Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici.
Identifieur interne : 000085 ( Main/Exploration ); précédent : 000084; suivant : 000086Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici.
Auteurs : Melania Figueroa [États-Unis] ; Narayana M. Upadhyaya [Australie] ; Jana Sperschneider [Australie] ; Robert F. Park [Australie] ; Les J. Szabo [États-Unis] ; Brian Steffenson [États-Unis] ; Jeff G. Ellis [Australie] ; Peter N. Dodds [Australie]Source :
- Frontiers in plant science [ 1664-462X ] ; 2016.
Abstract
The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.
DOI: 10.3389/fpls.2016.00205
PubMed: 26941766
PubMed Central: PMC4764693
Affiliations:
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Upadhyaya</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author><author><name sortKey="Sperschneider, Jana" sort="Sperschneider, Jana" uniqKey="Sperschneider J" first="Jana" last="Sperschneider">Jana Sperschneider</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation Perth, WA, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation Perth, WA</wicri:regionArea><wicri:noRegion>WA</wicri:noRegion></affiliation></author><author><name sortKey="Park, Robert F" sort="Park, Robert F" uniqKey="Park R" first="Robert F" last="Park">Robert F. Park</name><affiliation wicri:level="1"><nlm:affiliation>Faculty of Agriculture and Environment, Plant Breeding Institute, The University of Sydney Narellan, NSW, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Faculty of Agriculture and Environment, Plant Breeding Institute, The University of Sydney Narellan, NSW</wicri:regionArea><wicri:noRegion>NSW</wicri:noRegion></affiliation></author><author><name sortKey="Szabo, Les J" sort="Szabo, Les J" uniqKey="Szabo L" first="Les J" last="Szabo">Les J. Szabo</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA; Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research ServiceSt. Paul, MN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA; Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research ServiceSt. Paul, MN</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author><author><name sortKey="Steffenson, Brian" sort="Steffenson, Brian" uniqKey="Steffenson B" first="Brian" last="Steffenson">Brian Steffenson</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota St. Paul, MN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota St. Paul, MN</wicri:regionArea><placeName><region type="state">Minnesota</region></placeName></affiliation></author><author><name sortKey="Ellis, Jeff G" sort="Ellis, Jeff G" uniqKey="Ellis J" first="Jeff G" last="Ellis">Jeff G. Ellis</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author><author><name sortKey="Dodds, Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N" last="Dodds">Peter N. Dodds</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">26941766</PMID><DateCompleted><Year>2016</Year><Month>03</Month><Day>04</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>29</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici.</ArticleTitle><Pagination><MedlinePgn>205</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2016.00205</ELocationID><Abstract><AbstractText>The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Figueroa</LastName><ForeName>Melania</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota St. Paul, MN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Upadhyaya</LastName><ForeName>Narayana M</ForeName><Initials>NM</Initials><AffiliationInfo><Affiliation>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sperschneider</LastName><ForeName>Jana</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Agriculture, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation Perth, WA, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Robert F</ForeName><Initials>RF</Initials><AffiliationInfo><Affiliation>Faculty of Agriculture and Environment, Plant Breeding Institute, The University of Sydney Narellan, NSW, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Szabo</LastName><ForeName>Les J</ForeName><Initials>LJ</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA; Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research ServiceSt. Paul, MN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Steffenson</LastName><ForeName>Brian</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota St. Paul, MN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ellis</LastName><ForeName>Jeff G</ForeName><Initials>JG</Initials><AffiliationInfo><Affiliation>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dodds</LastName><ForeName>Peter N</ForeName><Initials>PN</Initials><AffiliationInfo><Affiliation>Agriculture, Commonwealth Scientific and Industrial Research Organisation Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D016454">Review</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>02</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant 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IdType="pubmed">8986840</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Australie</li><li>États-Unis</li></country><region><li>Minnesota</li></region></list><tree><country name="États-Unis"><region name="Minnesota"><name sortKey="Figueroa, Melania" sort="Figueroa, Melania" uniqKey="Figueroa M" first="Melania" last="Figueroa">Melania Figueroa</name></region><name sortKey="Steffenson, Brian" sort="Steffenson, Brian" uniqKey="Steffenson B" first="Brian" last="Steffenson">Brian Steffenson</name><name sortKey="Szabo, Les J" sort="Szabo, Les J" uniqKey="Szabo L" first="Les J" last="Szabo">Les J. Szabo</name></country><country name="Australie"><noRegion><name sortKey="Upadhyaya, Narayana M" sort="Upadhyaya, Narayana M" uniqKey="Upadhyaya N" first="Narayana M" last="Upadhyaya">Narayana M. Upadhyaya</name></noRegion><name sortKey="Dodds, Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N" last="Dodds">Peter N. Dodds</name><name sortKey="Ellis, Jeff G" sort="Ellis, Jeff G" uniqKey="Ellis J" first="Jeff G" last="Ellis">Jeff G. Ellis</name><name sortKey="Park, Robert F" sort="Park, Robert F" uniqKey="Park R" first="Robert F" last="Park">Robert F. Park</name><name sortKey="Sperschneider, Jana" sort="Sperschneider, Jana" uniqKey="Sperschneider J" first="Jana" last="Sperschneider">Jana Sperschneider</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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