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

在接下来的50年里，我们将需要在不断减少的农业用地上生产比整个人类历史上更多的粮食。因此，21世纪的一个主要挑战是利用最先进的基因技术提高大豆等主要农作物的产量，以便利用可用于种植作物的有限土地增加粮食产量。种子是人类和动物消费的主要食物来源。本项目中的实验将研究高等植物的种子分化。该项目的长期目标是使用最先进的基因组技术来发现“播种”所需的基因调控网络或DNA控制电路。支持本研究选择大豆的原因有几个。大豆种子是世界上最大的蛋白质饲料和植物油来源之一，每年为美国提供300亿美元的农业价值。大豆种子特别适合于研究控制种子发育的基本过程。最后，大豆有巨大的遗传资源，这将促进进展，包括其整个DNA序列的可用性。来自三所大学的理科和人文专业的本科生也将参加这个项目，以便第一手了解科学发现的兴奋感和作物基因工程在社会中的作用。该项目的目标是识别在整个发育过程中负责控制主要大豆种子区域和亚区域的分化和功能的基因调控网络--包括胚胎、胚乳和种皮。ChIP-Seq实验将用于确定下游基因靶标和转录因子(TF)的同源DNA控制元件，这些转录因子从受精到成熟都是针对每个种子区域和区域的。生物信息学方法将被用于构建调控网络，在发育过程中在空间上指导和控制特定的种子功能。SELEX-SEQ实验将通过在体外鉴定每个区域和次区域特异性转运蛋白的DNA结合基序来补充芯片序列研究。使用种子原生质体系统的功能研究将被用于扰乱和验证在体内用Chip-Seq鉴定的TF基因靶点。这些实验的意义在于，它们将为基因电路和顺式控制模块提供新的见解，这些电路和顺式控制模块对于“制造大豆种子”非常重要。通过了解建立种子形式和功能所需的DNA“连接”，可以设计新的方法来提高种子产量，从而提高粮食产量。

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.