The soybean cyst nematode (Heterodera glycines) is the major pathogen of soybean (Glycine max), and causes an estimated $0.5-$0.8 billion in losses per annum in the U.S. We identified genes expressed in soybean roots and by SCN before and during infection using microarrays containing 37,500 soybean and 7,500 SCN gene probes. We used laser capture microdissection (LCM) to isolate syncytia from roots to study gene expression specifically at the feeding site. This provided a group of soybean genes that may influence soybean resistance to SCN. Then we identified cyst nematode genes that may be useful in developing soybean resistant to nematodes by comparing the SCN EST database with genes from Caenorhabditis elegans. SCN homologs of C. elegans genes were identified that would cause death of C. elegans if mutated or silenced. We developed a system to rapidly transform soybean roots and screen DNA constructs to determine their effect on SCN survival. A series of transformation vectors, designated as pRAP, was constructed using Gateway (Invitrogen) technology to rapidly clone DNA without restriction digestion. Gene over-expression, gene silencing (RNAi), and promoter analysis can be studied using these vectors. The vectors contain the tetracycline resistance gene for easy selection of transformed Agrobacterium rhizogenes K599 and the gene encoding enhanced green fluorescent protein for easy selection of transformed roots. We transformed soybean roots with a series of vector constructs.  The transformed soybean roots were challenged with soybean cyst nematodes and analyzed to determine if there were changes in resistance compared to control roots. This system also can be used for general studies in functional genomics using plant roots.