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

  • Nat Commun. 2025 Mar 5;16(1):2200. doi: 10.1038/s41467-025-57550-x.
Ning Zhang  #  1 ,  Li Tang  #  2 ,  Songgang Li  3 ,  Lu Liu  3 ,  Mengjuan Gao  3 ,  Sisheng Wang  3 ,  Daiying Chen  3 ,  Yichao Zhao  2 ,  Ruiqing Zheng  2 ,  Armin Soleymaniniya  4 ,  Lingran Zhang  3 ,  Wenkang Wang  2 ,  Xia Yang  3 ,  Yan Ren  3 ,  Congwei Sun  3 ,  Mathias Wilhelm  4 ,  Daowen Wang  5 ,  Min Li  6 ,  Feng Chen  7
Affiliations
  • 1. State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping /Agronomy College, Henan Agricultural University, Zhengzhou, 450046, China. [email protected].
  • 2. School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
  • 3. State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping /Agronomy College, Henan Agricultural University, Zhengzhou, 450046, China.
  • 4. Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, 84104, Germany.
  • 5. State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping /Agronomy College, Henan Agricultural University, Zhengzhou, 450046, China. [email protected].
  • 6. School of Computer Science and Engineering, Central South University, Changsha, 410083, China. [email protected].
  • 7. State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping /Agronomy College, Henan Agricultural University, Zhengzhou, 450046, China. [email protected].
  • # Contributed equally.
PMID: 40038279 DOI: 10.1038/s41467-025-57550-x
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.

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