CRISPR/Cas9 Mediated Genome Editing for Enhancing Abiotic Stress Tolerance in Rice: An Omics Guided Perspective

The cultivation of rice (Oryza sativa L.) has become increasingly challenging due to various abiotic stresses such as elevated salinity and drought conditions, and these challenges will only worsen with climate change. This review highlights recent advancements in CRISPR/Cas9 genome editing technology as applied to developing rice for greater tolerance of abiotic stresses. Functional genomics analysis (including transcriptomic, proteomic, and metabolomic data) has identified and validated key regulatory genes and networks that affect plant response to abiotic stress. Researchers using CRISPR/Cas9 technology have made changes to both negative regulators (e.g., OsRR22 for salinity; OsDST for drought/salt) and positive (e.g., OsSAPK2 for drought) regulatory genes, producing transgene-free mutants displaying enhanced ion homeostasis and ROS scavenging as well as stomatal regulation and stability of yield under stress. Results from functional genomics indicate that polygenic regulatory networks, including the transcriptional regulators (NAC, WRKY, bHLH) and abscisic acid (ABA) signalling systems, are suitable for multiplex applications to produce a plant with broad-based stress resilience. Although functional genomic methods have been successful in the lab, there are still major issues with performance under field conditions when multiple stresses are present (e.g., genotype dependence, japonica bias, pleiotropic effects, and regulatory issues). The future integration of prime-editing, network mapping, and multi-site trial work will assist in the development of sustainable, superior quality indica varieties to help fulfill the UN's Sustainable Development Goals (SDGs) for food security.