Synergistic optimization enhancing the precision and efficiency of cytosine base editors in poplar.

Abstract

CRISPR/Cas9 genome editing technology, particularly cytosine base editing (CBE) systems, emerges as a powerful tool for precise genomic modification in plants, offering transformative applications across agricultural and forestry research and breeding programs. However, current CBE systems in poplar exhibit low efficiency and imprecise base substitutions, and optimization of base editing systems specifically for poplar remains a significant challenge. To address these limitations, we engineer a high-efficiency poplar CBE system (hyPopCBE) by integrating the MS2-UGI system, fusing Rad51 DNA-binding domain, and modifying the nuclear localization signal. Through stepwise optimization, we develop hyPopCBE-V4, which exhibits a synergistic effect in woody plants. Compared to the original hyPopCBE-V1, hyPopCBE-V4 improves C to T editing efficiency while reducing byproducts and exhibiting a narrower editing window. The proportion of plants with clean C to T edits (without byproducts) increases from 20.93% to 40.48%, and the efficiency of clean homozygous C to T editing rises from 4.65% to 21.43%. Using hyPopCBE-V1 and its variants, we induce Pro197Leu mutation in the herbicide target gene PagALS. Poplar lines with edits in all four PagALS homologues exhibit high resistance to tribenuron and nicosulfuron. This study employs a multi-component synergistic optimization strategy that specifically enhances the efficiency and precision of CBE editing in poplar while improving synchronous editing of alleles. Through editing the herbicide resistance gene PagALS, we obtain the herbicide-resistant poplar germplasm. Our research provides a more precise and efficient CBE tool for genetic modification in poplar that can also be applied to other forestry species, demonstrating its potential for advancing forestry research and breeding programs.