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Analysis of allohexaploid wheatgrass genome reveals its Y haplome origin in Triticeae and high-altitude adaptation

Author

Listed:
  • Yi Xiong

    (Sichuan Agricultural University)

  • Shuai Yuan

    (Lanzhou University)

  • Yanli Xiong

    (Sichuan Agricultural University
    Sichuan Academy of Grassland Sciences)

  • Lizuiyue Li

    (Southwest Forestry University
    Southwest Forestry University)

  • Jinghan Peng

    (Sichuan Agricultural University)

  • Jin Zhang

    (Lanzhou University)

  • Xing Fan

    (Sichuan Agricultural University)

  • Chengzhi Jiang

    (University of Electronic Science and Technology of China)

  • Li-na Sha

    (Sichuan Agricultural University)

  • Zhaoting Wang

    (Sichuan Agricultural University)

  • Xue Peng

    (Sichuan Agricultural University)

  • Zecheng Zhang

    (Sichuan Agricultural University)

  • Qingqing Yu

    (Sichuan Academy of Grassland Sciences)

  • Xiong Lei

    (Sichuan Academy of Grassland Sciences)

  • Zhixiao Dong

    (Sichuan Agricultural University)

  • Yingjie Liu

    (Sichuan Agricultural University)

  • Junming Zhao

    (Sichuan Agricultural University)

  • Guangrong Li

    (University of Electronic Science and Technology of China)

  • Zujun Yang

    (University of Electronic Science and Technology of China)

  • Shangang Jia

    (China Agricultural University)

  • Daxu Li

    (Sichuan Academy of Grassland Sciences)

  • Ming Sun

    (Southwest University of Science and Technology)

  • Shiqie Bai

    (Southwest University of Science and Technology)

  • Jianquan Liu

    (Lanzhou University)

  • Yongzhi Yang

    (Lanzhou University)

  • Xiao Ma

    (Sichuan Agricultural University)

Abstract

Phylogenetic origin of the Y haplome present in allopolyploid Triticeae species remains unknown. Here, we report the 10.47 Gb chromosome-scale genome of allohexaploid Elymus nutans (StStYYHH). Phylogenomic analyses reveal that the Y haplome is sister to the clade comprising V and Jv haplomes from Dasypyrum and Thinopyum. In addition, H haplome from the Hordeum-like ancestor, St haplome from the Pseudoroegneria-like ancestor and Y haplome are placed in the successively diverged clades. Resequencing data reveal the allopolyploid origins with St, Y, and H haplome combinations in Elymus. Population genomic analyses indicate that E. nutans has expanded from medium to high/low-altitude regions. Phenotype/environmental association analyses identify MAPKKK18 promoter mutations reducing its expression, aiding UV-B adaptation in high-altitude populations. These findings enhance understanding of allopolyploid evolution and aid in breeding forage and cereal crops through intergeneric hybridization within Triticeae.

Suggested Citation

  • Yi Xiong & Shuai Yuan & Yanli Xiong & Lizuiyue Li & Jinghan Peng & Jin Zhang & Xing Fan & Chengzhi Jiang & Li-na Sha & Zhaoting Wang & Xue Peng & Zecheng Zhang & Qingqing Yu & Xiong Lei & Zhixiao Dong, 2025. "Analysis of allohexaploid wheatgrass genome reveals its Y haplome origin in Triticeae and high-altitude adaptation," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58341-0
    DOI: 10.1038/s41467-025-58341-0
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    as
    1. Nadia Kamal & Nikos Tsardakas Renhuldt & Johan Bentzer & Heidrun Gundlach & Georg Haberer & Angéla Juhász & Thomas Lux & Utpal Bose & Jason A. Tye-Din & Daniel Lang & Nico Gessel & Ralf Reski & Yong-B, 2022. "The mosaic oat genome gives insights into a uniquely healthy cereal crop," Nature, Nature, vol. 606(7912), pages 113-119, June.
    2. Xianhui Huang & Yuejin Wang & Sainan Zhang & Liuling Pei & Jiaqi You & Yuexuan Long & Jianying Li & Xianlong Zhang & Longfu Zhu & Maojun Wang, 2024. "Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    3. Yinguang Hou & Junwei Gan & Zeyu Fan & Lei Sun & Vanika Garg & Yu Wang & Shanying Li & Pengfei Bao & Bingchen Cao & Rajeev K. Varshney & Hansheng Zhao, 2024. "Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. repec:plo:pcbi00:1004574 is not listed on IDEAS
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