Enhanced Rice Yellow Mottle Virus Resistance via CRISPR/Cas9-Targeted Mutagenesis of the Rice eIF(iso)4G Gene

Rice is a staple crop primarily recognised for its high content of carbohydrates and proteins. Rice yellow mottle disease (RYMD) is a destructive disease affecting rice fields in sub-Saharan Africa and is caused by the rice yellow mottle virus (RYMV). Development of virus-resistant genotypes is a highly recommended and effective approach to controlling RYMV. A genetic approach that exploits recessive mutations in susceptibility (S) genes may enhance resistance to the virus. Reports indicate that most rice genotypes grown in Kenya are vulnerable to RYMV infection. Genome editing has shown promise in enhancing agronomic traits in crops. We obtained enhanced resistance to RYMV in the Indica rice cv. IR2793-80-01 using the CRISPR-Cas9 system. The eIF(iso)4G susceptibility gene was targeted because natural mutations in this gene confer recessive resistance to RYMV. A Cas9-OseIF(iso)4G-gRNA-expressing vector targeting the eIF(iso)4G gene was introduced into rice calli via Agrobacterium-mediated transformation. Ten T₂ homozygous mutant plant lines were assessed for their reaction to RYMV, and infection was significantly reduced. There were no significant differences in the agronomic characteristics between the T₂ mutant lines and the wild-type plants. CRISPR/Cas9-mediated knockout alleles of the eIF(iso)4G gene conferred enhanced resistance to RYMV, which may be classified as partial. Findings underscore the need to embrace precise editing strategies, such as prime editing, to generate superior resistance alleles. Overall, the study provides an alternative resistance enhancement strategy that can create knockout resistance alleles that can be incorporated into breeding programmes for RYMV resistance.