In a landmark study published in Molecular Plant, researchers from the Chinese Academy of Sciences’ Institute of Genetics and Developmental Biology, in close collaboration with BGI-Research, Yazhouwan National Laboratory, and the CAS Institute of Genomics, have unveiled the first comprehensive spatiotemporal gene atlas for a Chinese soybean variety Zhonghuang 13. By integrating over 300 bulk RNA-seq samples with high-resolution single-nucleus RNA sequencing (snRNA-seq) and state-of-the-art spatial transcriptomics (Stereo-seq), the team has mapped the dynamic gene expression landscape across the entire developmental cycle of soybean organs. 

This innovative multi-layered approach not only deciphers the genetic mystery underlying soybean organogenesis but also lays the groundwork for precision molecular breeding, offering unprecedented insight into the regulatory networks that shape plant growth.

The study “A large-scale integrated transcriptomic atlas for soybean organ development” was published in Molecular Plant.

The achievement was realized through a meticulous integration of three complementary genomic technologies. BGI’s advanced sequencing platforms and computational pipelines played a crucial role in handling and integrating these vast datasets, ensuring that the resulting atlas is both high-resolution and highly reliable.

Bulk RNA sequencing provided an overview of gene expression across 314 organ samples, capturing the average transcriptomic signatures at different developmental stages. In addition, single-nucleus RNA sequencing offered a window into the cellular heterogeneity within key tissues—such as roots, nodules, shoot apices, leaves, and stems—by isolating and profiling individual cell nuclei. 

                                                                          Spatial Transcriptomic Atlas of Soybean Organ Development.

The Stereo-seq technology added a spatial dimension by precisely mapping the expression patterns back onto the tissue architecture, generating detailed three-dimensional (3D) atlases of gene activity. This tiered approach not only enhances the current understanding of tissue-specific and cell type–specific gene expression but also allows researchers to visualize the intricate spatial dynamics that drive organ development. 

The impact of this breakthrough is multifaceted. The integration of bulk, single-cell, and spatial transcriptomics in a single study has set a new standard in plant functional genomics by enabling the detection of subtle regulatory events that were previously obscured in average tissue-level analyses. This comprehensive mapping provides valuable insights into key developmental processes, such as the regulation of cell differentiation in the root apex and the orchestration of gene expression during nodule formation - a process vital for nitrogen fixation. 

By identifying specific gene modules and alternative splicing events that define distinct developmental stages and organ identities, the atlas not only uncovers potential genetic targets for crop improvement but also deepens our understanding of the fundamental biology of soybean.

With global soybean demand poised to double by 2050, insights gleaned from this research are expected to drive the next generation of molecular breeding strategies. By pinpointing critical regulators - such as gene families involved in root nodule development and those that modulate leaf expansion and wax biosynthesis - the study provides a powerful genetic toolkit to enhance yield, stress resilience, and nitrogen-fixing efficiency. These advancements are particularly significant in the context of sustainable agriculture and food security, where precision breeding can lead to more resilient and productive crop varieties.

The research data is publicly accessible through the SoyOmics Transcriptome Atlas and the Soybean Organ Transcriptomic Atlas (SOTA) databases.

Moreover, the establishment of publicly accessible databases - the SoyOmics Transcriptome Atlas and Soybean Organ Transcriptomic Atlas (SOTA) - empowers researchers and breeders to explore gene expression profiles in detail and visualize the 3D spatial localization of genes, thereby accelerating scientific discovery and practical applications. These initiatives, backed by the technological expertise and innovation at BGI-Research, emphasis the transformative potential of integrated genomic approaches in advancing precision molecular breeding and sustainable crop improvement.

This study can be accessed here: https://www.sciencedirect.com/science/article/pii/S1674205225000693