RESEARCH-PGR: System approaches to study soybean root biology at high resolution

RESEARCH-PGR：高分辨率研究大豆根生物学的系统方法

• 批准号: 1734145
• 负责人: Gary Stacey
• 金额: $ 369.04万
• 依托单位: University of Missouri-Columbia
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1734145&HistoricalAwards=false
• 关键词: RESEARCH; PGR; System; approaches; study

Soybean is a major crop with the ability to fix atmospheric nitrogen through symbiosis with soil bacteria. Legumes like soybean annually fix 60 million metric tons of nitrogen, which have a fertilizer replacement value of $7- 10 billion. A long-term goal of N2 fixation research is to transfer the symbiotic ability of legumes to non-legume crops like corn or tomato. However, there are gaps in our understanding of the complex events that occur after the bacteria penetrate the root. These gaps are hindering efforts to engineer nitrogen fixation into non-legumes. Hence, the main objective of this project is to elucidate the initial events that take place during the formation of structures that mediate the movement of bacteria through the root. This project will use high-resolution methods to characterize macromolecular events at a single-cell level. The experimental data will be analyzed with sophisticated modeling tools to improve our understanding of the first events of the legume-bacterial interactions that lead to symbiosis. The knowledge gained will support efforts to transfer the rhizobial symbiosis to non-leguminous plants. In addition to the research mission, the project will create new programs to provide transformative elementary education, as well as training programs for the professional development of middle school and high school teachers. Finally, this project will develop an innovative Sophomore Bioinformatics/Plant Science program to provide integrated training in plant research and bioinformatics.Data integration and system modeling of complex biological processes require detailed, functional genomic data, preferably obtained in a cell-specific way in order to avoid the effects of signal dilution due to the presence of non-responding cells. The long-term goal of this project is to further basic understanding of the agronomically important soybean N2 fixing symbiosis. A unique focus of this project is the ability to sample and analyze the transcriptome, proteome and metabolome at a single-cell resolution. These methods, as well as sophisticated data analysis and modeling tools, will be applied to the intermediate stages of soybean nodulation; specifically, the infection thread progression and bacterial release into nodule cells. These are key events in nodule formation/function that remain largely undefined. The data generated will be used to construct predictive, computational models of the plant response to rhizobial infection thread initiation and growth. The knowledge gained from this research, together with precision breeding techniques, will be instrumental to improving soybean quality and meeting the growing demand for food and fuel expected in the forthcoming years. Moreover, filling in the gaps in our understanding of the rhizobial-legume infection process will be critical to ongoing efforts to transfer this symbiosis to non-leguminous plants (e.g., maize). The project also includes strong outreach programs focusing on the introduction of plant science to elementary, high school and undergraduate students.

大豆是一种主要的农作物，通过与土壤细菌的共生，具有固定大气氮的能力。像大豆这样的豆类每年固定6000万公吨的氮，其肥料替代价值为70 - 100亿美元。固氮研究的一个长期目标是将豆科植物的共生能力转移到玉米或番茄等非豆科作物上。然而，我们对细菌穿透根部后发生的复杂事件的理解存在差距。这些差距阻碍了在非豆类植物中进行固氮工程的努力。因此，该项目的主要目标是阐明介导细菌通过根部运动的结构形成期间发生的初始事件。该项目将使用高分辨率方法来表征单细胞水平的大分子事件。实验数据将用复杂的建模工具进行分析，以提高我们对导致共生的豆类-细菌相互作用的第一个事件的理解。所获得的知识将支持将根瘤菌共生转移到非豆科植物的努力。除了研究使命，该项目将创建新的方案，提供变革性的小学教育，以及培训方案，为中学和高中教师的专业发展。最后，本项目将开发一个创新的生物信息学/植物科学二年级课程，提供植物研究和生物信息学的综合培训。复杂生物过程的数据集成和系统建模需要详细的功能基因组数据，最好是以细胞特异性的方式获得，以避免由于无响应细胞的存在而导致的信号稀释效应。本项目的长期目标是进一步了解具有重要农学意义的大豆固氮共生关系。该项目的一个独特的重点是能够以单细胞分辨率对转录组、蛋白质组和代谢组进行采样和分析。这些方法以及复杂的数据分析和建模工具将应用于大豆结瘤的中间阶段;特别是感染线进展和细菌释放到根瘤细胞中。这些是结核形成/功能中的关键事件，在很大程度上仍不明确。产生的数据将用于构建预测，计算模型的植物根瘤菌感染线程的启动和增长。从这项研究中获得的知识，加上精确的育种技术，将有助于提高大豆质量，满足未来几年对粮食和燃料日益增长的需求。此外，填补我们对根瘤菌-豆科植物感染过程的理解中的空白对于将这种共生关系转移到非豆科植物（例如，玉米）。该项目还包括强大的推广计划，重点是向小学，高中和本科生介绍植物科学。

项目成果

Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations

• DOI: 10.1021/acs.analchem.0c00936
• 发表时间: 2020-05-19
• 期刊: ANALYTICAL CHEMISTRY
• 影响因子: 7.4
• 作者: Samarah, Laith Z.;Khattar, Rikkita;Vertes, Akos
• 通讯作者: Vertes, Akos

Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries

• DOI: 10.1186/s12864-019-6287-8
• 发表时间: 2019-12
• 期刊: BMC Genomics
• 影响因子: 4.4
• 作者: Shuai Zeng;Zhen Lyu;Siva Ratna Kumari Narisetti;Dong Xu;T. Joshi

High-Throughput Analysis of Tissue-Embedded Single Cells by Mass Spectrometry with Bimodal Imaging and Object Recognition

采用双峰成像和物体识别的质谱法对组织包埋的单细胞进行高通量分析

• DOI: 10.1021/acs.analchem.1c00569
• 发表时间: 2021
• 期刊: Analytical Chemistry
• 影响因子: 7.4
• 作者: Stopka, Sylwia A.;Wood, Ellen A.;Khattar, Rikkita;Agtuca, Beverly J.;Abdelmoula, Walid M.;Agar, Nathalie Y.;Stacey, Gary;Vertes, Akos
• 通讯作者: Vertes, Akos

Characterization of the Spatial and Temporal Expression of Two Soybean miRNAs Identifies SCL6 as a Novel Regulator of Soybean Nodulation

• DOI: 10.3389/fpls.2019.00475
• 发表时间: 2019-04-16
• 期刊: FRONTIERS IN PLANT SCIENCE
• 影响因子: 5.6
• 作者: Hossain, Md Shakhawat;Hoang, Nhung T.;Stacey, Gary
• 通讯作者: Stacey, Gary

Suppression of LjBAK1-mediated immunity by SymRK promotes rhizobial infection in Lotus japonicus

• DOI: 10.1016/j.molp.2021.07.016
• 发表时间: 2021-11-01
• 期刊: MOLECULAR PLANT
• 影响因子: 27.5
• 作者: Feng, Yong;Wu, Ping;Cao, Yangrong
• 通讯作者: Cao, Yangrong