Exploiting eIF4E-based and associated broad-spectrum recessive resistance to potyviruses in dicots and monocots.
Lead Research Organisation:
University of Warwick
Department Name: Warwick HRI
Abstract
The project is a collaboration between Warwick HRI working on the dicotyledonous brassica plants and Rothamsted Research working on the monocotyledonous plants barley. The main aim is to: exploit sources of recessive eIF4E-based resistance to potyviruses in these plants. The involvement of the plant gene eIF4E in the life-cycle of viruses was first discovered in experiments on Turnip mosaic virus (TuMV, a potyvirus) and Arabidopsis. Subsequently it was found that the genes eIF4E or its isoform (eIF(iso)4E) are responsible for natural resistance to potyviruses in a range of crop types. The basis of the resistance is that potyviruses require one of these genes in order to complete their life-cycle. It is known that plants with specific alterations in these genes that affect the binding between the plant protein it codes and a viral protein (VPg) are resistant to infection. We have shown that eIF4E is associated with resistance to potyviruses in brassica and barley. The resistances described so far in other plant types involving eIF4E alone are not effective against all strains of the particular potyvirus. However, we have shown that in a brassica, eIF4E in combination with another gene (retr01), confers resistance against all strains of the potyvirus (TuMV). Other genes are involved in the interaction between the viral VPg protein and eIF4E, these include a the very similar gene eIF(iso)4E and other associated genes (eIF4G, eIF4A and isoforms of these). By studying the natural variation in the eIF4E and eIF(iso)4E genes from resistant and susceptible Brassica rapa and barley lines we aim to find new sources of resistance and understand the mechanism of the resistance. We will screen a collection of plants representing 95% of the genetic variation available within the brassica species and a barley diversity panel consisting of up to 800 landraces. Those plants that differ within the eIF4E gene will be tested with informative isolates of the potyviruses to check for resistance/susceptibility. Any eIF4E or eIF(iso)4E variants conferring resistance will be sequenced. This will be supported by looking at plants that have been mutated with chemicals to identify other novel changes in eIF4E and eIF(iso)4E alleles. Lines with such changes will be tested for resistance to a panel of BaMMV and BaYMV isolates. The aim is to identify forms of eIF4E that confer resistance that is durable to all (or most) virus isolates. Using the crystal structures available for eIF4E a model will be generated for eIF4E from barley and B. rapa. Natural and chemically-induced changes in the building blocks (amino acids) of the eIF4E associated with virus resistance in barley and B. rapa will be mapped on the 3D model of the normal eIF4E proteins. The effect of the changes on the potential ability of barley and B. rapa eIF4E to bind to the viral VPg protein will then be investigated. The outcome of this work will be the prediction of superior resistance genes of barley and B. rapa eIF4E for deployment in breeding. A gene retr01 which in combination with eIF4E confers the broad-spectrum resistance to TuMV in B. rapa will be fine mapped to identify the gene's position in the plant genome. The sequence of the gene will be used to search databases to predict its function, understand the mechanism of the broad-spectrum resistance and how retr01 might interact with eIF4E. Based on the best sources of virus resistance in brassicas and barley, changes associated with the genes conferring resistance will be used to design assays which can be used by breeders to incorporate the resistances into their elite breeding stocks by normal breeding methods (crossing). The project will provide an understanding of the scientific basis of the broad-spectrum resistance. Once the mechanism is understood it should be possible to deploy such resistance in a wide range of economically important crop species.
Technical Summary
The Potyviridae is the largest family of plant viruses in the world and cause some of the most important virus diseases of crops in the world. Plant resistance to viruses is the only reliable and sustainable means of control. Potyviruses seem to require the eukaryotic translation initiation factor 4E (eIF4E plant gene) for successful multiplication in the host. Incompatibility between variants of eIF4E genes and the potyvirus VPg has been found to be the basis of natural resistance to potyviruses in several species. eIF4E-based resistance is frequently strain-specific. This project aims to look for natural allelic variation in eIF4Ee within brassica and barley. Chemically induced allelic variants of eIF4E identified using barley TILLING populations currently available will increase the likelihood of finding novel variants capable of conferring resistance to potyviruses. Using these approaches and through modelling the likely effect of the different alleles on the known binding sites within the protein from both monocots and dicots we aim to identify and predict those likely to confer resistance to resistance breaking strains of the potyviruses. Other genes have been identified that have a role in the eukaryotic initiation complex (EIC) including eIF(iso)4E which has also been shown to be capable of conferring resistance. Allelic variation and possible associated resistance in this gene will also be investigated. In B. rapa we have already mapped a second gene (retr01) which with eIF4Ee confers broad-spectrum resistance to TuMV. This presents the opportunity to develop more durable resistance. By identifying this gene we will be able to determine if it is involved in the EIC and whether it interacts with eIF4Ee to confer broad-spectrum resistance. Discovery of the gene/s underlying broad-spectrum potyvirus resistance associated with eIF4E and markers for these provides the exciting possibility of developing durable potyvirus resistance in a wide range of crops.
People |
ORCID iD |
John Walsh (Principal Investigator) | |
Guy Barker (Co-Investigator) |
Publications
Jenner CE
(2010)
Turnip mosaic virus (TuMV) is able to use alleles of both eIF4E and eIF(iso)4E from multiple loci of the diploid Brassica rapa.
in Molecular plant-microbe interactions : MPMI
Ho T
(2010)
Nucleotide bias of DCL and AGO in plant anti-virus gene silencing.
in Protein & cell
Qian W
(2013)
Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chinese cabbage (Brassica rapa L.).
in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Nguyen HD
(2013)
Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago.
in PloS one
Lydiate DJ
(2014)
Genetic control of immunity to Turnip mosaic virus (TuMV) pathotype 1 in Brassica rapa (Chinese cabbage).
in Genome
Nellist CF
(2014)
Multiple copies of eukaryotic translation initiation factors in Brassica rapa facilitate redundancy, enabling diversification through variation in splicing and broad-spectrum virus resistance.
in The Plant journal : for cell and molecular biology
Schwinghamer M
(2014)
Turnip mosaic virus: potential for crop losses in the grain belt of New South Wales, Australia
in Australasian Plant Pathology
Sánchez F
(2015)
Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns.
in Molecular plant-microbe interactions : MPMI
Shopan J
(2017)
Eukaryotic translation initiation factor 2B-beta (eIF2Bß), a new class of plant virus resistance gene.
in The Plant journal : for cell and molecular biology
Michelmore R
(2017)
Foundational and Translational Research Opportunities to Improve Plant Health.
in Molecular plant-microbe interactions : MPMI
Description | BBSRC-funded researchers have described a mechanism conferring resistance in brassica plants to Turnip mosaic virus, a discovery which it is hoped will lead to durable resistance being introduced in to food crops. The University of Warwick, Chinese Academy of Agricultural Sciences and Syngenta Seeds team report their finding in The Plant Journal. Turnip mosaic virus (TuMV) can infect all kinds of plants, including oilseed rape, peas, cabbages, broccoli, Brussels sprouts, turnips, radish and cauliflower; it causes significant damage and losses to crops. TuMV is a member of the largest taxonomic group of plant viruses causing major diseases in most crop plants and hence the discovery has tremendous generic relevance. In their paper the researchers have unravelled the mechanism behind a novel broad-spectrum, recessive and potentially durable resistance to the virus and identified the gene involved. The resistance, which arises from a particular form of a gene called eIF4E, has been shown to be effective against different strains of TuMV from across the world. The University of Warwick has patented the generic resistance mechanism; Syngenta Seeds have purchased the generic patent and are currently introducing the resistance gene into commercial varieties of brassicas via a breeding programme. The breeding programme has been speeded up dramatically by the identification of the gene at Warwick, this has allowed Syngenta to use marker-assisted selection for the gene. Pre-commercial field trials are planned for 2016. Lead investigator Dr John Walsh, from the University of Warwick, said: "This is the culmination of careful and detailed research built on in depth knowledge of the virus and its interactions with brassica plants. The research programme has involved collaborations with valued colleagues at the University of Warwick, particularly Dr Guy Barker, Dr Carol Jenner and Dr Jay Moore, and colleagues in Canada, China, Taiwan, Japan, Holland and Spain, culminating with BBSRC-funded, Warwick PhD student Charlotte Nellist completing the final piece of the jigsaw. "The nature and mechanism of the resistance suggests that unlike many forms of plant resistance to disease, this particular resistance has the potential to be durable." Reference: Multiple copies of eukaryotic translation initiation factors in Brassica rapa facilitate redundancy, enabling diversification through variation in splicing and broad-spectrum virus resistance. http://onlinelibrary.wiley.com/doi/10.1111/tpj.12389/abstract |
Exploitation Route | As explained above, the findings are being taken forward by a commercial seed company who have purchased the rights to our patent and are pursuing it worldwide. They are also introgressing our novel broad-spectrum virus resistance in to commercial plant varieties. It is anticipated new varieties based on our resistance will be released in 2022. |
Sectors | Agriculture Food and Drink Education Environment |
Description | BBSRC-funded researchers have described a mechanism conferring resistance in brassica plants to Turnip mosaic virus, a discovery which it is hoped will lead to durable resistance being introduced in to food crops. The University of Warwick, Chinese Academy of Agricultural Sciences and Syngenta Seeds team report their finding in The Plant Journal. Turnip mosaic virus (TuMV) can infect all kinds of plants, including oilseed rape, peas, cabbages, broccoli, Brussels sprouts, turnips, radish and cauliflower; it causes significant damage and losses to crops. TuMV is a member of the largest taxonomic group of plant viruses causing major diseases in most crop plants and hence the discovery has tremendous generic relevance. In their paper the researchers have unravelled the mechanism behind a novel broad-spectrum, recessive and potentially durable resistance to the virus and identified the gene involved. The resistance, which arises from a particular form of a gene called eIF4E, has been shown to be effective against different strains of TuMV from across the world. The University of Warwick has patented the generic resistance mechanism; Syngenta Seeds have purchased the generic patent and are currently introducing the resistance gene into commercial varieties of brassicas via a breeding programme. The breeding programme has been speeded up dramatically by the identification of the gene at Warwick, this has allowed Syngenta to use marker-assisted selection for the gene. Pre-commercial field trials are planned for 2016. Lead investigator Dr John Walsh, from the University of Warwick, said: "This is the culmination of careful and detailed research built on in depth knowledge of the virus and its interactions with brassica plants. The research programme has involved collaborations with valued colleagues at the University of Warwick, particularly Dr Guy Barker, Dr Carol Jenner and Jay Moore, and colleagues in Canada, China, Taiwan, Japan, Holland and Spain, culminating with BBSRC-funded, Warwick PhD student Charlotte Nellist completing the final piece of the jigsaw. "The nature and mechanism of the resistance suggests that unlike many forms of plant resistance to disease, this particular resistance has the potential to be durable." Syngenta anticipate release of commercial plant varieties possessing the virus resistance discovered at Warwick by 2022. Reference: Multiple copies of eukaryotic translation initiation factors in Brassica rapa facilitate redundancy, enabling diversification through variation in splicing and broad-spectrum virus resistance. http://onlinelibrary.wiley.com/doi/10.1111/tpj.12389/abstract. Patents have been filed by the University of Warwick: patent WO 2011/161466 A1, https://patentimages.storage.googleapis.com/9a/4a/0d/d605689db7248c/WO2011161466A1.pdf and Syngenta US 2013/0117879 A1, https://patents.google.com/patent/US20130117879/en |
First Year Of Impact | 2010 |
Sector | Agriculture, Food and Drink,Education,Environment |
Description | I was invited to and participated in the UK-US Plant Health Workshop organised by BBSRC, USDA, UK Science & Innovation Network, Research Councils UK United States and the US National Institute of Food and Agriculture in the British Embassy on 19-21 September, 2016. The workshop produced a white paper 'Foundational and Translational Research Opportunities to Improve Plant Health', Molecular Plant-Microbe Interactions 30 (7). |
Geographic Reach | North America |
Policy Influence Type | Membership of a guideline committee |
URL | https://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-01-17-0010-CR |
Description | Invited to and participated in the Industrial Strategy Challenge Fund Workshop - Agricultural Productivity held in Solihull on 15 August, 2017 attended by industry representatives, BBSRC, NERC, academics, levy boards etc. |
Geographic Reach | National |
Policy Influence Type | Membership of a guideline committee |
Description | BBSRC iCASE studentship |
Amount | £111,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2015 |
End | 09/2019 |
Description | Warwick Impact Fund |
Amount | £45,643 (GBP) |
Funding ID | 15LFHF02 |
Organisation | University of Warwick |
Sector | Academic/University |
Country | United Kingdom |
Start | 07/2017 |
End | 07/2019 |
Title | Broad-spectrum resistance |
Description | Plant lines with broad-spectrum, potentially durable disease resistance along with within-gene molecular markers. |
Type Of Material | Biological samples |
Year Produced | 2010 |
Provided To Others? | Yes |
Impact | Syngenta are introgressing the gene conferring the broad-spectrum disease resistance into commercial plant lines, utilising the molecular markers we jointly developed. |
URL | http://www.bbc.co.uk/programmes/b00vy38g |
Description | Syngenta CASE studentship |
Organisation | Syngenta International AG |
Country | Switzerland |
Sector | Private |
PI Contribution | PhD studentship outputs |
Collaborator Contribution | Plant lines for crossing to and molecular marker services |
Impact | Identity of gene involved in broad-spectrum disease resistance |
Start Year | 2009 |
Description | Syngenta material purchase |
Organisation | Syngenta International AG |
Country | Switzerland |
Sector | Private |
PI Contribution | Provided plant germplasm with broad-spectrum disease resistance |
Collaborator Contribution | A route to exploitation / commercialisation |
Impact | Reported eslsewhere in Researchfish |
Start Year | 2009 |
Title | PLANT EUKARYOTIC TRANSLATION INITIATION FACTOR 4E |
Description | The invention relates to plants, and in particular to virus-resistant plants, and to methods of generating such plants. The invention extends to eukaryotic translation initiation factor variants and isoforms thereof, and to nucleic acids involved in the splicing of such variant factors, and uses thereof in methods for producing plants that are resistant to viral infections. |
IP Reference | WO2011161466 |
Protection | Patent granted |
Year Protection Granted | 2011 |
Licensed | Yes |
Impact | Syngenta Seeds are pursuing the patent worldwide. |
Description | CSI dissemination / publicity |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Radio 4's Science programme 'Material World' with Quentin Cooper: http://www.bbc.co.uk/programmes/b00vy38g An article on our research was published in the Guardian: http://www.theguardian.com/education/2010/dec/07/christmas-sprouts-black-spots-scientists An article on our research was published in the Daily Telegraph: http://www.telegraph.co.uk/topics/christmas/8143302/Brussel-sprout-will-be-resistant-to-black-spot.html A Warwick iCast: http://www2.warwick.ac.uk/newsandevents/icast/archive/s2week19/vegvirus/ |
Year(s) Of Engagement Activity | 2008,2010 |
URL | http://www.bbc.co.uk/programmes/b00vy38g |
Description | Challenges for Crop Production & Quality, Annals of Applied Biology Centenary Conference, Rothamsted, Harpenden |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Centenary meeting to celebrate 100 years of the Annals of Applied Biology attended by senior researchers, industry etc. where I was able to highlight outcomes of BBSRC CSI project and BBSRC iCASE studentship |
Year(s) Of Engagement Activity | 2014 |
URL | http://www.aab.org.uk/images/annals_centenary_pbf.pdf |
Description | Fascination of Plants Day |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | We had an exhibit at the Fascination of Plants Day on May 18th 2017 at our campus. |
Year(s) Of Engagement Activity | 2017 |
URL | https://warwick.ac.uk/study/outreach/news/celebrating_fascination_of/ |
Description | Innovate UK Industrial Strategy Challenge Fund Workshop - Agricultural Productivity |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | I participated in Innovate UK's Industrial Strategy Challenge Fund Workshop - Agricultural Productivity at the Ardlen Hotel, Solihul on 15 August, 2017. |
Year(s) Of Engagement Activity | 2017 |
Description | International Advances in Plant Virology conference (London) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A talk by PhD student Tongtong Wang at this international conference focussed on advances in virus research at which I was a member of the organising committee. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.aab.org.uk/images/virology_2016_ann_pbf.pdf |
Description | International Advances in Plant Virology conference (London) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A poster presented by PhD student Lawrence Bramham at this international conference focussed on advances in virus research at which I was a member of the organising committee. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.aab.org.uk/images/virology_2016_ann_pbf.pdf |
Description | International Advances in Plant Virology conference (London) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A poster presented by Brazilian collaborator Dr Marcelo Eiras at this international conference focussed on advances in virus research at which I was a member of the organising committee. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.aab.org.uk/images/virology_2016_ann_pbf.pdf |
Description | Invited presentation at Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA). Campus Montegancedo. Autopista M-40, km 38. Pozuelo de Alarcón. 28223 Madrid. Spain. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Invited presentation at Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA). Campus Montegancedo. Autopista M-40, km 38. Pozuelo de Alarcón. 28223 Madrid. Spain. |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.cbgp.upm.es/files/seminarios/SEMINARIOS_CBGP_2016_17.pdf |
Description | Invited seminar, University of York |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | Invited seminar presentation at Univewrsity of York, 17th April, 2018. |
Year(s) Of Engagement Activity | 2018 |
Description | Keynote conference presentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Keynote presentation entitled 'The quest for durable plant diease resistance' at the 10th International Virology Summit, 2-4 July, 2018 in Vienna, Austrai. |
Year(s) Of Engagement Activity | 2018 |
URL | https://virology.conferenceseries.com/europe/2018/ |
Description | Midlands Integrative Biosciences Training Partnership (MIBTP) BBSRC Doctoral Training Partnership Student Symposium Invited Presentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | Midlands Integrative Biosciences Training Partnership (MIBTP) BBSRC Doctoral Training Partnership Student Symposium Invited Presentation |
Year(s) Of Engagement Activity | 2017 |
Description | Public engagement event Gibbet Hill |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | A display at School of Life Sciences, University of Warwick public engagement event |
Year(s) Of Engagement Activity | 2017 |
URL | http://www2.warwick.ac.uk/fac/sci/lifesci/outreach/next/ |
Description | The Elizabeth Creak Charitable Trust Warwick Food Security Lecture; Keeping Pathogens at Bay |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Poster and plant exhibit at The Elizabeth Creak Charitable Trust Warwick Food Security Lecture; Keeping Pathogens at Bay outreach activity. |
Year(s) Of Engagement Activity | 2017 |
URL | https://warwick.ac.uk/fac/sci/lifesci/outreach/publicscievents/programme_for_event_final.pdf |
Description | UK-US Plant Health Workshop to discuss plant health and develop a white paper |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | the UK-US Plant Health Workshop held in the British Embassy, Washington DC was held to discuss biotic challenges to plant health and develop a white paper for future directions of research. |
Year(s) Of Engagement Activity | 2016 |
URL | https://apsjournals.apsnet.org/doi/full/10.1094/MPMI-01-17-0010-CR |
Description | UK-US Plant Health Workshop, British Embassy, Washington DC |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Policymakers/politicians |
Results and Impact | A UK-US workshop to: - facilitate new collaborations and build on existing links - increase community knowledge for international research collaborations - inform future funding priorities |
Year(s) Of Engagement Activity | 2016 |
Description | University visit (Saga University, Japan) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | Visit to Saga University, Japan, 18-24th May, 2019. Lecture to undergraduate and post-graduate students and discussions with postgraduate (MSc and PhD) students. |
Year(s) Of Engagement Activity | 2019 |
Description | Video, open day JW YouTube |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | A video to highlight the outcomes of the BBSRC funded projects |
Year(s) Of Engagement Activity | 2014 |
Description | Virology conference, Haarlem, The Netherlands |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | An oral presentation by PhD student Tongtong Wang at the international conference focussed on virus disease of legumes and vegetables at which I was the president of the group. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.plant-virology.nl/IWGLVV2015/ |
Description | Virology conference, Haarlem, The Netherlands |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | An international conference focussed on virus disease of legumes and vegetables at which I was the president of the group. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.plant-virology.nl/IWGLVV2015/ |