DeepWheat: predicting the effects of genomic variants on gene expression and regulatory activities across tissues and varieties in wheat using deep learning

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-09-29 DOI:10.1186/s13059-025-03809-x

Zhigang Ma, Jiazi Zhang, Hongcui Pei, Yanhong Liu, Hongning Tong, Lei Wang, Zefu Lu

引用次数: 0

Abstract

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.

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DeepWheat：利用深度学习预测基因组变异对小麦组织和品种间基因表达和调控活动的影响

时空基因表达决定了关键的农艺性状，但在复杂作物中，组织特异性预测仍然具有挑战性。我们提出了DeepWheat，一个广泛适用的深度学习框架，包括DeepEXP和DeepEPI，用于准确的组织特异性基因表达预测。DeepEXP整合序列和表观基因组特征来预测基因表达（PCC 0.82-0.88），而DeepEPI预测DNA序列的表观基因组图谱，以支持品种间的模型转移。在5个小麦品种上的验证验证了该方法的稳健性和准确性。DeepWheat还可以识别出具有强表达效应的调控变异，从而实现靶向顺式调控元件的编辑，为作物功能基因组学和育种提供强大的工具。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.