Engineered geminivirus replicons enable rapid in planta directed evolution

Abstract

Directed evolution can rapidly generate genetic variants with new and enhanced properties, yet efficient platforms for performing such evolution directly in plant cells have been lacking. We developed geminivirus replicon–assisted in planta directed evolution (GRAPE), a system that links gene function to geminivirus rolling circle replication to enable high-throughput selection for desired activities. GRAPE supports the screening of up to 10 5 variants on a single Nicotiana benthamiana leaf within 4 days. Using GRAPE, we evolved the immune receptor NRC3 to resist inhibition by the nematode effector SPRYSEC15 and broadened the recognition spectrum of the rice ( Oryza sativa ) immune receptor Pikm-1 to recognize all six alleles of the fungal effector AVR-Pik. GRAPE provides a rapid, scalable, and generalizable platform for directed evolution of diverse genes in the plant cellular context.