The role of endophytes in affecting symptom development of European apple canker caused by Neonectria ditissima

European Canker, caused by Neonectria ditissima, has become the most damaging disease of apple in recent years across all major apple growing regions worldwide. Modern cultivars lack resistance to this pathogen and in Europe most effective methods of chemical control are no longer available. Cultivars differ in their susceptibility but there is no absolute resistance.

We obtained preliminary data that indicate a possible link of antagonist fungal endophytes with cultivar tolerance to N. ditissima. The most damaging aspect of the disease is from latent infections in nurseries that become active and develop into canker on the main trunk soon after planting in orchards - leading to tree death. Ample empirical evidence suggests that stresses following planting can promote symptom expression of those nursery-origin latent infections.

In this proposal, we aim to investigate whether cultivar differences in tolerance to N. ditissima are associated with specific endophytes and, if so, identify the organism(s) for further biocontrol assay. Expression of specific genes in the SA and JA pathways will be assayed following inoculation of candidate endophytes to ascertain whether endophytes induce host defence responses that may contribute to canker suppression. Next, we will use a mapping population from a cross between canker resistant and susceptible cultivars to map QTLs that are responsible for recruiting specific endophytes and to determine the extent of overlapping of these QTLs with those mapped for canker resistance. Then, we shall study the extent to which endophyte profiles of a specific genotype are affected by individual or combined soil water deficit, AMF and PGPR treatments. Finally, we shall conduct a common garden experiment to assess (1) to what extent recruitment of endophyte profiles is influenced by soil characteristics, soil microbiota, and host genotypes, and (2) whether canker development is influenced by specific endophytes and plant defence signalling in response to biotic and abiotic factors (represented by different sites). Plant hormone response is measured in terms of specific hormones - JA, SA and ABA; endophyte composition will be characterised by next generation sequencing technology.

The output of this work will not only lead to a deeper understanding of the biology and epidemiology of the disease, but also develop tools and knowledge for practical disease management, which can be efficiently adopted by the industry due to their active involvement in the project.

The industry is supporting this proposal through the LINK scheme, as they recognise the need for a comprehensive strategy to manage the canker disease. Six industry partners will provide both cash and in-kind contribution to this proposal.

European Canker, caused by Neonectria ditissima, has become the most damaging disease of apple in recent years across all major apple growing regions worldwide. Modern cultivars lack effective resistance to this pathogen; in Europe most effective methods of chemical control are no longer available. Cultivars differ in their susceptibility but there is no absolute resistance. Ample empirical evidence suggests that stresses following planting can promote symptom expression of those latent infections of nursery-origin.

We propose to investigate whether cultivar differences in tolerance to N. ditissima are associated with specific endophytes (i.e., those microbes living inside plants without causing visual symptoms) and, if so, identify the organism(s) for further biocontrol assay. Studies will then be carried out to determine whether these endophytes induce host defence responses that may contribute to canker suppression. Next, we will map quantitative trait loci (QTLs) that are responsible for recruiting specific endophytes and to determine the extent of overlapping of these QTLs with those mapped for canker resistance. Then, we will study the extent to which endophyte composition of a specific apple genotype is influenced by individual or combined soil water deficit, AMF (beneficial fungi) and PGPR (beneficial bacteria) treatments. Finally, a field experiment will be conducted to assess (1) to what extent endophyte composition is influenced by soil characteristics, soil microbiota, and host genotypes, and (2) whether canker development is influenced by specific endophytes and plant defence signalling.

The output of this work will not only lead to a better understanding of the biology and epidemiology of the disease, but also develop tools and knowledge for practical disease management, which can be efficiently adopted by the industry because of their active involvement in the project.

The principal beneficiaries are the fruit tree nursery industry and the apple industry. European canker is the most important problem for apple production, affecting the production of rootstocks by the nurseries, establishment of healthy orchards, and subsequent fruit production.

The nursery industry
Our commercial project partners include Frank P. Matthews (FPM), the only fruit tree nursery in the UK producing apple trees for commercial orchards. In addition, NIAB EMR is leading a BBSRC HAPI project on apple replant disease in which Fruittree Rootstock Group (FTRG) is a project partner. FTRG are a consortium representing 17 EU members (propagators, fruit growers and breeders) mainly based in the Netherlands, Belgium and France. Therefore, the results from the present project on canker biology and epidemiology can be used by the project partner directly and disseminated to other commercial nurseries via FTRG initially.

Growers/levy body
Three partners (WWF, Avalon and Scripts) are three large apple producers in the UK and accounting for most dessert apple production in the UK. They will act as a focal point in adopting project results to reduce apple canker in practice, particularly in the early phase of orchard establishment. NIAB EMR and AHDB (project partner) will be responsible for disseminating project outcomes to the apple industry. Our New Zealand (NZ) partner (ENZA) will be engaged in knowledge exchange between researchers/growers in the UK and NZ.

Impact through commercial breeding programmes
EMR is currently leading a breeding programme on apple rootstocks funded by the International New variety Network (INN) and the AHDB Horticulture, and scion breeding programme funded by WWF and ENZA. Subject to agreement of the consortium members, the knowledge on QTLs for endophytes may be used in these breeding programmes.

Endophytes as biocontrol
If candidate biocontrol endophytes can be cultured in vitro, we may license a commercial company to develop this into commercial product. Indeed, NIAB EMR has obtained two biocontrol strains against other diseases; these two microbes are being formulated into commercial products by a company.

General Public
This project will generate results that will lead to improved apple production in the UK, whilst promoting sustainable production practices. This will benefit the general public in terms of secure provision of quality fruit as part of healthy diets, and help the government in delivering policies on food security and safety.