SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China.
Identifieur interne : 000F54 ( Main/Exploration ); précédent : 000F53; suivant : 000F55SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China.
Auteurs : Sandesh Shrestha [États-Unis] ; Jian Hu [République populaire de Chine] ; Rebecca Trout Fryxell [États-Unis] ; Joann Mudge [États-Unis] ; Kurt Lamour [États-Unis]Source :
- Mycologia [ 0027-5514 ]
Descripteurs français
- KwdFr :
- Amorces ADN (génétique), Analyse de séquence d'ADN (MeSH), Chine (MeSH), Colocasia (parasitologie), Génotype (MeSH), Génétique des populations (MeSH), Géographie (MeSH), Hawaï (MeSH), Iles (MeSH), Maladies des plantes (parasitologie), Marqueurs génétiques (MeSH), Perte d'hétérozygotie (MeSH), Phytophthora (génétique), Polymorphisme de nucléotide simple (génétique), Variation génétique (MeSH), Vietnam (MeSH).
- MESH :
- génétique : Amorces ADN, Phytophthora, Polymorphisme de nucléotide simple.
- parasitologie : Colocasia, Maladies des plantes.
- Analyse de séquence d'ADN, Chine, Génotype, Génétique des populations, Géographie, Hawaï, Iles, Marqueurs génétiques, Perte d'hétérozygotie, Variation génétique, Vietnam.
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- China (MeSH), Colocasia (parasitology), DNA Primers (genetics), Genetic Markers (MeSH), Genetic Variation (MeSH), Genetics, Population (MeSH), Genotype (MeSH), Geography (MeSH), Hawaii (MeSH), Islands (MeSH), Loss of Heterozygosity (MeSH), Phytophthora (genetics), Plant Diseases (parasitology), Polymorphism, Single Nucleotide (genetics), Sequence Analysis, DNA (MeSH), Vietnam (MeSH).
- MESH :
- chemical , genetics : DNA Primers.
- geographic : China, Genetic Markers, Hawaii, Vietnam.
- genetics : Phytophthora, Polymorphism, Single Nucleotide.
- parasitology : Colocasia, Plant Diseases.
- Genetic Variation, Genetics, Population, Genotype, Geography, Islands, Loss of Heterozygosity, Sequence Analysis, DNA.
Abstract
Taro (Colocasia esculenta) is an important food crop, and taro leaf blight caused by Phytophthora colocasiae can significantly affect production. Our objectives were to develop single nucleotide polymorphism (SNP) markers for P. colocasiae and characterize populations in Hawaii (HI), Vietnam (VN) and Hainan Island, China (HIC). In total, 379 isolates were analyzed for mating type and multilocus SNP profiles including 214 from HI, 97 from VN and 68 from HIC. A total of 1152 single nucleotide variant (SNV) sites were identified via restriction site-associated DNA (RAD) sequencing of two field isolates. Genotyping with 27 SNPs revealed 41 multilocus SNP genotypes grouped into seven clonal lineages containing 2-232 members. Three clonal lineages were shared among countries. In addition, five SNP markers had a low incidence of loss of heterozygosity (LOH) during asexual laboratory growth. For HI and VN, >95% of isolates were the A2 mating type. On HIC, isolates within single clonal lineages had A1, A2 and A0 (neuter) isolates. The implications for the wide dispersal of clonal lineages are discussed.
DOI: 10.3852/13-165
PubMed: 24895424
Affiliations:
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wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville</wicri:cityArea></affiliation></author><author><name sortKey="Mudge, Joann" sort="Mudge, Joann" uniqKey="Mudge J" first="Joann" last="Mudge">Joann Mudge</name><affiliation wicri:level="2"><nlm:affiliation>National Center for Genome Resources, Santa Fe, New Mexico.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Nouveau-Mexique</region></placeName><wicri:cityArea>National Center for Genome Resources, Santa Fe</wicri:cityArea></affiliation></author><author><name sortKey="Lamour, Kurt" sort="Lamour, Kurt" uniqKey="Lamour K" first="Kurt" last="Lamour">Kurt Lamour</name><affiliation wicri:level="1"><nlm:affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee klamour@utk.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville</wicri:regionArea><wicri:noRegion>Knoxville</wicri:noRegion></affiliation></author></analytic><series><title level="j">Mycologia</title><idno type="ISSN">0027-5514</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>China (MeSH)</term><term>Colocasia (parasitology)</term><term>DNA Primers (genetics)</term><term>Genetic Markers (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genetics, Population (MeSH)</term><term>Genotype (MeSH)</term><term>Geography (MeSH)</term><term>Hawaii (MeSH)</term><term>Islands (MeSH)</term><term>Loss of Heterozygosity (MeSH)</term><term>Phytophthora (genetics)</term><term>Plant Diseases (parasitology)</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Vietnam (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amorces ADN (génétique)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Chine (MeSH)</term><term>Colocasia (parasitologie)</term><term>Génotype (MeSH)</term><term>Génétique des populations (MeSH)</term><term>Géographie (MeSH)</term><term>Hawaï (MeSH)</term><term>Iles (MeSH)</term><term>Maladies des plantes (parasitologie)</term><term>Marqueurs génétiques (MeSH)</term><term>Perte d'hétérozygotie (MeSH)</term><term>Phytophthora (génétique)</term><term>Polymorphisme de nucléotide simple (génétique)</term><term>Variation génétique (MeSH)</term><term>Vietnam (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Primers</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term><term>Genetic Markers</term><term>Hawaii</term><term>Vietnam</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phytophthora</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Amorces ADN</term><term>Phytophthora</term><term>Polymorphisme de nucléotide simple</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Colocasia</term><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Colocasia</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genetic Variation</term><term>Genetics, Population</term><term>Genotype</term><term>Geography</term><term>Islands</term><term>Loss of Heterozygosity</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Chine</term><term>Génotype</term><term>Génétique des populations</term><term>Géographie</term><term>Hawaï</term><term>Iles</term><term>Marqueurs génétiques</term><term>Perte d'hétérozygotie</term><term>Variation génétique</term><term>Vietnam</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Taro (Colocasia esculenta) is an important food crop, and taro leaf blight caused by Phytophthora colocasiae can significantly affect production. Our objectives were to develop single nucleotide polymorphism (SNP) markers for P. colocasiae and characterize populations in Hawaii (HI), Vietnam (VN) and Hainan Island, China (HIC). In total, 379 isolates were analyzed for mating type and multilocus SNP profiles including 214 from HI, 97 from VN and 68 from HIC. A total of 1152 single nucleotide variant (SNV) sites were identified via restriction site-associated DNA (RAD) sequencing of two field isolates. Genotyping with 27 SNPs revealed 41 multilocus SNP genotypes grouped into seven clonal lineages containing 2-232 members. Three clonal lineages were shared among countries. In addition, five SNP markers had a low incidence of loss of heterozygosity (LOH) during asexual laboratory growth. For HI and VN, >95% of isolates were the A2 mating type. On HIC, isolates within single clonal lineages had A1, A2 and A0 (neuter) isolates. The implications for the wide dispersal of clonal lineages are discussed. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24895424</PMID><DateCompleted><Year>2014</Year><Month>10</Month><Day>16</Day></DateCompleted><DateRevised><Year>2014</Year><Month>08</Month><Day>29</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0027-5514</ISSN><JournalIssue CitedMedium="Print"><Volume>106</Volume><Issue>4</Issue><PubDate><MedlineDate>2014 Jul-Aug</MedlineDate></PubDate></JournalIssue><Title>Mycologia</Title><ISOAbbreviation>Mycologia</ISOAbbreviation></Journal><ArticleTitle>SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China.</ArticleTitle><Pagination><MedlinePgn>676-85</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3852/13-165</ELocationID><Abstract><AbstractText>Taro (Colocasia esculenta) is an important food crop, and taro leaf blight caused by Phytophthora colocasiae can significantly affect production. Our objectives were to develop single nucleotide polymorphism (SNP) markers for P. colocasiae and characterize populations in Hawaii (HI), Vietnam (VN) and Hainan Island, China (HIC). In total, 379 isolates were analyzed for mating type and multilocus SNP profiles including 214 from HI, 97 from VN and 68 from HIC. A total of 1152 single nucleotide variant (SNV) sites were identified via restriction site-associated DNA (RAD) sequencing of two field isolates. Genotyping with 27 SNPs revealed 41 multilocus SNP genotypes grouped into seven clonal lineages containing 2-232 members. Three clonal lineages were shared among countries. In addition, five SNP markers had a low incidence of loss of heterozygosity (LOH) during asexual laboratory growth. For HI and VN, >95% of isolates were the A2 mating type. On HIC, isolates within single clonal lineages had A1, A2 and A0 (neuter) isolates. The implications for the wide dispersal of clonal lineages are discussed. </AbstractText><CopyrightInformation>© 2014 by The Mycological Society of America.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shrestha</LastName><ForeName>Sandesh</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Jian</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, and China Agricultural University, Beijing.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fryxell</LastName><ForeName>Rebecca Trout</ForeName><Initials>RT</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mudge</LastName><ForeName>Joann</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>National Center for Genome Resources, Santa Fe, New Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lamour</LastName><ForeName>Kurt</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee klamour@utk.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>06</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mycologia</MedlineTA><NlmUniqueID>0400764</NlmUniqueID><ISSNLinking>0027-5514</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002681" MajorTopicYN="N" Type="Geographic">China</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031060" MajorTopicYN="N">Colocasia</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017931" MajorTopicYN="N">DNA Primers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="N">Genetics, Population</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005843" MajorTopicYN="N">Geography</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006254" MajorTopicYN="N" Type="Geographic">Hawaii</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D062312" MajorTopicYN="N">Islands</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019656" MajorTopicYN="N">Loss of Heterozygosity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014744" MajorTopicYN="N" Type="Geographic">Vietnam</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">SNP</Keyword><Keyword MajorTopicYN="N">loss of heterozygosity</Keyword><Keyword MajorTopicYN="N">population genetics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>6</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>6</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>10</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24895424</ArticleId><ArticleId IdType="pii">13-165</ArticleId><ArticleId IdType="doi">10.3852/13-165</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Nouveau-Mexique</li><li>Tennessee</li></region><settlement><li>Pékin</li></settlement></list><tree><country name="États-Unis"><region name="Tennessee"><name sortKey="Shrestha, Sandesh" sort="Shrestha, Sandesh" uniqKey="Shrestha S" first="Sandesh" last="Shrestha">Sandesh Shrestha</name></region><name sortKey="Fryxell, Rebecca Trout" sort="Fryxell, Rebecca Trout" uniqKey="Fryxell R" first="Rebecca Trout" last="Fryxell">Rebecca Trout Fryxell</name><name sortKey="Lamour, Kurt" sort="Lamour, Kurt" uniqKey="Lamour K" first="Kurt" last="Lamour">Kurt Lamour</name><name sortKey="Mudge, Joann" sort="Mudge, Joann" uniqKey="Mudge J" first="Joann" last="Mudge">Joann Mudge</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Hu, Jian" sort="Hu, Jian" uniqKey="Hu J" first="Jian" last="Hu">Jian Hu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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