microsatellites (MeSH)</term><term>Typage moléculaire (MeSH)</term><term>Variation génétique (MeSH)</term><term>Étiquettes de séquences exprimées (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Réaction de polymérisation en chaîne</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Basidiomycota</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Expressed Sequence Tags</term><term>Gene Library</term><term>Genetic Variation</term><term>Genome, Fungal</term><term>Iowa</term><term>Microsatellite Repeats</term><term>Molecular Typing</term><term>Polymorphism, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Banque de gènes</term><term>Basidiomycota</term><term>Génome fongique</term><term>Iowa</term><term>Marqueurs génétiques</term><term>Polymorphisme génétique</term><term>Répétitions microsatellites</term><term>Typage moléculaire</term><term>Variation génétique</term><term>Étiquettes de séquences exprimées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P. novopanici. This study reports the development and characterization of novel simple sequence repeat (SSR) markers from a Puccinia emaculata s.l. microsatellite-enriched library and expressed sequence tags (ESTs). Microsatellites were evaluated for polymorphisms on P. emaculata s.l. urediniospores collected in Iowa (IA), Mississippi (MS), Oklahoma (OK), South Dakota (SD) and Virginia (VA). Puccinia novopanici single spore whole genome amplifications were used as templates to validate the SSR reactions protocol and to assess a preliminary population genetics statistics of the pathogen. Eighteen microsatellite markers were polymorphic (average PIC=0.72) on individual urediniospores, with an average of 8.3 alleles per locus (range 3 to 17). Of the 49 SSRs loci initially identified in P. emaculata s.l., 18 were transferable to P. striiformis f. sp. tritici, 23 to P. triticina, 20 to P. sorghi and 31 to P. andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28457942</PMID><DateCompleted><Year>2017</Year><Month>11</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>01</Month><Day>26</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1872-8359</ISSN><JournalIssue CitedMedium="Internet"><Volume>139</Volume><PubDate><Year>2017</Year><Month>08</Month></PubDate></JournalIssue><Title>Journal of microbiological methods</Title><ISOAbbreviation>J Microbiol Methods</ISOAbbreviation></Journal><ArticleTitle>Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici.</ArticleTitle><Pagination><MedlinePgn>113-122</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0167-7012(17)30098-2</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.mimet.2017.04.011</ELocationID><Abstract><AbstractText>Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P. novopanici. This study reports the development and characterization of novel simple sequence repeat (SSR) markers from a Puccinia emaculata s.l. microsatellite-enriched library and expressed sequence tags (ESTs). Microsatellites were evaluated for polymorphisms on P. emaculata s.l. urediniospores collected in Iowa (IA), Mississippi (MS), Oklahoma (OK), South Dakota (SD) and Virginia (VA). Puccinia novopanici single spore whole genome amplifications were used as templates to validate the SSR reactions protocol and to assess a preliminary population genetics statistics of the pathogen. Eighteen microsatellite markers were polymorphic (average PIC=0.72) on individual urediniospores, with an average of 8.3 alleles per locus (range 3 to 17). Of the 49 SSRs loci initially identified in P. emaculata s.l., 18 were transferable to P. striiformis f. sp. tritici, 23 to P. triticina, 20 to P. sorghi and 31 to P. andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species.</AbstractText><CopyrightInformation>Copyright © 2017 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Orquera-Tornakian</LastName><ForeName>Gabriela K</ForeName><Initials>GK</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States. Electronic address: orquera@okstate.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Garrido</LastName><ForeName>Patricia</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad Tecnológica Equinoccial, EC171029 Quito, Ecuador.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kronmiller</LastName><ForeName>Brent</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hunger</LastName><ForeName>Robert</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tyler</LastName><ForeName>Brett M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Garzon</LastName><ForeName>Carla D</ForeName><Initials>CD</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Marek</LastName><ForeName>Stephen M</ForeName><Initials>SM</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>04</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Microbiol Methods</MedlineTA><NlmUniqueID>8306883</NlmUniqueID><ISSNLinking>0167-7012</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000472" MajorTopicYN="N">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="Y">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007484" MajorTopicYN="N">Iowa</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="Y">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058889" MajorTopicYN="N">Molecular Typing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="N">Polymorphism, Genetic</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Expressed sequence tags (ESTs)</Keyword><Keyword MajorTopicYN="Y">Puccinia</Keyword><Keyword MajorTopicYN="Y">Simple sequences repeats (SSRs)</Keyword><Keyword MajorTopicYN="Y">Switchgrass</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>09</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>04</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>04</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>5</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>11</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>5</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28457942</ArticleId><ArticleId IdType="pii">S0167-7012(17)30098-2</ArticleId><ArticleId IdType="doi">10.1016/j.mimet.2017.04.011</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Équateur</li><li>États-Unis</li></country><region><li>Oklahoma</li><li>Oregon</li></region></list><tree><country name="États-Unis"><region name="Oklahoma"><name sortKey="Orquera Tornakian, Gabriela K" sort="Orquera Tornakian, Gabriela K" uniqKey="Orquera Tornakian G" first="Gabriela K" last="Orquera-Tornakian">Gabriela K. Orquera-Tornakian</name></region><name sortKey="Garzon, Carla D" sort="Garzon, Carla D" uniqKey="Garzon C" first="Carla D" last="Garzon">Carla D. Garzon</name><name sortKey="Hunger, Robert" sort="Hunger, Robert" uniqKey="Hunger R" first="Robert" last="Hunger">Robert Hunger</name><name sortKey="Kronmiller, Brent" sort="Kronmiller, Brent" uniqKey="Kronmiller B" first="Brent" last="Kronmiller">Brent Kronmiller</name><name sortKey="Marek, Stephen M" sort="Marek, Stephen M" uniqKey="Marek S" first="Stephen M" last="Marek">Stephen M. Marek</name><name sortKey="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. Tyler</name></country><country name="Équateur"><noRegion><name sortKey="Garrido, Patricia" sort="Garrido, Patricia" uniqKey="Garrido P" first="Patricia" last="Garrido">Patricia Garrido</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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