During the course of this action, we developed a new toolset for automated assembly scaffolding and generated chromosome-level assemblies for a novel fast-cycling genotype called S100 that we established as system for high-throughput genome editing (Alonge et al., Genome Biol, 2022). We expect that this novel genotype, which nearly doubles the number of generations per year, will become the foundation for genome-wide editing experiments in tomato. Finally, our approach outlines strategies for rapidly generating diverse personalized reference systems in other species. Since genome editing experiments in tomato are still limited by laborious protocols to regenerate stably transformed plants that express editing reagents, we set out to enhance plant regeneration. We constructed a tomato morphogenic regulator chimera (SlGRF-GIF), which reliably improves of regeneration efficiency by nearly two-fold, while also shortening the time to obtain transgenic plants by approximately one month (Swinnen, Lizé et al., Plant Biotech J, 2025). We utilized this new system for CRISPR-Cas experiments to target meristem regulator genes in tomato, showing a simplified isolation of desired genome edits in both single and multiplex targeting approaches. We investigated how crop domestication led to potenitally harmful mutations that are deleterious for gene activity by computing the accumulation of deleterious mutations during tomato domestication (Glaus et al., Nat Genet, 2025). We identified a deleterious variant that disrupts the DNA-binding domain of a transcription factor and floral regulator. The loss of transcription factor activity broke functional redundancy with a closely related gene and allowed the utilization of a mutation to optimize tomato productivity. Finally, we used base editing to directly repair the deleterious mutation in domesticated tomato and obtained compact plants with early fruit yield. These findings illustrate how deleterious variants can become adaptive due to interactions with mutations that are introduced during breeding, which has an impact on genome editing in agriculture.
