Studying Co-evolution in agriculture to inform NLR deployment

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.

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.

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.