Precision Breeding for a Global Staple Food: A Systematic Review with a Strategic Framework for CRISPR-Cas Applications in Rice (Oryza sativa L.)
Abstract
1. Introduction
2. Materials and Methods
2.1. Literature Search Strategy and Study Selection
2.2. Eligibility Criteria and Screening Rationale
2.3. Data Extraction and Synthesis
Protocol and Registration
3. Results and Critical Analysis
3.1. Study Selection and Characteristics
3.2. Comparative Analysis of Editing Modalities: Efficacy and Constraints
3.2.1. NHEJ-Mediated Knockouts
3.2.2. Base Editing (CBE/ABE)
3.2.3. Homology-Directed Repair (HDR)
3.2.4. Prime Editing
| Editing Modality | Primary Mechanism | Reported Efficiency | Representative Use Cases | Major Constraints | Sources |
|---|---|---|---|---|---|
| NHEJ-Mediated Knockout | Error-prone repair of DSBs generating indels that disrupt gene function | High (commonly >70% in rice; up to 75–90% in mammalian systems) | Loss-of-function traits, including knockout of negative regulators and susceptibility genes | Inherently error-prone; unpredictable indel size; genotype-dependent transformation efficiency | [5,6,7,8,10,11,12,13,14] |
| Base Editing (CBE/ABE) | Direct single-nucleotide conversion without DSB formation | High transformation efficiency (up to 100% in Nipponbare); variable editing frequency | Herbicide resistance alleles and precise amino acid substitutions | Restricted editing window; strict PAM requirement; limited to specific base transitions | [9,16,17,20,22] |
| HDR-mediated Editing | Donor-template-guided homology-directed repair | Low (generally <10%) | Precise gene replacement or targeted gene insertion | Extremely low donor DNA incorporation; strong competition with NHEJ; genotype dependence; technically demanding | [23,24,25,26,28,34] |
| Prime Editing | Reverse transcriptase-mediated DNA synthesis guided by pegRNA without DSBs | Highly variable: <1% in many studies; up to 77.08–88.5% at specific loci under optimized conditions | Precise base substitutions, small insertions, and deletions for molecular breeding | Low reproducibility; difficulty recovering stable transgenic lines; large construct size; extensive optimization required | [29,30,31,32,33,34] |
3.3. Analysis of Key Trait Categories and Editing Success
3.3.1. Yield and Grain Quality
3.3.2. Biotic Stress Resistance
3.3.3. Abiotic Stress Tolerance
3.3.4. Nutritional Biofortification
3.4. The CRISPR Trait Prioritization and Readiness Framework (CTPRF)
3.5. Application to Case Studies
3.5.1. Japan: Herbicide-Tolerant Rice
3.5.2. United States: High-Yield Rice
3.5.3. China: Disease-Resistant Rice
3.6. Technical Challenges and Recent Mitigation Strategies
3.6.1. Overcoming HDR Inefficiency
3.6.2. Addressing Genotype-Dependent Transformation
3.6.3. Manipulating Polygenic Traits
3.7. Regulatory Landscapes
4. Conclusions and Future Perspectives
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Machel Gica, N.G.; Gica, W.T.; La, H.; Mi, Y.; Zhou, Y. Precision Breeding for a Global Staple Food: A Systematic Review with a Strategic Framework for CRISPR-Cas Applications in Rice (Oryza sativa L.). Genes 2026, 17, 165. https://doi.org/10.3390/genes17020165
Machel Gica NG, Gica WT, La H, Mi Y, Zhou Y. Precision Breeding for a Global Staple Food: A Systematic Review with a Strategic Framework for CRISPR-Cas Applications in Rice (Oryza sativa L.). Genes. 2026; 17(2):165. https://doi.org/10.3390/genes17020165
Chicago/Turabian StyleMachel Gica, Nlhavat Gabriel, Wilard Tuto Gica, Honggui La, Yi Mi, and Yi Zhou. 2026. "Precision Breeding for a Global Staple Food: A Systematic Review with a Strategic Framework for CRISPR-Cas Applications in Rice (Oryza sativa L.)" Genes 17, no. 2: 165. https://doi.org/10.3390/genes17020165
APA StyleMachel Gica, N. G., Gica, W. T., La, H., Mi, Y., & Zhou, Y. (2026). Precision Breeding for a Global Staple Food: A Systematic Review with a Strategic Framework for CRISPR-Cas Applications in Rice (Oryza sativa L.). Genes, 17(2), 165. https://doi.org/10.3390/genes17020165

