Tian Shuangrui, Yao Lan, Zhang Yuhong, Rao Xiaoyu, Zhu Hongliang
College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
Sichuan Advanced Agricultural & Industrial Institute, China Agricultural University, Chengdu 611430, China.
Genes (Basel). 2025 Aug 16;16(8):965. doi: 10.3390/genes16080965.
Prime editing (), a novel "search-and-replace" genome editing technology, demonstrates significant potential for crop genetic improvement due to its precision and versatility. However, since its initial application in plants, technology has consistently faced challenges of low and variable editing efficiency, representing a major bottleneck hindering its broader application. Therefore, this study conducted a systematic review following the 2020 guidelines. We systematically searched databases-Web of Science, PubMed, and Google Scholar-for studies published up to June 2025 focusing on enhancing performance in crops. After a rigorous screening process, 38 eligible primary research articles were ultimately included for comprehensive analysis. Our analysis revealed that early systems such as could perform diverse edits, including all 12 base substitutions and small insertions or deletions , but their efficiency was highly variable across species, targets, and edit types. To overcome this bottleneck, researchers developed four major optimization strategies: (1) engineering core components such as , reverse transcriptase (), and editor architecture; (2) enhancing expression and delivery via optimized promoters and vectors; (3) improving reaction processes by modulating repair pathways or external conditions; and (4) enriching edited events through selectable or visual markers. These advancements broadened 's targeting scope with novel variants and enabled complex, kilobase-scale insertions and rearrangements. The application of technology in plants has evolved from basic functional validation, through systematic optimization for enhanced efficiency, to advanced stages of functional expansion. This review charts this trajectory and clarifies the key strategies driving these advancements. We posit that future breakthroughs will increasingly depend on synergistically integrating these strategies to enable the efficient, precise, and predictable application of technology across diverse crops and complex breeding objectives. This study provides an important theoretical framework and practical guidance for subsequent research and application in this field.
碱基编辑是一种新型的“搜索并替换”基因组编辑技术，因其精准性和多功能性在作物遗传改良方面展现出巨大潜力。然而，自其最初应用于植物以来，该技术一直面临着编辑效率低且不稳定的挑战，这是阻碍其更广泛应用的主要瓶颈。因此，本研究遵循2020年指南进行了系统综述。我们系统地在Web of Science、PubMed和谷歌学术等数据库中搜索截至2025年6月发表的、聚焦于提高作物中碱基编辑性能的研究。经过严格筛选过程，最终纳入了38篇符合条件的初级研究文章进行综合分析。我们的分析表明，早期的碱基编辑系统，如碱基编辑器1，能够进行多种编辑，包括所有12种碱基替换以及小的插入或缺失，但它们在不同物种、靶点和编辑类型中的效率差异很大。为克服这一瓶颈，研究人员开发了四种主要的优化策略：（1）对核心组件如Cas9、逆转录酶（RT）和编辑器结构进行工程改造；（2）通过优化启动子和载体增强表达和递送；（3）通过调节DNA修复途径或外部条件改善反应过程；（4）通过选择或视觉标记富集编辑事件。这些进展通过新型碱基编辑器变体拓宽了碱基编辑的靶向范围，并实现了复杂的、千碱基规模的插入和重排。碱基编辑技术在植物中的应用已从基本功能验证，经过提高效率的系统优化，发展到功能扩展的高级阶段。本综述描绘了这一轨迹，并阐明了推动这些进展的关键策略。我们认为，未来的突破将越来越依赖于协同整合这些策略，以实现碱基编辑技术在各种作物和复杂育种目标中的高效、精准和可预测应用。本研究为该领域后续的研究和应用提供了重要的理论框架和实践指导。
