Identification of positive and negative regulators of antiviral RNA interference in Arabidopsis thaliana

• Published in: Nature communications Vol. 13; no. 1; p. 2994
• Main Authors: Liu, Si, Chen, Meijuan, Li, Ruidong, Li, Wan-Xiang, Gal-On, Amit, Jia, Zhenyu, Ding, Shou-Wei
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.05.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 45/22; 45/23; 45/29; 45/43; 45/71; 45/77; 45/88; 45/90; 631/208/205/2138; 631/326/596/2557; 631/449/1870; 631/449/2661/2666; Antiviral Agents; Arabidopsis; Arabidopsis thaliana; Coevolution; CRISPR; Cucumbers; Cucumovirus; Cucumovirus - genetics; Cytomegalovirus Infections - genetics; Disease resistance; Dormancy; Down-regulation; Gene expression; Genes; Genome-wide association studies; Genome-Wide Association Study; Genomes; Humanities and Social Sciences; Humans; Inactivation; Interference; multidisciplinary; Plant Diseases; Plant viruses; Ribonucleic acid; RNA; RNA Interference; RNA-mediated interference; Science; Science (multidisciplinary); Viruses
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-30771-0

Virus-host coevolution often drives virus immune escape. However, it remains unknown whether natural variations of plant virus resistance are enriched in genes of RNA interference (RNAi) pathway known to confer essential antiviral defense in plants. Here, we report two genome-wide association study screens to interrogate natural variation among wild-collected Arabidopsis thaliana accessions in quantitative resistance to the endemic cucumber mosaic virus (CMV). We demonstrate that the highest-ranked gene significantly associated with resistance from both screens acts to regulate antiviral RNAi in ecotype Columbia-0. One gene, corresponding to Reduced Dormancy 5 ( RDO5 ), enhances resistance by promoting amplification of the virus-derived small interfering RNAs (vsiRNAs). Interestingly, the second gene, designated Antiviral RNAi Regulator 1 ( VIR1 ), dampens antiviral RNAi so its genetic inactivation by CRISPR/Cas9 editing enhances both vsiRNA production and CMV resistance. Our findings identify positive and negative regulators of the antiviral RNAi defense that may play important roles in virus-host coevolution. Whether natural variations of plant virus resistance are enriched in genes of RNA interference pathway is unknown. Here, via genome-wide association studies, the authors identify regulators of the RDR6 and DCL2 antiviral pathways are involved in quantitative resistance to cucumber mosaic virus in Arabidopsis.