The first involves structural and comparative genomics of legumes. We are using the annual legume, Medicago truncatula, as a model for genome structure throughout the Papilionoid legumes. Projects in this area include determining the genomic architecture of resistance gene homologs, developing a sequence-based genetic map of Medicago truncatula, and examining conserved genome structure across the Papilionoideae by means of comparative mapping and phylogenetic methods. A current NSF funded project aims to develop a complete physical map for this species. The physical map serves as the basis of an international effort to segment the gene space of Medicago truncatula.

In a second area of emphasis, researchers in the group are involved in the genetic and molecular characterization of plant genes that regulate associations with symbiotic and pathogenic microorganisms. Research projects include the genetic characterization and map-based cloning of plant genes that regulate infection by symbionts and/or pathogens. In particular, we have cloned plant genes that function to transduce exogenous bacterial signals and endogenous hormonal cues. A current project focuses on biochemical and functional characterization of signaling proteins. We are also interested in the mechanistic overlaps between genetic programs for plant development and interactions with symbionts and pathogens.

The third area of investigation in the Cook lab involves characterizing transcriptional pathways in Vitis vinifera (grape) that are either correlated with infection by the bacterial pathogen Xylella fastidiosa, or influenced by viticultural practices. The activities in this area include EST sequencing, bioinforamtics and microarray expression analysis.