Genome editing techniques, such as the CRISPR/Cas9 system, offer a game-changing opportunity for crop improvement by enabling precise modifications to be made at targeted genomic loci. The CRISPR/Cas9 system has been employed successfully in many plant species; however, in order to use the system to its full potential, it is important to understand precisely how it functions and the factors that may limit its effectiveness. The mechanistic details of Cas9-induced double-strand breaks (DSBs), that underpin the mutational ability of the system, have been well-described. It also is known that the efficiency of editing varies for different target sequences. However, the impact of epigenetic modifications on CRISPR/Cas9 efficacy and subsequent DNA repair is poorly understood, especially in plants.

This article comments on: Kalinka A, Starczak M, Gackowski D, Stępień E, Achrem M. 2023. Global DNA 5-hydroxymethylcytosine level and its chromosomal distribution in four rye species. Journal of Experimental Botany 74, 3488–3502.