WheatFspm

About

WheatFspm is a Functional Structural Plant Model (FSPM) of wheat which fully integrates shoot morphogenesis and the metabolism of carbon (C) and nitrogen (N) at organ scale within a 3D representation of plant architecture. Plants are described as a collection of tillers, each consisting in individual shoot organs (lamina, sheath, internode, peduncle, chaff), a single root compartment, the grains, and a phloem.

WheatFspm simulates:

• Organ photosynthesis, temperature and transpiration from light distribution within the 3D canopy.
• Leaf and internode elongation.
• Leaf, internode and root growth in mass.
• N acquisition, synthesis and allocation of C and N metabolites at organ level and among tiller organs.
• Senescence of shoot organs and roots.

Model inputs are the pedoclimatic conditions (temperature, light, humidity, CO₂, wind, soil NO₃^-) and initial dimensions, mass and metabolic composition of individual organs.

Description

WheatFspm consists in a set of sub-models (named submodules in git) which share inputs/outputs through an MTG object:

Adapted from Gauthier et al. (2020)

• Farquhar-Wheat: Farquhar-based model of photosynthesis, stomatal conductance, organ temperature and transpiration.
• Elong-Wheat: regulation of leaf and internode elongation by C and N metabolites, temperature and coordination rules.
• Growth-Wheat: growth in biomass of leaves, internodes and roots ; related consumption in C and N metabolites.
• CN-Wheat: synthesis and degradation of C and N metabolites at organ level and allocation between tillers' organs. See doc at https://wheatfspm.readthedocs.io/
• Respi-Wheat: respiratory-costs related to the main biological processes.
• Senesc-Wheat: organ senescence and consequences in organ biomass, green area and remoblisation of C and N metabolites.
• Fspm-Wheat: is the submodule containing the interfaces (facades) for reading/updating information between each sub-model and the MTG. Also includes the scripts to be run for using all sub-models.

Table of Contents

• Table of Contents
• Installation
  • Prerequisites
  • Installing
    • Users
    • Developers
• Documentation
• Usage
  • NEMA
  • Vegetative stages
  • Scenarios monoculms
• Credits
  • Authors
  • Contributors
  • Funding
• License

Installation

Prerequisites

WheatFspm has the following dependencies (see documentation in the links provided, instructions for their installation are given in Installing):

• To run the model:
  • openalea.MTG
  • openalea.Plantgl
  • openalea.Lpy
  • openalea.Caribu
  • openalea.Adel
  • openalea.Astk

Installing

For general information about OpenAlea installation, see https://openalea.readthedocs.io/en/latest/install.html

Users

mamba create -n wheatfspm openalea.wheatfspm -c conda-forge -c openalea3

To activate the environment: mamba activate wheatfspm

Developers

1. To clone the project, please use:

git clone https://github.com/openalea/WheatFspm

2. create and activate a conda environment with dependencies:

mamba env create -n wheatfspm -f conda/environment.yml 
activate wheatfspm

Documentation

https://wheatfspm.rtfd.io

Usage

To date, WheatFspm has been used in four main contexts described below.

The scripts to run WheatFSPM are located in:

• WheatFspm\example\NEMA
• WheatFspm\example\Papier_FSPMA2016
• WheatFspm\example\Vegetative_stages
• WheatFspm\example\Scenarii_monoculms

NEMA

This example deals with the post-flowering stages of wheat development under 3 nitrogen fertilisation regimes (H0, H3 and H15). The main processes described are leaf senescence, C and N remobilisation, grain filling). During that stages, all vegetative organs have completed their growth. This work led to the research articles Barillot et al. (2016a) and Barillot et al. (2016b).

To run the example:

• Open a command line interpreter in WheatFspm\example\NEMA
• To run the 3 scenarios, use : python Multi_script_launcher.py

Vegetative stages

This example simulates the early vegetative stages of wheat growth as measured from a field experiment conducted in 1998-99 in Grignon (France). It mainly covers the processes of leaf, internode and roots growth. Tillering is simplified: tiller emergence is a model input while tiller metabolism and growth is approximated from that of the main stem. This work led to the research article Gauthier et al. (2020). Results were obtained from the tag paper_JXBot_2020.

To run the example:

• Open a command line interpreter in WheatFspm\example\Vegetative_stages
• Run script main.py: python main.py

Scenarios monoculms

This example explores the plasticity of leaf growth during the vegetative stages of wheat development. The growth of wheat monoculms was simulated for highly contrasting conditions of soil nitrogen concentration, incident light and planting density. This work led to the research article Gauthier et al. (2021).

The original outputs as well as a singularity container with the code version used for the paper can be found at

To run the example:

• Open a command line interpreter in WheatFspm\example\Scenarios_monoculms
• For a single scenario, run the script main.py: python main.py
• The whole set of scenarios was run in the high-performance computing center MESO@LR (Université de Montpellier, France)

Credits

Authors

• Romain BARILLOT - model designing, development and validation - rbarillot
• Marion GAUTHIER - model designing, development and validation - mngauthier
• Camille CHAMBON - software designing, development, deployment and optimization - cachambon
• Bruno ANDRIEU - model designing and validation, scientific project management - bandrieu

Contributors

• Christian FOURNIER - christian34
• Christophe PRADAL - pradal

Funding

• INRAE: salaries of permanent staff
• French Research National Agency: projects Breedwheat (ANR-10-BTBR-03) and Wheatamix (ANR-13-AGRO0008): postdoctoral research of R.Barillot
• itk company and ANRT: funded the Cifre PhD thesis of M.Gauthier

License

This project is licensed under the CeCILL-C License - see file LICENSE for details