Genome editing technologies have greatly accelerated crop improvement by enabling targeted modifications of plant genomes. Although Class 2 CRISPR systems, including Cas9 and Cas12, have become widely used tools for plant genome engineering, the discovery of diverse CRISPR systems with distinct molecular mechanisms continues to expand the possibilities for genome manipulation. Type I CRISPR systems employ a multi-subunit Cascade complex and the Cas3 nuclease to recognize target DNA and mediate processive DNA degradation, providing unique opportunities for applications such as targeted large-fragment deletion and expanded-window base editing.
Recently, a research team led by Associate Professor Jian Chen at China Agricultural University developed two novel Type I-C CRISPR systems, Aca I-C and Cja I-C, that enable efficient genome editing in maize. The study establishes Type I-C CRISPR systems as additional platforms for plant genome engineering and highlights the potential of microbial genome mining for discovering editing tools. These technologies may contribute to future crop improvement by providing alternative strategies for targeted genome modification.
The study was published online in The Crop Journal on July 28, 2026.
“By systematically mining microbial genomic resources, we identified new Type I-C CRISPR systems and demonstrated their potential for large-fragment genome deletion and base editing in crops,” shares Chen. “These systems provide new resources for expanding the plant genome-editing toolbox and advancing precision breeding applications.”
To discover new Type I-C systems, the research team established a bioinformatic pipeline and analyzed approximately 10.35 TB of genomic and metagenomic data from public databases. “From nearly 1.7 million CRISPR arrays, we identified 4258 Type I-C CRISPR systems, revealing a rich reservoir of previously unexplored genome-editing resources,” says Chen. “Among these candidates, Aca I-C from Acidobacterium capsulatum and Cja I-C from Cellvibrio japonicus exhibited robust genome-editing activity in maize.”
In maize protoplasts, Aca I-C and Cja I-C efficiently induced large-fragment DNA deletions, with average editing efficiencies of 47.41% and 44.89%, respectively. Further validation in stable transgenic maize demonstrated that both systems generated targeted large-fragment deletions at the GA20ox3 locus and produced edited plants with reduced plant height, highlighting their potential for crop trait improvement.
The researchers further engineered Aca I-C and Cja I-C into adenine base editors (ABEs) by integrating an adenine deaminase domain. “These Type I-C-derived editors enabled A-to-G base conversions in maize, representing the first demonstration of Type I-C CRISPR-based adenine base editing in plants,” Chen adds. “The Aca-ABE and Cja-ABE systems achieved editing efficiencies of up to 2.48% and 9.51%, respectively, with negligible unwanted indels.”
“This work expands the diversity of CRISPR technologies available for plant genome engineering,” says Dr. Zhimeng Li, first author of this study. “The unique features of Type I-C systems, including their longer spacer sequences and potential for broader editing windows, may provide new opportunities for functional genomics and crop improvement.”
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Contact Author:
Jian Chen
Email address: jianchen@cau.edu.cn
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The Crop Journal
Experimental study
Not applicable
Systematic mining identifies two Type I-C CRISPR systems for efficient genome editing in maize
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.