Minimal Plant Genomes Made Possible by New Genetic Strategy

Background: Ancient events in plant evolution have left behind large, duplicated regions in their genomes.

New discovery: Salk Institute scientists found that deleting these large blocks of DNA can still lead to normal plants.

The findings demonstrate that large chromosomal deletions are a viable strategy in plant genetic engineering, which could now accelerate the development of streamlined, minimal plant genomes-a major goal in industries looking to create new plant-based biotechnologies.

The new study, led by Salk Research Professor Todd Michael and computational scientist Ashot Papikian, was published in Proceedings of the National Academy of Sciences on August 11, 2025.

More details: The researchers used CRISPR-Cas9 to delete four large, duplicated blocks in Arabidopsis thaliana, a model plant commonly used in plant biology research. The deletions were then verified using whole-genome sequencing, which revealed minimal off-target effects.

While two deletion lines showed distinct phenotypes resulting from the loss of many genes, two others displayed no obvious defects. RNA-sequencing revealed that expression compensation, where deletions of duplicated genes led to the upregulation of intact duplicates, was not a general response to the deleted regions under these conditions.

The results suggest that it is possible to obtain viable plants when deleting large fragments that may be redundant or that contain non-essential genes.

Why this is important: These findings challenge the assumption that these duplicated regions are essential and highlight the potential redundancy or modularity within plant genomes. The scientists' approach of removing entire duplicated blocks now offers a powerful strategy to functionally dissect conserved genomic regions, investigate gene linkage and dosage effects, and accelerate the development of streamlined, minimal plant genomes with broad implications for plant biology, synthetic genomics, and biotechnology.

Other authors include: Rachel J. Rattner, Jenni Kao, Neil Hauser, Nicholas Allsing, Allen Mamerto, Nolan T. Hartwick, and Kelly Colt at Salk.

Funding: This work was supported by the Harnessing Plants Initiative at the Salk Institute, with funding from TED Audacious and the Bezos Earth Fund.