DeepWheat: predicting the effects of genomic variants on gene expression and regulatory activities across tissues and varieties in wheat using deep learning
Spatiotemporal gene expression shapes key agronomic traits, yet tissue-specific prediction remains challenging in complex crops. We present DeepWheat, a broadly applicable deep learning framework comprising DeepEXP and DeepEPI, for accurate, tissue-specific gene expression prediction. DeepEXP integrates sequence and epigenomic features to predict gene expression (PCC 0.82-0.88), while DeepEPI predicts epigenomic maps from DNA sequence to support model transfer across varieties. Validations in five wheat cultivars confirm robustness and accuracy. DeepWheat also identifies regulatory variants with strong expression effects, enabling targeted cis-regulatory elements editing and offering a powerful tool for crop functional genomics and breeding.
Authors
- Zefu Lu (ORCID: https://orcid.org/0000-0001-9322-8351)
- Jiazi Zhang (ORCID: https://orcid.org/0000-0003-0440-8102)
- Hongcui Pei (ORCID: https://orcid.org/0000-0001-9096-6826)
- Yanhong Liu (ORCID: https://orcid.org/0000-0002-0759-7597)
- Hongning Tong (ORCID: https://orcid.org/0000-0002-8749-5346)
- Lei Wang (ORCID: https://orcid.org/0000-0002-0356-3592)
- Zhigang Ma
Institutions
- Chinese Academy of Sciences (CN)
- Center for Agricultural Resources Research (CN)
- Institute of Genetics and Developmental Biology (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Institute of Crop Sciences (CN)
Publication Details
- Journal
- Genome biology
- Published
- 2025-09-29
- DOI
- https://doi.org/10.1186/s13059-025-03809-x
- Citations
- 3
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 5.45
Funders
- National Natural Science Foundation of China
- Chinese Academy of Sciences
- Chinese Academy of Agricultural Sciences
- China Agricultural Research System
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
- Agricultural Science and Technology Innovation Program
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
- Institute of Genetics