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.

This proposal describe our plans regarding the continuation of an on-going project. 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”

Key Performance Indicators (KPI)/Milestones/Deliverables:
KPI1: October 2021; Major deliverable from Year 1 of this project: Generation of sequencing datasets. KPI2: March 2022; Data analyzed and preliminary map of the transcriptome of soybean single cell.
KPI3: Summer 2022; Characterization of the programs and GRNs controlling soybean seed development.

Project economic impact:
This project will allow the identification of complex genetic programs controlling seed development, oil, and protein accumulation. Accessing this information will enable a better understanding of the regulation of oil and protein accumulation, protein and oil quality, and soybean yield. Hence, these fundamental discoveries will enable researchers (including the Libault lab) to control with unprecedented accuracy these various soybean traits. Ultimately, patents will be submitted to protect these discoveries.

Updated May 26, 2023:

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This project will have a profound impact on soybean productivity. It will help identify the genes that contribute to soybean development. 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 2022 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 later 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.