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Updated: Apr 10, 2026
Author Spotlight: Streamlining Rice Breeding with CRISPR/Cas for Obtaining Optimal Phenotypic and Agronomic Traits
Published on: January 3, 2025
Harnessing diverse tRNAs and AI-guided mining for compact and efficient plant multiplex genome editing
Yao He1, Yanqin Ma2, Yuechao Wu3
1Agricultural Microbial Agents Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
This study introduces a compact CRISPR genome editing system using plant transfer RNAs (tRNAs) for efficient multiplexed gene editing in crops. It also presents an AI tool to discover novel tRNAs for advanced plant engineering.
Area of Science:
- Plant biotechnology
- Molecular biology
- Genomics
Background:
- CRISPR-Cas9 technology is vital for plant genome editing.
- Efficient multiplexed editing requires optimized single-guide RNA (sgRNA) expression.
- Existing systems can be improved for compactness and efficiency.
Purpose of the Study:
- To optimize sgRNA expression for multiplexed CRISPR-Cas9 editing in plants using endogenous tRNA processing.
- To develop a compact and efficient tRNA-based multiplexed genome editing platform.
- To create an AI-driven framework for discovering novel tRNAs for plant genome engineering.
Main Methods:
- Screening of endogenous tRNAs in Arabidopsis thaliana and Oryza sativa for superior sgRNA processing.
- Leveraging tRNA's dual function in sgRNA processing and RNA polymerase III promoter activity.
- Development and application of plant tRNA large language models for tRNA mining.
Main Results:
- Identified superior tRNAs that enhance sgRNA expression compared to existing methods.
- Established a compact multiplexed system enabling simultaneous editing of at least ten genomic loci in rice and soybean.
- Discovered thousands of previously unidentified canonical and noncanonical tRNAs using AI models.
Conclusions:
- A robust tRNA-based CRISPR platform for multiplexed plant genome editing has been developed.
- An AI-guided tRNA mining framework significantly expands the repertoire of usable tRNAs.
- This work provides a valuable resource for advanced plant genome engineering and germplasm innovation.
