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

氮肥需要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了土壤和水污染。因此，有必要找到替代和可持续的氮源来帮助作物生长。豆科植物（如大豆、紫花苜蓿、普通豆）与一组称为根瘤菌的细菌形成独特的共生关系，根瘤菌将大气中的氮转化为一种可用于支持寄主植物生长和繁殖的化学形式。这种被称为结瘤的生物过程在经济上很重要，有利于农业的可持续性和粮食安全。豆科植物根瘤形成始于根瘤菌侵染植物根毛细胞。虽然这种细胞类型存在于所有开花植物中，但只有在豆科植物中，根毛细胞能够启动这种共生关系。虽然已经确定了参与这一过程的几个豆科基因，但在考虑根毛结瘤能力向非豆科作物的转移之前，需要更好地了解控制根毛感染的遗传程序。该项目的研究人员将利用植物单细胞技术表征这些遗传程序。除了对我们对豆科植物结瘤和生物固氮的理解产生影响外，该项目还将通过支持开发专门针对STEM高中和本科生的独特教育项目，促进研究与教育之间的整合。该项目建立在植物细胞分化、生物功能的获得和对外部刺激的反应是由进化保守的转录模块控制的假设基础上。本项目着眼于豆科植物根毛细胞的生物学特性及其对根瘤菌接种的反应，将解决三个关键问题：豆科植物根毛转录组在根瘤菌感染的不同阶段发生了哪些动态变化？在豆科植物在5000万年的分化和最近（5- 1000万年）的大豆多倍体之后，这些程序的保存水平是什么？在根瘤菌侵染根毛时，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，研究人员将利用铬单细胞多组ATAC +基因表达技术对分离的豆科植物根毛细胞进行分析，详细分析与结瘤过程早期阶段相关的分子机制。了解基因活性和染色质可及性的变化，将有助于更深入地了解植物细胞对微生物感染的动态反应，以及豆类物种和全基因组复制时这些反应的保存水平。该奖项由植物基因组研究计划和植物生物相互作用计划共同资助。该奖项反映了美国国家科学基金会的法定使命，并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，被认为值得支持。

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.