HealthyPlants: A systematic survey of cultivated plant viruses and cereal virus reservoirs.

Project Information

HealthyPlants

Grant agreement ID: 101106728

DOI

10.3030/101106728

Project closed

EC signature date 20 July 2023

Start date 1 February 2024

End date 31 January 2026

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 199 694,40

Coordinated by

TEAGASC - AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY
Ireland

Periodic Reporting for period 1 - HealthyPlants (HealthyPlants: A systematic survey of cultivated plant viruses and cereal virus reservoirs.)

Reporting period: 2024-02-01 to 2026-01-31

Summary of the context and overall objectives of the project

Plant viruses are an under‑recognised but growing threat to European agriculture. Their impact is being amplified by climate change, the evolution of pesticide resistance, and the loss of crop protection chemistries. Europe’s Farm to Fork ambitions increase the need for robust integrated pest management (IPM) strategies and real time decision support systems for farmers. Effective disease management depends on rapid, sensitive and specific diagnostic tools built on a clear understanding of viral diversity and reservoirs in the landscape. This project set out to build the knowledge and tools needed for effective molecular surveillance of plant viruses in Ireland by (1) completing the first survey of viruses associated with major cultivated plants in Ireland and establish an open, national baseline of viral sequences to underpin development of new diagnostic and surveillance tools; (2) determining whether field margins, hedgerows and pastures act as reservoirs for cereal and other crop viruses; and (3) screening newly imported tuber crops with potential phytosanitary risks. The intended impact was to underpin early detection, evidence‑based integrated pest management (IPM) and policy decisions governing crop introductions and plant‑health preparedness.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

More than 360 plant samples were collected from symptomatic and asymptomatic cultivated crops (including barley, wheat, oats, potato, rye, beet, faba bean, peas, lupin and pasture swards) and processed using an RNA sequencing workflow optimised during a pilot comparison of enrichment and bioinformatics methods; sequence data were generated for 80+ samples and analysed with validated pipelines. All raw sequence data and assembled viral genomes have been deposited in public repositories (SRA, GenBank) and collated into an open, central database of Irish plant virus sequences, made available on Zenodo to support reuse by researchers and diagnosticians. A landscape reservoir study collected and pooled over 300 individual plants from arable margins, hedgerows and pastures into plant‑community samples, confirming that grasslands and pasture are important reservoirs of cereal‑relevant yellow dwarf viruses (including the species dominant in spring barley), and sampling of margins led to the first record of soybean dwarf virus (SbDV) in Ireland, detected in red and white clover. Four alternative tuber crops (yacon, oca, Chinese artichoke, Jerusalem artichoke) were screened and no high‑risk pathogens (e.g. potato yellowing virus) were found. Beet yellows virus (BYV) was identified as causing yellowing in fodder beet, prompting development and publication of a rapid, field‑amenable RT‑LAMP assay for BYV. Finally, a secondment to a national plant‑health laboratory produced a case study and report on implementing high‑throughput sequencing (HTS) for routine diagnostics.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

In summary, this project provides open data, validated methods and practical diagnostics that together strengthen Ireland’s ability to detect, assess and manage plant‑virus risks, supporting resilient, sustainable crop production and informing policy on crop diversification and plant‑health preparedness; it fills a critical information gap by delivering the first open, large‑scale collection of plant virus sequences for Ireland and demonstrating the practical value of untargeted high‑throughput sequencing (HTS) for national surveillance. The work establishes a new baseline for surveillance by making a publicly available sequence database that enables development and validation of molecular assays tailored to locally circulating viral strains and supports rapid screening of vectors and plants. Taking an ecosystem perspective, systematic sampling of field margins and pastures assessed their role as reservoirs and notably revealed abundant soybean dwarf virus (SbDV) in clover, a finding directly relevant to risk assessments for introducing legume crops such as soybeans adapted to cooler climates. The survey of viruses in Irish legume crops detected a total of eight viruses and highlighted three of potential concern: the Pea enation mosaic virus complex (PEMV), which was widespread and can cause substantial yield loss but for which tolerance or resistance exists; Turnip yellows virus (TuYV), found in both peas and visually healthy faba beans and warranting further study because resistance is currently limited; and Pea necrotic yellow dwarf virus (PNYDV), identified in faba bean and known to cause severe outbreaks elsewhere in Europe. Together these results point to priorities for molecular surveillance and varietal resistance work as legume production expands. On the diagnostics front, Beet yellows virus (BYV) was confirmed as the cause of yellowing in fodder beet and a rapid, field‑amenable RT‑LAMP assay for BYV was developed and published, offering a low‑cost tool for in‑field screening and for vector and crop surveillance. For broader impact, further uptake will require integrating sequence data into national high‑throughput surveillance platforms, feeding outputs into decision‑support systems for farmers, and sustaining landscape‑scale monitoring to detect shifts in virus and vector prevalence driven by changes in farming practices and climate.

Individual plant specimens sampled from potential viral reservoirs

Improving diagnostics for crop viruses using information from HTS surveys