Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation (Part 2/2)
Creators
- 1. University of Zurich
- 2. LPIXEL Inc.*
- 3. Yokohama City University
- 4. Kyoto University
- 5. University of Tokyo
- 6. National Agriculture and Food Research Organization
- 7. Kanazawa University
- 8. University of Tsukuba
- 9. Humanome Lab Inc.*
Description
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 analyzed >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".
Notes
Labelling data (.json files) can be opened using labelme in python.
R scripts (.r files) can be opened in R or as a text file.
Python scripts (in script_7_for_Dataset_8_Fig_S29) can be opened in Python or as a text file.
Funding provided by: Japan Science and Technology Agency
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002241
Award Number: JPMJCR16O3
Funding provided by: Japan Science and Technology Agency
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002241
Award Number: JPMJCR15O1
Funding provided by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001711
Award Number: 31003A_182318
Funding provided by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001711
Award Number: CRSII5_183578
Funding provided by: Japan Society for the Promotion of Science
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001691
Award Number: 22H02316
Funding provided by: Japan Society for the Promotion of Science
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001691
Award Number: 17H06990
Funding provided by: Japan Society for the Promotion of Science
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001691
Award Number: 21H04977
Funding provided by: Universität Zürich
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100006447
Award Number: University Research Priority Program in Evolution in Action
Funding provided by: Japan Society for the Promotion of Science
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001691
Award Number: 22H05179
Funding provided by: Kyoto University
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100005683
Award Number: 2017jurc-cer05
Funding provided by: Universität Zürich
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100006447
Award Number: Global Affairs of the University of Zurich
Funding provided by: Japan Society for the Promotion of Science
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001691
Award Number: 22K21352
Funding provided by: Kyoto University
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100005683
Award Number: 2018jurc-cer09
Funding provided by: Kyoto University
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100005683
Award Number: 2019jurc-cer02
Funding provided by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001711
Award Number: 310030_212551
Funding provided by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001711
Award Number: 310030_212674
Files
PlantServation_demo_set.zip
Files
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Additional details
Related works
- Is cited by
- 10.1101/2022.11.21.517294 (DOI)
- Is source of
- 10.5061/dryad.h70rxwdnk (DOI)