ZLab collaboration advances precise large-fragment genome editing in rice

Homologous replacement of large genomic fragments (>100 bp) remains a major bottleneck in precision crop breeding. A collaborative study involving ZLab has now been published in New Phytologist under the title “Efficient homologous replacement and deletion of large genomic fragments through template-jumping prime editing in rice.”

The team developed a rice template-jumping prime-editing system assisted by the Csy4 pegRNA processing system (Csy4PS). Compared with canonical prime editing and GRAND editing, TJ-PE delivered substantially higher replacement efficiency and precision at the tested loci. It supported efficient equal-length replacement of 71–275 bp fragments, with a maximum demonstrated replacement length of 340 bp and precision reaching 100% at selected sites.

The system also enabled precise deletion of 944–2024 bp genomic segments. Precise deletion of a 2024 bp fragment reached 34.6%, and multiplex large-fragment deletions were achieved simultaneously at C1, BADH2, and DEP1. The edits were stably inherited in T₁ homozygous lines, while the evaluated off-target risk remained low.

By extending TJ-PE from large-fragment insertion to homologous replacement and precise deletion, this work establishes a versatile plant genome-editing toolkit for insertion, replacement, and deletion. It provides a new route for rice functional genomics, allele reconstruction, and precision molecular breeding.