Rice's Resistance To Genetic Tweaks Poses Challenge For Crop Scientists

Advanced methods for temporarily switching plant genes on or off do not work in rice, but setback could be a springboard for innovation

Efforts to use viruses as tools for genetic research in rice have hit a roadblock, according to a new study by scientists from Rothamsted and the Federal University of Rio Grande do Sul (UFRGS) in Brazil. The collaboration tested two popular viral vectors — barley stripe mosaic virus (BSMV) and foxtail mosaic virus (FoMV) — for their ability to alter gene expression in rice plants.

While the technique, known as virus-enabled reverse genetics (VERG), has proven effective in wheat and other monocots, researchers found that neither BSMV nor FoMV successfully altered gene expression in six different rice cultivars. The findings suggest rice may possess intrinsic resistance mechanisms that block these viral vectors, making it harder to study gene function in this crop.

VERG techniques, which harness plant viruses to silence or overexpress a specific gene, are a cornerstone of functional genomics in species where stable transformation is difficult. While VERG tools have enabled researchers ask questions about what specific genes do in a range of monocots and dicots, including in blackgrass, the new data clearly show that rice (Oryza sativa) is recalcitrant.

If we’re going to transiently alter gene expression in rice, we will need new approaches.

“We tested everything - different rice subspecies, different inoculation methods, used the ideal growth conditions - but no matter what we did, it worked in wheat, but not in rice,” said Guilherme M. Turra, a PhD student at UFRGS who undertook the study whilst based at Rothamsted.

When it is successful, the most tried-and-tested method to assess successful silencing is through removing one of the genes associated with chlorophyll production. This causes a change from green leaves to white, otherwise known as photobleaching. Alternatively, using the viruses to drive expression of fluorescent proteins like GFP will result in plants with fluorescent patches. Neither outcome was observed in rice, despite extensive optimisation.

By publishing these negative results, the researchers hope to save others from repeating the same experiments and to encourage the development of alternative viral systems tailored to rice.

“This result suggests rice has some intrinsic resistance mechanisms that block the viruses from successfully mounting a VERG response in rice.” said Dr. Dana MacGregor, senior Rothamsted co-author on the article. “Although BSMV and FoMV driven VERG have a good track record in other species, our data show they also have their limitations. What works in wheat, Setaria, or blackgrass didn’t translate easily to rice. If we’re going to transiently alter gene expression in rice, we will need new approaches.”

This study was funded by the Brazilian Government's Institutional Internationalization Program (PRINT) from Coordination for the Improvement of Higher Education Personnel (CAPES) with additional strategic funding from the UK Biotechnology and Biological Sciences Research Council allocated to the Growing Health Institute Strategic Programme.