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

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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.