Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans.
Identifieur interne : 000328 ( Main/Corpus ); précédent : 000327; suivant : 000329Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans.
Auteurs : Yanfeng Duan ; Shaoguang Duan ; Miles R. Armstrong ; Jianfei Xu ; Jiayi Zheng ; Jun Hu ; Xinwei Chen ; Ingo Hein ; Guangcun Li ; Liping JinSource :
- G3 (Bethesda, Md.) [ 2160-1836 ] ; 2020.
Abstract
Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato.
DOI: 10.1534/g3.119.400818
PubMed: 31818876
PubMed Central: PMC7003068
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Armstrong</name><affiliation><nlm:affiliation>The University of Dundee, Division of Plant Sciences at the James Hutton Institute, Dundee, DD2 5DA, UK, and.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Jianfei" sort="Xu, Jianfei" uniqKey="Xu J" first="Jianfei" last="Xu">Jianfei Xu</name><affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Jiayi" sort="Zheng, Jiayi" uniqKey="Zheng J" first="Jiayi" last="Zheng">Jiayi Zheng</name><affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.</nlm:affiliation></affiliation></author><author><name sortKey="Hu, Jun" sort="Hu, Jun" uniqKey="Hu J" first="Jun" last="Hu">Jun Hu</name><affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Xinwei" sort="Chen, Xinwei" uniqKey="Chen X" first="Xinwei" last="Chen">Xinwei Chen</name><affiliation><nlm:affiliation>Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Hein, Ingo" sort="Hein, Ingo" uniqKey="Hein I" first="Ingo" last="Hein">Ingo Hein</name><affiliation><nlm:affiliation>The University of Dundee, Division of Plant Sciences at the James Hutton Institute, Dundee, DD2 5DA, UK, and.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Guangcun" sort="Li, Guangcun" uniqKey="Li G" first="Guangcun" last="Li">Guangcun Li</name><affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China, liguangcun@caas.cn jinliping@caas.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Jin, Liping" sort="Jin, Liping" uniqKey="Jin L" first="Liping" last="Jin">Liping Jin</name><affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China, liguangcun@caas.cn jinliping@caas.cn.</nlm:affiliation></affiliation></author></analytic><series><title level="j">G3 (Bethesda, Md.)</title><idno type="eISSN">2160-1836</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">Late blight, caused by <i>Phytophthora infestans</i> (<i>P. infestans</i>), is a devastating disease in potato worldwide. Our previous study revealed that the <i>Solanum andigena</i> genotype 03112-233 is resistant to <i>P. infestans</i> isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new <i>R</i> gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as <i>SWEET</i> compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between <i>P. infestans</i> and potato.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">31818876</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>15</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2160-1836</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>2</Issue><PubDate><Year>2020</Year><Month>02</Month><Day>06</Day></PubDate></JournalIssue><Title>G3 (Bethesda, Md.)</Title><ISOAbbreviation>G3 (Bethesda)</ISOAbbreviation></Journal><ArticleTitle>Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward <i>Phytophthora infestans</i>.</ArticleTitle><Pagination><MedlinePgn>623-634</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1534/g3.119.400818</ELocationID><Abstract><AbstractText>Late blight, caused by <i>Phytophthora infestans</i> (<i>P. infestans</i>), is a devastating disease in potato worldwide. Our previous study revealed that the <i>Solanum andigena</i> genotype 03112-233 is resistant to <i>P. infestans</i> isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new <i>R</i> gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as <i>SWEET</i> compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between <i>P. infestans</i> and potato.</AbstractText><CopyrightInformation>Copyright © 2020 Duan et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Duan</LastName><ForeName>Yanfeng</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Duan</LastName><ForeName>Shaoguang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Armstrong</LastName><ForeName>Miles R</ForeName><Initials>MR</Initials><AffiliationInfo><Affiliation>The University of Dundee, Division of Plant Sciences at the James Hutton Institute, Dundee, DD2 5DA, UK, and.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Jianfei</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Jiayi</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Xinwei</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hein</LastName><ForeName>Ingo</ForeName><Initials>I</Initials><Identifier Source="ORCID">0000-0002-0128-2084</Identifier><AffiliationInfo><Affiliation>The University of Dundee, Division of Plant Sciences at the James Hutton Institute, Dundee, DD2 5DA, UK, and.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Guangcun</ForeName><Initials>G</Initials><Identifier Source="ORCID">0000-0003-2024-9914</Identifier><AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China, liguangcun@caas.cn jinliping@caas.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jin</LastName><ForeName>Liping</ForeName><Initials>L</Initials><Identifier Source="ORCID">0000-0001-9119-3474</Identifier><AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China, liguangcun@caas.cn jinliping@caas.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>G3 (Bethesda)</MedlineTA><NlmUniqueID>101566598</NlmUniqueID><ISSNLinking>2160-1836</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Phytophthora infestans</Keyword><Keyword MajorTopicYN="Y">Potato</Keyword><Keyword MajorTopicYN="Y">RNAseq</Keyword><Keyword MajorTopicYN="Y">dRenSeq</Keyword><Keyword MajorTopicYN="Y">late 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