Using Genome-Wide Approaches to Dissect Seed Development

Seeds are a major source of food for human and animal consumption and can account for a large majority of the caloric intake by human. A detailed understanding of seed development should provide strategies for improving seed yield or enhance seed nutrients. Seed development consists of three major structure — the embryo, endosperm, and seed coat — all developing in parallel. Each of these structures undergo major developmental and physiological changes during seed development; however, it is not known how the different developmental programs in these structure are coordinated to form a seed.How are genes regulated during seed development? What are the transcription factors playing a major role in controlling seed development? Are there genome-wide methylation changes during seed development, and if so, how do these changes affect seed activity? These were the driving questions that formed the basis of my Ph.D. research. To begin to address these questions, I used a variety of genomics tools [e.g., Sanger sequencing, next generation sequencing (NGS), GeneChip microarrays, laser capture microdissection (LCM)], with several plant species [e.g., Arabidopsis, soybean, scarlet runner bean (SRB)], to characterize seed transcriptomes and methylomes on a genome-wide basis. In addition, I used reverse genetics to knockout seed-specific transcription factors and determine what role they may play in seed development. Collectively, data generated from my Ph.D. research can contribute to understanding gene activity during seed development