Prime editing: a new frontier in precision genome engineering for rice improvement

Rice (Oryza sativa) is a primary cereal crop that provides food for more than half of the global population, however, its production is increasingly threatened by climate change and diverse biotic and abiotic stresses. While traditional breeding and early genome editing technologies, such as CRISPR/Cas9 and base editors, have accelerated crop improvement, they remain limited by off-target effects, dependence on double-stranded breaks (DSBs), and narrow base conversion possibilities. Prime editing (PE), introduced in 2019, overcomes many of these limitations by enabling precise substitutions, insertions, and deletions without requiring donor DNA or DSBs, and with reduced off-target activity. In this review, we review the evolution of PE systems from PE1 to PEmax and highlight key innovations that enhance their efficiency and applicability. Including recent advances in pegRNA engineering, mismatch repair modulation, and editor architecture optimization that have improved editing efficiency and applicability in plants. We further discuss recent applications of PE in rice improvement, including grain quality enhancement via the Waxy (wx) gene editing, engineered resistance to bacterial blight and herbicide, enhanced heat resilience, and restoration of nutritional traits. Finally, we discuss current challenges related to editing efficiency, delivery, scalability, biosafety, and genetic stability, while outlining future prospects for advanced PE-derived platforms such as twin prime editing (twinPE) and PASTE. Collectively, these advances position PE as a transformative genome editing platform for creating climate-resilient, high-yield, and nutritionally enhanced rice varieties capable of meeting future food security challenges.