RESEARCH-PGR: Single-Cell Analysis of the Dynamics and Evolution of Gene Expression in Legumes

RESEARCH-PGR：豆类基因表达动态和进化的单细胞分析

• 批准号: 2425989
• 负责人: Marc Libault
• 金额: $ 150万
• 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: 2023
• 资助国家: 美国
• 起止时间: 2023-10-01 至 2024-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2425989&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Single; Cell; Analysis

Nitrogen fertilizers are required to maximize crop growth and yields to feed a growing population. However, their extensive use leads to soil and water pollution. Therefore, there is a need to find alternative and sustainable sources of nitrogen to aid crop growth. Legumes (e.g., soybean, Medicago, common bean) develop unique symbiotic relationships with a group of bacteria called rhizobia that convert atmospheric nitrogen to a chemical form available to support the host plant’s growth and reproduction. This biological process, called nodulation, is economically important and benefits agricultural sustainability and food security. Legume nodulation starts with the infection of the plant root hair cell by rhizobia. Although this cell type is found in all flowering plants, in only a subset of plants, among them legumes, is the root hair cell capable of initiating this symbiotic relationship. While several legume genes involved in this process have been characterized, a better understanding of the genetic programs controlling root hair infection is needed before considering the transfer of nodulation capacity to non-legume crop plants. The investigators in this project will characterize these genetic programs using plant single-cell technologies. In addition to its impact on our understanding of legume nodulation and biological nitrogen fixation, this project will promote the integration between research and education by supporting the development of unique educational programs dedicated to STEM high-school and undergraduate students.This project is built on the hypothesis that plant cell differentiation, gain of biological functions, and response to external stimuli are controlled by evolutionarily conserved transcriptional modules. Focusing on the biology of legume root hair cells and their response to rhizobia inoculation, this project will address three key questions: What dynamic changes occur in the legume root hair transcriptome at different stages of their infection by rhizobia? What is the level of conservation of these programs among legumes after their divergence over 50 million years and after recent (5-10 million years) polyploidy in soybean? What is the contribution of chromatin accessibility in controlling the dynamic changes of the transcriptomic programs in response to root hair infection by rhizobia? To answer these questions, the investigators will analyze in detail the molecular mechanisms associated with the early stages of the nodulation process by using the Chromium Single Cell Multiome ATAC + Gene Expression technology on isolated legume root hair cells. Accessing changes in both gene activity and the profiles of chromatin accessibility will provide a deeper understanding of the dynamic response of a plant cell to microbial infection, and the level of conservation of these responses among legume species and upon whole-genome duplication.This award was co-funded by the Plant Genome Research Program and the Plant Biotic Interactions Program.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

需要氮肥来最大限度地提高作物生长和产量，以养活不断增长的人口。然而，它们的广泛使用导致土壤和水污染。因此，需要找到替代和可持续的氮源来帮助作物生长。豆类（例如，大豆、苜蓿、普通菜豆）与一组称为根瘤菌的细菌发展了独特的共生关系，根瘤菌将大气中的氮转化为可用于支持宿主植物生长和繁殖的化学形式。这一生物过程被称为生物转化，具有重要的经济意义，有利于农业的可持续性和粮食安全。豆科植物的繁殖始于根瘤菌对植物根毛细胞的侵染。虽然这种细胞类型存在于所有开花植物中，但只有一部分植物，其中包括豆类，根毛细胞能够启动这种共生关系。虽然参与这一过程的几个豆科植物基因的特点，更好地了解控制根毛感染的遗传程序之前，需要考虑到非豆科作物植物的繁殖能力的转移。该项目的研究人员将使用植物单细胞技术来表征这些遗传程序。除了对我们理解豆科植物的生长和生物固氮产生影响外，该项目还将通过支持专门针对STEM高中和本科生的独特教育计划的开发，促进研究与教育之间的整合。该项目建立在植物细胞分化，获得生物功能，对外界刺激的反应是由进化上保守的转录模块控制的。该项目将重点关注豆科植物根毛细胞的生物学及其对根瘤菌接种的反应，将解决三个关键问题：在根瘤菌感染的不同阶段，豆科植物根毛转录组发生了什么样的动态变化？这些程序在豆科植物中的保护水平是多少？在它们分化超过5000万年之后，以及在大豆中最近（500 - 1000万年）的多倍化之后？根瘤菌根毛感染后，染色质可及性在控制转录组程序动态变化中的作用是什么？为了回答这些问题，研究人员将通过使用Chromium Single Cell Multiome ATAC + Gene Expression技术对分离的豆类根毛细胞进行详细分析，以了解与生长过程早期阶段相关的分子机制。基因活性和染色质可接近性的变化将提供对植物细胞对微生物感染的动态响应的更深入的理解，以及这些反应在豆类物种之间和全基因组复制时的保护水平。由植物基因组研究计划和植物生物相互作用计划资助。该奖项反映了NSF的法定使命，并已被视为通过使用基金会的知识价值和更广泛的影响审查标准进行评估，