CRISPR-Cas Mediated Genome Editing for Disease Resistance in Crops: Advances and Challenges

Abstract

The increasing menace of phytopathogens to food security in the world demands the creation of a type of crop with long-term and extensive disease resistance. CRISPR-associated protein (Cas) systems and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) have transformed the way the genome of plants are engineered, providing unprecedented specificity, efficiency, and ease in the development of resistant crops. This review starts by describing the molecular processes of various CRISPR-Cas types (Cas9, Cas12a, and Cas13) and their use in plants. We then address some of the important strategies, such as targeted editing of host susceptibility (S) genes to generate recessive resistance, introducing broad-spectrum resistance (R) gene variants using homology-directed repair (HDR) and base editing, and producing transgene-free genome-edited plants by delivery of ribonucleoproteins (RNPs). Practical achievements are presented through successful case studies of major crops including rice, wheat, tomato and citrus. Moreover, we discuss novel technologies like CRISPR-Cas13 to interfere with viral RNA and multiplexed editing to overlay resistance characteristics against several pathogens. Though impressive advances have been made, there are still major issues to deal with, such as the effective transfer of CRISPR components to recalcitrant crop species, off-target effects and unwanted genomic modifications, regulatory barriers to transgene vs. transgene-free edited plants, and social acceptance. Lastly, we present future directions, including the combination of CRISPR and speed breeding, synthetic biology, and accelerated breeding technologies to create disease-resistant and robust crops to support sustainable agriculture