Manitoba is the second largest potato producer in Canada after Prince Edward Island. This crop faces many disease problems including the most famous and devastating one, late blight, caused by the oomycete pathogen Phytophthora infestans. More than 150 years have elapsed since this disease caused the Irish potato famine, but strategies for managing it often remain unsustainable and costly. With the advent of molecular biology, genetic engineering, and now, genomics-based approaches, it may be possible to initiate studies which will address important questions regarding very complex host-pathogen interactions. Dr. Daayf’s lab has shown that the most aggressive strains of P. infestans suppress potato defense mechanisms, through transcriptional inhibition of PAL and HMGR pathways. Therefore, the objective of the current study was to carry out a molecular characterization of potato defense suppression by Phytophthora infestans. Gene expression profiling was accomplished by developing a new subtractive hybridization (SH)/cDNA-AFLP combinational approach. This approach is a gel-based subtractive hybridization profiling technique that uses the advantages of cDNA-AFLP and subtractive hybridization in order to amplify cDNA products in a polyacrylamide gel and remove the constitutively/commonly expressed sequences. Using this approach differentially expressed genes involved in the potato-Phytophthora infestans interaction were identified. These included genes potentially controlling pathogenesis or avr genes in P. infestans as well as those potentially involved in potato resistance or susceptibility to this pathogen. Using the subtractive hybridization (SH)/cDNA-AFLP combinational approach, DOXP-MEP pathway genes were identified for first time in potato and its regulation in response to the oomycete P. infestans. The DOXP-MEP pathway, also called the non-mevalonate route is an alternative terpenoids' biosynthetic route that was discovered first in eubacteria and soon after in photosynthetic organisms such as higher plants, algae as well as in cyanobacteria. In addition, potato plants treated with glucans extracted from P. infestans, the elicitor eicosapentanoic acid (EPA) and P. infestans isolates were analyzed to study the accumulation of phenolic compounds and expression level of genes from the phenylpropanoid, mevalonate and DOXP-MEP pathway.