Fig. 1

Application of CRISPR/Cas-based technologies for engineering disease-resistant plants. CRISPR technology, most widely with the Cas9, can be applied to achieve precise genome editing of the plant genome to develop resistance against various pathogens. CRISPR/Cas9 can be used to disrupt plant susceptibility (S) genes by targeting coding regions to knock out these genes, or to alter sequences of promoter regions (for example, pathogen promoter’s effector-binding site), precluding pathogen effector binding to the promoter and thus disrupting plant susceptibility. In addition, the ability of performing Cas9-mediated multiplex targeting can facilitate the chromosomal deletion of S gene clusters, generating long-term resistance to the target pathogen. Homology-directed repair (HDR) mediated by Cas9 can be used to introduce resistance (R) genes against pathogens in cases where the plant-pathogen interaction (and S genes) is not well studied. To develop pathogen resistance without disrupting or replacing whole genes, base-editors or Cas9 technology (via synthetic directed evolution under the biotic selective pressure) can be applied to achieve specific mutations (biomimicking) or evolution of genes resistant to pathogens of interest. Apart from utilizing CRISPR technologies for plant genome engineering to develop disease-resistant plants, the native function of CRISPR can be mimicked to directly target and interfere with the genomes of pathogens of interest without affecting plant genome. For example, CRISPR can interfere with DNA genomes of pathogens, such as DNA viruses, through DNA-targeting CRISPR systems, including Cas9. CRISPR systems can also be used to target and disrupt pathogen’s RNA genomes (or RNA transcript of pathogens with DNA genomes) through RNA-targeting CRISPR systems, such as Cas13 and FnCas9