Research Topics
Department of Crop Sciences and Plant Biology
Research Topics
Research Interests
All genes function as part of functional networks, where final outputs are governed by complex regulatory circuits. Many of the connections within gene networks are defined by interactions between regulatory DNA binding proteins and promoter DNA sequences. My laboratory's research interests focus on defining and characterizing these regulatory networks in maize, a model species for plant genomics research and an economically valuable crop. We use a variety of complementary genomics approaches to identify key regulatory nodes within maize gene expression networks. Where regulatory DNA binding proteins are known, we use directed mutagenesis and transgenic over-expression strategies to identify target genes - those whose promoters are likely to be bound by the regulatory factor. We make use of microarrays to profile genome-scale changes in gene transcription among maize genotypes that differ significantly in the expression of economically important traits such as grain composition. We are also exploring a "bottom-up" approach where large numbers of gene promoter sequences are analyzed computationally for sequence patterns that suggest their corresponding genes function in common regulatory networks. Hypotheses based on these computational analyses are then tested in the laboratory using biochemical assays of DNA-protein interactions and functional analysis of promoter sequences in transgenic plants.
All of our studies take advantage of the recently completed genome sequence of rice, which is closely related to maize and allows for comparative genomics analyses that allow us to determine to what extent gene regulatory networks have evolved among these important cereal crops. The above approaches are primarily being applied to the study of gene networks that influence the nutritional composition and processing qualities of maize seeds. These include the synthesis of protein, oil, starch, and fiber (the cell wall). In addition, we are also characterizing genes associated with cellular differentiation and carbon and nitrogen import. A more detailed understanding of gene networks that operate during seed development will lead to the more efficient modification of maize grain through biotechnology for feed and processing traits.