Plant breeding is a key tool for addressing global food security by improving crop yields, nutritional quality and resilience to climate change.
But traditional plant transformation methods are often inefficient, expensive and incompatible with many important species. A new study led by UCLA and published in Nature Plants introduces a simpler approach: a heritable, transgene-free genome editing technique using a compact CRISPR system delivered by a common plant virus. The method could streamline crop improvement and expand genome editing to a wider range of plants.
Steven Jacobsen, a professor of molecular, cell and developmental biology at UCLA, led the research in collaboration with CRISPR-Cas9 co-inventor Jennifer Doudna and microbiologist Jill Banfield of UC Berkeley.
Their team engineered the tobacco rattle virus to deliver a CRISPR-like enzyme, ISYmu1, into Arabidopsis thaliana, a model plant. The tool targeted specific DNA sequences, resulting in inheritable genetic edits without leaving behind the virus or any foreign DNA.
“CRISPR has the potential to make a huge impact in agriculture — one that can be customized to local needs around the world,” said Doudna, a Nobel laureate and founder of the Innovative Genomics Institute, in a UCLA news release.
Key Breakthrough
The innovation centers on using the virus as a delivery system to reach germ cells, enabling the changes to pass down through generations. Unlike conventional techniques that require tissue culture and cell regeneration, this method simplifies the process into a single step.
“One of the biggest hurdles in plant breeding is getting gene-editing tools into the right cells,” said Jacobsen. “Our system lets us bypass that bottleneck.”
Traditional CRISPR systems are too large to be packaged into plant viruses. By using a smaller enzyme, the team was able to fit the tool into the virus and ensure it traveled throughout the plant, reaching even reproductive cells.
From Concept to Field
The team tested several compact CRISPR systems and identified ISYmu1 as the most effective. Using a natural soil bacterium to introduce the engineered virus into the plant, they observed clear markers indicating successful edits — white patches on the plant where changes had occurred.
Because the virus doesn’t enter the seeds, only the targeted DNA changes are inherited. This creates plants that are genetically modified without containing viral or foreign material.
Broader Implications
The tobacco rattle virus can infect more than 400 plant species, offering broad potential for future applications. Jacobsen sees particular promise for improving crops that are difficult to modify using current techniques.
“I grew up on an almond ranch and have spent my career in agriculture,” he said. “There’s real opportunity here to make this technology accessible for under-resourced crops in developing regions.”
Collaborative Strengths
The study reflects the combined expertise of the three labs. Doudna’s team specializes in CRISPR development, Banfield’s group identifies novel CRISPR systems and Jacobsen’s lab focuses on plant applications. Together, they developed and tested a platform with potential to significantly advance crop breeding.
What’s Next
The researchers are now testing the system in additional plant species, including major crops. They also plan to expand the tool’s capabilities, enabling multiple edits at once, and improve its overall efficiency.
Other contributors include Trevor Weiss, Maris Kamalu, Honglue Shi, Zheng Li, Jasmine Amerasekera, Zhenhui Zhong, Benjamin Adler, Michelle Song, Kamakshi Vohra, Gabriel Wirnowski, Sidharth Chitkara, Charlie Ambrose, Noah Steinmetz, Ananya Sridharan and Diego Sahagun.
Funding came from the NSF Plant Genome Research Program, the Howard Hughes Medical Institute, the Jane Coffin Childs Fund for Medical Research, Lawrence Berkeley National Laboratory, the U.S. Department of Energy and the UCLA Broad Stem Cell Research Center Sequencing Core.
