Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance.
Identifieur interne : 000025 ( Main/Exploration ); précédent : 000024; suivant : 000026Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance.
Auteurs : Roshan Sharma Poudel [États-Unis] ; Jonathan Richards [États-Unis] ; Subidhya Shrestha [États-Unis] ; Shyam Solanki [États-Unis] ; Robert Brueggeman [États-Unis]Source :
- BMC genomics [ 1471-2164 ] ; 2019.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (méthodes), Analyse de séquence d'ADN (MeSH), Analyse de séquence d'ARN (MeSH), Basidiomycota (génétique), Basidiomycota (pathogénicité), Hordeum (génétique), Hordeum (microbiologie), Interactions hôte-pathogène (MeSH), Maladies des plantes (microbiologie), Protéines fongiques (génétique), Protéines fongiques (métabolisme), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes fongiques (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Résistance à la maladie (MeSH), Substitution d'acide aminé (MeSH), Virulence (MeSH), Études d'associations génétiques (MeSH).
- MESH :
- génétique : Basidiomycota, Hordeum, Protéines fongiques, Protéines végétales.
- microbiologie : Hordeum, Maladies des plantes.
- métabolisme : Protéines fongiques, Protéines végétales.
- méthodes : Analyse de profil d'expression de gènes.
- pathogénicité : Basidiomycota.
- Analyse de séquence d'ADN, Analyse de séquence d'ARN, Interactions hôte-pathogène, Régulation de l'expression des gènes fongiques, Régulation de l'expression des gènes végétaux, Résistance à la maladie, Substitution d'acide aminé, Virulence, Études d'associations génétiques.
English descriptors
- KwdEn :
- Amino Acid Substitution (MeSH), Basidiomycota (genetics), Basidiomycota (pathogenicity), Disease Resistance (MeSH), Fungal Proteins (genetics), Fungal Proteins (metabolism), Gene Expression Profiling (methods), Gene Expression Regulation, Fungal (MeSH), Gene Expression Regulation, Plant (MeSH), Genetic Association Studies (MeSH), Hordeum (genetics), Hordeum (microbiology), Host-Pathogen Interactions (MeSH), Plant Diseases (microbiology), Plant Proteins (genetics), Plant Proteins (metabolism), Sequence Analysis, DNA (MeSH), Sequence Analysis, RNA (MeSH), Virulence (MeSH).
- MESH :
- chemical , genetics : Fungal Proteins, Plant Proteins.
- genetics : Basidiomycota, Hordeum.
- chemical , metabolism : Fungal Proteins, Plant Proteins.
- methods : Gene Expression Profiling.
- microbiology : Hordeum, Plant Diseases.
- pathogenicity : Basidiomycota.
- Amino Acid Substitution, Disease Resistance, Gene Expression Regulation, Fungal, Gene Expression Regulation, Plant, Genetic Association Studies, Host-Pathogen Interactions, Sequence Analysis, DNA, Sequence Analysis, RNA, Virulence.
Abstract
BACKGROUND
Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley.
RESULTS
Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses.
CONCLUSIONS
This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.
DOI: 10.1186/s12864-019-6369-7
PubMed: 31842749
PubMed Central: PMC6915985
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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<term>Basidiomycota (genetics)</term>
<term>Basidiomycota (pathogenicity)</term>
<term>Disease Resistance (MeSH)</term>
<term>Fungal Proteins (genetics)</term>
<term>Fungal Proteins (metabolism)</term>
<term>Gene Expression Profiling (methods)</term>
<term>Gene Expression Regulation, Fungal (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genetic Association Studies (MeSH)</term>
<term>Hordeum (genetics)</term>
<term>Hordeum (microbiology)</term>
<term>Host-Pathogen Interactions (MeSH)</term>
<term>Plant Diseases (microbiology)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Sequence Analysis, DNA (MeSH)</term>
<term>Sequence Analysis, RNA (MeSH)</term>
<term>Virulence (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (méthodes)</term>
<term>Analyse de séquence d'ADN (MeSH)</term>
<term>Analyse de séquence d'ARN (MeSH)</term>
<term>Basidiomycota (génétique)</term>
<term>Basidiomycota (pathogénicité)</term>
<term>Hordeum (génétique)</term>
<term>Hordeum (microbiologie)</term>
<term>Interactions hôte-pathogène (MeSH)</term>
<term>Maladies des plantes (microbiologie)</term>
<term>Protéines fongiques (génétique)</term>
<term>Protéines fongiques (métabolisme)</term>
<term>Protéines végétales (génétique)</term>
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<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Résistance à la maladie (MeSH)</term>
<term>Substitution d'acide aminé (MeSH)</term>
<term>Virulence (MeSH)</term>
<term>Études d'associations génétiques (MeSH)</term>
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<term>Plant Proteins</term>
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<term>Hordeum</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Basidiomycota</term>
<term>Hordeum</term>
<term>Protéines fongiques</term>
<term>Protéines végétales</term>
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<term>Maladies des plantes</term>
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<term>Protéines végétales</term>
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<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Substitution</term>
<term>Disease Resistance</term>
<term>Gene Expression Regulation, Fungal</term>
<term>Gene Expression Regulation, Plant</term>
<term>Genetic Association Studies</term>
<term>Host-Pathogen Interactions</term>
<term>Sequence Analysis, DNA</term>
<term>Sequence Analysis, RNA</term>
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<term>Analyse de séquence d'ARN</term>
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<term>Régulation de l'expression des gènes fongiques</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Résistance à la maladie</term>
<term>Substitution d'acide aminé</term>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b>
</p>
<p>This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.</p>
</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31842749</PMID>
<DateCompleted><Year>2020</Year>
<Month>04</Month>
<Day>13</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>04</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>20</Volume>
<Issue>1</Issue>
<PubDate><Year>2019</Year>
<Month>Dec</Month>
<Day>16</Day>
</PubDate>
</JournalIssue>
<Title>BMC genomics</Title>
<ISOAbbreviation>BMC Genomics</ISOAbbreviation>
</Journal>
<ArticleTitle>Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance.</ArticleTitle>
<Pagination><MedlinePgn>985</MedlinePgn>
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<ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-019-6369-7</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sharma Poudel</LastName>
<ForeName>Roshan</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>Department of Plant Pathology, North Dakota State University, Fargo, ND, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Richards</LastName>
<ForeName>Jonathan</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Department of Plant Pathology and Crop Physiology, Louisiana State University, Baton Rouge, LA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Shrestha</LastName>
<ForeName>Subidhya</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Department of Plant Pathology, North Dakota State University, Fargo, ND, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Solanki</LastName>
<ForeName>Shyam</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Brueggeman</LastName>
<ForeName>Robert</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA. bob.brueggeman@wsu.edu.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
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<Agency>National Science Foundation</Agency>
<Country></Country>
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<Month>12</Month>
<Day>16</Day>
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<MedlineTA>BMC Genomics</MedlineTA>
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<ISSNLinking>1471-2164</ISSNLinking>
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<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D019943" MajorTopicYN="N">Amino Acid Substitution</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000472" MajorTopicYN="Y">pathogenicity</QualifierName>
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<MeshHeading><DescriptorName UI="D060467" MajorTopicYN="Y">Disease Resistance</DescriptorName>
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<MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
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<MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
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<MeshHeading><DescriptorName UI="D015966" MajorTopicYN="N">Gene Expression Regulation, Fungal</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D056726" MajorTopicYN="N">Genetic Association Studies</DescriptorName>
</MeshHeading>
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