Technical Abstract: Tobacco rattle virus (TRV) recombinant viral vectors are commonly used to mediate virus-induced gene silencing (VIGS) of target genes in Nicotiana benthamiana and tomato; however, the efficiency of TRV-based VIGS is more variable in tomato. Our goal was to use real-time RT-PCR to quantify the effect of VIGS on transcript levels of phytoene desaturase (PDS) in leaf tissue of both hosts and monitor the relative abundance of the recombinant TRV vector (rTRV) coat protein (CP) RNA to estimate viral replication. Primer sets designed to amplify the 5' or 3' regions of endogenous PDS transcripts in tomato yielded similar reductions in transcript levels indicating a uniform degradation of target RNA. VIGS in N. benthamiana resulted in complete photo-bleaching of all foliar tissue compared to the chimeric bleaching in tomato. PDS transcript levels were reduced 11 and 7-fold in photobleached leaves of N. benthamiana and tomato, respectively, while sampling tomato leaflets on the basis of age and not phenotypic silencing resulted in only a 17% reduction in PDS coupled with a large leaf-to-leaf variation. There was a significant inverse relationship (R2 = 76%, P = 0.01) between the relative abundance of CP RNA and the amount of PDS transcript in rTRV::tPDS-infected tomato. Our findings in tomato supports the hypothesis that rTRV replication necessitates RNA-silencing and that the silencing inducer acts locally in tissue infected with the virus.