Rapid identification disease resistance genes from plant genomes by resistance gene enrichment sequencing (RenSeq) of EMS-derived susceptible mutants

Lead Research Organisation: John Innes Centre
Department Name: Crop Genetics

Abstract

Plant disease causes significant yield losses in agriculture. Wheat and potato are two of the most important crops worldwide, including India and the UK. Among the most damaging diseases of wheat are the rusts. Stripe rust occurs wherever the crop is grown causing average yearly yield losses of up to 10% in some regions. Stem rust was until the green revolution associated with regular crop failures and famine. The resistance introduced then has now been broken by new strains of the fungus, which started appearing in Africa 14 years ago. The potato late blight disease, the cause of the Great Irish Potato famine in the 1840s, is still a serious impediment to potato cultivation today. Pesticides can control these diseases but they are expensive, at odds with sustainable intensification of agriculture, and in developing countries and for subsistence farmers, they are simply unaffordable.

Wild relatives of domesticated crops contain many useful disease resistance (R) genes. Introducing this natural resistance is an elegant way of managing disease. However, traditional methods for introducing R genes typically involve long breeding trajectories to avoid linkage drag, i.e. the simultaneous introduction of deleterious traits. Furthermore, R genes tend to be overcome by the pathogen within a few seasons when deployed one at a time.

Our long-term strategy is to isolate, by molecular cloning, as many new R genes as possible, and introduce them in combinations using GM methods. Molecular cloning makes it possible, indeed straightforward, to put several new genes together in the same location in the genome, allowing breeders to work with them as a "single" gene and avoiding linkage drag. Moreover, from first principles, a pyramid of R genes with distinct specificities should be more durable.

Traditional map-based cloning of R genes, however, is still challenging. First, large tracts of plant genomes are inaccessible to map-based genetics due to lack of recombination. Second, most R genes belong to a structural class of genes called NB-LRRs, which tend to reside in complex clusters, and many hundreds of NB-LRRs populate a typical plant genome. The scientist therefore frequently delimits a map interval containing multiple NB-LRRs and must find out which confers the resistance of interest. An approach, which has been successfully used to narrow down the candidate list to a single NB-LRR, is mutagenesis and screening for susceptible mutants. This creates discrete variations whereby a simple comparison of mutant and wildtype can identify the R gene.

We propose a strategy that will significantly increase the rate of R gene identification. In a first step of our workflow, we will screen large numbers of mutagenized plants for susceptible mutants. In a second step, we will use a state-of-the art sequencing technique recently implemented in our lab to selectively capture and sequence all the NB-LRRs in a plant genome. This will allow us to rapidly and cheaply compare wildtype with mutants to identify and clone resistance genes.

The outputs of this research will be three-fold: (i) using known controls we will implement our generic strategy to isolate R genes from complex genomes, (ii) we will apply this strategy to identify novel R genes from potato and wheat (against late blight and wheat rusts respectively), and (iii) we will test our key wheat rust R genes in Indian and UK environments.

We envisage that not only will our strategy significantly accelerate R gene cloning, it could also be used to pursue R genes not amenable to standard genetics, e.g. in low- or non-recombinogenic regions of the genome including centromeres, alien introgressed segments, and translocations. In wheat, this would allow accessing a plethora of useful R genes currently unusable due to linkage to deleterious yield-depressing alleles.

Technical Summary

The isolation of plant disease resistance (R) genes by traditional map-based cloning is typically an expensive and time consuming process, requiring development of thousands of molecular markers and screening of large segregating populations. Furthermore, many perfectly good R genes reside in genetically inaccessible regions of the genome.

We recently developed a NextGen resistance gene enrichment-sequencing (RenSeq) workflow that allows rapid scrutiny of the hundreds of NB-LRR R gene candidates within a plant genome.

In this proposal we will use RenSeq to quickly and cheaply compare the NB-LRRome of resistant parents and EMS-derived susceptible mutants to accelerate the identification of agriculturally relevant R genes.

In particular we will:

Improve RenSeq by adapting it to long read technologies (MiSeq and PacBio). Next, we will perform RenSeq on a recombinant inbred line population. This will allow us to test and optimise various bioinformatics parameters - the best parameters will be those that allow the integration of most NB-LRR markers into the genetic map with a low false discovery rate. As a proof of concept, we will use our optimised RenSeq workflow to re-clone R genes from previously published EMS-derived mutants.

Apply optimised RenSeq to agriculturally relevant R genes. We will generate EMS mutant populations in (i) a wild diploid potato relative with resistance to potato late blight, (ii) a wild diploid wheat relative with resistance to wheat stem rust, and (iii) various introgression lines of hexaploid bread wheat with resistance to wheat stripe rust and/or leaf rust. The choice of germplasm will allow us to test our RenSeq workflow on increasingly complex situations from a small diploid genome (1 Gb) to a large hexaploid genome (17 Gb).

Assay germplasm for resistance in Indian and UK environments. We will exchange our key wheat germplasm lines between the UK and India to test their resistance efficacy under local conditions.

Planned Impact

A durable solution to wheat stem and stripe rust is a paramount problem in global food security. In recent years, new, more aggressive races of these two pathogens have appeared globally, increasing the potential for economic damage and food scarcity. Because the pathogens have shown the ability to overcome each new resistance gene that is deployed in agriculture, developing a capability to isolate large numbers of useful genes and deploy them in combinations is critical to successfully overcome these diseases. The proposed research aims to do exactly that: develop new methods for rapidly accessing novel resistance genes that can be deployed in wheat breeding programs.

Direct beneficiaries of this work include public wheat germplasm improvement programs (such as those at CIMMYT), the country-level breeding efforts that they support in the developing world (including Kenya, Ethiopia, Pakistan, India, and China), growers of wheat, and consumers of wheat in those countries. In the absence of a durable solution to wheat stem and wheat stripe rust, wheat agriculture, particularly in Africa and South Asia, will live under the constant threat of epidemics and resulting crop failure caused by this disease.

In the UK, new races of wheat stripe rust have appeared in recent years that infect previously resistant UK wheat cultivars. In addition, although stem rust has not been important in the UK or in most European wheat production for many years, climate change brings a new threat from this disease, which requires relatively warm conditions early in the growing season to have full impact. Although in high-value agriculture the pathogen can be controlled with chemical fungicide application, genetic resistance is vastly preferable from the standpoints of cost and environmental sustainability. Thus, UK and European wheat breeding companies, wheat growers, and consumers are also potential direct beneficiaries of this.

Identification of resistance genes that can be deployed for transgenic resistance to stem and stripe rust in wheat, in combinations to maximize durability of resistance are longterm (10-15) years, depending on acceptance of GM wheat.

Aegilops sharonensis, our choice as source for several of the novel resistance genes in the present proposal, is of interest to the global community of wheat researchers because its genome is closely related to the D and B genomes of hexaploid bread wheat. As part of another BBSRC-funded grant we have recently sequenced the genome of Ae. sharonensis and we are presently collaborating with the IWSC to perform genome-wide comparisons with the other wheat progenitors. The combined tools from these projects, including a deep sequence and vastly improved genetic map of this organism, will enable any interested researcher to more easily identify genes associated with useful agronomic traits in Ae sharonenesis. In addition to resistance genes for other diseases, these will include genes for tolerance to abiotic stresses such as heat and drought, and increased efficiency of nutrient utilization. These resources are already being made available to the research community.

The research staff working on this project will develop additional technical expertise in a diverse range of skills, including molecular genetics, bioinformatics, and plant biotechnology, specifically in wheat, an exceedingly important crop in UK and Indian agriculture. They will develop an increased understanding of the application of how basic science discoveries get translated into practical outcomes for agriculture by working with our downstream deployment partners. This expertise can be applied in future career positions in academia, research institutes, and in companies, both small agricultural biotech firms and global multi-national agriculture companies. These benefits will be realized immediately upon the next career progression steps taken by the individuals involved in the project.

Publications

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Bevan M (2017) Genomic innovation for crop improvement in Nature

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Hickey LT (2019) Breeding crops to feed 10 billion. in Nature biotechnology

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Kawashima CG (2016) A pigeonpea gene confers resistance to Asian soybean rust in soybean. in Nature biotechnology

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Mago R (2017) Generation of Loss-of-Function Mutants for Wheat Rust Disease Resistance Gene Cloning. in Methods in molecular biology (Clifton, N.J.)

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Narang D (2019) Fine mapping of Aegilops peregrina co-segregating leaf and stripe rust resistance genes to distal-most end of 5DS. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Steuernagel B (2017) MutRenSeq: A Method for Rapid Cloning of Plant Disease Resistance Genes. in Methods in molecular biology (Clifton, N.J.)

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Steuernagel B (2015) NLR-parser: rapid annotation of plant NLR complements. in Bioinformatics (Oxford, England)

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Steuernagel B (2017) Rapid Gene Isolation Using MutChromSeq. in Methods in molecular biology (Clifton, N.J.)

 
Title Wrestling genes out of the giant barley and wheat genomes 
Description Blog for general science audience on how to rapidly clone genes from wheat or barley 
Type Of Art Creative Writing 
Year Produced 2016 
Impact Postive feedback from friends and colleagues. 
URL http://blogs.biomedcentral.com/on-biology/2016/10/24/wrestling-genes-out-of-the-giant-barley-and-whe...
 
Description Optimising the RenSeq workflow:
We optimised resistance gene enrichment sequencing (RenSeq) using PacBio long read technology to accelerate the cloning of the blight resistance genes Rpi-amr3 and Rpi-amr1E in wild potato (Witek et al., 2016; Witek et al., unpublished). In tomato and potato, the PacBio long read technology leads to assembly of the near-complete NLR repertoires (Witek et al., 2016; Giolai et al. 2016). However, in hexaploid wheat, large introns permitted only ~1300 (out of ~3400) NLR loci to be assembled into full-length molecules with PacBio. In the future, we propose to use other technologies such as mate-pair or linked-reads combined with NLR capture to overcome this technical hurdle in wheat.

Other key outputs from this grant include a series of workshops on RenSeq and gene cloning (JIC, UK, June 2015), bioinformatics (PAU, India, March, 2017) and scientific soft skills (PAU, India, March 2017. Our Indian collaborators have also visited JIC to receive hands on training in RenSeq wet-lab and bioinformatics procedures. These visitors included Dr Satinder Kaur (1 June to 31 August, 2015), Prof. Parveen Chhuneja (16 May to 15 August 2016) and Dr Inderjit Singh Yadav (27 March to 26 June 2017). Our outputs have been well received by the community as evidenced by many citations, high Altmetric scores, and the invitations received to present at conferences and public good and commercial breeding companies by the lead PI (Brande Wulff, n = 21) and the named postdocs (8). Finally, we have filed five patent applications, two on methods, and three on gene discoveries.
We delivered on another key aim of the proposal, by demonstrating the power of combining RenSeq with mutagenesis by cloning the wheat stem rust resistance genes Sr22 and Sr45 in a matter of months (Steuernagel et al., 2016).

In recognising that not all disease resistance genes will be clonable using RenSeq approaches, due to technical limitations (as outlined above with obtaining fully assembled NLR complements from exome capture), or due to the bias introduced by bait design (after all, not all disease resistance genes are NLRs), we developed the MutChromSeq technology (Sanchez-Martin et al., 2016). In this workflow, we flow-sorted chromosomes from wildtype and mutant plants (in collaboration with Jaroslav Dolezel in the Czech Republic) followed by sequencing and sequence comparison. We demonstrated proof-of-concept, by cloning the wax biosynthesis gene Eceriferum-q in barley and the powdery mildew resistance gene Pm2 in wheat in a matter of months.
Exploitation Route Many colleagues in the UK and abroad are now using our enabling technologies to speed up gene cloning in complex plant genomes.

Note added: 08 March 2019: The 2Blades Foundation have sponsored a field trial in Rosemont, Minnesota, in which a GM stack containing 5 stem rust resistance genes was tested against local pathogen isolates and found to be completely immune. 2Blades are planning to engineer and test additional stacks, including in stem rust hot spots, e.g. Kenya.
Sectors Agriculture, Food and Drink

 
Description Our findings have stimulated ongoing discussions between multiple partners (2Blades Foundation, CSIRO, JIC, and CIMMYT) for establishing an international framework for cloning wheat stem rust resistance genes and engineering a transgenic stack for deployment in developing countries. Two of the stem rust resistance (Sr) genes we have cloned have been used to engineer a multigene stack with three other Sr genes. The five gene stack was tested in the field in Minnesota during the 2018 growing season, where it was found to confer complete immunity to local isolates of the pathogen (http://2blades.org/2019/03/12/wheat-lines-from-2blades-csiro-and-umn-exhibit-exceptional-stem-rust-resistance-in-the-field/). Further tests are planned for this summer. We have since cloned additional Sr genes, and these are being incorporated into the new stacks containing more/different combinations of Sr genes. We have developed improved technologies to speed up the cloning of disease resistance genes by combining association gentics to resistance gene enrichment sequencing (Arora et al. 2019; Nature Biotechnology) and this has led to additional funding (e.g. BBSRC GCRF-IAA BB/GCRF-IAA/17/11, BBSRC DTP, BBSRC iCASE, Newton Institutional Links grant) and collaborations on other disease and pest targets (e.g. wheat stripe rust, wheat leaf rust, wheat blast, powdery mildew, aphids, hessian fly, etc). We have cloned >10 high confidence candidate resistance genes, including two wheat blast resistance genes. For wheat blast we have initiated discussions with potential future Bangladeshi collaborators to realise practical outcomes for these genes. We have filed patent applications on the new technology and proceeded to PCT (January 2019), and in collaboration with 2Blades, we have patented three stem rust resistance genes. Realising that GM crops, and in particular GM wheat, is locked in a socio-political impasse (Wulff et al., 2018, Science), we have (in collaboration with the Lee Hickey lab in University of Queensland) developed methods for accelerated generation advancement (dubbed 'speed breeding') for wheat, barley, oat, brassica, pea, grasspea, etc. (Watson et al., 2018, Nature Plants; Ghosh et al., 2018, Nature Protocols). Speed breeding allows halving the generation time for many crops by modulating light intensiy, quality and day length. Speed breeding has been very well received by the plant research and breeding community. Our protocols were widely distributed before publication to resaerchers and breeders in different countries. Upon publicaiton, the enabling technology was covered widely by the national and international press and media (including The Times, The Guardian, News Week, National Geographic, BBC Radio4, BBC World Service, etc), translated into Chinese, Japanese, Russian, German, Spanish and Arabic, and reaching an estimated audience of >7M.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
Impact Types Cultural,Societal,Economic

 
Description 2Blades Foundation
Amount $20,000 (USD)
Organisation 2Blades Foundation 
Sector Charity/Non Profit
Country United States
Start 07/2017 
End 07/2018
 
Description A multi-R gene stack for durable resistance to wheat stem rust (with 2Blades Foundation)
Amount £939,147 (GBP)
Organisation Two Blades Foundation 
Sector Charity/Non Profit
Country United States
Start 07/2014 
End 06/2017
 
Description BBSRC "Impact Acceleration Account"
Amount £13,078 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 02/2018
 
Description BBSRC - ISCF Agri-food Technology Catalyst
Amount £29,943 (GBP)
Funding ID BB/SCA/JIC/17 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 02/2018
 
Description BBSRC iCASE
Amount £113,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2018 
End 09/2022
 
Description Doctoral Trainingship Programme
Amount £97,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
 
Description FSOV
Amount € 279,216 (EUR)
Organisation French Wheat Research Fund (FSOV) 
Sector Charity/Non Profit
Country France
Start 02/2017 
End 01/2020
 
Description FSOV
Amount € 255,538 (EUR)
Organisation French Wheat Research Fund (FSOV) 
Sector Charity/Non Profit
Country France
Start 02/2017 
End 01/2020
 
Description Global Challenges Research Fund
Amount £316,622 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 07/2018
 
Description Global Challenges Research Fund - Data and Resources
Amount £897,694 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 07/2017
 
Description John Innes Centre KEC Innovation Fund
Amount £40,499 (GBP)
Organisation John Innes Centre 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2015 
End 12/2016
 
Description Marie Sklodowska Curie Action International Training Network
Amount € 238,507 (EUR)
Organisation Marie Sklodowska-Curie Actions 
Department Initial Training Networks (ITN)
Sector Charity/Non Profit
Country Global
Start 01/2016 
End 12/2019
 
Description Monsanto Beachel-Borlaug International Scholarship
Amount $220,000 (USD)
Funding ID MBBIS 06-400258-12580 
Organisation Monsanto 
Sector Private
Country United States
Start 07/2016 
End 06/2020
 
Description Newton Institutional Links Grant
Amount £299,973 (GBP)
Organisation Newton Fund 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2020
 
Description Norwich Research Park Translational Fund
Amount £41,272 (GBP)
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 11/2016 
End 06/2017
 
Title Wheat stem rust resistance genes and methods of use 
Description The patent describes the cloning and characterisation of two stem rust resistance genes in wheat. 
IP Reference WO2017024053 
Protection Patent application published
Year Protection Granted 2015
Licensed No
Impact The genes have been added to multi-R gene stacks and transformed into wheat and barley. These will be field trialled in Minnesota, USA in the 2018 growing season.
 
Title AgRenSeq - GitHub 
Description AgRenSeq is a pipeline to identify candidate resistance (R) genes in plants directly from a diversity panel. The diversity panel needs to be sequenced (R gene enrichment sequencing - RenSeq) and phenotyped. Phenotype scores need to be converted to AgRenSeq scores that assign positive values to resistance and negative values to suscetibility. An intermediate phenotype should have an AgRenSeq score close to zero. For RenSeq you will need a bait library that targets R genes in your plant species. A bait library for Aegilops tauschii can be found here. We reccomend Arbor biosciences for synthesis of baits. They also offer the enrichment service. 
Type Of Technology Software 
Year Produced 2018 
Impact Requests for collaboration from academia and industry. 
 
Title MutChromSeq - GitHub 
Description MutChromSeq is a method to clone genes in plants. Prerequisites are that the gene must be related to a specific phenotype and that chromosome flow sorting is established in the species. In a nutshell, you do an EMS mutagenesis screen of your wildtype and look for mutants that have lost the phenotype related to your gene. You need at least 5 or 6 independent mutants. If you have been working on that gene for a while, you most problably know on which chromosome it is. Otherwise find out. Flow sort chromosomes of your wildtype and mutants. Sequence amplified DNA from your chromosomes on Illumina. You need about a HiSeq2000 lane per chromosome. A denovo assembly of the wildtype data will be used as reference. You map the mutants against that reference and will find one or very few genes that have a mutation in every of your mutants. Here you find the pipeline and scripts for the analysis of the data. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Requests for collaborations and requests for participation in responsive mode grants, and foundation for PhD fellowship proposal to international funding organisation. 
URL https://github.com/steuernb/MutChromSeq
 
Title MutRenSeq Mutant Hunter 
Description The MutRenSeq Mutant Hunter is a pipeline to combine resistance gene enrichment sequencing (RenSeq) with EMS mutant screens to identify NLR-type resistance genes. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact This pipeline has resulted in collaborations (some on responsive mode grants), research agreements, and further funding (e.g. from the 2Blades Foundation, USA). 
URL https://github.com/steuernb/MutantHunter/
 
Description 5th Plant Genomics Workshop, Amsterdam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented my work on rapid gene cloning and speed breeding at the 5th Plant Genomics Workshop, Amsterdam. This lead to questions and discussion with other scientists and representatives from industry, and I was invited back to present again in 2018, as well as invited to the advisory board.
Year(s) Of Engagement Activity 2017
 
Description Annual Science Meeting 2018, JIC and TSL 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I was called upon to give an update of my work at the JIC and TSL Annual Science Meeting 2018.
Year(s) Of Engagement Activity 2018
 
Description BMGF Grand Challenges Meeting, Berlin, Germany 
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 I was invited to the BMGF Grand Challenges Meeting, in Berlin, Germany. This has since led to further interactions with the BMGF and DFID funded DGGW project, and a request for a workshop at the next DGGW meeting which will be held in the John Innes Centre in 2020.
Year(s) Of Engagement Activity 2019
 
Description CerealPath PhD Course on Scientific Soft Skills 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I co-organised and taught a course on scientific soft skills for a group of PhD students from the EU funded CerealPath programme.
Year(s) Of Engagement Activity 2016
URL https://cerealpath.eu/
 
Description Cranfield University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact I was called upon to give a lecture to MSc students on the Cranfield University bioinformatics course. I was asked to come back again in May for a two day visit to teach scientific soft skills for early career scientists.
Year(s) Of Engagement Activity 2019
 
Description DivSeek Workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I was called upon at short notice to give a presentation at the DivSeek workshop on how to exploit germplasm collections for rapid trait identificaiton and deployment.
Year(s) Of Engagement Activity 2019
 
Description Interview by Jerome Starkey, The Times 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Following our press release on the appearance of stem rust in the UK for the first time in 50 years, I was interviewed by The Times correspondent Jereme Starkey. This resulted in a short article in The Times.
Year(s) Of Engagement Activity 2018
URL https://www.thetimes.co.uk/article/plague-that-scared-the-romans-is-back-g6nzm5d0k
 
Description Interview with Newsweek on genetic diversity 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact I was interviewed by Newsweek on the importance of genetic diversity in crops.
Year(s) Of Engagement Activity 2018
URL http://www.newsweek.com/feed-world-scientists-have-plan-save-chickpeas-destruction-806925
 
Description Interviews with press and media on speed breeding 
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 Public/other audiences
Results and Impact JIC External Relations department released a press release on our work on 'speed breeding'. This sparked considerable attention from the press and media. I expect I gave about 20 interviews in the ensuing days, featured on BBC Look East, the local press, two national newspapers (The Times and The Guardian), Newsweek, as well as countless other media outlets across the world, including in Japanese, Chinese and Arabic.
Year(s) Of Engagement Activity 2018
 
Description Invited presentaiton at G20 Wheat Meeting in Frankfurt 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a presentation at the G20 wheat meeting in Frankfurt. The presentation sparked questions and led to requests for futher information and collaboration.
Year(s) Of Engagement Activity 2016
URL https://www.bmel.de/SharedDocs/TermineVeranstaltungen/EN/16-12-08-InternationalWheatCongress.html
 
Description Invited presentation at AgriTech East, NIAB, Cambridge, UK 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact AgriTech East dissemination activity to local farmers, breeders and industry stake holders on rust diseases of wheat.
Year(s) Of Engagement Activity 2016
URL https://www.cambridgenetwork.co.uk/events/pollinator-rusts-and-other-cereal-killers/
 
Description Invited presentation at BeCA-ILRI (Nairobi, Kenya) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact This presentation sparked questions and discussions.

Expansion of my scientific network and opportunities for future collaborations.
Year(s) Of Engagement Activity 2014
 
Description Invited presentation at Elsoms Ltd, Spalding 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Industry/Business
Results and Impact I was invited to give a presentation to the vegatble and herb breeding company Elsoms Ltd in Spalding, Lincolnshire. The presentation lead to request for further information and
Year(s) Of Engagement Activity 2016
 
Description Invited presentation at IPK, Gatersleben, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I gave a presentation on engineering resistance to the stem rust fungus in wheat using cloned resistance genes from wild grasses.
Year(s) Of Engagement Activity 2016
 
Description Invited presentation at Institute of Experimental Botany, Czech Republic 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to the Institute of Experimental Botany in the Czech Republic to give a presentation about my work on rapid gene discovery and cloning in Triticeae.
Year(s) Of Engagement Activity 2018
 
Description Invited presentation at Julius Kühn Institute, Quedlinburg, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Policymakers/politicians
Results and Impact I gave a presentation on engineering resistance to the stem rust fungus in wheat using cloned resistance genes from wild grasses.
Year(s) Of Engagement Activity 2016
 
Description Invited presentation at Kew 
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 was invited to give a short seminar on how to exploit genetic variation in crop wild relatives at a joint workshop organised between the John Innes Centre and Kew.
Year(s) Of Engagement Activity 2018
 
Description Invited presentation at National Institute of Botany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I gave a presentation on next generation disease resistance breeding in wheat.
Year(s) Of Engagement Activity 2015
 
Description Invited presentation at The Sainsbury Laboratory, Norwich, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Was invited to give a presentation of my work on wheat rusts at the annual Sainsbury Lab retreat.
Year(s) Of Engagement Activity 2016
 
Description Invited presentation at University College Dublin 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I gave a presentaiton to undergraduates and research scientists on the use of mutational genomics to isolate disease resistance genes.
Year(s) Of Engagement Activity 2016
 
Description Invited presentation at University of Nottingham 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact I was invited to give a presentation on my work at the University of Nottingham to share my latest results on rapid resistance gene discovery, cloning and deployment. This resulted in long discussions.
Year(s) Of Engagement Activity 2019
 
Description Invited presentation at the Australian National University, Canberra, Australia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I gave a presentation on cloning and stacking stem rust resistance genes in wheat.
Year(s) Of Engagement Activity 2015
 
Description Invited presentation at the Bill and Melinda Gates Foundation Grand Challenges Meeting in London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was asked to give a presentation on molecular breeding for durable disease resistance, including my work on speed breeding and speed cloning. The presentation sparked considerable interest and I was asked to chair two round table discussions on the topic where I answered many questions and was requested additional information.
Year(s) Of Engagement Activity 2016
URL http://grandchallenges.org/videos
 
Description Invited presentation at the Institute of Cereal Crop Research, Tel Aviv, Israel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Gave a presentation on the use of genetic diversity from wild grasses to improve wheat disease resistance
Year(s) Of Engagement Activity 2016
 
Description Invited presentation at the Molecular Plant Microbes Interaction Meeting in Portland, USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a presentation on my work on speed breeding and wheat rusts at the biennial congress on Molecular Plant-Microbe Interactions.
Year(s) Of Engagement Activity 2016
URL http://www.ismpmi.org/Congress/2016/MeetingSchedule/Pages/default.aspx
 
Description Invited presentation at the University of Copenhagen 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I gave a presentation on the cloning of stem rust resistance genes from wheat and wild relatives and their potential use in transgenic wheat.
Year(s) Of Engagement Activity 2015
 
Description Invited presentation at the Wheat Durable Resistance Meeting, Minneapolis, USA 
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 I was invited to give a presentation at the Wheat Durable Resistance Meeting in Minneapolis, USA. The presentation lead to debate and request for additional information and collaboration.
Year(s) Of Engagement Activity 2016
URL https://www.ag.ndsu.edu/wheatresistance
 
Description Invited presentation at the Wheat Initiative Expert Working Group, Minneapolis, USA 
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 I was invited to join the wheat Expert Working Group on Control of Wheat Pathogens and Pests and deliver a presentation on available genomics and germplasm resources and what the community needs in this respect. The presentation lead to debate and requests for germplasm sharing with other labs.
Year(s) Of Engagement Activity 2016
URL http://www.wheatinitiative.org/activities/expert-working-groups/control-wheat-pathogens-and-pests
 
Description Invited presentation at the wheat breeding company KWS 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I visited the wheat breeding company KWS at their Cambridge site and gave a presentation on how to use mutational genomics approaches to identify markers that can be used in breeding. The presentation sparked interest and generated significant debate.
Year(s) Of Engagement Activity 2015
 
Description Keynote Speaker, Advances in Integrated Pest Management, Association of Applied Biologists, Harper Adams University, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I was invited to be a Keynote Speaker, at the meeting entitled Advances in Integrated Pest Management, Association of Applied Biologists, Harper Adams University, UK. This led to futher request to be involved in a responsive mode GCRF collaboration, which regretfully was not funded.
Year(s) Of Engagement Activity 2017
 
Description Keynote Speaker, German Plant Breeding Society, Wernigerode, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was the Keynote Speaker, German Plant Breeding Society, Wernigerode, Germany. This resulted in additional interest from a range of colleagues in academia and industry, including policy makers.
Year(s) Of Engagement Activity 2018
 
Description Plant Genomics and Gene Editing Congress, Rotterdam, The Netherlands 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I was invited to present at a Congress in Rotterdam.
Year(s) Of Engagement Activity 2018
 
Description Plenary Speaker, 4th International Conference on Plant Genetics, Genomics, Bioinformatics and Biotechnology, Almaty, Kazakhstan 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to present my work on speed cloning and speed breeding as a Plenary Speaker at the 4th International Conference on Plant Genetics, Genomics, Bioinformatics and Biotechnology, Almaty, Kazakhstan. This led to stimulating discussions and contributed to requests for further involvment.
Year(s) Of Engagement Activity 2017
 
Description Presentation at Institute of Genetics and Developmental Biology, Beijing, China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to visit the Institute of Genetics and Developmental Biology, Beijing, China and present my work on speed cloning and speed breeding. This has led to follow up requests for further visits, collaboration, and applicaiton for joint funding opportunities.
Year(s) Of Engagement Activity 2017
 
Description Presentation at Nanjing Agricultural University, China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to Nanjing Agricultural University, China where I gave a presentation on my work on speed cloning and speed breeding. I was invited to participate in further collaborations based on this visit.
Year(s) Of Engagement Activity 2017
 
Description Presentation at Science Innovation Showcase, JIC, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I was invited to present at the Science Innovation Showcase, JIC, UK. This has led to requests for further information and ongoing disussions with inustrial partners for collaboration / contract research.
Year(s) Of Engagement Activity 2018
 
Description Presentation at Tel Aviv University, Israel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to present my work on speed breeding and speed cloning at Tel Aviv University, Israel. This led to further discussions and resulted in an active collaboration and exchange of germplasm.
Year(s) Of Engagement Activity 2017
 
Description Presentation to Appolinaire Dijkeng and Jacob Mignouna, BecA 
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 I gave a presentation to Appolinaire Dijkeng and Jacob Mignouna from the BecA-ILRI Hub in Nairobi, Kenya. This was part of ongoing discussions and collaborative work between JIC and BecA-ILRI.
Year(s) Of Engagement Activity 2017
 
Description Presentation to Elsoms Seeds, Spalding, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I was invited to present my work on speed breeding and resistance gene cloning to Elsoms Seeds, Lincolnshire, and to troubleshoot their LED lighting in the glasshouse. This has since resulted in further interactions and dicussions.
Year(s) Of Engagement Activity 2017
 
Description Presentation to Joe Cerrell & James Birch, BMGF 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact Joe Cerrell & James Birch frin the Bill and Melinda Gates Foundation came to visit JIC and I was called upon to present my work on wheat stem rust and the solution we are working on to try to mitigate this problem for small holder farmers in Africa.
Year(s) Of Engagement Activity 2016
 
Description Presentation to KWS, Einbech, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I was invited to present my work on speed cloning and speed breeding at KWS, Einbech, Germany. KWS are currently considering how our enabling technologies could be integrated in one of their own crop breeding programmes and how we may collaborate to achieve this.
Year(s) Of Engagement Activity 2018
 
Description Presentation to delegation from Elsoms Seeds, Lincolnshire, UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact I invited 8 delegates from Elsoms Seeds to visit JIC for some bespoke presentations from my group and a colleauge, and for an inspection of our speed breeding facilities. This has helped cement a relationship that now stretches back more than one year.
Year(s) Of Engagement Activity 2018
 
Description Science Collaboration Agritech, Aquaculture and Food Safety Forum, Muscat, Sultanate of Oman 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to present at the Science Collaboration Agritech, Aquaculture and Food Safety Forum, Muscat, Sultanate of Oman.
Year(s) Of Engagement Activity 2018
 
Description Short presentation to Eric Danquah, WACCI, Ghana 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was called upon to give a presentation to a visiting dignitary, Eric Danquah from the WACCI, Ghana. This lead to a lively discussion and exhange of ideas and request for further collaboration.
Year(s) Of Engagement Activity 2016
 
Description Teleconference discussion with Syngenta 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Participated in a teleconference with Syngenta with participation from China, UK and USA. Follow-on discussions are ongoing.
Year(s) Of Engagement Activity 2018
 
Description The Sainsbury Laboratory Annual Retreat 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I presented my yearly update to The Sainsbury Laboratory as part of my Adjunct Affiliation with this institution.
Year(s) Of Engagement Activity 2018
 
Description The Sainsbury Laboratory Retreat 2017, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I was invited to present my work on R gene cloning and speed breeding at The Sainsbury Laboratory 2017 retreat. This sparked questions and discussions and has since contributed to further collaboration with colleagues in TSL.
Year(s) Of Engagement Activity 2017
 
Description Workshop at BecA-ILRI, Kenya on Molecular Breeding in Small Grain Cereals 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I co-organised and taught a short 4-day course on molecular breeding in small grain cereals (wheat, barley and teff) for African scientist and breeders. Participants came from Ethiopia (~12), Kenya, Uganda, Tanzania, Madagascar, Nigeria and Burundi. The course was well received, led to requests for additional information, request to repeat the course the following year, and the possibility of a new strategically interesting collaboration with young career wheat scientist from Ethiopia.
Year(s) Of Engagement Activity 2017
URL http://hpc.ilri.cgiar.org/beca/training/jic_beca_2016/index.html
 
Description Workshop on Scientific Softskills, Punjab Agricultural University, Ludhiana, India 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I organised and presented, with colleagues, a workshop on scientific soft skills to early career scientists primarily from India, but also from the UK, Tunisia and Iran.
Year(s) Of Engagement Activity 2017
 
Description Young Anglia Grows: LEP agri-tech 6th form taster course 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Myself, members of my lab, and a few colleagues entertained a group of ~10 year 12 pupils (top end of ability range) sourced by recommendations from Norfolk heads of biology. The day included a session on wheat diseases (formal lecture), a practical on using microscopes to observe wheat infected by stripe rust, a tour of the John Innes Centre and TGAC facilities, and a hands-on bioinformatics practical.
Year(s) Of Engagement Activity 2015
URL http://www.newanglia.co.uk/