Tiny Pathogens, Big Losses: How RNA Sprays Could Help Protect Crops from Viroids

ViroiDoc MSCA Fellow Lara Palatinus is aiming to understand how viroids interact with their host plants at a molecular level.

Plant diseases are often associated with fungi, bacteria, or viruses. Yet some of the most damaging plant pathogens are even simpler. Viroids are extremely small infectious RNA molecules that do not encode proteins but nevertheless cause severe diseases in important crops such as potato, tomato, citrus, hop, and avocado. Viroid infections can reduce yields by up to 60% and are particularly problematic because, once a plant is infected, there is currently no curative treatment.

Today, viroid control relies almost entirely on prevention by using clean planting material, monitoring fields, and removing infected plants. These measures are costly, imperfect, and difficult to maintain in long-lived or vegetatively propagated crops. New, sustainable approaches to protect plants from viroids are therefore urgently needed.

Using a natural plant mechanism: RNA interference

Plants possess a conserved regulatory mechanism called RNA interference (RNAi). RNAi allows cells to recognize RNA molecules based on their sequence or structure and enables them to regulate their abundance by processing them into small RNAs. This mechanism plays an important role in normal gene regulation and also contributes to plant defense against invasive nucleic acids.

RNA-based plant protection strategies aim to exploit this natural pathway. Instead of modifying the plant genome, specially designed RNA molecules can be applied externally to plants as sprays. Once taken up, these RNAs can be processed by the plant’s RNAi machinery and lead to sequence-specific silencing of complementary RNA molecules.

RNA sprays against viroids

RNA sprays can be used against viroid diseases in two different ways.

The first strategy aims to directly target the viroid RNA. Sprayed RNAs, including antisense RNAs or circular RNAs, can bind to viroid sequences and interfere with essential steps of the viroid life cycle, such as replication or intracellular trafficking. This approach focuses on the viroid itself rather than on the plant.

The second strategy targets the interaction between the viroid and its host plant. Viroids depend on specific plant proteins for replication and movement. RNA sprays can be designed to temporarily reduce the expression of such host genes, thereby limiting viroid replication. These effects are reversible and rely on short-lived RNA-mediated regulation rather than permanent genetic changes.

Together, these approaches illustrate how RNA sprays can be adapted to different molecular targets within the viroid–host system.

Why this approach matters

RNA sprays offer several advantages over traditional plant protection methods. They are highly specific, affecting only the intended RNA targets. They are non-transgenic, as no DNA is integrated into the plant genome. And because RNA molecules naturally degrade, they have the potential to be environmentally compatible when properly designed and applied.

In the face of increasing disease pressure, climate change, and the need to reduce chemical inputs in agriculture, RNA-based technologies could become valuable tools for sustainable crop protection.

Looking ahead

My PhD research within the ViroiDoc project focuses on understanding how viroids interact with their host plants at the molecular level and how RNA-based approaches can be optimized to interfere with these interactions. By combining fundamental research with innovative RNA technologies, this work aims to contribute to future strategies for protecting crops against viroid diseases.

*The photo was created with Biorender.

Lara Palatinus is an MSCA fellow within the ViroiDoc Network. Lara is working on an individual research project entitled “RNA sprays - precision tools for the modulation of host genes to develop viroid resistance” at the University of Regensburg (UREG) in Germany under supervision of Aline Koch, while also pursuing her PhD at the Regensburg International Graduate School of Life Sciences (RIGeL).