Tomato is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV.

The tomato encode four functional families, of which is poorly studied. Here, we generated loss-of-function mutants for a tomato gene, , and we identified its major role in defending against tomato mosaic virus in relation to both natural and manual infections. Genome-wide small RNA expression profiling revealed that was required for the processing 22-nt small RNAs, including a few species of miRNAs. Interestingly, these -dependent 22-nt miRNAs functioned similarly to the -produced 22-nt miRNAs in and could serve as triggers to generate a class of secondary siRNAs. In particular, the majority of secondary siRNAs were derived from plant defense genes when the plants were challenged with viruses. We also examined differentially expressed genes in through RNA-seq and observed that numerous genes were associated with mitochondrial metabolism and hormone signaling under virus-free conditions. Notably, when the loss-of-function mutant was challenged with tomato mosaic virus, a group of defense response genes was activated, whereas the genes related to lipid metabolism were suppressed. Together, our findings provided new insights into the roles of tomato in small RNA biogenesis and in antiviral defense.