Molecular tools for engineering resistance in hosts against plant viruses

Clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein (Cas)–mediated genome editing, derived from prokaryotic adaptive immunity, is rapidly emerging as a potential tool for targeted alterations in eukaryotic genomes. Eclectic application of CRISPR includes insertion/deletion of a part of DNA, loss-of-function mutation, expression and repression of a gene, and epigenomic reprogramming. The CRISPR system is not limited to editing DNA but can also be deployed to target RNA, resulting in an effect similar to that of RNA interference. The system is characterized by ease of cloning, cost-effectiveness, and multiplexing-targeting multiple sites simultaneously. The system has been extensively used for creating gene knockdowns in planta. Several molecular and breeding approaches have identified genes that confer resistance against viruses and elucidated their mode of inheritance in plants. Dominant resistance (R) genes recognize the viral component and initiate a defense response, whereas recessive resistance genes (also known as susceptibility [S] genes, or proviral genes) help viruses complete their life cycle; to achieve this, the S gene must be nonfunctional. To acquire resistance in plants, several studies have targeted viral genomes and host genes. Although, the CRISPR system is a powerful tool for gene stacking and gene knockdown, the identification of new resistance genes remains a challenge. Current losses in food and fiber crops due to viral diseases necessitates the development of durable resistance against viruses to meet the demands of the escalating world population. In this chapter, we describe the mechanism of CRISPR-Cas system and its diverse applications, Cas variants, and resources for developing resistance against viruses.