Crop gene therapy is an emerging technology that seeks to optimize a mature plant’s response to abiotic stress by delivering therapeutic genes in a manner and timing informed by human forecasting of environmental conditions. This thesis seeks to support the development of crop gene therapy to sustain crop production despite increasingly volatile environmental conditions due to anthropogenic climate change. The specific focus of this work is the development of reporter gene systems to track the movement within plants of viral vectors for delivery of therapeutic genes to address plant stressors. The proposed model system is comprised of bipartite begomovirus (single-stranded DNA) vectors acting on a tomato (Solanum lycopersicum var. Florida lanai) host with transmission facilitated by the silverleaf whitefly (Bemisa tabaci). A key aspect of this work was the development of the fungal bioluminescence pathway from Neonothopanus nambi towards the ability to facilitate bioluminescence in plants based on endogenously produced substrate that does not require the destructive sampling of tissue. In addition to taking on the challenge of a working with a non-model crop, tomato, a newly discovered biosynthetic pathway, and novel viral vectors, this work applied remnant-free polyprotein technology for expression of a biosynthetic pathway in transgenic plants for the first time with multiple luciferin biosynthesis enzymes expressed from a single plant promoter to minimize transgene size. This was accomplished using self-cleaving Intein-F2A peptide linkers between enzymes. This novel approach was shown to facilitate functional expression of four fungal luciferin biosynthesis genes using transient co-expression of the luciferase to complete the cyclic metabolic pathway to produce bioluminescence. The generation of transgenic tomato lines with these genes was also undertaken and confirmed via PCR of the transgene. However, luminescence was not observed when the luciferase was transiently expressed in these tomato plants due either to insufficient stable transgenic expression of the luciferin biosynthesis pathway or insufficient transient expression of the luciferase enzyme. This thesis also contains additional contributions to crop gene therapy development including transient reporter genes with introns to prevent Agrobacterium expression, as well as improvements to procedures for tomato and Arabidopsis plant transformation.