Altered Expression of MicroRNAs and Target mRNAs in Tomato Root and Stem Tissues upon Different Viral Infection

MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in numerous biological processes in both plants and animals. In plants, root and stem tissues play essential roles in their anchorage to soil as well as in nutrient and water uptake and transfer. We have quantified the expression alterations of eleven miRNAs and their target mRNAs in tomato root and stem tissues after infection with Cucumber mosaic virus (CMV)-Fny, CMV-Fny?2b (a CMV-Fny 2b-deletion mutant), CMV-Fny-satT1 (CMV-Fny plus an aggressive satellite (sat) RNA variant satT1) and Tomato aspermy virus (TAV)-Bj. From 21 days postinoculation onwards, we found the stem tissues were hollow in CMV-Fny-satT1 infected tomatoes, and a fibrosis phenotype was observed in stems of TAV-Bj infected plants. In addition, this phenotype was associated with the decreasing of tomato lateral root numbers upon the two infections. Consistence with these phenotypic alterations, tomato miRNA/mRNA levels upon different viral infections were changed by different degrees. Based on our results, the interference of different viral infections with tomato miRNA pathways were analysed and the correlations between miRNAs/mRNAs expression alterations and tomato symptoms were discussed.