Research-PGR: Gene Regulatory Networks Required to Make a Soybean Seed

University Of California-Los Angeles, Los Angeles CA

Investigators

Abstract

During the next 50 years we will need to produce more food than in the entire history of humankind on a decreasing amount of land for agriculture. A major challenge for the 21st century, therefore, is to increase the yields of major crop plants, such as soybean, using state-of-the-art genetic technologies in order to increase food production using the limited amount of land available for growing crops. Seeds represent a major source of food for human and animal consumption. The experiments in this project will investigate seed differentiation in higher plants. The long-term objective of this project is to use state-of-the-art genomic technologies to uncover the gene regulatory networks, or DNA control circuits, required to "make a seed." There are several reasons that support the selection of soybean for this study. Soybean seeds are one of the largest sources of protein feed and vegetable oil in the world, providing $30 billion annually in farm value to the U.S. Soybean seeds are uniquely suited to study the basic processes controlling seed development. Finally, there are enormous genetic resources for soybeans that will facilitate progress, including the availability of its entire DNA sequence. Undergraduates majoring in both science and humanities from three universities, including a historically African-American university, will also participate in this project in order to learn first-hand about the "excitement of scientific discovery" and the role crop genetic engineering plays in society. The goal of this project is to identify the gene regulatory networks that are responsible for controlling the differentiation and function of major soybean seed regions and subregions throughout development- including the embryo, endosperm, and seed coat. Chip-Seq experiments will be used to identify downstream gene targets and cognate DNA control elements of transcription factors (TFs) that are specific for each seed region and subregion from fertilization through maturation. Bioinformatic approaches will be used to construct regulatory networks that guide and control specific seed functions spatially during development. SELEX-Seq experiments will complement the Chip-Seq studies by identifying the DNA binding motifs for each region- and subregion-specific TF in vitro. Functional studies using a seed protoplast system will be used to perturb and validate TF gene targets identified with Chip-Seq in vivo. The significance of these experiments is that they will provide new insights into the gene circuits and cis-control modules that are important for "making a soybean seed." By understanding the DNA "wiring" required for the establishment of seed form and function, novel approaches can be designed for increasing seed yield and, therefore, food production.