Transposon elements drive subgenomic divergence of homoeologous genes to shape wheat domestication and improvement

Jizeng Jia; Pingchuan Deng; Tianbao Li; Kai Wang; Lifeng Gao; Guangyao Zhao; Dangqun Cui; Zhongdong Dong; Chengdao Li; Kehui Zhan; Wanquan Ji; Zhengang Ru; Daowen Wang; Liang Wu

doi:10.1016/j.xplc.2025.101341

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Transposon elements drive subgenomic divergence of homoeologous genes to shape wheat domestication and improvement

Journal article

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Transposon elements drive subgenomic divergence of homoeologous genes to shape wheat domestication and improvement

Jizeng Jia, Pingchuan Deng, Tianbao Li, Kai Wang, Lifeng Gao, Guangyao Zhao, Dangqun Cui, Zhongdong Dong, Chengdao Li, Kehui Zhan, …

Plant communications, Vol.6(9), 101341

2025

DOI: https://doi.org/10.1016/j.xplc.2025.101341

PMID: 40247620

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Abstract

Polyploidy

Wheat

Transposable elements

Subgenome gene divergence

Polyploidization is a fundamental evolutionary process in plants, including bread wheat. Here, we performed a comprehensive genome-wide analysis of dynamic homoeologous gene divergence in Aikang58 (AK58), a modern elite polyploidy wheat cultivar with a recently released reference genome, and in several other wheat genomes, including landraces, synthetic wheat, and wheat breeding materials. Over 40% of transposable element (TE) families have a biased distribution across the three subgenomes in wheat. Approximately 95.0% (113,421) of genes were co-located with TEs, and these variable TEs contributed greatly to homoeologous divergence. We revealed that around 80% of the triad homoeologs were divergent due to expression or sub-functionalization. The subgenome divergences contribute to polyploid wheat domestication and improvement through increased favorable homoeoallele combinations. Our findings suggest that homoeolog divergence contributes to the adaptation, domestication, and improvement of hexaploidy wheat. These subgenomic divergence that contributes to polyploidy heterosis was discussed. Together, this study provides a wealth of resources for elucidating the role of TEs in increasing homoeologous divergence during wheat domestication and improvement.

Details

Title: Transposon elements drive subgenomic divergence of homoeologous genes to shape wheat domestication and improvement
Authors/Creators: Jizeng Jia - Henan Agricultural University
Pingchuan Deng - Northwest A&F University
Tianbao Li - Henan Agricultural University
Kai Wang - Novogene Bioinformatics Institute
Lifeng Gao - Institute of Crop Sciences
Guangyao Zhao - Institute of Crop Sciences
Dangqun Cui - Henan Agricultural University
Zhongdong Dong - Henan Agricultural University
Chengdao Li - Murdoch University
Kehui Zhan - Henan Agricultural University
Wanquan Ji - Northwest A&F University
Zhengang Ru - Henan Institute of Science and Technology
Daowen Wang - Henan Agricultural University
Liang Wu - Zhejiang University
Publication Details: Plant communications, Vol.6(9), 101341
Publisher: Elsevier Inc. on behalf of CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, and Chinese Society for Plant Biology.; CAMBRIDGE
Number of pages: 20
Identifiers: 991005764902107891
Copyright: © 2025 The Author(s)
Murdoch Affiliation: Centre for Crop and Food Innovation
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.1122 Transposable Elements
Web Of Science research areas: Biochemistry & Molecular Biology; Plant Sciences
ESI research areas: Plant & Animal Science