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

RESEARCH-PGR：阐明玉米基因调控网络以加速转化基因组学

• 批准号: 1733633
• 负责人: Erich Grotewold
• 金额: $ 488.43万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-02-01 至 2024-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1733633&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Elucidating; Maize; Gene

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.

玉米是最广泛种植的谷物作物之一，支持全球不断增长的人群。通过上个世纪农业的改善，尽管这些进展有这些进展，但在美国，玉米产量已大大提高，目前，农业面临着重大的环境挑战，从增加水压力到新疾病的传播。因此，需要采用新的育种方法来生产有弹性的植物并维持玉米农业的健康和生产力。该领域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素，这些因素是控制重要特征表达的“主要调节剂”。当前，这些因素何时或在何处或它们如何控制特征。该项目使用全新技术来查找和表征基因组中表达控制的隐藏位点，并测试其功能。这项研究的突破将为产生农作物的弹性提供新的方法，并将提高玉米的繁殖潜力。通过公共网站，该项目的成果可供其他研究人员，种植者和育种者提供，从而确保了社区协调的努力，以改善玉米研究和农业。对学生和博士后研究人员进行了农作物基因组学培训，以维持美国阐明​​基因调节网络的科学企业的强度，连续性和安全性，涉及将顺式调节守则（CISTROME）与跨性因素联系起来，通过识别蛋白-DNA的相互作用将其联系起来。 Cistrome取决于转录启动开始的位置，必须在经验上定义。近交系之间基因表达的差异有助于杂种活力，最终是影响蛋白质-DNA相互作用空间的顺式和反式作用变化的结果。了解这些变化为加速作物育种提供了机会。在团队先前开发的工具以识别蛋白质-DNA相互作用的基础上，该跨学科项目具有三个主要目标：1）在玉米中建立全基因组转录启动的全基因组景观，2）开发了玉米基因调节性相互作用的全面目录，以及3）将功能转录因子信息纳入了可观的特征发现。该项目将继续开发植物基因调节网络必需的全基因组工具，并建立在其他农作物中进行类似研究所必需的知识。数据将通过可见的知识库Grassius（www.grassius.org）和MaizeGDB（www.maizegdb.org）来可视化，以确保结果最广泛的结果。该研究的跨学科性质将通过火灾（促进研究与本科教育的融合）计划与本科生的培训相结合，最近通过Sigue（研究生教育的成功）计划，来自代表性不足的小组的毕业生。

项目成果

Mutator transposon insertions within maize genes often provide a novel outward reading promoter

• DOI: 10.1093/genetics/iyad171
• 发表时间: 2023-11-01
• 期刊: GENETICS
• 影响因子: 3.3
• 作者: Ellison，Erika L.;Zhou，Peng;Springer，Nathan M.
• 通讯作者: Springer，Nathan M.

Rhamnose in plants - from biosynthesis to diverse functions

• DOI: 10.1016/j.plantsci.2020.110687
• 发表时间: 2021-01-01
• 期刊: PLANT SCIENCE
• 影响因子: 5.2
• 作者: Jiang, Nan;Dillon, Francisco M.;Grotewold, Erich
• 通讯作者: Grotewold, Erich

Discovery of modules involved in the biosynthesis and regulation of maize phenolic compounds

• DOI: 10.1016/j.plantsci.2019.110364
• 发表时间: 2020-02-01
• 期刊: PLANT SCIENCE
• 影响因子: 5.2
• 作者: Gomez-Cano, Lina;Gomez-Cano, Fabio;Gray, John
• 通讯作者: Gray, John

Should I stay or should I go? Trafficking of plant extra-nuclear transcription factors

• DOI: 10.1093/plcell/koad277
• 发表时间: 2024-01-02
• 期刊: PLANT CELL
• 影响因子: 11.6
• 作者: Marathe，Sarika;Grotewold，Erich;Otegui，Marisa S.
• 通讯作者: Otegui，Marisa S.