Applications of Base Editors in Plants

Many agriculturally important traits result from single-nucleotide polymorphisms (SNPs) located in both coding and noncoding regions of the genome. Base editing has therefore become a valuable tool in plant breeding and crop improvement. In coding regions, one key application of base editing is the development of herbicide-resistant crops. Resistance to various herbicides has been achieved in multiple plant species by targeting genes such as ALS with cytidine base editors, and by editing the ACCase gene using adenine base editors. In polyploid species like wheat, however, base editing outcomes can be highly variable particularly when multiple guide RNAs are used highlighting the complexity of editing in such genomes.

In addition to modifying protein-coding sequences, base editors can also influence gene expression by targeting RNA splicing. Alternative splicing enables a single gene to produce multiple protein isoforms, contributing to phenotypic diversity. Most splicing follows the canonical GU/AG rule, with GU at the 5′ donor site and AG at the 3′ acceptor site of introns. Base editing can introduce mutations at these conserved sites, leading to altered splicing outcomes, including intron retention or loss of specific splice forms. This strategy has been used to disrupt normal splicing, resulting in changes to gene function and the creation of null mutants in various plant species.