ESTABLISHMENT OF THE SOYBEAN SINGLE CELL TRANSCRIPTOME ATLAS.

The transcriptome of each soybean cell is unique, depending on cell type (i.e., cell fate determination), cell state (i.e., cell differentiation stage, age, degree of elongation, and functional status [11, 29, 47]), and environmental factors (e.g., photoperiod affects plant transcriptomes [48]). Taking advantage of existing soybean genomic resources, the expertise of the PI in single cell/nucleus genomic, and preliminary results (Fig. 2), we propose to apply snRNA-seq technology to analyze soybean cell-type gene expression across organs and establish the first single cell transcriptome atlas. Specifically, we propose to:Objective 1 (Years 1-3): Establish the transcriptomic signature of each soybean cell-types. This will be achieved upon isolation of soybean nuclei from various organs and their use to synthesize then sequence snRNA-seq libraries. These data will be used to compare the transcriptome of the soybean single cell-types in and between plant organs (see Objective 2).Objective 2 (Years 2-4): Create the "Soybean Single Cell Types Transcriptome Atlas" to characterize cell-type-specific differentially expressed genes. To fulfill this second objective, we will utilize modern computational tools specifically develop to support the analysis of single cell transcriptomic datasets [40, 41]. The major outcome of this analysis will be the development of an online resource, the "Soybean Single Cell Types Transcriptome Atlas", to allow the scientific community to access and analyze the transcriptional pattern of the soybean genes.Objective 3 (Years 3-5): Comprehensive analysis of the transcriptional regulation of the soybean root hair genes. The root hair cell plays a central role in the uptake of water and nutrients from the soil, and it is the first cell infected by nitrogen-fixing Bradyrhizobium diazoefficiens, soil bacteria involved in the nodulation process. In this third objective, we propose to characterize the dynamic regulation of the soybean root hair transcriptome during the lifetime of the cell (i.e., starting by its cellular differentiation, continuing with its typical polar elongation, and finishing with the gain of its biological functions). We also propose to reveal co-expressed gene modules [49] which are composed of specialized genes essential for the establishment of the soybean root hair function. The characterization of the co-expressed gene modules will benefit from the current development of MiReN (Minimal Regulatory Network; [50]) by co-PI Saha, an optimization-based tool for transcriptomic data-driven discovery of global regulatory phenomena.