Potato PCN Resistance: Cloning effective resistances against potato cyst nematodes

Potato is the world's most important non-cereal food crop and production is threatened by pathogens that severely reduce crop yield, quality, and impede seed potato production. Potato Cyst Nematodes (PCN) are widespread pathogens of potato that are difficult to eradicate once established. The potato industry is dependent on access to PCN-free land to produce healthy seed tubers as well as PCN resistant potato varieties to suppress populations of this economically damaging pest.

Current control methods for PCN often depend on nematicides which can be environmentally damaging and are consequently being phased out in many potato producing countries. Further, crop rotations, which in the UK typically span between six to seven years, can help reduce the disease pressure, but fail to clean-up contaminated land as PCN cysts in the soil can remain viable for over 20 years.

The realisation that cultivated potatoes can be protected from pathogens such as PCN by the introduction of disease resistance genes from wild species led to the deployment into cultivars of the H1 resistance effective against the PCN species Globodera rostochiensis and Gpa5 and Gpa4 that are effective against G. pallida. Previous genetic mapping studies of these resistances have provided evidence that the hitherto elusive genes are likely members of the plant nucleotide-binding, leucine-rich-repeat gene family (NLRs).

This project aims to identify the functional NLRs that are responsible for the resistances against both nematode species and to understand the molecular mechanism by which these genes provide protection upon recognition of pathogen molecules known as effectors. It is this combined knowledge about the host and pathogen molecules that determine the ability of potatoes to be infected or to defend themselves that breeders require to develop resistant potato varieties for the future.

Our consortium brings together experts on potato NLRs from The James Hutton Institute and The Sainsbury Laboratory alongside PCN experts from The James Hutton Institute and the University of Cambridge. We have obtained support from the international companies PepsiCo Solynta and Averis, as well as the 2Blades foundation to ensure immediate impact of the research.

Key resources for this project are already in place. For potatoes, this includes our ability to preferentially re-sequence NLRs using a technology known as RenSeq that was jointly developed by members of this consortium. Using RenSeq, we have been able to represent the NLRs in existing potato varieties that contain the genes H1, Gpa5 and Gpa4. This enables powerful association studies to identify gene candidates. By taking advantage of existing high-throughput transformation capabilities, these candidate NLRs can be assessed quickly to identify the functional nematode resistance genes.

For PCN, we have in place genomic resources such as genome assemblies of both PCN species and established pipelines to identify likely candidate effector genes. In addition, we have PCN populations of G. rostochiensis and G. pallida that have been selected for virulence on potato plants carrying H1, Gpa5 or Gpa4, respectively. These populations will allow us to prioritise candidate avirulence genes that trigger the potato resistance responses upon detection. Through Solynta and Averis we have access to PCN populations that can evade Gpa5 resistance and allow us to study virulence.

These resources combined make the project extremely timely and feasible. The knowledge generated in this project will a) address a scientific gap in our understanding of resistances against plant-parasitic nematodes and b) will deliver an applied outcome to protect potato production. Indeed, we anticipate reaching a position where we can inform breeders about the nature of resistances that can be combined and predict their effectiveness by considering pathogen effector diversity including changes to bona fide avirulence genes.

Potato Cyst Nematodes (PCN) are a persistent threat to potato production and could lead to the demise of the UK's seed potato industry in the next 10 years if not controlled. Resistances against the PCN species Globodera rostochiensis and G. pallida are available in selected cultivars, but the genes, H1 (G. rostochiensis) and Gpa5 and/or Gpa4 (G. pallida), that underpin these resistances remain elusive.

Using state of the art genetics and genomics, our evidence strongly supports that H1, Gpa5 and Gpa4 are members of the NLR gene family. To specifically study NLRs, this consortium has jointly developed RenSeq-based technologies that enable the rapid identification of candidates for these resistances. Using existing RenSeq data from 380 cultivars and breeding clones alongside established computational approaches for SMRT-AgRenSeq-based analysis, we have identified five candidates for H1 and nine candidates for Gpa5. For Gpa4, we have in place populations and phenotypic information that will enable similar studies and can draw on resources from our partners Solynta and Averis.

In addition to cloning H1, Gpa5 and Gpa4, this project aims to identify the corresponding PCN Avr genes. By comparing the effector repertoires of avirulent PCN populations, populations selected for virulence on these resistances, and recently identified virulent populations from the Netherlands, we will be able to identify Avr candidate and, simultaneously, virulent variants thereof.

This knowledge will aid the mechanistic understanding of host resistances against plant-parasitic nematodes. In addition, we will reach a position through these studies where we can facilitate the stacking of complimentary resistances and predict their durability in light of Avr gene diversity in the pathogen population. With the help of our commercial partners, PepsiCo, Solynta, Averis and the 2Blades foundation, we will be able to deliver impact for the international potato market.