VernalisationPhase
The VernalisationPhase defines a phenological development phase that is completed when vernalisation requirements are fulfilled. It integrates gene expression signals into crop phenology progression, making it essential for modeling genotypic and environmental responses affecting vernalisation.
Overview
The VernalisationPhase utilises the Cereal Anthesis Molecular Phenology (CAMP) model (Brown et al. 2013) to control phase development. The phase completes when vernalisation saturation is achieved, as determined by the CAMP gene expression interface. This phase is crucial for modeling winter crops, such as wheat and barley, that require exposure to cold temperatures (vernalisation) before they can proceed to reproductive development.
Vernalisation is a biological process where plants require a period of cold exposure to become competent to flower. This phase translates complex gene expression signals from the CAMP model into phenological progress, allowing APSIM NG to accurately simulate the interaction between genotype, temperature, and photoperiod in determining flowering time in winter cereals.
Model Structure
This section describes how this model is positioned within the APSIM framework. It outlines the broader structural and computational components that define its role and interactions in the simulation system.
This model inherits structural and functional behaviour from the following core APSIM components:
Connections to Other Components
This section describes how the model interacts with other components in the APSIM Next Generation framework.
These connections allow the model to exchange information—such as environmental conditions, developmental stage, or physiological responses—with other parts of the simulation system. For a general overview of how model components are connected in APSIM, see the Connections Overview.
| Component | Model | Connection Type | Description |
|---|---|---|---|
| CAMP | IVrnExpression | Link | Provides vernalisation gene expression signals (Vrn1, Vrn2, Vrn3, BaseVrn, MaxVrn) |
| Clock | IClock | Link | Provides the current simulation date and time |
Model Variables
This section lists the key variables that describe or control the behaviour of this component. Some variables can be adjusted by the user to modify how the model behaves (configurable), while others are calculated internally and can be viewed as model outputs (reportable). For a general explanation of variable types and how they are used within the APSIM Next Generation framework, see the Model Variables Overview.
Configurable and Reportable Properties
| Property | Type | Description |
|---|---|---|
| Start | string | Name of the phenological stage that initiates this phase |
| End | string | Name of the phenological stage that ends this phase |
| IsEmerged | bool | Whether the phase assumes the crop is emerged (default: true) |
| Target | double | Target vernalisation saturation threshold (default: 1.0) |
Read-Only Reportable Properties
| Property | Type | Description |
|---|---|---|
| FractionComplete | double | Proportion (0–1) of progress through this phase |
| ProgressThroughPhase | double | Accumulated units of progress through this phase (0–1) |
| DateToProgress | string | Optional external completion date. If set, the phase ignores its normal mechanism and waits for this date |
Events
This section describes the events associated with this component. Events are signals or notifications that indicate when a particular process occurs within the simulation, or when a component needs to respond to a change in another part of the system. Some events are listened for by this component to trigger its processes, while others are raised to inform other components about changes. For a general overview of how APSIM Next Generation uses events to coordinate processes between components, see the Events Overview.
Events Listened For
These are signals or notifications that the function listens for from other parts of the simulation:
| Event | Purpose |
|---|---|
| Commencing | Resets internal counters and state for simulation startup |
Events Raised to
No events are raised by this function.
Processes and Algorithms
This section describes the scientific processes and algorithms represented by this component. Each process corresponds to a biological, physical, or chemical mechanism simulated during a model time step. Where appropriate, equations or conceptual summaries are provided to explain how the process operates within the APSIM Next Generation framework.
Vernalisation Target Calculation
The vernalisation target represents the threshold level of gene expression required for the phase to complete. It is calculated using the Vrn2 gene expression from the CAMP model:
\[ \text{Target}_{\text{Vrn}} = 1 + Vrn2 \]
where \(Vrn2\) is the photoperiod-induced repressor of flowering. Higher \(Vrn2\) expression increases the vernalisation requirement, meaning the crop needs more cold exposure to satisfy vernalisation.
Relative Vernalisation Expression
On each timestep, the model calculates the current relative vernalisation expression \(R_{\text{Vrn}}\) by combining multiple gene expression components from the CAMP model:
\[ R_{\text{Vrn}} = \min\left(\frac{Vrn_{\text{base}} + Vrn1 + Vrn3}{\text{Target}_{\text{Vrn}}},\ Vrn_{\text{max}} \right) \]
where:
- \(Vrn_{\text{base}}\) is the baseline (constitutive) vernalisation gene expression
- \(Vrn1\) is the cold-induced vernalisation gene expression that accumulates during exposure to cold temperatures
- \(Vrn3\) is a photoperiod-dependent promoter of flowering
- \(Vrn_{\text{max}}\) is the maximum possible vernalisation expression (an upper limit)
The minimum function ensures that relative vernalisation cannot exceed the maximum value, even if gene expression would otherwise suggest higher levels.
Phase Initialization
When the phase first becomes active, the model records the current relative vernalisation expression as the baseline:
\[ R_{\text{Vrn},\ \text{emergence}} = R_{\text{Vrn}} \]
This baseline represents the vernalisation state at the start of the phase (typically at emergence). Any vernalisation that occurred before emergence is accounted for in this initial value, but further progress during the phase is measured relative to this starting point.
Progress Calculation
Progress through the phase is calculated as the fraction of the remaining vernalisation requirement that has been satisfied:
\[ P = \min\left(1,\ \frac{R_{\text{Vrn}} - R_{\text{Vrn},\ \text{emergence}}}{1 - R_{\text{Vrn},\ \text{emergence}}} \right) \]
where \(P\) is the progress through the phase (ranging from 0 to 1).
This formulation ensures that: - Progress starts at 0 when the phase begins - Progress reaches 1.0 when vernalisation is complete - The denominator \((1 - R_{\text{Vrn},\ \text{emergence}})\) represents the remaining vernalisation requirement at the start of the phase
Phase Completion
The phase is considered complete when the CAMP model sets its IsVernalised flag to true. This occurs when the accumulated vernalisation gene expression has reached the threshold required for the specific genotype and environmental conditions.
The completion criterion integrates: - Cold accumulation (via Vrn1) - Photoperiod effects (via Vrn2 and Vrn3) - Genotype-specific vernalisation requirements (via CAMP parameters)
External Date Override
If an external model sets the DateToProgress property, the phase will ignore its normal gene expression-based progression mechanism and instead complete on the specified date. This allows for simplified control of phase timing when detailed vernalisation modeling is not required.
User Interface
VernalisationPhase is added as a child of a Phenology node to simulate development that depends on cold exposure.
To add this phase:
- Right-click the
Phenologynode in the model tree - Select “Add Model…”
- Search for and select “VernalisationPhase” in the Filter Box
- Configure the
StartandEndstage names - Ensure a CAMP component is available to provide gene expression signals
Practical Example
No practical example available.
See Also
- Source code: VernalisationPhase.cs on GitHub