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.
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
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.
Song, Y. H., Shim, J. S., Kinmonth-Schultz, H. A. & Imaizumi, T. Photoperiodic flowering: time measurement mechanisms in leaves. Annu. Rev. Plant Biol. 66, 441–464 (2015).
Mouradov, A., Cremer, F. & Coupland, G. Control of flowering time: interacting pathways as a basis for diversity. Plant Cell 14, S111–S130 (2002).
Song, Y. H., Ito, S. & Imaizumi, T. Flowering time regulation: photoperiod- and temperature-sensing in leaves. Trends Plant Sci. 18, 575–583 (2013).
Golembeski, G. S. & Imaizumi, T. Photoperiodic regulation of florigen function in Arabidopsis thaliana. Arabidopsis Book 13, e0178 (2015).
Blümel, M., Dally, N. & Jung, C. Flowering time regulation in crops—what did we learn from Arabidopsis? Curr. Opin. Biotechnol. 32, 121–129 (2015).
Kubota, A. et al. Co-option of a photoperiodic growth-phase transition system during land plant evolution. Nat. Commun. 5, 3668 (2014).
Mockler, T. et al. Regulation of photoperiodic flowering by Arabidopsis photoreceptors. Proc. Natl Acad. Sci. USA 100, 2140–2145 (2003).
Ratcliffe D. The Geographical and Ecological Distribution of Arabidopsis and Comments on Physiological Variation (Arabidopsis Information Service, 1965); https://www.arabidopsis.org/ais/1965/ratcl-1965-aagli.html
Effmertova E. The Behaviour of “Summer Annual”, “Mixed”, and “Winter Annual” Natural Populations as Compared with Early and Late Races in Field Conditions (Arabidopsis Information Service, 1967); https://www.arabidopsis.org/ais/1967/effme-1967-aagph.html
Thompson, L. The spatiotemporal effects of nitrogen and litter on the population dynamics of Arabidopsis thaliana. J. Ecol. 82, 63–68 (1994).
Donohue, K. Germination timing influences natural selection on life-history characters in Arabidopsis thaliana. Ecology 83, 1006–1016 (2002).
Griffith, C., Kim, E. & Donohue, K. Life-history variation and adaptation in the historically mobile plant Arabidopsis thaliana (Brassicaceae) in North America. Am. J. Bot. 91, 837–849 (2004).
Wilczek, A. M. et al. Effects of genetic perturbation on seasonal life history plasticity. Science 323, 930–934 (2009).
Picó, F. X. Demographic fate of Arabidopsis thaliana cohorts of autumn- and spring-germinated plants along an altitudinal gradient. J. Ecol. 100, 1009–1018 (2012).
Chiang, G. C. K. et al. Pleiotropy in the wild: the dormancy gene DOG1 exerts cascading control on life cycles. Evolution 67, 883–893 (2013).
Bieniawska, Z. et al. Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol. 147, 263–279 (2008).
Imaizumi, T., Tran, H. G., Swartz, T. E., Briggs, W. R. & Kay, S. A. FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 426, 302–306 (2003).
Imaizumi, T., Schultz, T. F., Harmon, F. G., Ho, L. A. & Kay, S. A. FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science 309, 293–297 (2005).
Kinmonth-Schultz, H. A. et al. Cool night-time temperatures induce the expression of CONSTANS and FLOWERING LOCUS T to regulate flowering in Arabidopsis. New Phytol. 211, 208–224 (2016).
Yamaguchi, A., Kobayashi, Y., Goto, K., Abe, M. & Araki, T. TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT. Plant Cell Physiol. 46, 1175–1189 (2005).
Krzymuski, M. et al. The dynamics of FLOWERING LOCUS T expression encodes long-day information. Plant J. 83, 952–961 (2015).
Mizoguchi, T. et al. Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis. Plant Cell 17, 2255–2270 (2005).
Amasino, R. Seasonal and developmental timing of flowering. Plant J. 61, 1001–1013 (2010).
Holmes, M. G. & Smith, H. The function of phytochrome in plants growing in the natural environment. Nature 254, 512–514 (1975).
Wollenberg, A. C., Strasser, B., Cerdan, P. D. & Amasino, R. M. Acceleration of flowering during shade avoidance in Arabidopsis alters the balance between FLOWERING LOCUS C-mediated repression and photoperiodic induction of flowering. Plant Physiol. 148, 1681–1694 (2008).
Kim, S. Y., Yu, X. & Michaels, S. D. Regulation of CONSTANS and FLOWERING LOCUS T expression in response to changing light quality. Plant Physiol. 148, 269–279 (2008).
Bouché, F., Lobet, G., Tocquin, P. & Périlleux, C. FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. Nucleic Acids Res. 44, D1167–D1171 (2016).
Koornneef, M., Alonso-Blanco, C. & Vreugdenhil, D. Naturally occurring genetic variation in Arabidopsis thaliana. Annu. Rev. Plant Biol. 55, 141–172 (2004).
Lee, J. H. et al. Regulation of temperature-responsive flowering by MADS-box transcription factor repressors. Science 342, 628–632 (2013).
Pruneda-Paz, J. L. & Kay, S. A. An expanding universe of circadian networks in higher plants. Trends Plant Sci. 15, 259–265 (2010).
Reed, J. W., Nagatani, A., Elich, T. D., Fagan, M. & Chory, J. Phytochrome A and phytochrome B have overlapping but distinct functions in Arabidopsis development. Plant Physiol. 104, 1139–1149 (1994).
Johnson, E., Bradley, M., Harberd, N. P. & Whitelam, G. C. Photoresponses of light-grown phyA mutants of Arabidopsis (phytochrome A is required for the perception of daylength extensions). Plant Physiol. 105, 141–149 (1994).
Genoud, T. et al. FHY1 mediates nuclear import of the light-activated phytochrome A photoreceptor. PLoS Genet. 4, e1000143 (2008).
Mockler, T. C., Guo, H., Yang, H., Duong, H. & Lin, C. Antagonistic actions of Arabidopsis cryptochromes and phytochrome B in the regulation of floral induction. Development 126, 2073–2082 (1999).
Valverde, F. et al. Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 303, 1003–1006 (2004).
Reed, J. W. et al. Independent action of ELF3 and phyB to control hypocotyl elongation and flowering time. Plant Physiol. 122, 1149–1160 (2000).
Leivar, P. & Quail, P. H. PIFs: pivotal components in a cellular signaling hub. Trends Plant Sci. 16, 19–28 (2011).
Nusinow, D. A. et al. The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475, 398–402 (2011).
Jang, S. et al. Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response. EMBO J. 27, 1277–1288 (2008).
Laubinger, S. et al. Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability. Development 133, 3213–3222 (2006).
Nakamichi, N. et al. Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway. Plant Cell Physiol. 48, 822–832 (2007).
Park, M. J., Kwon, Y. J., Gil, K. E. & Park, C. M. LATE ELONGATED HYPOCOTYL regulates photoperiodic flowering via the circadian clock in Arabidopsis. BMC Plant Biol. 16, 114 (2016).
Lazaro, A., Valverde, F., Pineiro, M. & Jarillo, J. A. The Arabidopsis E3 ubiquitin ligase HOS1 negatively regulates CONSTANS abundance in the photoperiodic control of flowering. Plant Cell 24, 982–999 (2012).
Huang, H. et al. Identification of evening complex associated proteins in Arabidopsis by affinity purification and mass spectrometry. Mol. Cell. Proteomics 15, 201–217 (2016).
Schwartz, C. J., Lee, J. & Amasino, R. Variation in shade-induced flowering in Arabidopsis thaliana results from FLOWERING LOCUS T allelic variation. PLoS ONE 12, e0187768 (2017).
Song, Y. H. et al. FKF1 conveys timing information for CONSTANS stabilization in photoperiodic flowering. Science 336, 1045–1049 (2012).
Yu, J. W. et al. COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Mol. Cell 32, 617–630 (2008).
Sheerin, D. J. et al. Light-activated phytochrome A and B interact with members of the SPA family to promote photomorphogenesis in Arabidopsis by reorganizing the COP1/SPA complex. Plant Cell 27, 189–201 (2015).
Kim, W. Y., Hicks, K. A. & Somers, D. E. Independent roles for EARLY FLOWERING 3 and ZEITLUPE in the control of circadian timing, hypocotyl length, and flowering time. Plant Physiol. 139, 1557–1569 (2005).
Lin, M. K. et al. FLOWERING LOCUS T protein may act as the long-distance florigenic signal in the cucurbits. Plant Cell 19, 1488–1506 (2007).
Yoo, S. C. et al. Phloem long-distance delivery of FLOWERING LOCUS T (FT) to the apex. Plant J. 75, 456–468 (2013).
Mitchell, D. E., Gadus, M. V. & Madore, M. A. Patterns of assimilate production and translocation in muskmelon (Cucumis melo L.): I. Diurnal patterns. Plant Physiol. 99, 959–965 (1992).
Savage, J. A., Zwieniecki, M. A. & Holbrook, N. M. Phloem transport velocity varies over time and among vascular bundles during early cucumber seedling development. Plant Physiol. 163, 1409–1418 (2013).
Yasunaga, E., Yano, T., Araki, T., Setoyama, S. & Kitano, M. Effect of environmental condition on xylem and phloem transport of developing fruit. IFAC Proc. 46, 297–301 (2013).
Shim, J. S., Kubota, A. & Imaizumi, T. Circadian clock and photoperiodic flowering in Arabidopsis: CONSTANS is a hub for signal integration. Plant Physiol. 173, 5–15 (2017).
Pittendrigh, C. S. & Minis, D. H. The entrainment of circadian oscillations by light and their role as photoperiodic clocks. Am. Nat. 98, 261–294 (1964).
Gattermann, R. et al. Golden hamsters are nocturnal in captivity but diurnal in nature. Biol. Lett. 4, 253–255 (2008).
Daan, S. et al. Lab mice in the field: unorthodox daily activity and effects of a dysfunctional circadian clock allele. J. Biol. Rhythms 26, 118–129 (2011).
Vanin, S. et al. Unexpected features of Drosophila circadian behavioural rhythms under natural conditions. Nature 484, 371–375 (2012).
Montelli, S. et al. period and timeless mRNA splicing profiles under natural conditions in Drosophila melanogaster. J. Biol. Rhythms 30, 217–227 (2015).
Shimizu, K. K., Kudoh, H. & Kobayashi, M. J. Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology. Ann. Bot. 108, 777–787 (2011).
Kudoh, H. Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments. New Phytol. 210, 399–412 (2016).
Kotake, T., Takada, S., Nakahigashi, K., Ohto, M. & Goto, K. Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. Plant Cell Physiol. 44, 555–564 (2003).
Takada, S. & Goto, K. TERMINAL FLOWER2, an Arabidopsis homolog of HETEROCHROMATIN PROTEIN1, counteracts the activation of FLOWERING LOCUS T by constans in the vascular tissues of leaves to regulate flowering time. Plant Cell 15, 2856–2865 (2003).
Reed, J. W., Nagpal, P., Poole, D. S., Furuya, M. & Chory, J. Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. Plant Cell 5, 147–157 (1993).
Liu, X. L., Covington, M. F., Fankhauser, C., Chory, J. & Wagner, D. R. ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell 13, 1293–1304 (2001).
McNellis, T. W. et al. Genetic and molecular analysis of an allelic series ofcop1 mutants suggests functional roles for the multiple protein domains. Plant Cell 6, 487–500 (1994).
Laubinger, S., Fittinghoff, K. & Hoecker, U. The SPA quartet: a family of WD-repeat proteins with a central role in suppression of photomorphogenesis in Arabidopsis. Plant Cell 16, 2293–2306 (2004).
Leivar, P. et al. Multiple phytochrome-interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness. Curr. Biol. 18, 1815–1823 (2008).
Yanovsky, M. J., Mazzella, M. A., Whitelam, G. C. & Casal, J. J. Resetting of the circadian clock by phytochromes and cryptochromes in Arabidopsis. J. Biol. Rhythms 16, 523–530 (2001).
Yakir, E. et al. Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis. Plant Physiol. 150, 844–857 (2009).
Nakamichi, N., Kita, M., Ito, S., Yamashino, T. & Mizuno, T. PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana. Plant Cell Physiol. 46, 686–698 (2005).
Kubota, A. et al. TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis. PLoS Genet. 13, e1006856 (2017).
Baudry, A. et al. F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression. Plant Cell 22, 606–622 (2010).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57, 289–300 (1995).
Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
Shinomura, T. et al. Action spectra for phytochrome A- and B-specific photoinduction of seed germination in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 93, 8129–8133 (1996).
Jefferson, R. A., Kavanagh, T. A. & Bevan, M. W. GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 6, 3901–3907 (1987).
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.
The authors declare no competing interests.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figs 1–25 and Supplementary Table 2.
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)
Actual p-values obtained by statistical analysis in flowering time experiments
About this article
Cite this article
Song, Y.H., Kubota, A., Kwon, M.S. et al. Molecular basis of flowering under natural long-day conditions in Arabidopsis. Nature Plants 4, 824–835 (2018). https://doi.org/10.1038/s41477-018-0253-3
New Phytologist (2020)
Tree Physiology (2020)
Genetic diversity in developmental responses to light spectral quality in barley (Hordeum vulgare L.)
BMC Plant Biology (2020)
The Plant Journal (2020)
Journal of Experimental Botany (2020)