A research team from the Higher Council of Scientific Research (CSIC), part of the Ministry of Science, Innovation and Universities, has made a significant breakthrough in plant biotechnology by developing a new gene-silencing method. This innovative technique uses ultra-short RNA sequences delivered by genetically modified viruses to silence specific genes, enabling precise customization of plant traits. Published in Plant Biotechnology Journal, the work opens new possibilities for crop improvement, functional genomics, and sustainable agriculture.

Viral vector technology modifies viruses by removing their disease-causing genetic material, turning them into carriers that deliver targeted RNA sequences into plants. This approach has already shown promise in experimental settings — inducing flowering, speeding up the development of improved crop varieties, altering plant architecture for easier mechanization, enhancing drought tolerance, and producing health-beneficial metabolites.

The new method, developed by CSIC in collaboration with the University Research Institute of Conservation and Improvement of Valencian Agrodiversity (COMAV) and Italy’s Department of Applications and Innovation in Supercomputing (Cineca), optimizes technological platforms to accelerate the development and testing of viral vector-based agricultural applications, according to a press release.

“We have implemented synthetic biology approaches compatible with future production on an industrial scale,” says Fabio Pasin, Ramón y Cajal researcher at the Margarita Salas Biological Research Center (CIB-CSIC) that has directed the study.

The new technique, called virus-transported short RNA insertions (vsRNAi), marks an important advance in using viral vectors to enhance crop traits. By employing a harmless plant virus to deliver short RNA molecules, vsRNAi activates RNA interference (RNAi)—a natural process that switches off specific genes by preventing their instructions from producing proteins. This approach improves the efficiency of suppressing target plant genes.

Using comparative genomics and transcriptomics, researchers designed vsRNAi sequences targeting particular plant genes. They demonstrated that ultra-short RNA inserts — just 24 nucleotides long — can effectively silence genes. This is a significant reduction compared to the typical 300-nucleotide sequences used in viral vector technology. “This innovation drastically reduces the size and complexity of traditional virus-induced gene silencing constructs, enabling faster, cheaper, and more scalable applications,” explains Pasin.

To test the method, the team targeted the CHLI gene, vital for chlorophyll biosynthesis, by designing viral vectors carrying inserts between 20 and 32 nucleotides. When introduced into a model plant, these vectors caused visible yellowing of the leaves and a strong drop in chlorophyll levels, confirming effective gene silencing.

“Small RNA sequencing revealed that the vsRNAi approach triggers the production of small RNAs, of 21 and 22 nucleotides, which correlates with a negative regulation, a process by which the expression of a gene is reduced or stopped, effective transcription,” adds the CIB-CSIC researcher.

An Effective Technique to Boost Agriculture

The researchers applied this new technique to the model plant Nicotiana benthamiana, demonstrating its ability to produce desired traits in crops from the Solanaceae family—one of the world’s most important plant families that includes staple vegetables like potatoes. The method was also tested on tomato and scarlet eggplant (Solanum aethiopicum), an underutilized crop with significant potential to expand cultivation beyond its current regions in Africa and Brazil, and even grow in Europe, where it holds niche markets and local varieties such as Italy’s “Rossa di Rotonda.”

Key advantages of this new approach over traditional RNAi methods include its simplicity, high specificity, cost-effectiveness, and the fact that it does not introduce permanent genetic changes into the plants.

“This is a great advance in plant biotechnology and we are excited about its possible applications,” says Pasin. “We believe that the technique could mean a revolutionary change for basic research, especially for non-model plants with limited availability of genetic resources and biotechnological tools, but also for agriculture, since it allows the on-demand alteration of the traits of the crops and the selective control of pests and diseases of these.”

The results have important implications for agriculture, since they could be used to temporarily alter the features of crops in order to obtain specific phenotypes that improve their performance, disease resistance and nutritional content. In addition, the portability of vsRNAi between species highlights its potential for high-yield functional genomics and the modulation of specific traits in both model and underutilized cultures.