IPN - Instituto Pedro Nunes

IPN     IPN Incubadora

Epidemiologia, Ecogenómica e Modelação das Doenças Reguladas de Prunus


The impact of plant diseases has increased due to intensification, globalisation, commercial development and climate change. Despite investment in protection and control, they still account for more than 15% of total losses. Plant protection products play an important role but are constrained due to the reduction in the number of approved substances. This is a major issue contributing to the unfavourable agricultural production global context and the UN proclaimed 2020 as the International Year of Plant Health.

The Beira Interior (BI) region of Portugal is the most productive in Prunus sp. (Prunus avium-cherry and P. persicae-peach), being these agri-food resources pillars for the regional economy, corresponding to 69% and 48% of the national production. Fundão and Cova da Beira are Protected Geographical Indications of BI for cherry and peach production that occurs in mixed orchards. The recent implementation in BI of considerable areas of almond (P. dulci) in intensive system is a relevant factor for the dynamics of the agroecosystem, namely at the phytosanitary level. The Prunus production in BI is highly affected by diseases, whose intensity and severity is increasing without the etiological agents having been identified. The most devastating diseases that affect transversely these crops are caused by the regulated bacteria Pseudomonas syringae (PS), Xanthomonas arboricola (XA) and Xylella fastiosa (XF), with the team having experience with these organisms. Although PS has already been described in BI, the impact and prevalence have not been assessed. On the other hand, XF is present in national territory, isolated on Prunus sp. in the Porto region, and similarly, XA is present at the border with Spain responsible for considerable losses in almond orchards.


The agroecosystem of BI is characterized by a high density of genetically heterogeneous Prunus sp. where these pathogens can coexist in the plant, enhancing the development of highly adapted strains and/or the occurrence of coevolution phenomena associated with the expansion and emergence of new diseases. Strains considered non-pathogenic or weakly virulent that coexist with pathogenic strains in the same plant have been described. This coexistence of phylogenetically close strains, but drastically different in their phenotype constitutes a critical challenge for diagnosis. Studies carried out at BI are limited and scarce, and based on the team's knowledge acquired in projects, contracts and studies, we determined after an initial inspection, that the symptoms observed coincide with those described for PS and XA.

In this framework, the project has five major objectives:
1. Assess disease incidence on Prunus orchard in Beira Interior region;

2. Molecular epidemiology (who, when, where) using the long-read sequencing Oxford Nanopore Technologies targeting Prunus sp. disease-related bacteria isolation;

3. Using the whole-genome sequence of isolates we intend to explore the host range and the virulence determinants repertoire;

4. Using a metagenomic approach evaluate the effect of disease-related bacteria on the structure and functions of the microbiota of the Prunus phyllosphere to identify taxonomic groups relevant for disease control as part of potential bio-based solutions;

5. Infer the risk of disease establishment and spread under climate change scenarios using spatial models based on ecological and environmental data collected in the project.

Objectives, Activities and Results expected / achieved

Overall, the integration of all data generated in this project allows the definition of the first policy guidelines contributing to implement local control measures, prevent dissemination and reduce susceptibility to disease, fostering the sustainable production of Prunus sp. and the agroecosystem resilience in BI. Given the relevance of the proposed approaches and the urgency to take early action for controlling the main diseases affecting Prunus orchards in BI, we present an innovative project to multidimensionally characterise bacterial diseases and assess their long-term impact. We also intend to use metagenomics-based methods for diagnosis.

The work team has the necessary skills to successfully achieve the proposed objectives, combining know-how in disease diagnosis, metagenomic tools applied to plant-pathogen interactions, expertise in population genomics of bacterial pathogens with modelling of biotic agent dispersion.

The project also benefits from the support of COTHN and the partners APPIZEZERE and CNCFS, which will ensure the fieldwork. Several international consultants with relevant experience in this area will actively contribute to the project. In this context it will be possible to carry out an in-depth study on Prunus diseases in Beira Interior, contributing to a deeper knowledge of pathogens and new methodological applications fostering sustainable production in vulnerable and agriculture-dependent regions.

Project Reference

DOI: 10.54499/PTDC/ASP-PLA/3145/2021


Intervention Region

North and Center of Portugal

Total Investment


IPN Investment


Total Eligible


IPN Eligible


EC Funding – Total


EC Funding – IPN



36 Months

Start Date


End Date


Approval Date



Instituto Pedro Nunes;
Associação Centro de Apoio Tecnológico Agro Alimentar;
Associação de Protecção Integrada e Agricultura Sustentável do Zêzere;
Centro Nacional de Competências dos Frutos Secos - Associação CNCFS;
Universidade de Coimbra.




Xanthomonas Xylella;
Population structure;
Host range;
Structural and Functional Microbiota;
Disease predictive spatial modelling.