Every year, farmers battle an invisible, relentless, formidable enemy: plant viruses. Unlike bacteria or fungi, which can be controlled with pesticides or fungicides, there is no straightforward way to cure crops of viral infections. According to the U.N. Food and Agriculture Organisation (FAO), plant pests and diseases destroy nearly 40% of the world’s annual crop, costing the world more than $220 billion. Of that, plant viruses alone contribute to over $30 billion in losses each year.
In response, scientists started tapping the power of RNA-based technology to help plants defend themselves better — just the way our immune system fights off viruses. At Martin Luther University Halle-Wittenberg in Germany, a team of researchers recently reported developing an RNA-based antiviral agent that confers strong protection against cucumber mosaic virus (CMV), a widespread and destructive plant virus.
CMV infects more than 1,200 plant species, including critical food crops like cucumbers, squash, and cereals, and medicinal plants. It spreads through small sap-sucking insects called aphids. With nearly 90 aphid species capable of transmitting CMV, outbreaks are often difficult to contain.
In India, CMV is responsible for 25-30% yield losses in banana plantations. In pumpkins, cucumbers, and melons, infection rates can soar up to 70%. Affected plants develop a mosaic discoloration, stunted growth, and commercially unviable fruits.
HIGS and SIGS
In the new study, the researchers used RNA silencing, a natural defence mechanism found in plants. When a virus infects a plant, it introduces double-stranded RNA (dsRNA), which is a red flag for the plant’s immune system.
The plant responds by activating Dicer-like enzymes (DCLs), which slice the dsRNA into small fragments called small interfering RNAs (siRNAs). These siRNAs then guide the plant’s defence system to recognise and destroy the viral RNA, preventing the infection from spreading.
But this process is far from perfect. Not all siRNA generated by the plant are effective and the virus often mutates rapidly, evading the plant’s natural defences. To strengthen plant immunity, researchers are exploring RNA-based crop protection techniques such as host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS).
HIGS works by genetically modifying plants to produce virus-fighting dsRNA in their own cells. This provides continuous protection throughout the plant’s life. But regulations, high production costs, and the potential for viral resistance limit its widespread use.
SIGS is a more flexible alternative. Plants are treated with RNA sprays instead of being genetically modified. Leaves absorb the RNA, triggering the plant’s natural immune response without altering its DNA.
While SIGS doesn’t require genetic modification and is cost-effective and environmentally friendly, its effectiveness is limited: traditional dsRNA formulations produce a random mix of siRNAs, many of which fail to silence the virus efficiently.
Effective dsRNA
To overcome the limitations of existing RNA-based approaches, the researchers developed a new approach that enhanced the effectiveness of RNA silencing against CMV.
Instead of using randomly generated dsRNA, they designed “effective dsRNA” — genetically engineered dsRNA enriched with highly functional siRNA. These specially selected siRNA bind to the virus’s genetic material to trigger a stronger antiviral response. Their findings were published in Nucleic Acids Research.
In a laboratory setting, researchers first screened siRNA candidates and identified the most potent siRNAs against CMV. These e-siRNA were assembled into dsRNA constructs to ensure that when the plant’s defence system processed them, they’d produce a high concentration of functional siRNA. This method resulted in a more targeted, more efficient form of RNA-based plant protection.
The researchers also tested their new method by applying the more-effective siRNA and dsRNA directly to a model plant, Nicotiana benthamiana, infected with CMV. They wrote in their paper that plants treated with this siRNA had almost 80% lower viral load, with some experiments achieving complete protection. The dsRNA formulation outperformed traditional dsRNA because the plant processed them into active siRNA more efficiently, creating a stronger immune response.
The team also found this method to be more effective against multiple CMV strains.
The new approach has three key advantages: (i) It’s more precise because the plant’s immune system is directed toward the viral particles’ most vulnerable genetic regions, boosting its ability to fight infection. (ii) It provides a stronger defence because the more-effective dsRNA targets multiple regions of the viral genome simultaneously, making it harder for the virus to mutate and escape. (iii) The effective dsRNA can be redesigned in about a month to target new viral strains.
Researchers currently apply RNA-based agents manually in laboratory conditions either by injecting or by rubbing them onto plant leaves. To make the treatment possible for real-world use, the team is currently developing spray-based solutions, and preparing for field trials to test their effectiveness in natural conditions.
While the study focused on CMV, the principles of the new dsRNA technology can be applied to combat other major plant viruses, such as the tomato yellow leaf curl virus, the potato virus Y, and the tobacco mosaic virus. The researchers have also expressed belief that RNA-based approaches can be extended to target fungal and bacterial diseases as well as insect pests.
More time
Despite its immense potential, one major hurdle is stability in outdoor conditions. RNA molecules degrade quickly when exposed to sunlight, rain, and soil microbes. The researchers are working on nanoparticle-based delivery systems to improve RNA stability and ensure long-lasting protection.
Another challenge is cost and scalability. While production costs are falling, large-scale use remains expensive. This requires further innovation that makes it economically viable for farmers.
Finally, regulatory approvals pose a challenge. The US Environmental Protection Agency granted the world’s first approval for an RNA-based crop protection product only in 2023; the regulatory processes in other countries including India may take more time.
Manjeera Gowravaram has a PhD in RNA biochemistry and works as a freelance science writer.
Published – April 28, 2025 05:30 am IST