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Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

Author

Listed:
  • Yong Zhou

    (King Abdullah University of Science and Technology (KAUST)
    University of Arizona)

  • Zhichao Yu

    (Huazhong Agricultural University)

  • Dmytro Chebotarov

    (International Rice Research Institute (IRRI), Los Baños)

  • Kapeel Chougule

    (Cold Spring Harbor Laboratory)

  • Zhenyuan Lu

    (Cold Spring Harbor Laboratory)

  • Luis F. Rivera

    (King Abdullah University of Science and Technology (KAUST))

  • Nagarajan Kathiresan

    (King Abdullah University of Science and Technology (KAUST))

  • Noor Al-Bader

    (King Abdullah University of Science and Technology (KAUST))

  • Nahed Mohammed

    (King Abdullah University of Science and Technology (KAUST))

  • Aseel Alsantely

    (King Abdullah University of Science and Technology (KAUST))

  • Saule Mussurova

    (King Abdullah University of Science and Technology (KAUST))

  • João Santos

    (King Abdullah University of Science and Technology (KAUST))

  • Manjula Thimma

    (King Abdullah University of Science and Technology (KAUST))

  • Maxim Troukhan

    (Persephone Software, LLC)

  • Alice Fornasiero

    (King Abdullah University of Science and Technology (KAUST))

  • Carl D. Green

    (King Abdullah University of Science and Technology (KAUST))

  • Dario Copetti

    (University of Arizona)

  • David Kudrna

    (University of Arizona)

  • Victor Llaca

    (Research and Development, Corteva Agriscience)

  • Mathias Lorieux

    (DIADE, University of Montpellier, CIRAD, IRD)

  • Andrea Zuccolo

    (King Abdullah University of Science and Technology (KAUST)
    Crop Science Research Center (CSRC), Scuola Superiore Sant’Anna)

  • Doreen Ware

    (Cold Spring Harbor Laboratory
    USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit)

  • Kenneth McNally

    (International Rice Research Institute (IRRI), Los Baños)

  • Jianwei Zhang

    (University of Arizona
    Huazhong Agricultural University)

  • Rod A. Wing

    (King Abdullah University of Science and Technology (KAUST)
    University of Arizona
    International Rice Research Institute (IRRI), Los Baños)

Abstract

Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.

Suggested Citation

  • Yong Zhou & Zhichao Yu & Dmytro Chebotarov & Kapeel Chougule & Zhenyuan Lu & Luis F. Rivera & Nagarajan Kathiresan & Noor Al-Bader & Nahed Mohammed & Aseel Alsantely & Saule Mussurova & João Santos & , 2023. "Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37004-y
    DOI: 10.1038/s41467-023-37004-y
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    References listed on IDEAS

    as
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    Cited by:

    1. Xuezhu Liao & Dejin Xie & Tingting Bao & Mengmeng Hou & Cheng Li & Bao Nie & Shichao Sun & Dan Peng & Haixiao Hu & Hongru Wang & Yongfu Tao & Yu Zhang & Wei Li & Li Wang, 2024. "Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Zeyu Zheng & Mingjia Zhu & Jin Zhang & Xinfeng Liu & Liqiang Hou & Wenyu Liu & Shuai Yuan & Changhong Luo & Xinhao Yao & Jianquan Liu & Yongzhi Yang, 2024. "A sequence-aware merger of genomic structural variations at population scale," Nature Communications, Nature, vol. 15(1), pages 1-9, December.

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