Transcriptional Regulatory Networks Controlling the Development of the Soybean Seed

Seed development in flowering plants is divided into two main contrasting developmental phases, morphogenesis and maturation. The morphogenesis phase is characterized by a series of cell division and differentiation events that establish the basic body plan of the embryo. Following morphogenesis, the seeds enter the maturation phase which is characterized by the accumulation of storage compounds and the embryo’s acquisition of desiccation tolerance. Because seed development is a complex yet highly coordinated period of the plant life cycle, the temporal and spatial control of gene expression is crucial to ensure the proper development of the plant. The focus of my dissertation research was to investigate the complex network of transcription factors and their combinatorial efforts to control the onset of specific biological programs during the development of the soybean seed.My first research topic investigated the function of four putative regulators of seed development in flowering plants: LEAFY COTYLEDON1 (LEC1), ABA-RESPONSIVE ELEMENT BINDING PROTEIN3 (AREB3), BASIC LEUCINE ZIPPER67 (bZIP67), and ABA INSENSITIVE3 (ABI3). I showed through genome-wide analyses of transcription factor binding sites that distinct transcription factor combinatorial interactions are controlling distinct biological programs in the soybean seed, such as embryo morphogenesis, photosynthesis, and seed storage protein accumulation. I also showed that these combinatorial interactions are assembled in cis-regulatory modules (CRMs) to control the expression of specific target genes. These distinct combinatorial interactions in CRMs are determined by the unique composition of DNA motifs in the CRMs and the ability of transcription factors to physically interact with each other. I also explored the ability of CRMs to act as cis-acting enhancers. The second topic of my dissertation described the role of the WRINKLED1 (WRI1) transcription factor in the regulation of lipid storage accumulation in soybean seeds. Lipid accumulation in seeds is a complex metabolic pathway that requires the action of many enzymes that act in processing carbohydrates into long chain fatty acids in addition to packaging triacyl-glycerol molecules into oil bodies. Genome-wide characterization of WRI1 binding sites revealed that this TF can bind to several genes that encode enzymes involved with every step of the fatty acid and triacylglycerol metabolic pathway. We also explored the collaboration between LEC1 and WRI1 in the regulation of genes involved with this metabolic process. Our results provided important and novel insights into the mechanisms of WRI1 in the control of lipid biosynthesis in soybean seeds