Gene Networks in Soybean Seed Development

The seed is an excellent model system for studies of plant development. The seed is a complex yet elegant structure that is comprised of three major regions, each with a distinct genetic composition.  The diploid embryo and triploid endosperm arise from separate fertilization events, and the diploid seed coat is of maternal origin. Each region is partitioned further into subregions that consist of specific tissues and cell types. Another unique aspect of seed development is that it is biphasic.  During the morphogenesis phase early in seed development, both the embryo and endosperm undergo morphogenetic events that are required for formation of the seed regions.  Late in seed development, the embryo and endosperm undergo the maturation phase during which storage macromolecules accumulate to massive amounts, and the embryo becomes tolerant of desiccation.  A comprehensive understanding of seed development requires knowledge of the gene regulatory networks that operate temporally and spatially within the seed.

We have profiled mRNA and small RNA populations genome-wide in every organ, tissue, and cell type of soybean seeds throughout development using laser-capture microdissection coupled with RNA sequencing experiments. We have characterized the DNA methylome of soybean seeds at several stages of development. To complement this information, we have also identified the binding sites of specific transcription factors and modified histones that affect the transcriptional activities of genes.  Our studies to dissect the gene regulatory networks that operate during seed development will be discussed.