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Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation

Author

Listed:
  • Reiko Akiyama

    (University of Zurich)

  • Takao Goto

    (Research and Development Division, LPIXEL Inc., Chiyoda-ku)

  • Toshiaki Tameshige

    (Yokohama City University
    Nara Institute of Science and Technology (NAIST))

  • Jiro Sugisaka

    (Yokohama City University
    Kyoto University)

  • Ken Kuroki

    (The University of Tokyo)

  • Jianqiang Sun

    (Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization)

  • Junichi Akita

    (Kanazawa University, Kakuma)

  • Masaomi Hatakeyama

    (University of Zurich
    Functional Genomics Center Zurich)

  • Hiroshi Kudoh

    (Kyoto University)

  • Tanaka Kenta

    (University of Tsukuba)

  • Aya Tonouchi

    (Research and Development Division, LPIXEL Inc., Chiyoda-ku)

  • Yuki Shimahara

    (Research and Development Division, LPIXEL Inc., Chiyoda-ku)

  • Jun Sese

    (Artificial Intelligence Research Center
    Humanome Lab, Inc.
    AIST-Tokyo Tech RWBC-OIL)

  • Natsumaro Kutsuna

    (Research and Development Division, LPIXEL Inc., Chiyoda-ku)

  • Rie Shimizu-Inatsugi

    (University of Zurich)

  • Kentaro K. Shimizu

    (University of Zurich
    Yokohama City University)

Abstract

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software that extracts leaf color by detecting plant individuals automatically. As a case study, we applied PlantServation to examine environmental and genotypic effects on the pigment anthocyanin content estimated from leaf color. We processed >4 million images of small individuals of four Arabidopsis species in the field, where the plant shape, color, and background vary over months. Past radiation, coldness, and precipitation significantly affected the anthocyanin content. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation facilitates the study of plant responses to complex environments termed “in natura”.

Suggested Citation

  • Reiko Akiyama & Takao Goto & Toshiaki Tameshige & Jiro Sugisaka & Ken Kuroki & Jianqiang Sun & Junichi Akita & Masaomi Hatakeyama & Hiroshi Kudoh & Tanaka Kenta & Aya Tonouchi & Yuki Shimahara & Jun S, 2023. "Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41260-3
    DOI: 10.1038/s41467-023-41260-3
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    References listed on IDEAS

    as
    1. Timothy Paape & Roman V. Briskine & Gwyneth Halstead-Nussloch & Heidi E. L. Lischer & Rie Shimizu-Inatsugi & Masaomi Hatakeyama & Kenta Tanaka & Tomoaki Nishiyama & Renat Sabirov & Jun Sese & Kentaro , 2018. "Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    2. Nobutoshi Yamaguchi & Satoshi Matsubara & Kaori Yoshimizu & Motohide Seki & Kouta Hamada & Mari Kamitani & Yuko Kurita & Yasuyuki Nomura & Kota Nagashima & Soichi Inagaki & Takamasa Suzuki & Eng-Seng , 2021. "H3K27me3 demethylases alter HSP22 and HSP17.6C expression in response to recurring heat in Arabidopsis," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    3. Sean P. Gordon & Bruno Contreras-Moreira & Joshua J. Levy & Armin Djamei & Angelika Czedik-Eysenberg & Virginia S. Tartaglio & Adam Session & Joel Martin & Amy Cartwright & Andrew Katz & Vasanth R. Si, 2020. "Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
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