Plants sense light and temperature changes to regulate flowering time. Here, we show that expression of the Arabidopsis florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a different pattern than we observe in the laboratory. Providing our laboratory growth conditions with a red/far-red light ratio similar to open-field conditions and daily temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Under the adjusted growth conditions, key light signalling components, such as phytochrome A and EARLY FLOWERING 3, play important roles in morning FT expression. These conditions stabilize CONSTANS protein, a major FT activator, in the morning, which is probably a critical mechanism for photoperiodic flowering in nature. Refining the parameters of our standard growth conditions to more precisely mimic plant responses in nature can provide a powerful method for improving our understanding of seasonal response.

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Data availability

All data are available in the main text or the Supplementary Materials. The raw sequence data (GSE110605) were deposited in the NCBI Sequence Read Archive. The mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD010518 and 10.6019/PXD010518.

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We thank M. Endo, M. Zeidler, X. W. Deng, U. Hoecker, R. Green, S. Harmer, T. Yamashino and J. H. Ahn for providing the mutant seeds, J. Nemhauser for critical reading of the manuscript and J. Milne for technical support. This work was supported by a NIH grant (GM079712) to T.I., NSF grants (IOS-1656076 to T.I. and IOS-1456796 to D.A.N.), Next-Generation BioGreen 21 Program (SSAC, PJ013386, Rural Development Administration, Republic of Korea) to Y.H.S. and T.I., BBSRC award (BB/N012348/1) to A.J.M., JST CREST grant (JPMJCR16O3), MEXT Kakenhi (18H04785) and Swiss National Science Foundation to K.K.S., and NRF grant (NRF-2015R1D1A1A01058948) to Y.H.S. We acknowledge a NSF grant (DBI-0922879) for LTQ-Velos Pro Orbitrap liquid chromatography–tandem mass spectrometry acquisition. A.K. is supported by the JSPS Postdoctoral Fellowships for Research Abroad.

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Author notes

  1. These authors contributed equally: Young Hun Song, Akane Kubota.


  1. Department of Biology, University of Washington, Seattle, WA, USA

    • Young Hun Song
    • , Akane Kubota
    • , Michael S. Kwon
    • , Nayoung Lee
    • , Ella R. Taagen
    • , Dianne Laboy Cintrón
    • , Nhu H. Nguyen
    •  & Takato Imaizumi
  2. Department of Life Sciences, Ajou University, Suwon, Korea

    • Young Hun Song
    •  & Dae Yeon Hwang
  3. Amaryllis Nucleics, Oakland, CA, USA

    • Michael F. Covington
  4. Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland

    • Reiko Akiyama
    •  & Kentaro K. Shimizu
  5. School of Biological Sciences and SynthSys, University of Edinburgh, Edinburgh, UK

    • Sarah K. Hodge
    •  & Andrew J. Millar
  6. Donald Danforth Plant Science Center, St. Louis, MO, USA

    • He Huang
    •  & Dmitri A. Nusinow
  7. Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan

    • Kentaro K. Shimizu


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T.I. conceived the project. Y.H.S., A.K. and T.I. designed the experiments. Y.H.S., A.K., M.S.K., M.F.C., N.L., E.R.T., D.L.C., D.Y.H., R.A., S.K.H., H.H., N.H.N., D.A.N., A.J.M. and T.I. performed the experiments and analyses. Y.H.S., A.K. and T.I. wrote the manuscript with the help of R.A., D.A.N., A.J.M. and K.K.S.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Young Hun Song or Takato Imaizumi.

Supplementary information

  1. Supplementary Information

    Supplementary Figs 1–25 and Supplementary Table 2.

  2. Reporting Summary

  3. Supplementary Table 1

    A list of genes upregulated outside in late spring 2013 compared to lab LD conditions on ZT4 (logFC>1, FDR<0.05, adjusted p-values for multiple comparisons using Benjamini–Hochberg Procedure)

  4. Supplementary Table 3

    Actual p-values obtained by statistical analysis in flowering time experiments

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