Student Number : 9610284H - MSc dissertation - School of Molecular and Cell Biology - Faculty of Science / Cassava Mosaic Disease is the most devastating disease affecting cassava (Manihot esculenta Crantz) crops worldwide. This disease is associated with eight species of geminiviruses, all belonging to the genus Begomovirus of the family Geminiviridae. In South Africa, in particular, CMD is caused by South African cassava mosaic virus (SACMV). Currently, there are no adequate methods for control of this disease as mechanisms within virus-host interactions are poorly understood. This brings about the need for development of virus-disease control strategies. This study was therefore conducted to identify the host’s response to an invading virus. The model plant, Arabidopsis was chosen as it is a well-characterized plant system, with expression databases readily available as its entire genome has been sequenced. This study was conducted, firstly, to phenotypically determine if Arabidopsis was resistant or susceptible to SACMV infection, and secondly, to identify the host’s response to pathogen infection on a molecular level through gene expression studies utilizing microarrays. Results from the symptomatology study revealed that Arabidopsis plants were fully symptomatic 28 days post-inoculation, displaying characteristic disease symptoms such as stunting, yellowing, and leaf deformation. This indicated that Arabidopsis was susceptible to SACMV infection. Microarray analyses revealed 86 differentially expressed genes, of which 48 showed up-regulation and 38 down-regulation. Relative quantification real-time PCR was performed on selected genes to confirm these results. Many up-regulated genes were shown to be primarily involved in a general stress response induced by the host, whereas those genes that were downregulated seemed to be involved in more specific responses to viral invasion, probably a consequence of suppression of host genes by SACMV to enhance its own replication. The majority of genes identified fell under the predominant functional categories involved in metabolism, transcription, and transport. To our knowledge, this is the first study in which a DNA geminivirus has been used in a host-pathogen interaction utilizing microarrays.