RESEARCH-PGR: Elucidating Maize Gene Regulatory Networks to Accelerate Translational Genomics

玉米是种植最广泛的谷类作物之一，支持世界各地不断增长的人口。通过上个世纪农业的改进，美国各地的玉米产量显著增加。尽管取得了这些进展，但农业目前面临着重大的环境挑战，从日益严重的水资源压力到新疾病的传播。因此，需要新的育种方法来生产有弹性的植物，并保持玉米农业的健康和生产力。这一竞技场的主要新进展来自玉米遗传学和基因组学的最新发现：研究人员已经确定了基因组中的关键因子，这些因子作为“主调节因子”来控制重要性状的表达。目前，人们对这些因素何时、何地发挥作用以及它们如何控制性状知之甚少。该项目使用全新的技术来寻找和表征基因组中隐藏的表达控制位点，并测试它们的功能。这项研究的突破将提供新的方法来产生作物的韧性，并将提高玉米的育种潜力。通过公共网站，该项目的成果可供其他研究人员、种植者和育种者使用，从而确保社区协调努力，改善玉米研究和农业。学生和博士后研究人员接受作物基因组学培训，以保持美国科学企业的实力，连续性和安全性阐明基因调控网络涉及通过识别蛋白质-DNA相互作用将顺式调控代码（顺式组）与反式作用因子联系起来。顺反序列取决于转录起始的位置，这必须根据经验来定义。近交系之间基因表达的差异有助于杂种优势，最终是影响蛋白质-DNA相互作用空间的顺式和反式作用变异的结果。了解这些变异为加速作物育种提供了机会。基于该团队先前开发的识别蛋白质-DNA相互作用的工具，该跨学科项目有三个主要目标：1）建立玉米转录起始的全基因组景观，2）开发玉米基因调控相互作用的综合目录，3）整合功能转录因子信息以加速性状发现。该项目将继续开发植物基因调控网络解剖所需的全基因组工具，并积累必要的知识，以便在其他作物中进行类似的研究。将通过可上网查阅的知识库GRASSIUS（www.grassius.org）和MaizeGDB（www.maizegdb.org）使数据可视化，以确保尽可能广泛地传播结果。研究的跨学科性质将通过FIRE（促进研究与本科教育的融合）计划与本科生的培训相结合，并通过SIGUE（研究生教育的成功）计划从代表性不足的群体中毕业的学生。

Maize is one of the most widely grown cereal crops that supports growing populations across the world. Through improvements in agriculture over the last century, corn yields have increased significantly across the U.S. Despite these advances, agriculture currently faces significant environmental challenges, from increasing water stress to spread of new diseases. New breeding approaches are thus needed to produce resilient plants and to maintain the health and productivity of maize agriculture. Major new advances in this arena come from recent discoveries in maize genetics and genomics: Researchers have identified key factors in the genome that serve as "master regulators" to control expression of important traits. Currently, little is known about when or where these factors function or how they control traits. The project uses all-new technologies to find and characterize hidden sites of expression control in the genome, and tests their function. The breakthroughs from this research will provide new ways to generate crop resilience and will improve the breeding potential of maize. Through public websites, outcomes from the project are made available to other researchers, growers and breeders, thereby ensuring a coordinated community effort to improve maize research and agriculture. Students and post-doctoral researchers are trained in crop genomics to maintain the strength, continuity and security of the scientific enterprise in the U.S. Elucidating gene regulatory networks involves linking the cis-regulatory code (cistrome) with the trans-acting factors through identifiying protein-DNA interactions. The cistrome hinges on where transcription initiation starts, which must be empirically defined. Differences in gene expression between inbred lines contribute to hybrid vigor, and are ultimately a consequence of cis- and trans-acting variations that affect the protein-DNA interaction space. Understanding these variations provides opportunities to accelerate crop breeding. Building on the team's previously developed tools to identify protein-DNA interactions, this interdisciplinary project has three main objectives: 1) Establish the genome-wide landscape of transcriptional initiation in maize, 2) develop a comprehensive catalog of maize gene regulatory interactions, and 3) incorporate functional transcription factor information to accelerate trait discovery. The project will continue to develop genome-wide tools necessary for plant gene regulatory network dissection, and build the knowledge necessary to enable similar studies in other crops. Data will be visualized through the Web-accessible knowledge base GRASSIUS (www.grassius.org) and MaizeGDB (www.maizegdb.org) to ensure the broadest possible dissemination of results. The interdisciplinary nature of the research will be integrated with the training of undergraduate students through the FIRE (Fostering Integration of Research and undergraduate Education) program, and recently graduated students from underrepresented groups through the SIGuE (Success In Graduate Education) program.