Tomatoes are one of the world’s most consumed vegetable crops with production of fresh market and processing tomatoes increasing in greenhouse, high tunnels, and the field. Several viroids (small, unencapsidated, single-stranded, covalently closed circular, highly structured, noncoding RNAs) are seed transmitted and easily spread mechanically in tomato; control relies on limiting introduction of the viroid to prevent disease outbreaks. Disease symptoms-including stunting, reduced vigor, flower abortion, reduced size and number of fruits, and reduced root growth-can result in significant crop losses. These dramatic alterations in plant development are the result of differential gene expression patterns, including the transcriptional activation of genes encoding transcription factors and a protein kinase involved in phospholipid signaling. Silencing of the protein kinase gene in tobacco resulted in substantially increased vigor, including increases in plant and root biomass. Our studies involved a two-pronged approach to determine if symptoms of viroid infection can be mitigated to reduce crop losses in tomato: 1) silencing of key genes responsible for symptom production, and 2) grafting susceptible tomato cultivars onto either tolerant, engineered, or commercially employed rootstocks to evaluate changes in gene expression, water use efficiency, plant vigor, and the effects of viroid infection on fruit development.