Ectopically expressing viral suppressors of RNA silencing (VSR) in transgenic Arabidopsis overcome host range limitation and viral titer variation, and have similar VSR levels to investigate RNA silencing suppression. Therefore, identifying the insertion of the transgenic VSR gene and developing an endogenous AGO1-based in vitro RNA-inducing silencing complex (RISC) assay prompted further investigation into VSR-mediated suppression. Three P1/HC-Pro plants from turnip mosaic virus (TuMV) (P1/HC-ProTu), zucchini yellow mosaic virus (P1/HC-ProZy), and tobacco etch virus (P1/HC-ProTe) were investigated for in vitro RISC cleavage efficiency. We identified T-DNA insertion for these P1/HC-Pro plants and applied these plant materials to compare the endogenous AGO1 levels and RISC activity. Our results indicated that P1/HC-ProTu plants have lower AGO1 levels and lower RISC activity than the other P1/HC-Pro plants. In addition, the phenomena are consistent with those in TuMV-infected Arabidopsis, implying that HC-ProTu could directly interfere with AGO1 stability. In this study, we demonstrated the application of various plant materials with an in vitro RISC assay in VSR-mediated RNA silencing suppression.