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

为了最大限度地提高作物生长和产量，养活不断增长的人口，需要氮肥。然而，它们的广泛使用导致了土壤和水的污染。因此，有必要寻找替代和可持续的氮源来帮助作物生长。豆类(如大豆、紫花苜蓿、菜豆)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。豆科植物的结瘤始于根瘤菌对植物根毛细胞的侵染。虽然这种细胞类型在所有开花植物中都能找到，但只有少数植物，其中包括豆类，是能够启动这种共生关系的根毛细胞。虽然参与这一过程的几个豆科植物基因已经被表征，但在考虑将结瘤能力转移到非豆科作物植物之前，需要更好地了解控制根毛侵染的遗传程序。该项目的研究人员将使用植物单细胞技术来描述这些遗传程序。除了影响我们对豆科植物结瘤和生物固氮的理解外，该项目还将通过支持针对STEM高中生和本科生的独特教育计划的发展，促进研究和教育的整合。该项目建立在植物细胞分化、生物学功能的获得和对外部刺激的反应受进化保守的转录模块控制的假设基础上。该项目将重点研究豆科植物根毛细胞的生物学及其对根瘤菌接种的反应，以解决三个关键问题：豆科植物根毛转录组在根瘤菌感染的不同阶段发生了什么动态变化？这些计划在豆类植物中的保存水平如何，在它们分化超过5000万年后，以及最近(500万-1000万年)大豆多倍体之后？染色质的可及性在控制转录程序的动态变化以响应根瘤菌感染根毛方面有何贡献？为了回答这些问题，研究人员将利用分离的豆科植物根毛细胞上的铬单细胞多聚体ATAC基因表达技术，详细分析与结瘤过程早期阶段相关的分子机制。获取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，以及豆科植物物种之间和全基因组复制时这些反应的保守水平。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NSF的法定使命，并通过使用基金会的智力优势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.