Research conducted by the Laboratory of Nematology is part of the research prgram of the Graduate School Experimental Plant Sciences (EPS) and the C.T. de Wit Graduate School for Production Ecology & Resource Conservation (PE&RC)
Research funded by Hudson River Biotechnology B.V. (Wageningen, The Netherlands), developer of MADTiGER®.
CRISPR-based genome editing is a critical tool for crop improvement to meet the challenges of population growth, climate change, and diminishing arable land area. Although genome editing with CRISPR can be easily performed in cells of various species, including plants, the success rate is highly variable and dependent on the target sequence, genomic location, and species. In addition, diminishing returns on editing efficiency are observed when multiplexing CRISPR edits required to research and breed for complex traits. These drawbacks severely limit the application of CRISPR-mediated crop improvement. Current efforts to explain differences in CRISPR editing efficiencies focus mainly on CRISPR enzyme activity and/or their guide properties and have not been able to explain most of the variability observed. Likely, the under highlighted host-specific genome characteristics and DSB repair mechanisms have a much larger impact on editing efficiency.
Host genome characteristics that are believed to have an adverse effect on editing efficiency in plants are genome size, GC content, chromatin structure, and ploidy. It is easily argued that the host genomic structure can have a strong effect on achievable genome editing efficiencies, however, to date, the exact underlying mechanisms modulating accessibility and in turn editing efficiencies in plants are only poorly characterized. Furthermore, a wide range of potential DNA repair mechanisms are represented in plants, which contribute to DSB repair at different extents. This leads to highly variable mutation patterns following DSB repair which can result in undesired editing outcomes.
I aim to elucidate how host-specific genome characteristics and DNA repair mechanisms affect genome editing efficiencies and mutation types, ultimately allowing the application of this knowledge to maximize the utilization of CRISPR in plants.