Monitoring of fungal crop pathogens with the Oxford Nanopore MinION | LC 25

Biography

Rute Rego holds an MSc in Plant Molecular Biology, Biotechnology and Bioentrepreneurship, having previously worked at the University of Minho and Polytechnic Institute of Viana do Castelo, Portugal, on the identification of bacteriophages targeting phytopathogenic bacteria in Actinidia. Rute currently works as a MSc researcher at InnovPlantProtect, Portugal, where she is applying her molecular skills to develop novel methods for monitoring crop pathogens, with a strong focus on environmental DNA (eDNA) analysis through nanopore sequencing.

Abstract

Agricultural production is expected to face significant challenges in the coming decades due to the increasing geographical spread and variable impacts of phytopathogenic organisms. These organisms, which currently cause productivity losses of 20 to 40%, are anticipated to pose greater risks in Europe and the Mediterranean. This is driven by climate change, global trade, the rising prevalence of endemic and emerging species, coupled with anthropogenic factors that facilitate their evolution. Addressing these challenges requires the development of robust systems for the early detection of diverse species and strains of phytopathogenic organisms in the environment. Monitoring of environmental DNA (eDNA) from airborne spores is emerging as a key approach for detecting multiple biotic threats. In this study we focused on identifying airborne spores, pathogens of two key crops for the Alentejo region (Portugal): wheat and olives. To achieve this, spore trap networks were deployed in wheat fields and olive orchards during the respective spore propagation seasons. Samples were collected bi-weekly, eDNA was extracted, and sequenced on the Oxford Nanopore MinION either with a metabarcoding or a genomics approach. The former enabled the detection of multiple pathogen species, whereas the latter enabled strain identification for two key pathogens: Puccinia striiformis f. sp. tritici (which causes yellow rust in wheat), and Colletotrichum (which causes olive anthracnose). This early detection capability will support improved pest management strategies, optimized pesticide application, and reduced crop losses, ultimately enhancing agricultural resilience to phytopathogenic threats.