A large-scale integrated transcriptomic atlas for soybean organ development
Soybean is one of the most important crops globally, and its production must be significantly increased to meet increasing demand. Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change. An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ development-related genes and thereby help us to understand organ developmental processes. Here, we constructed a comprehensive, integrated transcriptomic atlas for soybeans, integrating bulk RNA sequencing (RNA-seq) datasets from 314 samples across the soybean life cycle, along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs: root, nodule, shoot apex, leaf, and stem. Investigating genes related to organ specificity, blade development, and nodule formation, we demonstrate that the atlas has robust power for exploring key genes involved in organ formation. In addition, we developed a user-friendly panoramic database for the transcriptomic atlas, enabling easy access and queries, which will serve as a valuable resource to significantly advance future soybean functional studies.
Authors
- Zhifeng Deng (ORCID: https://orcid.org/0000-0003-3529-0549)
- Bohan Zhang (ORCID: https://orcid.org/0000-0002-8007-0214)
- Dongmei Tian (ORCID: https://orcid.org/0000-0003-0564-625X)
- Xiaofeng Wei (ORCID: https://orcid.org/0000-0002-6741-5505)
- Chuan Chen (ORCID: https://orcid.org/0009-0000-4316-4388)
- Tao Yang (ORCID: https://orcid.org/0000-0002-6840-6993)
- Zhixi Tian (ORCID: https://orcid.org/0000-0001-6051-9670)
- Hai‐Xi Sun (ORCID: https://orcid.org/0000-0003-2719-6456)
- Xiaoyue Yang (ORCID: https://orcid.org/0000-0002-9331-0512)
- Shu‐Lin Liu (ORCID: https://orcid.org/0000-0002-1043-4238)
- J. H. Fan (ORCID: https://orcid.org/0000-0002-7185-7365)
- Xi Chen (ORCID: https://orcid.org/0000-0003-2648-3146)
- Xun Xu (ORCID: https://orcid.org/0000-0002-5338-5173)
- Yu Wang (ORCID: https://orcid.org/0000-0001-6100-1312)
- Haixia Liu (ORCID: https://orcid.org/0000-0002-7792-8638)
- Min Zhang (ORCID: https://orcid.org/0000-0002-2893-701X)
- Can Liu (ORCID: https://orcid.org/0009-0006-8694-9322)
- Yuqiang Jiang
- Yanting Shen (ORCID: https://orcid.org/0000-0001-8129-0844)
- Guoan Zhou (ORCID: https://orcid.org/0009-0004-5121-8509)
- Ruiying Chen (ORCID: https://orcid.org/0000-0003-2556-7604)
- Xin Liu (ORCID: https://orcid.org/0000-0003-3187-3392)
Institutions
- BGI Group (China) (CN)
- Chinese Academy of Sciences (CN)
- Beijing Institute of Genomics (CN)
- Beijing Graphene Institute (CN)
- State Key Laboratory of Plant Genomics (CN)
- Institute of Genetics and Developmental Biology (CN)
- China National GeneBank (CN)
- University of Chinese Academy of Sciences (CN)
Publication Details
- Journal
- Molecular Plant
- Published
- 2025-02-18
- DOI
- https://doi.org/10.1016/j.molp.2025.02.003
- Citations
- 24
- Primary Topic
- Soybean genetics and cultivation
- Type
- article
- Field-Weighted Citation Impact
- 42.00
Funders
- National Natural Science Foundation of China