CRISPR, chimerism, and chromothripsis: A technique for studying DNA repair in plants

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Abstract
The discovery of Cas9 nuclease has revolutionized the field of gene editing, allowing for precise and programmable modifications to DNA. Many gene-editing techniques stemming from CRISPR-Cas9 (CRISPR) rely on the creation of double-stranded breaks (DSBs) in DNA. However, DSBs pose a threat to the replication process and therefore need to be repaired. The repair of CRISPR-induced DSBs can have varying effects on the genome, with nonhomologous end joining causing small insertions or deletions at the site of the break and homologous recombination potentially leading to crossovers between homologous chromosomes or gene conversion. Targeted crossovers and gene conversion are highly sought-after outcomes in plant breeding for segregating undesirable alleles. These events can enable targeted gene replacement or the elimination of undesirable transgenes, making this process invaluable to the improvement of crops ( He et al. 2022). Aviva Samach, Fabrizio Mafessoni, Or Gross, and colleagues (Samach et al. 2023) present an assay that detects loss of heterozygosity (LOH) and can be used to study the genomic consequences of DSBs. They induce and can visually identify targeted crossover induction (see Fig.) and also the occurrence of chromothripsis, a process not well studied in plants but characterized by large and severe chromosome rearrangements. This visual assay adds new uses to a growing group of unconventional tools that reduce the need for microscopes or other equipment for particular experiments and screens ( Liu et al. 2019, Chen et al. 2023, Sun et al. 2023). These may lower financial and infrastructure barriers to plant biology research, expanding the abilities of universities, field sites, and classrooms.