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

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 Sese, Natsumaro Kutsuna, Rie Shimizu-Inatsugi () and Kentaro K. Shimizu ()
Additional contact information
Reiko Akiyama: University of Zurich
Takao Goto: Research and Development Division, LPIXEL Inc., Chiyoda-ku
Toshiaki Tameshige: Yokohama City University
Jiro Sugisaka: Yokohama City 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
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
Natsumaro Kutsuna: Research and Development Division, LPIXEL Inc., Chiyoda-ku
Rie Shimizu-Inatsugi: University of Zurich
Kentaro K. Shimizu: University of Zurich

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: 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”.

Date: 2023
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DOI: 10.1038/s41467-023-41260-3

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