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Retrotranspositional landscape of Asian rice revealed by 3000 genomes

Author

Listed:
  • Marie-Christine Carpentier

    (Université de Perpignan Via Domitia)

  • Ernandes Manfroi

    (Universidade Federal do Rio Grande do Sul)

  • Fu-Jin Wei

    (Academia Sinica
    Forestry and Forest Products Research Institute)

  • Hshin-Ping Wu

    (Academia Sinica)

  • Eric Lasserre

    (Université de Perpignan Via Domitia)

  • Christel Llauro

    (Université de Perpignan Via Domitia)

  • Emilie Debladis

    (Université de Perpignan Via Domitia)

  • Roland Akakpo

    (Université de Perpignan Via Domitia)

  • Yue-Ie Hsing

    (Academia Sinica)

  • Olivier Panaud

    (Université de Perpignan Via Domitia
    Institut Universitaire de France)

Abstract

The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.

Suggested Citation

  • Marie-Christine Carpentier & Ernandes Manfroi & Fu-Jin Wei & Hshin-Ping Wu & Eric Lasserre & Christel Llauro & Emilie Debladis & Roland Akakpo & Yue-Ie Hsing & Olivier Panaud, 2019. "Retrotranspositional landscape of Asian rice revealed by 3000 genomes," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-018-07974-5
    DOI: 10.1038/s41467-018-07974-5
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    Cited by:

    1. Victoria L. Sork & Shawn J. Cokus & Sorel T. Fitz-Gibbon & Aleksey V. Zimin & Daniela Puiu & Jesse A. Garcia & Paul F. Gugger & Claudia L. Henriquez & Ying Zhen & Kirk E. Lohmueller & Matteo Pellegrin, 2022. "High-quality genome and methylomes illustrate features underlying evolutionary success of oaks," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Huanran Yuan & Weilong Yang & Jianing Zou & Mingxing Cheng & Fengfeng Fan & Ting Liang & Yajie Yu & Ronghua Qiu & Shaoqing Li & Jun Hu, 2021. "InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice ( Oryza sativa L.)," Agriculture, MDPI, vol. 11(7), pages 1-15, July.
    3. Hsin-Ya Huang & Siqi Zhang & Fadi Abou Choucha & Marion Verdenaud & Feng-Quan Tan & Clement Pichot & Hadi Shirazi Parsa & Filip Slavkovic & Qinghe Chen & Christelle Troadec & Fabien Marcel & Catherine, 2024. "Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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