Delivering Sustainable Wheat: Delivering Resilience to Biotic Stress (Rothamsted Research)
Lead Research Organisation:
Rothamsted Research
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
WP2 aims to improve the resilience of wheat production systems to biotic stresses frequently encountered in high yielding UK-European (and global) wheat regions. This WP will investigate biotic threats which typically cause grain yield losses in the range 10 to 25% even after the correct application of fully integrated control options. The WP will focus on major anticipated/recurrent UK European- global threats including stem rust wheat blast Fusarium Head Blight (FHB)/Scab caused by Fusarium graminearum (Fg) and F. culmorum (Fc) Septoria Leaf Blotch caused by Zymoseptoria tritici (Zt) take-all root disease yellow rust and two aphid species (Rhopalosiphum padi (Rp) and Sitobion avenae (Sa)) that transmit various viruses and exploit comparative analyses. As a result of DFW and other investments we will in this WP deliver molecular targets in wheat and in the major wheat pests and pathogens which can be exploited to sustain future productivity in the short medium and longer terms. Our approach will mirror that used to counter infectious diseases of humans as exemplified by the recent Covid-19 pandemic. These were to: (1) increase host immunity (vaccination) (2) understand the molecular basis of infection and deploy selective antiviral chemistry and (3) monitor (surveillance) of pathogen strains and predict new emergence/ epidemics. WP2 will deliver resilient wheat crop protection via a similar triple-pronged cross institute approach. Specifically we will identify and characterise wheat germplasm and genes which will (1) boost wheats natural immunity to multiple diseases whilst also identifying genes/processes which pathogens may exploit (“susceptibility factors”) as potential weaknesses with emphasis on those exploited by multiple pathogens. We will also (2) functionally identify the genes that are pathogen weaknesses based on their importance for wheat infection. Through large-scale comparative genomics and pangenomics we will refine these lists for “Accessible SMART targets” for future interventions which can be selectively targeted in pathogens/pests as opposed to beneficial/non-target organisms. Finally we will (3) further develop and deploy state of the art surveillance strategies to enable rapid identification and response to new variants of existing threats as well as detect new and emerging threats to UK-global wheat production.
Planned Impact
unavailable
Organisations
- Rothamsted Research (Lead Research Organisation)
- National Institute of Agricultural Botany (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- University of Neuchâtel (Collaboration)
- CABI Kenya (Collaboration)
- University of Bergen (Collaboration)
- Federal University of Viçosa (Collaboration)
- IPK Gatersleben (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- UNIVERSITY OF EXETER (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- University of California, Davis (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- Bayer (Collaboration)
- ExPASy, Swiss Institute of Bioinformatics (SIB) (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- University of Bath (Collaboration)
- John Innes Centre (Collaboration)
- National Institute of Agronomy and Botany (NIAB) (Collaboration)
- Brazilian Agricultural Research Corporation (Collaboration)
- University of Bristol (Collaboration)
Publications


Armer V
(2024)
Navigating the Fusarium species complex: Host-range plasticity and genome variations
in Fungal Biology


Armer VJ
(2024)
The trichothecene mycotoxin deoxynivalenol facilitates cell-to-cell invasion during wheat-tissue colonization by Fusarium graminearum.
in Molecular plant pathology

Blyth HR
(2023)
Fungal plant pathogen "mutagenomics" reveals tagged and untagged mutations in Zymoseptoria tritici and identifies SSK2 as key morphogenesis and stress-responsive virulence factor.
in Frontiers in plant science


Chancellor T
(2024)
A fungal endophyte induces local cell wall-mediated resistance in wheat roots against take-all disease
in Frontiers in Plant Science



Cuzick A
(2023)
A framework for community curation of interspecies interactions literature.
in eLife
Description | Application of microfluidics chip analyses to Fusarium graminearum research |
Amount | £5,000 (GBP) |
Organisation | British Society of Plant Pathoogy |
Sector | Learned Society |
Country | United Kingdom |
Start | 08/2023 |
End | 09/2024 |
Description | DFW - Designing Future Wheat - Work package 2 (WP2) - Added value and resilience |
Amount | £7,068,842 (GBP) |
Funding ID | BBS/E/C/000I0250 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2017 |
End | 03/2023 |
Description | Exploring resistance to take-all root disease in wheat by high throughput genotyping and functional characterisation of wheat defence genes |
Amount | £4,000 (GBP) |
Organisation | Royal Society of Biology (RSB) |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 05/2023 |
End | 09/2023 |
Description | IIP - • Establishing a universal high-throughput digital phenomics platform to study wheat responses to various biotic fungal threats and potential biocontrol bacteria |
Amount | £4,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2024 |
End | 06/2024 |
Description | IIP -Beyond the host plant, how Fusarium graminearum establishes beneficial interactions with the microbiome. |
Amount | £18,896 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2024 |
End | 06/2024 |
Description | Jade Smith - Investigating fungal pathogen effector localisation within plant cells - SWBioDTP 2023-2027 |
Amount | £130,000 (GBP) |
Funding ID | 229139594 SWBio DTP Rothamsted studentship - University of Bath |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 08/2023 |
End | 09/2027 |
Description | Phenotyping Barley yellow dwarf virus resistance in wheat, and quantification of the virus titre in different tissues of susceptible and resistant plants |
Amount | £4,000 (GBP) |
Organisation | The British Society of Plant Pathology |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2023 |
End | 09/2023 |
Description | RRes-Brazil partnership for protecting crops against bacterial / viral plant diseases and associated vectors |
Amount | £10,914 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2024 |
End | 05/2024 |
Description | X9 High-Throughput Genomics System for new and versatile research capabilities |
Amount | £158,270 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2023 |
End | 12/2023 |
Title | High Molecular Weight DNA extraction method for fungal tissues from soil dwelling species |
Description | Through collaborations with Rothamsted Research, Michelle Grey modified a method for extracting high molecular weight DNA for long-read sequencing (PacBio HiFi reads) during the time she worked on the DFW project. Modifications included overnight lysis, a robust RNase-A digestion, Proteinase K digestion, twisting out DNA before washing and then splitting the sample during the wash phase. This worked well using the Nucleon PhytoPure and Macherey-Nagel kits. |
Type Of Material | Technology assay or reagent |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This new protocol developed through a collaboration between Rothamsted Research and Earlham has lead to the development of a robust protocol to isolate HMW DNA from a range of very difficult fungal species that can then be used for both PacBio and IIlumina sequence used to de novo assemble chromosome scale whole genomes from new species. This protocol is now being exploited in the Fungal Tree of life project. |
Title | Identification and functional characterisation of a locus for target site integration in Fusarium graminearum |
Description | Background: Fusarium Head Blight (FHB) is a destructive floral disease of different cereal crops. The Ascomycete fungus Fusarium graminearum (Fg) is one of the main causal agents of FHB in wheat and barley. The role(s) in virulence of Fg genes include genetic studies that involve the transformation of the fungus with different expression cassettes. We have observed in several studies where Fg genes functions were characterised that integration of expression cassettes occurred randomly. Random insertion of a cassette may disrupt gene expression and/or protein functions and hence the overall conclusion of the study. Target site integration (TSI) is an approach that consists of identifying a chromosomal region where the cassette can be inserted. The identification of a suitable locus for TSI in Fg would avert the potential risks of ectopic integration. Results: Here, we identified a highly conserved intergenic region on chromosome 1 suitable for TSI. We named this intergenic region TSI locus 1. We developed an efficient cloning vector system based on the Golden Gate method to clone different expression cassettes for use in combination with TSI locus 1. We present evidence that integrations in the TSI locus 1 affects neither fungal virulence nor fungal growth under different stress conditions. Integrations at the TSI locus 1 resulted in the expression of different gene fusions. In addition, the activities of Fg native promoters were not altered by integration into the TSI locus 1. We have developed a bespoke bioinformatic pipeline to analyse the existence of ectopic integrations, cassette truncations and tandem insertions of the cassette that may occurred during the transformation process. Finally, we established a protocol to study protein secretion in wheat coleoptiles using confocal microscopy and the TSI locus 1. Conclusion: The TSI locus 1 can be used in Fg and potentially other cereal infecting Fusarium species for diverse studies including promoter activity analysis, protein secretion, protein localisation studies and gene complementation. The bespoke bioinformatic pipeline developed in this work together with PCR amplification of the insert could be an alternative to Southern blotting, the gold standard technique used to identify ectopic integrations, cassette truncations and tandem insertions in fungal transformation. |
Type Of Material | Technology assay or reagent |
Year Produced | 2024 |
Provided To Others? | Yes |
Impact | The method has been used in different projects of the lab to complement knock-out fungal strains and to express recombinant proteins in the fungus. |
URL | https://fungalbiolbiotech.biomedcentral.com/articles/10.1186/s40694-024-00171-8 |
Title | Identification of a locus for target site integration in Fusarium graminearum |
Description | We developed a vector system for target site integration (TSI) in an intergenic chromosomic region of the Fg genome. Insertion of the expression cassette in this chromosomic region (TSI locus1) does not alter either fungal growth of fungal virulence. Integrations in the TSI locus1 allow the expression of different genes fusions and activities of virulence specific promoters were not altered by integration into the TSI locus 1. Complementation tests were successfully done on three test genes. Finally, we established a protocol to study protein secretion in wheat coleoptiles using confocal microscopy and the TSI locus1 for stable expression of different gene fusions. |
Type Of Material | Technology assay or reagent |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | The TSI locus1 can be used for diverse studies including promoter activity analysis, secretion and gene complementation and localisation studies. Therefore, the vector system has already been used in multiple ongoing BBSRC funded research projects in the laboratory. A PhD student and a postdoctoral researcher have successfully used the vector system for gene complementation studies. The vector system will also be used to study protein secretion in a new collaborative project with US researchers. The project aims to identify fungal secreted proteinases that can be used to engineer fungal resistance in wheat. The new vector system is available from ADDGene. |
URL | https://doi.org/10.1186/s40694-024-00171-8 |
Title | PHI-Canto |
Description | This community curation tool and framework tool permits authors of in scope peer reviewed publication to manually enter all the data and findings from their publication into the open access PHI-base database, using controlled ontologies and evidence codes. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Highly fragment data sets on any pathogen host interaction or any chemical interaction with a pathogen species, published in all peer review articles is converted to FAIR data |
URL | https://doi.org/10.7554/eLife.84658 |
Title | PHI-Canto: Annotating a gene-for-gene interaction |
Description | PHI-Canto: Annotating a gene-for-gene interaction. This is a specific type of host-pathogen interaction that determines the overall outcome of the interaction namely the resistance or susceptibility of the host and the ability of the pathogen to cause disease or not. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | The authors of a relevant peer reviewed publication can curate their complicated data sets directly into the PHI-base database using the PHI-Canto tool. |
URL | https://youtu.be/_og3umfy4WU |
Title | PHI-Canto: Annotating an inverse gene-for-gene interaction |
Description | PHI-Canto: Annotating an inverse gene-for-gene interaction into the PHI-base database. https://youtu.be/KKhomX11TMs |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | The authors of a relevant peer reviewed publication can curate their complicated data sets directly into the PHI-base database using the PHI-Canto tool. The are genetically the rarer interaction types compared to gene-for-gene interaction types. |
URL | https://youtu.be/KKhomX11TMs |
Title | PHI-Canto: Why should I contribute? |
Description | PHI-Canto: the personal and professional benefits to authors of contributing a peer reviewed article using this community curation tool https://youtu.be/QQGZBnUYZcA |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Soon after publication, more authors will spend the time curating their research articles via PHI-Canto into the PHI-base database |
URL | https://youtu.be/QQGZBnUYZcA |
Title | The Pathogen-Host Interactions Database (PHI-base) |
Description | This is described in the Wikipedia entry - https://en.wikipedia.org/wiki/PHI-base |
Type Of Material | Improvements to research infrastructure |
Provided To Others? | Yes |
Impact | PHI-base makes two data releases per annum in May and November. In the reporting period the following has occurred The latest release of PHI-base, version 4.15, was on 2 May 2023 (http://www.phi-base.org/releaseNote.htm). Compared to version 4.14, released on 1 November 2022, the increase in data is: 384 genes, 1,069 interactions, 237 publications, 2 new pathogens, and 2 new hosts. The number of diseases was reduced by one, due to data cleaning efforts removing redundant and incorrect disease names. We continue to freely share phenotyping data with Ensembl ( since 2011), FungiDB (since 2019) and UniProtKB (since 2020). UK and international resource usage trends: PHI-base > 25,800 and > 1007 full database downloads, > 6,000 unique users and > 400 registered API users. Total users > 119,700 during the reporting period April 2023-March 2024. |
URL | http://www.phi-base.org/ |
Title | Video - PHI-Canto: Choosing a suitable publication |
Description | PHI-Canto: Choosing a suitable publication https://youtu.be/J6z4MlU8Bkc |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | How to select an in scope publication for author curation using the community curation tool - PHI-Canto |
URL | https://youtu.be/J6z4MlU8Bkc |
Title | Video - PHI-Canto: Introduction to PHI-base |
Description | https://youtu.be/5GlKRM9qshk |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Improved understanding of what PHI-base is about for first time users of the database |
URL | https://youtu.be/5GlKRM9qshk |
Title | Additional file 17: of Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum |
Description | Fusarium venenatum presence of TRI6 Fusarium greaminearum binding sites predicted by Nasmith et al. [39]. Fusarium venenatum BLASTP alignment percentages were added to identify presence or absence. (XLS 61Â kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | Placing the chromosome scale, fully annotated F. venenatum genome in the public domain has increased the power of comparative genomics for cereal infecting Fusarium species. |
URL | https://springernature.figshare.com/articles/Additional_file_17_of_Inter-genome_comparison_of_the_Qu... |
Title | Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen |
Description | Studying genomic variation in rapidly evolving pathogens potentially enables identification of genes supporting their "core biology", being present, functional and expressed by all strains or "flexible biology", varying between strains. Genes supporting flexible biology may be considered to be "accessory", whilst the "core" gene set is likely to be important for common features of a pathogen species biology, including virulence on all host genotypes. The wheat-pathogenic fungus Zymoseptoria tritici represents one of the most rapidly evolving threats to global food security and was the focus of this study. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | A new method for prioritising genes of interest from a pangenome |
URL | https://harvestirr.rothamsted.ac.uk/98q90/combined-pangenomics-and-transcr |
Title | Pathogen-Host Interactions database |
Description | Pathogen-Host Interactions database |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Two new releases Version 4.15 May 2nd 2023 Version 4.14 November 1st 2022 |
URL | http://www.phi-base.org |
Description | Apoplastic proteomics and activity testing |
Organisation | National Institute of Agronomy and Botany (NIAB) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Generating apoplastic fluids from infected wheat plants |
Collaborator Contribution | Enzyme activity testing and effector protein inhibitor modelling |
Impact | PhD student poster |
Start Year | 2023 |
Description | Apoplastic proteomics and activity testing |
Organisation | University of Oxford |
Department | Oxford Hub |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Generating apoplastic fluids from infected wheat plants |
Collaborator Contribution | Enzyme activity testing and effector protein inhibitor modelling |
Impact | PhD student poster |
Start Year | 2023 |
Description | Bayer Targets and Abraham Wald |
Organisation | Bayer |
Country | Germany |
Sector | Private |
PI Contribution | Generated materials for genome sequencing project |
Collaborator Contribution | Paid for and performed sequencing project |
Impact | Private datasets and new resources |
Start Year | 2019 |
Description | EMBL-EBI ENSEMBL |
Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Highly curated information on the genes in multiple pathogens shown to be required for the disease causing ability. Monthly curation of the peer reviewed literature , to link gene sequence information to phenotypic information for 250 pathogenic species |
Collaborator Contribution | The quarterly mapping of the single gene - phenotype information onto the pathogen genomes with ENSEMBL. Also the creation of a bespoke genome portal called PhytoPath to display the genomes of hundreds of plant pathogen genomes within which this gene-to-phenotype information is displayed on the genome browser and can be searched for via the BioMart tool. |
Impact | Several joint publications, quarterly joint data releases since 2013 via ENSEMBL, PhytoPath and PHI-base. New funding since 2017 via the Smart Crop Protection (SCP) strategic programme (BBS/OS/CP/000001) funded through Biotechnology and Biological Sciences Research Council's Industrial Strategy Challenge Fund to explore the possibility of curating new data types into PHI-base relating to fungicide insensitivity, resistance linked to pathogen target information. |
Start Year | 2010 |
Description | EMBRAPA Brazil - Passo fundo - Trigo (wheat) team |
Organisation | Embrapa Trigo |
Country | Brazil |
Sector | Private |
PI Contribution | The Rothamsted Team has sequenced the genomes of 16 Brazilian strains of the Fusarium head blight disease causing strain F. graminearum (Fg) and has now created a pan -genome for this species by comparing with the available Fg genomes for 6 six additional global isolates including the reference isolate PH-I. This has indicated that the Fg pan genome is relatively closed. The Rothamsted Team has stably transformed the Brazilian commercial wheat cultivar Guaramin for the first time |
Collaborator Contribution | The EMBRAPA Trigo team have generated various transgenic Arabidopsis harboring different Fg HIGS constructs. The EMBRAPA Team have also screened and identified lettuce cultivars that are fully susceptible to the nominated reference Brazilian strain. |
Impact | A major display at the annual Cereals event held in Cambridgeshire in June 2016 on the new HIGS and SIGS technologies for the control of FHB disease in wheat . A open evening public event entitled @ Healthy Crops- Healthy Food done at Rothamsted Research in July 2016. |
Start Year | 2014 |
Description | Fusarium NADases_University of Bergen_Norway |
Organisation | University of Bergen |
Country | Norway |
Sector | Academic/University |
PI Contribution | Unpublished data shared with the Norwegian research team lead by Professor Mathias Ziegler at the University of Bergen on two Fusarium graminearum NADase genes and their potential functions. |
Collaborator Contribution | Unpublished data shared with the Rothamsted research team on the crystal structure of three different types of NADases present in the fungal kingdom. |
Impact | None yet |
Start Year | 2024 |
Description | Fusarium graminearum effector characterisation using global pangenome analyses |
Organisation | University of Bath |
Department | Department of Biology and Biochemistry |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We designed this fungal effector PhD project based on soon to be published Fusarium graminearum pangenome analyses arising from an ongoing now unfunded collaboration with EMBRAPA in Brazil. This included detailed bioinformatics analyses and wet biology verification of the in planta destination location of small secreted candidate effector proteins. |
Collaborator Contribution | The two partners at the University of Bath will provide specialist transcriptome analyses (Dr Neil Brown) and genome analyses (Dr Hans -Wilhelm Nützmann to this PhD project. In 2023 , Hans -Wilhelm Nützmann moved to The University of Exeter. This collaboration continues with Drs Neil Brown and Hans -Wilhelm Nützmann. |
Impact | Hiring of the 4 year PhD student Jade Smith |
Start Year | 2022 |
Description | Fusarium-bacteria interactions_Pilar Junier_University of Neuchatel, Switzerland |
Organisation | University of Neuchatel |
Country | Switzerland |
Sector | Academic/University |
PI Contribution | Comprehensive literature search on Fusarium-bacteria interactions. Successfully winning a BBSRC research travel project entitled ' Beyond the host plant, how Fusarium graminearum establishes beneficial interactions with the microbiome' by Drs Martin Darino and Kim Hammond-Kosack |
Collaborator Contribution | Established multiple laboratory based techniques to explore fungal - bacterial interactions, including the isolation of bacteria that live on and /or within fungi. |
Impact | Collaboration just started |
Start Year | 2023 |
Description | GFP strand 11 delivery into GFP1-10 expressing plant cells - Gitta Coaker |
Organisation | University of California, Davis |
Country | United States |
Sector | Academic/University |
PI Contribution | None yet , we have just received the required Arabidopsis seed stock in Jan 2024 |
Collaborator Contribution | Provision of the following GM Arabidopsis line 35S promoter : GFP1-10 expressing homozygous line described in the publication : Henry E, Toruno TY, Jauneau A, Deslandes L, Coaker G (2017) Direct and indirect visualization of bacterial effector delivery into diverse plant cell types during infection. Plant Cell. 29:1555-70. https://www.ncbi.nlm.nih.gov/pubmed/28600390. |
Impact | None yet |
Start Year | 2023 |
Description | Green_Soil microbiome_Take-all_wheat_Bonnie Waring_Imperial College and CABI at Silwood Park |
Organisation | CABI |
Country | United Kingdom |
Sector | Private |
PI Contribution | Full day visit (Dec 2023) to Silwood Park and to meet Bonnie Waring and the other 10 PIs involved in their new project on UK soil microbiomes of wheat. Discussed methodologies, ongoing research activities on Take-all research at Rothamsted. Subsequently, provide specific advice on wheat genotypes, a highly virulent Take-all isolate for which a chromosome scale, fully annotated genome is now available, protocols on how to isolate Take-all from cereal roots and how to culture and store the fungus. |
Collaborator Contribution | Detailed information on their new 3 year project title 'Green Microbiome' which commenced in Jan 2024 which is funded by the MIchael Uren Foundation - £2.45 milion |
Impact | Root pieces with lesions collected from Take-all infected wheat plants sampled from different UK wheat fields by NIAB, will be sent to Rothamsted on a weekly basis throughout spring and summer 2024. The Imperial team will have sampled the soil microbiomes prior to sending Rothamsted the associated root samples. This will generate a large paired data set. The wheat genotype will also be known. |
Start Year | 2023 |
Description | Green_Soil microbiome_Take-all_wheat_Bonnie Waring_Imperial College and CABI at Silwood Park |
Organisation | Imperial College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Full day visit (Dec 2023) to Silwood Park and to meet Bonnie Waring and the other 10 PIs involved in their new project on UK soil microbiomes of wheat. Discussed methodologies, ongoing research activities on Take-all research at Rothamsted. Subsequently, provide specific advice on wheat genotypes, a highly virulent Take-all isolate for which a chromosome scale, fully annotated genome is now available, protocols on how to isolate Take-all from cereal roots and how to culture and store the fungus. |
Collaborator Contribution | Detailed information on their new 3 year project title 'Green Microbiome' which commenced in Jan 2024 which is funded by the MIchael Uren Foundation - £2.45 milion |
Impact | Root pieces with lesions collected from Take-all infected wheat plants sampled from different UK wheat fields by NIAB, will be sent to Rothamsted on a weekly basis throughout spring and summer 2024. The Imperial team will have sampled the soil microbiomes prior to sending Rothamsted the associated root samples. This will generate a large paired data set. The wheat genotype will also be known. |
Start Year | 2023 |
Description | Investigating Non host resistance in model plants to fungal pathogens |
Organisation | National Institute of Agronomy and Botany (NIAB) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Supervisors of PhD student Alina Igna |
Collaborator Contribution | Supervisors of PhD student Alina Igna |
Impact | PhD reports. poster presentations and draft thesis |
Start Year | 2019 |
Description | Investigating Non host resistance in model plants to fungal pathogens |
Organisation | University of Nottingham |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Supervisors of PhD student Alina Igna |
Collaborator Contribution | Supervisors of PhD student Alina Igna |
Impact | PhD reports. poster presentations and draft thesis |
Start Year | 2019 |
Description | Molecular and biological characterisation of Fusarium species and isolates collected from infected wheat fields in Southern Brazil |
Organisation | Federal University of Viçosa |
Country | Brazil |
Sector | Academic/University |
PI Contribution | Rothamsted team has used a next generation sequencing approach to explore the genomes of the five Fusarium Head Blight causing species in Southern Brazil, namely F. graminearum, F. meridionale, F.cortaderiae, F. austroamericanum and F. asiaticum.. The Rothamsted team are currently focussing on investigating and defining the core and variable parts of the pan genome of F. graminearum. The Rothamsted team also assembled and annotated the F. meridionale genome and has given this data to the University team for further analysis. |
Collaborator Contribution | The University team had collected field isolates during 2009 - 2012 and provided the 24 Fusarium isolates covering the five required species. The University team had also characterised the disease causing ability of each isolate on the floral spikes of various Brazilian wheat genotypes. Currently, the University team is exploring the genomes of the various F. meridionale, |
Impact | The two main output delivered so far has been (1) the biological characterisation of the 24 / 5 species collection for disease causing ability on both Brazilian and non-Brazilian wheat genotypes and (2) the 24 newly assembled and annotated genomes covering the five most important FHB causing species in Southern Brazil. |
Start Year | 2014 |
Description | PHI-Canto_curation of fungicide literature_Nichola Hawkins_NIAB |
Organisation | National Institute Of Agricultural Botany |
Country | United Kingdom |
Sector | Private |
PI Contribution | The PHI-Canto community curation tool for literature curation for multiple pathogenic species. Detailed literature searches to identify the in scope publications Development of controlled vocabularies, ontology terms and evidence codes to curate the literature on fungicide targets and resistance mechanisms |
Collaborator Contribution | In depth knowledge of the relevant fungicide resistance literature for key species , especially for those infecting wheat and barley. In depth knowledge of anew system to identify orthologous function mutations in protein structure across different species even when the amino acid sequence changes are not identical . |
Impact | This joint project has been a success and a joint manuscript is in preparation |
Start Year | 2022 |
Description | PHI-base collaboration with PomBase (PHI-CANTO and PHI-PO) |
Organisation | University of Cambridge |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Since Sept 2017 the PomBase team at the University of Cambridge and the PHI-base team at Rothamsted Research have held weekly meetings ( by Skype) as well as occasional face-to-face meetings to develop an new multi-species author curation tool called PHI-Canto as well as a new pathogen - host interaction ontology called PHI-PO and a new .pathogen host disease ontology called PHI-DO. The Rothamsted team have provided the biological, wet biology experimental and literature knowledge into this collaboration |
Collaborator Contribution | The PomBase team had already developed a highly successful single organism author curation tool called Canto. The PomBase team also bring a wealth of ontology development expertise into this collaborative project. |
Impact | Two joint posters will be given at the International Ontology Development conference to be held in Cambridge UK in April 2019. The presenting authors will be Dr Alayne Cuzick and Dr Val Wood. |
Start Year | 2017 |
Description | Plasmodesmata function in Arabidopsis and Wheat |
Organisation | John Innes Centre |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Devising and supervising of a SWBIo -DTP PhD student |
Collaborator Contribution | Devising and co-supervising of a SWBIo -DTP PhD student |
Impact | Unpublished Arabidopsis lines and constructs have been transferred from John Innes Centre to Rothamsted Research to explore plasmodesmata function during the F graminearum - floral infection process. A collaborative agreement is under development. |
Start Year | 2015 |
Description | Providing pathogen-host interaction data to UniprotKB |
Organisation | ExPASy, Swiss Institute of Bioinformatics (SIB) |
Country | Switzerland |
Sector | Academic/University |
PI Contribution | Providing pathogen-host interaction data to UniprotKB |
Collaborator Contribution | Providing pathogen-host interaction data to UniprotKB |
Impact | Providing pathogen-host interaction data to UniprotKB |
Start Year | 2019 |
Description | Proximity Labelling methodology - The Sainsbury Lab, Norwich |
Organisation | John Innes Centre |
Department | The Sainsbury Laboratory |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Described and discussed this project goals with this collaborator. Explored the proximity labelling methods developed at TSL Norwich in the group of Professor Jonathan Jones for proximity labelling in Arabidopsis and Nicotiana benthamiana. Methods piloted at Rothamsted and additional positive and negative constructs included in the experimental design Collaboration still on going |
Collaborator Contribution | Receive two types of detailed non-published proximity labelling protocols for Arabidopsis and Nicotiana benthamiana. . |
Impact | Still in method development phase at Rothamsted |
Start Year | 2023 |
Description | Regulation of LysM effector expression |
Organisation | University of Nottingham |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Supervising PhD student Luca Steel |
Collaborator Contribution | Supervising PhD student Luca Steel |
Impact | Posters, Reports, PhD thesis |
Start Year | 2019 |
Description | SWBiO collaboration on fungal cell walls |
Organisation | University of Exeter |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Building from joint BBSRC PhD project we are assembling new data towards joint funding application. |
Collaborator Contribution | Building from joint BBSRC PhD project we are assembling new data towards joint funding application. |
Impact | A PhD thesis and two published papers |
Start Year | 2018 |
Description | SWBio DTP - PhD student Erika Kroll |
Organisation | University of Bath |
Department | Department of Chemical Engineering |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | The PHI-base databases Unpublished transcriptome data sets on the interaction between the fungal pathogen Fusarium graminearum and wheat plants PHI-Nets datasets which report on predicted protein-protein interactions for Fusarium graminearum A recent review article on Fusarium -cereal plant interactions covering Fusarium genomics, transcriptomics, secondary metabolite gene clusters, virulence genes, effector genomes, cell biologies in different plant species and tissue types and novel approaches to disease control by targeting Fusarium virulence requirements. |
Collaborator Contribution | Unpublished transcriptome data sets on the interaction between the fungal pathogen Fusarium graminearum and wheat plants Unpublished single gene deletion mutants in Fusarium graminaerum |
Impact | During the 1st rotation project, the deletion of three different predicted secreted proteases was successfully completed by the PhD student. One of these single gene deletion mutants had reduced virulence. The gene deleted was a secreted protease This data will fit into another recently funded project being done jointly with two US based groups where Rothamsted receives funding directly from the USA. In 2023 a bilateral NSF-BBSRC project was funded based on some of the data generated in the 1st rotation project of this joint PhD project. |
Start Year | 2020 |
Description | SWBio DTP - PhD student Victoria Armer |
Organisation | University of Exeter |
Department | Biosciences |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Unpublished functional genomics datasets including the generation of single gene deletion mutants for the cereal infecting fungus Fusarium graminearum Unpublished transcriptomic datasets Unpublished cell biology studies. |
Collaborator Contribution | New microscopy methods to explore cereal-fungal interactions |
Impact | Too early |
Start Year | 2020 |
Description | SWBio-DTP Fusarium graminearum effector characterisation and genome analyses_Jade Smith_Exeter |
Organisation | University of Exeter |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Co-devising of a new SW-Bio DTP PhD project, which gives the appointed student a monthly researcher meeting where Dr Hans -Wilhelm Nützmann joins the rest of the supervisory team at Rothamsted. The techniques to be trained in are not those routinely available at Exeter. |
Collaborator Contribution | The student will spend a 5 month training period within the laboratory of the student will spend a 5 month training period in genome analyses of multiple species in the laboratory of Dr Hans -Wilhelm Nützmann during the period March 2024-July 2024). The techniques to be trained in are not those routinely available at Rothamsted |
Impact | Too early, this joint PhD project only formally commenced in Sept 2023 |
Start Year | 2023 |
Description | SWBio-DTP PhD student Izayana Sandoval (2022 onwards) |
Organisation | University of Bristol |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Hiring of the PhD student Preliminary data for PhD project obtained by Dr Lawrence Bramham via a defra funded project entitles ' The Wheat Genetic Improvement Network' as well as through a British Society for Plant Pathology undergraduate summer bursary project in 2021. Identified a suitable industrial partner , the UK wheat breeding company RAGT Devising the project which is entitled - Investigating resistance to Barley yellow dwarf virus in wheat |
Collaborator Contribution | To permit 30% of their SWBioDTP students to be international students. |
Impact | None yet - too early the PhD project only commenced in Oct 2021 |
Start Year | 2021 |
Description | Wheat Genetic Improvement Networks (WGIN) funded by defra |
Organisation | John Innes Centre |
Department | Department of Crop Genetics |
Country | United Kingdom |
Sector | Private |
PI Contribution | Kim Hammond-Kosack and Peter Shewry at Rothamsted Research co-founded the defra funded Wheat Genetic Improvement Network in 2003. This network is about to enter its 4th phase. Kim Hammond-Kosack is the project leader and Peter Shewry chairs all the meetings. WGIN ensures the wheat genetic, genotyping and phenotyping pre-breeding research ongoing within the project is focussed on improving the sustainability and resilience of the UK wheat crop. A very wide range of wheat traits have been investigated in WGIN over the years, numerous new genetic resources for wheat have been generated and distributed. An integral part of WGIN is the regular connections with the nine wheat breeding companies based in the UK. An annual stakeholder meeting is held each November to connect this project with the needs of the wider UK wheat industry. |
Collaborator Contribution | John Snape at The John Innes Centre co-founded WGIN in 2003. John Snape was trhe project leader up until 2008 and then this transferred to Simon Griffiths. The John Innes is involved in generating new genetic resources and in genotyping and phenotyping specific mapping populations as well as maintaining and distributing key germplasm. |
Impact | Over 60 peer reviewed publications, including many involving multiple teams based at different academic organisations and industry. 45 joint meetings with the wheat breeding industry. 15 stakeholder meeting. Annual or biannual community newsletters, Well maintained database contain all the project information, key data sets and the resources available. Training the next generation of wheat scientists, through summer placements funded by learned society summer bursary schemes and involving PhD students in specific large and long term experiments. Considerable new funding obtained for wheat research. Still need to add in the final numbers. |
Description | Wheat Pathogens_HTP Digital Phenomics_IPK Gaterslaben_Dimitar Douchkov |
Organisation | IPK Gatersleben |
Country | Germany |
Sector | Private |
PI Contribution | Well characterised isolates of the wheat fungal pathogens Fusarium graminearum and Zymoseptoria tritici with chromosome scale, fully annotated genomes Globally unique wheat introgression germplasm arising fro the Defra funded Wheat Genetic Improvemet Network. The NIFTYR lines in the elite UK spring cultivar Paragon harbour different segments of various Triticum monococcum (einkorn wheat ) lines. |
Collaborator Contribution | IPK Gaterslaben has establishing a universal high-throughput digital phenomics platform to study wheat responses to various biotic fungal threats and potential biocontrol bacteria |
Impact | Still in the planning stage. A funded research study period will take place in IPK Gaterslaben in Q2 2024 involving Dr Wanxin Chen from Rothamsted |
Start Year | 2022 |
Description | Zymoseptoria genome re-annotation |
Organisation | French National Institute of Agricultural Research |
Country | France |
Sector | Academic/University |
PI Contribution | We provided a reference genome re-annotation to intercompare with others |
Collaborator Contribution | They intercompared numerous gene set predictions |
Impact | Community manuscript under review and a public data release |
Start Year | 2022 |
Description | AICC_Jan 2024_Birmingham_Lawrence Bramham |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | 20 min talk followed by 5 mins Q & A on the aphid-barley Yellow dwarf virus risk in the UK and the three strain variation data obtained for the UK over the last three seasons. |
Year(s) Of Engagement Activity | 2024 |
Description | Cereals 2023_South Nottinghamshire_Take-all_Aphids_BYDV |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Diverse Wheat germplasm plot, poster and living material for take-all fungal root disease, cereal aphids and the barley yellow dwarf virus. Microscopes and hand lens to explore infected wheat material. Wheat plot tours to explain these biotic threats, the potential and real risks, and potential disease control strategies currently available and though being developed at Rothamsted. |
Year(s) Of Engagement Activity | 2023 |
Description | DSW Industry Engagement Event |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | To disseminate results from DSW research to Industrial groups. To foster / encourage future collaborations |
Year(s) Of Engagement Activity | 2024 |
Description | Hosting the visit of three MPs currently serving on the cross party Parliament Science Technology and Innovation Select Committee |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | The three visiting MPs to Rothamsted in October 2023 were MPs Greg Clark, Katherine Fletcher & Stephen Metcalfe accompanied by secretary of the committee Dr Claire Kanja . Together they explored topics on increasing insecticide resistance, lack of alternative modes of action, the need for novel IPM strategies, the emergence of new pest and virus threats in the UK due to climate change/ lack of effective insecticides/ withdrawal of active ingredients. There was also a facilities tour including the suction traps used for the ongoing UK wide Rothamsted Insect Survey. The DSW participating members were Dr Lawrence Bramham (a DSW post-doctoral specialist in cereal-aphid-virus interactions) and his 3rd year DSW aligned BBSRC-SWBio DTP student Izayana Sandoval-Carvajal. |
Year(s) Of Engagement Activity | 2024 |
Description | UK Civil Service Fast-stream programme _Nov 2023_Rothamsted |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | 30 min talk + 10 min Q&A on global food security and the biotic threats encounter both historic and recent. Then focussed on the current biotic threats to the UK wheat crop and the types of research approaches ongoing in DFW and DSW to help to provide alternative pest and pathogen control strategies and novel targets for intervention. Also discussed various UK policies which are in place to effectively minimise the biotic threat risk, whilst pointing out that air borne threats pose are the most challenging for policy makers. |
Year(s) Of Engagement Activity | 2023 |
Description | Visit of Prof Nichola Spence_Chief Plant Health Officer at Defra_11th July 2023 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Policymakers/politicians |
Results and Impact | 1-1 and small group discussions on plant health, new pest and pathogen threats UK quarantine policies and practices, new opportunities for Rothamsted Visit to Rothamsted pathogen and pest biological containment facilities and discussions on future opportunities these facilities may bring to UK research |
Year(s) Of Engagement Activity | 2023 |