Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development

Authors: ZHANG, HENGYOU - Danforth Plant Science Center; HU, ZHENBIN - Danforth Plant Science Center; YANG, YUMING - Henan Agricultural University; LIU, XIAOQIAN - Henan Agricultural University; LV, HAIYAN - Henan Agricultural University; SONG, BAO-HUA - University Of North Carolina; An, Yong-Qiang - Charles; LI, ZHIMIN - Henan Agricultural University; ZHANG, DAN - Henan Agricultural University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/8/2021
Publication Date: 6/16/2021
Citation: Zhang, H., Hu, Z., Yang, Y., Liu, X., Lv, H., Song, B., An, Y., Li, Z., Zhang, D. 2021. Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development. BMC Genomics. 22. Article e453. https://doi.org/10.1186/s12864-021-07783-z.
DOI: https://doi.org/10.1186/s12864-021-07783-z

Interpretive Summary: Soybean is one of the two most important seed crops in US. Seed development is one of the most important biological processes for soybean seed quality and yield, the two key determining factors for soybean economics. To understand the molecular basis underlying seed development and discover genes important for soybean seed quality and yield improvement, we applied next generation sequencing technology to determine expression levels of all 56,000 genes at four key seed developmental stages. We identified a set of genes highly abundant in seeds that contribute to seed storage protein content. In addition, we also identified 8,925 genes whose expression changed over the course of seed development and inferred a network revealing the relationship of those genes based on their expression pattern. Thus, the study provides a comprehensive depiction of the regulatory program underlying seed development at a gene, pathway and network level, and develop a set of new hypothesizes for future investigations. The new knowledge generated from the study also enhances our ability to develop effective strategies to improve soybean seed quality and yield, and eventually increase competitiveness of US soybean in world soybean market and US soybean farmers’ income.

Technical Abstract: Background Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement. Results In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40'days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules. Conclusions Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.