Integration of multi-omics data accelerates molecular analysis of common wheat traits

Ning Zhang (), Li Tang, Songgang Li, Lu Liu, Mengjuan Gao, Sisheng Wang, Daiying Chen, Yichao Zhao, Ruiqing Zheng, Armin Soleymaniniya, Lingran Zhang, Wenkang Wang, Xia Yang, Yan Ren, Congwei Sun, Mathias Wilhelm, Daowen Wang (), Min Li () and Feng Chen ()
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Ning Zhang: Henan Agricultural University
Li Tang: Central South University
Songgang Li: Henan Agricultural University
Lu Liu: Henan Agricultural University
Mengjuan Gao: Henan Agricultural University
Sisheng Wang: Henan Agricultural University
Daiying Chen: Henan Agricultural University
Yichao Zhao: Central South University
Ruiqing Zheng: Central South University
Armin Soleymaniniya: Technical University of Munich (TUM)
Lingran Zhang: Henan Agricultural University
Wenkang Wang: Central South University
Xia Yang: Henan Agricultural University
Yan Ren: Henan Agricultural University
Congwei Sun: Henan Agricultural University
Mathias Wilhelm: Technical University of Munich (TUM)
Daowen Wang: Henan Agricultural University
Min Li: Central South University
Feng Chen: Henan Agricultural University

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Integration of multi-omics data can provide information on biomolecules from different layers to illustrate the complex biology systematically. Here, we build a multi-omics atlas containing 132,570 transcripts, 44,473 proteins, 19,970 phosphoproteins, and 12,427 acetylproteins across wheat vegetative and reproductive phases. Using this atlas, we elucidate transcriptional regulation network, contributions of post-translational modification (PTM) and transcript level to protein abundance, and biased homoeolog expression and PTM in wheat. The genes/proteins related to wheat development and disease resistance are systematically analyzed, thus identifying phosphorylation and/or acetylation modifications for the seed proteins controlling wheat grain quality and the disease resistance-related genes. Lastly, a unique protein module TaHDA9-TaP5CS1, specifying de-acetylation of TaP5CS1 by TaHDA9, is discovered, which regulates wheat resistance to Fusarium crown rot via increasing proline content. Our atlas holds great promise for fast-tracking molecular biology and breeding studies in wheat and related crops.

Date: 2025
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DOI: 10.1038/s41467-025-57550-x

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