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 describes our plans regarding the continuation of an ongoing project. The main objective of this proposal is to develop and release an intuitive website to establish this fundamental knowledge by characterizing the soybean genes controlling seed development accessible by the scientific community, students, citizens, and farmers. 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”

This FY 2022-2023 proposal strictly focuses on developing transfer technology. The “Soybean Single??Cell Transcriptome Atlas” will be shared with the different communities:
1) through the publication of research manuscripts in international journals with open access format. These manuscripts will provide supplemental information to access the transcriptional datasets.
2) through the design and development of a dynamic website that fosters scientific advancement through sharing and exchange. This website will benefit from the expertise of co-PI Yao who has expertise in high throughput -omics including in using genomics and transcriptomics data, and in developing interactive designs to maximize the sharing of complex biological information. We intent to model our atlas after the two very popular atlases, the Arabidopsis eFP Browser (bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi) and the Human Single-Cell Atlas (www.humancellatlas.org), and the newly developed “The Plant scRNA-Seq Browser” (https://www.zmbp-resources.uni-tuebingen.de/timmermans/plant-single-cell-browser/).

This proposal directly addresses one of the overarching goals of the Nebraska Soybean Board for FY 2023 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.