Studying Co-evolution in agriculture to inform NLR deployment

Lead Research Organisation: University of Dundee
Department Name: School of Life Sciences

Abstract

Potato is the world's most important non-cereal food crop and production is threatened by pathogens that severely reduce crop yield and quality. The most important pathogen is late blight, the organism that caused the Irish potato famine. Current control methods for late blight in most parts of the world are based mainly on the use of chemical sprays which can be environmentally hazardous and expensive. The realisation that cultivated potatoes could be protected from pathogens such as late blight by the introduction of disease resistance genes from wild species, led to the molecular characterisation of numerous functional plant nucleotide-binding, leucine-rich-repeat resistance genes (NLRs). The deployment patterns of these functional NLRs in potato varieties remain largely unknown, which obstructs effective resistance breeding strategies and pathogen co-evolution studies in an agricultural context.

To this effect we refined a novel tool, referred to as dRenSeq, to detect the presence of characterised NLRs in potatoes. This enables us to track, for the first time, the current, historical and geographical deployment patterns of functional NLRs in varieties and (pre)-breeding material. Through recently established Pathogen enrichment Sequencing (PenSeq) technology, we are in a position to also study the late blight pathogen effector diversity including changes to bonafide avirulence genes which lead to resistance upon detection by NLRs. Therefore, we have now reached a position to study the impact of NLR gene deployment on the cognate pathogen Avr gene diversification.

Our preliminary data suggest that the most commercially valuable potato varieties grown in the UK and US contain a maximum of four already defeated NLRs specific against the late blight pathogen, P. infestans. The distinct patterns of NLR gene deployment in both countries is mirrored by the diversity of the cognate Avr genes in virulent extant US and UK P. infestans genotypes, respectively. Highly relevant for breeding, we identified recently characterised NLRs that remain effective against P. infestans and that already exist in advanced pre-breeding material or even varieties which have been trialed in the Netherlands. Critically, these 'new' resistances have not been used extensively in commercial potato production and have not yet been stacked in varieties. To date, only a limited number of P. infestans isolates exist that can overcome these new NLRs in isolation.

This proposal aims to discover the pathogen adaptation mechanisms that enable different and geographically distinct lineages of P. infestans to overcome host resistance in agriculture. This knowledge will be applied, through breeding programs with our global commercial partners, to produce more durable resistant varieties containing complementary and effective NLR stacks. The combination of effective NLRs will prolong the longevity of individual resistances and reduce the need for chemical applications.

Technical Summary

The most important commercial potato varieties that are currently grown are susceptible to late blight and require repeated applications of chemicals, which could be reduced by introducing more effective resistance gene stacks. This project will develop a new informed strategy for the deployment of effective late blight resistance gene combinations in potato based on studying Phytophthora infestans effector diversity in response to utilised resistances.

We need to know how many distinct resistances, which are typically members of the nucleotide-binding, leucine-rich-repeat resistance genes class (NLRs), are currently being utilised in potato varieties, how the pathogen has adapted to these by co-evolution, and how many effective NLRs remain immediately available for combining through breeding. To this effect, we refined established Resistance gene enrichment Sequencing, RenSeq, and developed a diagnostic form (dRenSeq) to detect the presence of previously characterised NLRs in diploid or tetraploid potato clones. This enables us to track with high accuracy the current, historical and geographical deployment patterns of functional NLRs in varieties and (pre)-breeding material. Through recently established Pathogen enrichment Sequencing (PenSeq), we are in a position to also study the P. infestans effector diversity including changes to bonafide avirulence (Avr) genes which lead to resistance upon detection by NLRs.

Therefore, we have now reached a position to study the impact of NLR gene deployment on the cognate pathogen Avr gene diversification. This knowledge will be applied, through breeding programs with our global commercial partners, to produce more durable resistant varieties containing complementary and effective NLR stacks.

Planned Impact

Who might benefit from this research?
The immediate beneficiaries of this research will include other academic researchers, as described in detail above. Phytophthora infestans dramatically impacts on the cultivation of potato. Currently, P. infestans populations are assessed through evolutionary neutral SSR markers and consequently little is known about the molecular diversity (e.g. effector diversity) within and between existing populations and the molecular diversity of this oomycete around the world.

This project has been developed by the academic partner, the University of Dundee, in collaboration with the commercial companies Greenvale, McCain, and James Hutton Limited. McCain, which has a major investment in potato through ownership of various processed potato products, operates globally. Complimentary to McCain is Greenvale, which is a major producer of fresh potatoes and the UK's largest grower of organic potatoes. James Hutton Limited breeds potatoes for both the fresh and processed market in the UK and globally. These companies will be able to advance any promising potato material established in this project for varietal development suitable for the fresh or processed market.


One of the main outputs of this project will be technical 'know-how' of how to efficiently determine and ultimately track resistance genes in potato varieties. Our approach, which is driven by dRenSeq (Objectives 2-3) and the development of transferable markers (Objective 4), will be applicable to any crop and disease that can be controlled by NLRs.

A second major output relates to the development of an informed strategy for NLR gene stacking and deployment that takes advantage of elucidating the pathogen population diversity (Objective 1). McCain, Greenvale and James Hutton Limited will benefit from the development of an informed NLR stacking and deployment approach. Therefore, this project will provide information, namely characterisation of current cultivars and breeding material for deployed NLRs and markers for functional resistances. These key findings will also benefit all those engaged in potato improvement, including companies that generate varieties for the UK fresh and processed markets. The commercial companies of this project are ideally placed to exploit this information as they are engaged through existing potato breeding programmes with all major national potato producers, enabling ready routes to translate research outcomes to UK industry. In the longer term, breeding in other crop species will benefit from the concepts and technologies developed in this proposal.

How will they benefit from this research?
In the shorter term, potato breeders will have a much improved 'toolbox' for breeding varieties with informed, complimentary resistances to late blight. As more and more functional and effective genes are being identified against other pathogens such as potato cyst nematodes and viruses, the approach developed here will be easily adaptable to new disease resistance traits. This is important not only for pathogens that impact on UK production but also for those countries to which the UK, and Scotland, in particular, exports seeds. The availability of novel resistance genes and diagnostic markers for these genes will allow more rapid development of new resistant varieties.

Stakeholders, including the public and farmers, will benefit from improved environmental conditions through the reduced use of fungicides, and, as eluded above, eventually nematicides and insecticides used to control blight, PCN and aphid vectors of viruses. The public will also benefit from the availability of fresh produce and process products containing less chemical residues.

Publications

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Torrance L (2020) Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

 
Description The project only commenced in December 2019 and therefore very few key findings can be reported to date. However, we have generated the first new RenSeq and PenSeq data sets and used the RenSeq information, in combination with existing sequences, to further develop NLR-gene specific KASP markers. Markers for R8, Rpi-vnt1 and Rpi-ber1 have been assessed in the established breeding consortium and confirmed dRenSeq data. Screening of F1 progenies from crosses designed to pyramid resistances has already identified individuals with at least two complementary and functional NLRs.
Exploitation Route Academia: The concept of developing unique and informative markers for key genes based on enrichment sequencing has been well received by academia and we have had multiple requests from international collaborators to share our computational pipeline for the marker development.

Industry: The stacking of complimentary NLRs in potato breeding programs, through the help of dRenSeq for the identification of suitable parents and the KASP markers, has been well received. We presented data at a recent Industry event which was organised by the James Hutton in collaboration with the University of Dundee and received multiple requests for further information.
Sectors Agriculture, Food and Drink

 
Description The BBSRC award was taken up by a number of media outlets including BBC Radio 4 and various international newspaper. As a consequence of the media coverage, we had questions from the public as well as communications with policymakers concerning our dRenSeq and PenSeq approach and the state of play of potato breeding. Examples of press coverage are detailed below: Radio: https://www.bbc.co.uk/sounds/play/m0007qg1 Newspaper: • http://digital.spudman.com/i/1195920-january-2020/31? • https://www.heraldscotland.com/business_hq/17864468.scientists-harness-wild-potatoes-bolster-commercial-spuds/ • https://www.thescottishfarmer.co.uk/news/17860991.scientists-harness-wild-potatoes-bolster-commercial-spuds/ • https://www.potatopro.com/news/2019/four-late-blight-resistancy-genes-current-commercial-potato-varieties-already-defeated • https://spudsmart.com/scientists-discover-wild-potatoes-key-for-stronger-spuds/ • https://www.farminglife.com/farming-news/wild-spuds-to-stop-threat-of-blight-1-9020072 • https://www.agf.nl/article/9130881/schotland-oude-aardappelrassen-veel-minder-phytophthora-gevoelig/ • https://www.heraldscotland.com/news/17815436.race-time-keep-humble-scots-tattie-menu/ • http://www.stackyard.com/news/2019/07/crop/04_dundee_potatoes.html • https://www.countrylife.co.uk/news/wild-potatoes-help-spuds-resist-deadly-blight-caused-irish-potato-famine-200323 • https://potatonewstoday.com/2019/07/25/wild-potatoes-key-for-stronger-spuds/ • http://www.deadlinenews.co.uk/2019/07/25/tatties-gone-scientists-discover-wild-potatoes-key-for-stronger-spuds/ • https://www.agriland.co.uk/farming-news/wild-potato-genes-may-be-key-to-stronger-spuds/
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Education
Impact Types Societal

 
Description Royal Society - IEC\R2\192090 - International Exchanges 2019 Cost Share (Russia)
Amount £12,000 (GBP)
Funding ID IEC\R2\192090 - International Exchanges 2019 Cost Share (Russia) 
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 11/2019 
End 10/2021
 
Description Collaboration with China Agricultural University 
Organisation China Agricultural University (CAU)
Country China 
Sector Academic/University 
PI Contribution I am currently supervising a student from the China Agricultural University of Beijing at my laboratory in Dundee and have been appointed an adjunct Professor at CAU in recognition of my research contributions. We have been able to send wild potato accessions from the CPC, in true seed form, to CAU following consultation with SASA and DEFRA.
Collaborator Contribution Material from the CPC is currently being assessed for disease resistances and effector recognition
Impact We already have a number of joint publication involving China Agricultural University, James Hutton Institute and the University of Dundee. We have also applied jointly for a Royal Society grant which is currently being reviewed.
Start Year 2019
 
Description Royal Society funded project with Vavilov Institute in Russia 
Organisation N. I. Vavilov All-Russian Institute of Plant Genetic Resources
Country Russian Federation 
Sector Public 
PI Contribution Hosting scientists from Russia
Collaborator Contribution providing plant material for analysis
Impact Exchange of personal and ideas
Start Year 2019
 
Title KASP markers for all currently used major potato disease resistance genes 
Description We have developed KASP markers, based on dRenSeq analysis of over 200 potato varieties, for all major disease resistance genes. These have been successfully introduced in commercial breeding programs. 
IP Reference  
Protection Protection not required
Year Protection Granted 2019
Licensed Commercial In Confidence
Impact Advanced Breeding and resistance gene stacking through markers assisted selection.
 
Title dRenSeq analysis for commercial breeding companies 
Description We are currently offering dRenSeq to commercial breeding companies 
IP Reference  
Protection Protection not required
Year Protection Granted 2019
Licensed Commercial In Confidence
Impact interest from industry has grown significantly
 
Description BBC Radio 4 - Farming today interview 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact BBC Radio 4 - Farming today interview with a focus on potato research and the Commonwealth Potato Collection
Year(s) Of Engagement Activity 2019
URL https://www.bbc.co.uk/sounds/play/m0007qg1
 
Description Invited presentation at SRUC - Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited presentation at SRUC
Year(s) Of Engagement Activity 2019
 
Description Invited presentation at the University of Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited presentation at the University of Edinburgh
Year(s) Of Engagement Activity 2019
 
Description National and International newspaper articles 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Our research featured in 13 international newspapers and magazines:

• http://digital.spudman.com/i/1195920-january-2020/31?
• https://www.heraldscotland.com/business_hq/17864468.scientists-harness-wild-potatoes-bolster-commercial-spuds/
• https://www.thescottishfarmer.co.uk/news/17860991.scientists-harness-wild-potatoes-bolster-commercial-spuds/
• https://www.potatopro.com/news/2019/four-late-blight-resistancy-genes-current-commercial-potato-varieties-already-defeated
• https://spudsmart.com/scientists-discover-wild-potatoes-key-for-stronger-spuds/
• https://www.farminglife.com/farming-news/wild-spuds-to-stop-threat-of-blight-1-9020072
• https://www.agf.nl/article/9130881/schotland-oude-aardappelrassen-veel-minder-phytophthora-gevoelig/
• https://www.heraldscotland.com/news/17815436.race-time-keep-humble-scots-tattie-menu/
• http://www.stackyard.com/news/2019/07/crop/04_dundee_potatoes.html
• https://www.countrylife.co.uk/news/wild-potatoes-help-spuds-resist-deadly-blight-caused-irish-potato-famine-200323
• https://potatonewstoday.com/2019/07/25/wild-potatoes-key-for-stronger-spuds/
• http://www.deadlinenews.co.uk/2019/07/25/tatties-gone-scientists-discover-wild-potatoes-key-for-stronger-spuds/
• https://www.agriland.co.uk/farming-news/wild-potato-genes-may-be-key-to-stronger-spuds/
Year(s) Of Engagement Activity 2019
 
Description Organiser, speaker and facilitator at University of Dundee, Plant Sciences 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 Organiser, speaker and facilitator at University of Dundee, Plant Sciences Retreat
Year(s) Of Engagement Activity 2019
 
Description Organiser, speaker and facilitator for Potato@Hutton workshop 
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 Organiser, speaker and facilitator for Potato@Hutton workshop
Year(s) Of Engagement Activity 2020