A New Approach to Controlling Crop Diseases: Viroid-like RNAs Against Fusarium

ViroiDoc MSCA Fellow Vjeko Hrabar aims to expand knowledge of the diversity of viroid-like RNAs in fungi. What if the key to protecting our food crops from destructive fungi lies not in chemicals, but in the fungi’s own viruses? 

Fungi of the genus Fusarium and related genera are among the most damaging and toxic fungal pathogens affecting agriculture. They have a major impact on food and feed production and safety worldwide. These fungi can survive in soil and plant residues and produce toxic compounds—known as mycotoxins—including zearalenone, trichothecenes, fumonisins, moniliformin, and beauvericin. These toxins accumulate in plant tissues and can enter the human and animal food chain.

Fusarium species infect staple crops such as maize, wheat, and rice, causing diseases like Fusarium wilt and Fusarium head blight. These infections lead to significant yield losses, reduced grain quality, and contamination problems at harvest. For farmers and the agri-food sector, this means economic losses, stricter quality controls, and potential market rejection of contaminated batches. Due to the persistence and severity of these infections, finding effective and sustainable control strategies remains a priority.

Viruses that infect fungi, known as mycoviruses, have long been recognized. What has become clearer in recent years is their potential agricultural relevance. Some mycoviral infections can alter fungal growth and toxin production, and in certain cases reduce the pathogen’s ability to cause disease in crops—a phenomenon known as hypovirulence.

These findings have led to an important question for agriculture: could these viruses, or similar infectious molecules such as viroid-like RNAs (vdlRNAs), be used as biological control agents to weaken harmful fungi?

My individual research project builds on this idea. The goal is to expand our knowledge of the diversity of viroid-like RNAs in fungi that are relevant to agriculture and food production. The research has three main objectives.

First, the project focuses on identifying and characterizing new viroid-like RNAs, especially in fungi of agronomic importance—both plant pathogens and beneficial fungi. Additional investigations include bacteria and plants to better understand how widespread these RNA agents are.

Second, the project evaluates how vdlRNA infection affects fungal characteristics such as growth, aggressiveness toward crops, and toxin production. Understanding these effects is essential to assess whether viroid-like RNAs could be developed as biological control tools, natural regulators of mycotoxin production, or even as biostimulants that support healthier crop systems.

Finally, the research examines the structure and function of potential proteins encoded by newly identified viroid-like RNAs, helping to clarify how these small RNA agents interact with their fungal hosts.

Previous studies have already shown that certain viroid-like RNAs can influence fungal behavior, including virulence and mycotoxin production. If these effects can be better understood and harnessed, they may provide a new, environmentally friendly complement to existing crop protection strategies.

At a time when agriculture faces increasing pressure to reduce chemical inputs while maintaining yield and food safety, exploring naturally occurring biological regulators such as viroid-like RNAs could open new avenues for sustainable disease management. Understanding these invisible interactions may ultimately help farmers produce safer crops with fewer losses and lower environmental impact.

Vjeko Hrabar is an MSCA fellow within the ViroiDoc Network. Vjeko is working on an individual research project entitled “Identification and characterization of novel infectious circular viroid-like RNAs in hosts belonging to different kingdoms” at the National Research Council (CNR) in Italy, while also pursuing her PhD at the University of Bari (UNIBA).