Comparative transcriptome analysis between a resistant and a susceptible Chinese cabbage in response to Hyaloperonospora brassicae.
Identifieur interne : 000194 ( Main/Exploration ); précédent : 000193; suivant : 000195Comparative transcriptome analysis between a resistant and a susceptible Chinese cabbage in response to Hyaloperonospora brassicae.
Auteurs : Han Zheng [République populaire de Chine] ; Yihui Zhang [République populaire de Chine] ; Jingjuan Li [République populaire de Chine] ; Lilong He [République populaire de Chine] ; Fengde Wang [République populaire de Chine] ; Yuping Bi [République populaire de Chine] ; Jianwei Gao [République populaire de Chine]Source :
- Plant signaling & behavior [ 1559-2324 ] ; 2020.
Abstract
Downy mildew caused by Hyaloperonosporabrassicae (H. brassicae) leads to up to 90% of the crop yield loss in Chinese cabbage in China. A transcriptome analysis was carried out between a resistant line (13-13, R) and a susceptible line (15-14, S) of Chinese cabbage in response to H. brassicae. The NOISeq method was used to find differentially expressed genes (DEGs) between these two groups and GO and KEGG were carried out to find R genes related to downy mildew response of Chinese cabbage. qRT-PCR was carried out to verify the reliability of RNA-seq expression data. A total of 3,055 DEGs were screened out from 41,020 genes and clustered into 6 groups with distinct expression patterns. A total of 87 candidate DEGs were identified by functional annotation based on GO and KEGG analysis. These candidate genes are involved in plant-pathogen interaction pathway, among which 54 and 33 DEGs were categorized into plant-pathogen interaction proteins and transcription factors, respectively. Proteins encoded by these genes have been reported to play an important role in the pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) processes of disease responses in some model plants, such as Arabidopsis, rice, tobacco, and tomato. However, little is known about the mechanisms of these genes in resistance to downy mildew in Chinese cabbage. Our findings are useful for further characterization of these candidate genes and helpful in breeding resistant strains.
DOI: 10.1080/15592324.2020.1777373
PubMed: 32538253
Affiliations:
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susceptible Chinese cabbage in response to <i>Hyaloperonospora brassicae</i>.</title><author><name sortKey="Zheng, Han" sort="Zheng, Han" uniqKey="Zheng H" first="Han" last="Zheng">Han Zheng</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Science, Shandong Normal University , Jinan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, Shandong Normal University , Jinan</wicri:regionArea><wicri:noRegion>Jinan</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Yihui" sort="Zhang, Yihui" uniqKey="Zhang Y" first="Yihui" last="Zhang">Yihui Zhang</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Science, Shandong Normal University , Jinan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, Shandong Normal University , 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Chine</country><wicri:regionArea>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan</wicri:regionArea><wicri:noRegion>Jinan</wicri:noRegion></affiliation></author><author><name sortKey="Gao, Jianwei" sort="Gao, Jianwei" uniqKey="Gao J" first="Jianwei" last="Gao">Jianwei Gao</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Science, Shandong Normal University , Jinan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, Shandong Normal University , Jinan</wicri:regionArea><wicri:noRegion>Jinan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan</wicri:regionArea><wicri:noRegion>Jinan</wicri:noRegion></affiliation></author></analytic><series><title level="j">Plant signaling & behavior</title><idno type="eISSN">1559-2324</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">Downy mildew caused by <i>Hyaloperonosporabrassicae</i> (<i>H. brassicae</i>) leads to up to 90% of the crop yield loss in Chinese cabbage in China. A transcriptome analysis was carried out between a resistant line (13-13, R) and a susceptible line (15-14, S) of Chinese cabbage in response to <i>H. brassicae</i>. The NOISeq method was used to find differentially expressed genes (DEGs) between these two groups and GO and KEGG were carried out to find R genes related to downy mildew response of Chinese cabbage. qRT-PCR was carried out to verify the reliability of RNA-seq expression data. A total of 3,055 DEGs were screened out from 41,020 genes and clustered into 6 groups with distinct expression patterns. A total of 87 candidate DEGs were identified by functional annotation based on GO and KEGG analysis. These candidate genes are involved in plant-pathogen interaction pathway, among which 54 and 33 DEGs were categorized into plant-pathogen interaction proteins and transcription factors, respectively. Proteins encoded by these genes have been reported to play an important role in the pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) processes of disease responses in some model plants, such as Arabidopsis, rice, tobacco, and tomato. However, little is known about the mechanisms of these genes in resistance to downy mildew in Chinese cabbage. Our findings are useful for further characterization of these candidate genes and helpful in breeding resistant strains.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32538253</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>07</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1559-2324</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>7</Issue><PubDate><Year>2020</Year><Month>07</Month><Day>02</Day></PubDate></JournalIssue><Title>Plant signaling & behavior</Title><ISOAbbreviation>Plant Signal Behav</ISOAbbreviation></Journal><ArticleTitle>Comparative transcriptome analysis between a resistant and a susceptible Chinese cabbage in response to <i>Hyaloperonospora brassicae</i>.</ArticleTitle><Pagination><MedlinePgn>1777373</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/15592324.2020.1777373</ELocationID><Abstract><AbstractText>Downy mildew caused by <i>Hyaloperonosporabrassicae</i> (<i>H. brassicae</i>) leads to up to 90% of the crop yield loss in Chinese cabbage in China. A transcriptome analysis was carried out between a resistant line (13-13, R) and a susceptible line (15-14, S) of Chinese cabbage in response to <i>H. brassicae</i>. The NOISeq method was used to find differentially expressed genes (DEGs) between these two groups and GO and KEGG were carried out to find R genes related to downy mildew response of Chinese cabbage. qRT-PCR was carried out to verify the reliability of RNA-seq expression data. A total of 3,055 DEGs were screened out from 41,020 genes and clustered into 6 groups with distinct expression patterns. A total of 87 candidate DEGs were identified by functional annotation based on GO and KEGG analysis. These candidate genes are involved in plant-pathogen interaction pathway, among which 54 and 33 DEGs were categorized into plant-pathogen interaction proteins and transcription factors, respectively. Proteins encoded by these genes have been reported to play an important role in the pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) processes of disease responses in some model plants, such as Arabidopsis, rice, tobacco, and tomato. However, little is known about the mechanisms of these genes in resistance to downy mildew in Chinese cabbage. Our findings are useful for further characterization of these candidate genes and helpful in breeding resistant strains.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Han</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Normal University , Jinan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yihui</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Normal University , Jinan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jingjuan</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0002-4983-0924</Identifier><AffiliationInfo><Affiliation>College of Life Science, Shandong Normal University , Jinan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>He</LastName><ForeName>Lilong</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Fengde</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Normal University , Jinan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bi</LastName><ForeName>Yuping</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Normal University , Jinan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Jianwei</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>College of Life Science, Shandong Normal University , Jinan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science , Jinan, China.</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>06</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Signal Behav</MedlineTA><NlmUniqueID>101291431</NlmUniqueID><ISSNLinking>1559-2316</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Chinese cabbage</Keyword><Keyword MajorTopicYN="Y">Downy mildew</Keyword><Keyword MajorTopicYN="Y">RNA-Seq analysis</Keyword><Keyword MajorTopicYN="Y">differentially expressed genes</Keyword><Keyword MajorTopicYN="Y">disease resistance</Keyword><Keyword MajorTopicYN="Y">transcription factors</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>6</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>6</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32538253</ArticleId><ArticleId IdType="doi">10.1080/15592324.2020.1777373</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Zheng, Han" sort="Zheng, Han" uniqKey="Zheng H" first="Han" last="Zheng">Han Zheng</name></noRegion><name sortKey="Bi, Yuping" sort="Bi, Yuping" uniqKey="Bi Y" first="Yuping" last="Bi">Yuping Bi</name><name sortKey="Bi, Yuping" sort="Bi, Yuping" uniqKey="Bi Y" first="Yuping" last="Bi">Yuping Bi</name><name sortKey="Gao, Jianwei" sort="Gao, Jianwei" uniqKey="Gao J" first="Jianwei" last="Gao">Jianwei Gao</name><name sortKey="Gao, Jianwei" sort="Gao, Jianwei" uniqKey="Gao J" first="Jianwei" last="Gao">Jianwei Gao</name><name sortKey="He, Lilong" sort="He, Lilong" uniqKey="He L" first="Lilong" last="He">Lilong He</name><name sortKey="Li, Jingjuan" sort="Li, Jingjuan" uniqKey="Li J" first="Jingjuan" last="Li">Jingjuan Li</name><name sortKey="Li, Jingjuan" sort="Li, Jingjuan" uniqKey="Li J" first="Jingjuan" last="Li">Jingjuan Li</name><name sortKey="Wang, Fengde" sort="Wang, Fengde" uniqKey="Wang F" first="Fengde" last="Wang">Fengde Wang</name><name sortKey="Wang, Fengde" sort="Wang, Fengde" uniqKey="Wang F" first="Fengde" last="Wang">Fengde Wang</name><name sortKey="Zhang, Yihui" sort="Zhang, Yihui" uniqKey="Zhang Y" first="Yihui" 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