CRISPR, Base Editing and Prime Editing for Climate-smart Crop Improvement: Advances, Challenges and Field Prospects

Abstract

Climate change is intensifying abiotic and biotic stresses that threaten global food security, whilst conventional breeding timelines remain poorly matched to the pace of environmental change. This review critically examines three precision genome editing platforms—clustered regularly interspaced short palindromic repeats and associated protein (CRISPR-Cas) nuclease editing, base editing, and prime editing—and their contributions to climate-smart crop improvement. This review synthesises current progress, benchmarks the technical profiles of the three platforms, identifies priority research gaps, and outlines a translational roadmap towards the field deployment of precision-edited, climate-resilient crop varieties. A structured literature search was conducted across multiple academic databases, including Web of Science, Scopus, PubMed, and Google Scholar. The date range for the primary search since January 2005 to present, with particular emphasis on publications from 2012 onwards reflecting the emergence of CRISPR-Cas technology.  CRISPR-Cas9-mediated gene disruption via non-homologous end-joining has been deployed successfully to engineer drought tolerance, disease resistance, flood adaptation, heat resilience, and salinity tolerance across major crop species, including rice, wheat, maize, and tomato. Base editors—comprising cytosine base editors (CBEs) and adenine base editors (ABEs)—extend editing precision to single-nucleotide transitions without inducing double-strand breaks, enabling the targeted introduction of naturally occurring adaptive alleles and the fine-tuning of stress-responsive regulatory elements with minimal off-target consequences. Prime editing, the most recently developed platform, employs a Cas9 nickase fused to an engineered reverse transcriptase and a prime editing guide RNA to install all 12 classes of point mutation as well as small insertions and deletions, circumventing both double-strand breaks and the requirement for exogenous donor templates. Despite remarkable advances, each platform faces technical challenges relating to delivery efficiency in recalcitrant crops editing precision in polyploid genomes, and regulatory frameworks that differ substantially across national jurisdictions.