Improving iSpyMacCas9 multiplex genome editing in rice by CRISPR-combo-mediated BBM1 activation

The recently developed CRISPR-Combo technology enables simultaneous targeted mutagenesis and transcriptional activation in plants. However, its reliance on SpCas9 limits its use at AT-rich genomic loci, such as promoter regions commonly targeted for transcription activation. To overcome this limitation, we explored the usage of Cas12b and iSpyMacCas9 in the CRISPR-Combo architecture for simultaneous genome editing and gene activation. We tested these expanded CRISPR-Combo systems for hormone-free regeneration of rice plants by transcriptional activation of a morphogenic gene, OsBBM1, while knocking out the genes of interest. The Cas12b-Combo system induced mild OsBBM1 upregulation (~3-fold), which did not affect the genome editing efficiency. By contrast, iSpyMacCas9-Combo achieved approximately 12-fold OsBBM1 transcriptional activation, supporting hormone-free regeneration at a high rate (42%). As a result, iSpyMacCas9-Combo conferred higher genome editing efficiency, including improved multiplex editing, than the standard iSpyMacCas9 system, either with or without hormones during rice regeneration. Hence, our data prove iSpyMacCas9-Combo to be a more efficient system for genome editing in rice, especially at low-efficiency target sites, when coupled with OsBBM1 transcriptional activation. These findings establish iSpyMacCas9-Combo as a useful addition to the CRISPR-Combo toolkit, expanding its genomic targeting scope and enabling more efficient genome editing by activation of an appropriate endogenous gene such as OsBBM1 in rice.