Technical Abstract: Soybean is one of the top five agricultural products in the United States with an estimated production of 3.36 billion bushels in 2009. Its protection from all pathogens is very important for soybean production. The Glycine max L. Merr. (soybean) defense response to Heterodera glycines Ichinohe (soybean cyst nematode [SCN]) was a model to phenotype its resistant reactions at cellular resolution. The defense response, leading to resistance occurs at the site of infection, a nurse cell known as the syncytium. Two major genotype-defined defense responses exist, the G. max[Peking]- and G. max[PI 88788]-types. Resistance in G. max[Peking] is a potent and rapid localized response, accompanied by the formation of cell wall appositions that perform important defense roles. The G. max[Peking] response halts parasitic second stage juveniles (p-J2) development. In contrast, defense occurs by a potent but more prolonged reaction in G. max[PI 88788], lacking cell wall appositions and stopping nematode development at the J3 or J4 stages. Comparative transcriptomic analyses of these cytologically and developmentally distinct defense responses along with the susceptible reaction related gene expression to the rhg1 locus, defined within a 67 kb region of DNA on chromosome 18. The analyses, using the sequenced G. max[Williams 82/PI 518671] identified an amino acid transporter, a soluble NSF attachment protein, and an extensin-family gene expressed in syncytia of both G. max[Peking/PI 548402] and G. max[PI 88788] expressed throughout their defense responses as compared to pericycle and syncytia undergoing a susceptible reaction. A custom-developed KEGG application known as Pathway Analysis and Integrated Coloring of Experiments (PAICE) visualizes gene expression for the 2207 identified pathways, allowing better understanding of gene activity across all chromosomes and in and around the rhg1 locus. Genes were identified that mapped to a known location on the genome carrying resistance to SCN. These are now candidate genes that can be tested to determine their role in resistance to SCN. This information is important to plant scientists interested in developing broad resistance in soybean to SCN.