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

在今后50年中，我们将需要在越来越少的农业用地上生产比人类整个历史上更多的粮食。因此，21世纪世纪的一个主要挑战是使用最先进的遗传技术来增加主要作物植物（如大豆）的产量，以便使用可用于种植作物的有限数量的土地来增加粮食产量。种子是人类和动物消费的主要食物来源。本计画的实验将探讨高等植物的种子分化。该项目的长期目标是利用最先进的基因组技术来揭示基因调控网络，或DNA控制电路，需要“制造种子”。“有几个原因支持选择大豆进行这项研究。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300亿美元的农场价值。最后，大豆有巨大的遗传资源，包括其整个DNA序列的可用性，这将促进进展。来自三所大学的科学和人文专业的本科生，包括一所历史上的非洲裔美国人大学，我也将参加这个项目，以了解第一手资料的“兴奋的科学发现”本项目的目标是确定负责控制主要大豆种子分化和功能的基因调控网络，在整个发育过程中的区域和亚区域-包括胚，胚乳和种皮。Chip-Seq实验将用于鉴定下游基因靶标和转录因子（TF）的同源DNA控制元件，这些转录因子对从受精到成熟的每个种子区域和亚区域具有特异性。生物信息学方法将用于构建调控网络，指导和控制特定的种子功能空间发育过程中。SELEX-Seq实验将通过在体外鉴定每个区域和亚区域特异性TF的DNA结合基序来补充Chip-Seq研究。使用种子原生质体系统的功能研究将用于干扰和验证用Chip-Seq在体内鉴定的TF基因靶标。这些实验的意义在于，它们将为了解基因回路和顺式控制模块提供新的见解，这些模块对于“制造大豆种子”至关重要。通过了解种子形态和功能建立所需的DNA“布线”，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.