An extended mathematical model for reproducing the phase response of  Arabidopsis thaliana  under various light conditions

Ohara, Takayuki; Fukuda, Hirokazu; Tokuda, Isao T.

doi:10.1016/j.jtbi.2015.07.016

Cited by 16 publications

(22 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This feature of our model is coherent with the existing literature, as it includes a complex network structure and multiple light inputs, both of which have been shown to be important factors in the ability of a system to respond to light cues (Troein et al, 2011 ; Dixon et al, 2014 ; Ohara et al, 2015 ).…”

Section: Resultssupporting

confidence: 85%

A Compact Model for the Complex Plant Circadian Clock

et al. 2016

View full text Add to dashboard Cite

The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock gene mRNA/protein and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes). Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24 h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the core clock as well as clock-dependent processes.

show abstract

Section: Resultssupporting

confidence: 85%

A Compact Model for the Complex Plant Circadian Clock

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Moreover, the blue LED light pulses for excitation of chlorophyll would provide no effect on the circadian rhythms. In our previous work (Ohara et al, 2015a , b ), it was investigated how plant circadian clock responds to light pulse perturbations. The phase shift of circadian rhythm became maximally to 0.4 rad/2π (~9.6 h) by a blue LED light pulse (80 μmol m −2 s −1 for 2 h).…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Growth Prediction for Lactuca sativa L. Seedlings Using Chlorophyll Fluorescence in a Plant Factory with Artificial Lighting

Moriyuki

Fukuda

2016

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

Poorly grown plants that result from differences in individuals lead to large profit losses for plant factories that use large electric power sources for cultivation. Thus, identifying and culling the low-grade plants at an early stage, using so-called seedlings diagnosis technology, plays an important role in avoiding large losses in plant factories. In this study, we developed a high-throughput diagnosis system using the measurement of chlorophyll fluorescence (CF) in a commercial large-scale plant factory, which produces about 5000 lettuce plants every day. At an early stage (6 days after sowing), a CF image of 7200 seedlings was captured every 4 h on the final greening day by a high-sensitivity CCD camera and an automatic transferring machine, and biological indices were extracted. Using machine learning, plant growth can be predicted with a high degree of accuracy based on biological indices including leaf size, amount of CF, and circadian rhythms in CF. Growth prediction was improved by addition of temporal information on CF. The present data also provide new insights into the relationships between growth and temporal information regulated by the inherent biological clock.

show abstract

“…First, the activation of P97 by CL protein is modified to repression based on recent studies ( Fogelmark and Troein 2014 ; Adams et al 2015 ), which showed that CL protein represses the expression of all other clock genes including P97. Second, to investigate the effect of red and/or blue lights on the hypocotyl growth, the single light-sensitive protein is replaced by three photoreceptors; phyA, phyB and cry1 following the approach described in Ohara et al (2015a) (see the following section for more detailed description of the light module). Thus, the revised PCS model is represented by the following ODEs:…”

Section: Model Descriptionsmentioning

confidence: 99%

“…Despite the aforementioned progress in PCS modelling, almost all the PCS models available considered regulation involving only white light. To the best of our knowledge, the only study that incorporated light quality into PCS model was carried out in Ohara et al (2015a) , where the authors replaced the commonly used light-responsive protein P proposed in Locke et al (2005) with three photoreceptors, namely Phytochrome A (phyA), Phytochrome B (phyB) and Cryptochrome 1 (cry1), which are sensitive to red and blue light, respectively. As a mean of model validation, the authors showed that the model was able to reproduce experimental Phase Response Curve (PRC) under different light quality.…”

Section: Introductionmentioning

confidence: 99%

“…In this study, we developed a mathematical model for PCS demonstrating the effect of various light quality conditions on plant growth. Specifically, we incorporated the light quality function from Ohara et al (2015a) into the compact model proposed in De Caluwé et al (2016) to develop a PCS model for characterizing hypocotyl growth under different light quality conditions. To account for plant growth through photomorphogenesis and skotomorphogenesis and their interactions with the photoreceptors ( Kim et al 2017 ; Lymperopoulos et al 2018 ), we included, for the first time, the interaction of a light signalling centre, COP1, with photoreceptors ( Lau and Deng 2012 ; Su et al 2017 ) into our model.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Modelling of plant circadian clock for characterizing hypocotyl growth under different light quality conditions

et al. 2022

View full text Add to dashboard Cite

To meet the ever-increasing global food demand, the food production rate needs to be increased significantly in the near future. Speed breeding is considered as a promising agricultural technology solution to achieve the zero-hunger vision as specified in the United Nations Sustainable Development Goal 2. In speed breeding, the photoperiod of the artificial light has been manipulated to enhance crop productivity. In particular, regulating the photoperiod of different light qualities rather than solely white light can further improve speed breading. However, identifying the optimal light quality and the associated photoperiod simultaneously remains a challenging open problem due to complex interactions between multiple photoreceptors and proteins controlling plant growth. To tackle this, we develop a first comprehensive model describing the profound effect of multiple light qualities with different photoperiods on plant growth (i.e., hypocotyl growth). The model predicts that hypocotyls elongated more under red light compared to both red and blue light. Drawing similar findings from previous related studies, we propose that this might result from the competitive binding of red and blue light receptors, primarily Phytochrome B (phyB) and Cryptochrome 1 (cry1) for the core photomorphogenic regulator, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). This prediction is validated through an experimental study on Arabidopsis thaliana. Our work proposes a potential molecular mechanism underlying plant growth under different light qualities and ultimately suggests an optimal breeding protocol that takes into account light quality.

show abstract

An extended mathematical model for reproducing the phase response of Arabidopsis thaliana under various light conditions

Cited by 16 publications

References 27 publications

A Compact Model for the Complex Plant Circadian Clock

A Compact Model for the Complex Plant Circadian Clock

High-Throughput Growth Prediction for Lactuca sativa L. Seedlings Using Chlorophyll Fluorescence in a Plant Factory with Artificial Lighting

Modelling of plant circadian clock for characterizing hypocotyl growth under different light quality conditions

Contact Info

Product

Resources

About