The purpose of this project is to precisely identify the genes, gene networks, and master regulators (e.g., transcription factors) controlling soybean seed development and, ultimately, soybean yield. To reach this objective, we propose to analyze the activity of the soybean genes in each cell composing the seed and during seed development. This project will have several major outcomes:
1- the identification of the genes that contribute to soybean seed biology and the establishment of the time-course of their activity during seed development;
2- the characterization of seed cell-type-specific gene networks;
3- the identification of seed cell-type-specific promoter sequences.
The latter will contribute to the development of synthesis promoters, a pre-requirement to the development of new strategies to specifically express transgenes in soybean seeds. We strongly believe that this project will lead to the submission of patents describing collections of seed-cell-type specific promoters and regulatory elements.

The main objective of this proposal is to establish this fundamental knowledge by characterizing the soybean genes controlling seed development. Applying a single cell approach, the goals of this project are to:
1- Identify seed-specific soybean genes in soybean seeds;
2- Precisely characterize the expression of the soybean genes for each cell-type composing the seed;
3- Reveal the temporal changes in gene expression during seed development;
4- Characterize soybean seed gene regulatory networks at the level of single cell-types.
5- Design and develop a dynamic website to share with the community the “Soybean Single-Cell Transcriptome Atlas”

One unique and innovative aspect of this proposal is the quantification of gene activity at the level of individual cells. This will be accomplished by using a single-nuclei approach to provide the highest resolution to better understand the transcriptional regulation of the soybean genes during seed development. This project is highly relevant to the Nebraska Soybean Board based on the need to develop new functional genomic resources to facilitate gene function studies. This proposal intends to support this goal through the creation of a website to access the transcriptional activity of soybean genes in seed single-cell-types. This project will also help in refining our current knowledge of the soybean gene regulatory pathways including those controlling the biosynthesis of seed oil and proteins.
Finally, combined to gene editing technologies, the characterization of the transcriptional activity of the soybean gene at the single cell-type level will support the development of precision genomic tools.

Updated May 19, 2023:

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This project will provide the highest resolution possible in the transcriptomic profile of each gene composing the soybean genome. Accessing this information will help understand the role of each gene and gene cluster. Considering the strong focus of this project on seed development, we will gain a deep understanding of the role of the soybean genes and their co-expression during seed development and protein/oil accumulation. This resource will allow soybean researchers to develop more accurate synthetic biology strategies to enhance soybean yield and oil/protein quality.

This proposal directly addresses one of the overarching goals of the Nebraska Soybean Board for FY 2021 Funding: “Conduct research aimed at genetic-based improvement in soybean yield potential”. Our innovative approach to analyze the activity of the soybean genes in seeds will lead to several deliverables:
1- the identification of the genes that contribute to soybean seed biology and the establishment of the time-course of their activity during seed development;
2- the characterization of seed cell-type-specific gene networks;
3- the identification of seed cell-type-specific promoter sequences. The latter will contribute to the development of synthesis promoters also leading to the submission of patents describing collections of seed-cell-type specific promoters and regulatory elements.