Chld_Chlf_in_soybean

Simulate the light distribution and photosynthesis in a soybean canopy

Model description

Using a 3D canopy model of soybean, reconstructed from a field crop, the potential for Chl-d and Chl-f utilization was assessed by simulating their effects on photon absorption and CO2 assimilation.

Contact Author

Yu Wang - https://github.com/yuwangcn

Reference

Wang Y., Oliver T. J., Croce R., Long S. P., Addition of longer wavelength absorbing chlorophylls into crops could increase their photosynthetic productivity up to 26%. A theoretical evaluation. (2024)

Software

Simulations were conducted in MATLAB 2019 (Mathworks, https://uk.mathworks.com).

Step 1 Reconstruct a soybean canopy

Folder

SoyCanopy

Run

Open matlab

Change the work path to the SoyCanopy folder

Run SoybeanCanopy('M_mean.txt', 'M_Vx.txt', 231, 1, true) in the command window

Output

CM_V231_rep1_M_mean.txt

References

Song, Q. F., Srinivasan, V., Long, S. P. & Zhu, X. G. Decomposition analysis on soybean productivity increase under elevated CO2 using 3-D canopy model reveals synergestic effects of CO2 and light in photosynthesis. Annals of Botany 126, 601-614 (2020). Wang, Y., Burgess, S. J., de Becker, E. M. & Long, S. H. P. Photosynthesis in the fleeting shadows: an overlooked opportunity for increasing crop productivity? Plant Journal 101, 874-884 (2020).

Step 2 Simulate the light distribution in the soybean canopy

Photon fluxes in different wavelengths at each leaf piece was predicted using a forward ray-tracing algorithm (FastTracer, https://github.com/PlantSystemsBiology/fastTracerPublic)

Folder

FastTracer

Run

Open Windows PowerShell

Change the work path to the FastTracer folder

Commands can be find in 'Sim.txt'

Input soybean canopy:

V231_rep1.txt

(The file was converted from the file 'CM_V231_rep1_M_mean.txt' to meet the requirement of the FastTracer, column 1-9 in 'CM_V231_rep1_M_mean.txt' to column 6-14 in 'V231_rep1.txt', column 10 in 'CM_V231_rep1_M_mean.txt' to column 1 in 'V231_rep1.txt')

Output

light profile with different leaf transmittance and reflectance settings (Check the 'Sim.txt' for simulation details)

PPFD_V231_*.txt

Reference

Song Q, Zhang G, Zhu X-G. 2013. Optimal crop canopy architecture to maximise canopy photosynthetic CO2 uptake under elevated CO2- a theoretical study using a mechanistic model of canopy photosynthesis. Functional Plant Biology 40, 109–124.

Step 3 Canopy photosynthesis estimation

Folder

CanopyPhotosynhesis

3.1

The leaf photosynthesis and transpiration were estimated by a leaf energy balance module (Drewry, et al., 2010)

Run

Use' CalPhotosynthesis_*.m' to run the simulations for each leaf transmittance and reflectance setting

Input:

'PPFD_V231_*.txt'

Output:

'CanopyAT_*.txt'

3.2

Net canopy CO2 assimilation was calculated by summing the A of all leaf pieces over the daylight hours.

Run

Use 'CanopyAT_*.m' to calculate the canopy CO2 uptake, light absorption, and generate figures.

Input:

'CanopyAT_*.txt'

Output：

'CanopyAT_* outA,txt', 'CanopyAT_* outPAR,txt' and figures.

3.3

All the data from 'CanopyAT_* outA,txt', 'CanopyAT_* outPAR,txt' has been organized and documened in 'Results_all_2404.elsx'

Reference

Drewry, D. T. et al. Ecohydrological responses of dense canopies to environmental variability: 1. Interplay between vertical structure and photosynthetic pathway. Journal of Geophysical Research-Biogeosciences 115 (2010).