1 Peanut. 1.1 Arbitrator

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1 Peanut

The Peanut model is constructed from the following list of software components. Details of the implementation and model parameterisation are provided in the following sections.

List of Plant Model Components.

Component Name Component Type

Arbitrator Models.PMF.OrganArbitrator Phenology Models.PMF.Phen.Phenology Leaf Models.PMF.Organs.SimpleLeaf Grain Models.PMF.Organs.ReproductiveOrgan Root Models.PMF.Organs.Root Nodule Models.PMF.Organs.Nodule Shell Models.PMF.Organs.GenericOrgan Stem Models.PMF.Organs.GenericOrgan AflotoxinRisk Models.Functions.BoundFunction MortalityRate Models.Functions.Constant

1.1 Arbitrator

The Arbitrator class determines the allocation of dry matter (DM) and Nitrogen between each of the organs in the crop model. Each organ can have up to three different pools of biomass:

· Structural biomass which is essential for growth and remains within the organ once it is allocated there.

· Metabolic biomass which generally remains within an organ but is able to be re-allocated when the organ senesces and may be retranslocated when demand is high relative to supply.

· Storage biomass which is partitioned to organs when supply is high relative to demand and is available for retranslocation to other organs whenever supply from uptake, fixation, or re-allocation is lower than demand.

The process followed for biomass arbitration is shown in Figure 1. Arbitration calculations are triggered by a series of events (shown below) that are raised every day. For these calculations, at each step the Arbitrator exchange information with each organ, so the basic computations of demand and supply are done at the organ level, using their specific parameters.

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1. doPotentialPlantGrowth. When this event occurs, each organ class executes code to determine their potential growth, biomass supplies and demands. In addition to demands for structural, non-structural and metabolic biomass (DM and N) each organ may have the following biomass supplies:

· Fixation supply. From photosynthesis (DM) or symbiotic fixation (N)

· Uptake supply. Typically uptake of N from the soil by the roots but could also be uptake by other organs (eg foliage application of N). · Retranslocation supply. Storage biomass that may be moved from organs to meet demands of other organs.

· Reallocation supply. Biomass that can be moved from senescing organs to meet the demands of other organs.

1. doPotentialPlantPartitioning. On this event the Arbitrator first executes the DoDMSetup() method to gather the DM supplies and demands from each organ, these values are computed at the organ level. It then executes the DoPotentialDMAllocation() method which works out how much biomass each organ would be allocated assuming N supply is not limiting and sends these allocations to the organs. Each organ then uses their potential DM allocation to determine their N demand (how much N is needed to produce that much DM) and the arbitrator calls DoNSetup() to gather the N supplies and demands from each organ and begin N arbitration. Firstly DoNReallocation() is called to redistribute N that the plant has available from senescing organs. After this step any unmet N demand is considered as plant demand for N uptake from the soil (N Uptake Demand).

2. doNutrientArbitration. When this event occurs, the soil arbitrator gets the N uptake demands from each plant (where multiple plants are growing in competition) and their potential uptake from the soil and determines how much of their demand that the soil is able to provide. This value is then passed back to each plant instance as their Nuptake and doNUptakeAllocation() is called to distribute this N between organs.

3. doActualPlantPartitioning. On this event the arbitrator call DoNRetranslocation() and DoNFixation() to satisfy any unmet N demands from these sources. Finally, DoActualDMAllocation is called where DM allocations to each organ are reduced if the N allocation is insufficient to achieve the organs minimum N concentration and final allocations are sent to organs.

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Figure 1: Schematic showing the procedure for arbitration of biomass partitioning. Pink boxes represent events that occur every day and their numbering shows the order of calculations. Blue boxes represent the methods that are called when these events occur. Orange boxes contain properties that make up the organ/arbitrator interface. Green boxes are organ specific properties.

1.2 Phenology

Peanut's phenological development is simulated as the progression through a series of developmental phases, each bound by distinct growth stages.

In the new model we simplified phenology by taking out stages that are not measurable (e.g. end of juvenile stage) and by adding new stages that are measurable (e.g. start pod). The new phenology follows the V/R staging system

1.2.1 ThermalTime

Look up a value based upon the current growth phase.

PreEmergence has a value between Sowing and Emergence calculated as: TT = [Phenology].PreemergentThermalTime

VegetativeGrowth has a value between Emergence and StartFlowering calculated as: TT = [Phenology].VegetativeThermalTime

ReproductiveGrowth has a value between StartFlowering and HarvestRipe calculated as: TT = [Phenology].ReproductiveThermalTime x PPModifier

Where:

PPModifier is calculated using linear interpolation.

X Y

13 1

16 1

20 1

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1.3 Phases

List of stages and phases used in the simulation of crop phenological development

Phase Number Phase Name Initial Stage Final Stage

1 Germinating Sowing Germination

2 Emerging Germination Emergence

3 Vegetative Emergence StartFlowering

4 EarlyFlowering StartFlowering StartPodDevelopment

5 EarlyPodDevelopment StartPodDevelopment StartGrainFilling 6 EarlyGrainFilling StartGrainFilling EndCanopyDevelopment 7 MidGrainFilling EndCanopyDevelopment EndPodDevelopment

8 LateGrainFilling EndPodDevelopment EndGrainFill

9 Maturing EndGrainFill Maturity

10 Ripening Maturity HarvestRipe

11 ReadyForHarvesting HarvestRipe Unused

1.3.1 Germinating Phase

The Germinating phase goes from Sowing stage to Germination stage and assumes germination Germination will be reached on the day after sowing or the first day thereafter when the extractable soil water at sowing depth is greater than zero."

1.3.2 Emerging Phase

The Emerging phase goes from Germination stage to Emergence stage and simulates time to emergence as a function of sowing depth. The ThermalTime Target for this phase is given by

Target = SowingDepth x ShootRate + ShootLag Where: ShootRate = + ShootRate + ShootLag \n and SowingDepth (mm) is sent from the manager with the sowing event; Progress toward emergence is driven by Thermal time accumulation from Phenology.Thermaltime

ThermalTime = [Phenology].PreemergentThermalTime 1.3.3 Vegetative Phase

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The Target for completion is calculated as Target = 390 (oD)

Progression through the Vegetative phase is calculated daily and accumulated until the Target is reached. Progression = [Phenology].ThermalTime

1.3.4 EarlyFlowering Phase

The EarlyFlowering phase goes from the StartFlowering stage to the StartPodDevelopment stage. The Target for completion is calculated as

Target = 200 (oD)

Progression through the EarlyFlowering phase is calculated daily and accumulated until the Target is reached. Progression = [Phenology].ThermalTime

1.3.5 EarlyPodDevelopment Phase

The EarlyPodDevelopment phase goes from the StartPodDevelopment stage to the StartGrainFilling stage. The Target for completion is calculated as

Target = 140 (oD)

Progression through the EarlyPodDevelopment phase is calculated daily and accumulated until the Target is reached. Progression = [Phenology].ThermalTime

1.3.6 EarlyGrainFilling Phase

The EarlyGrainFilling phase goes from the StartGrainFilling stage to the EndCanopyDevelopment stage. The Target for completion is calculated as

Target = FractionofGrainfilling x [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue Where:

FractionofGrainfilling = 0.05 (oD)

EntireGrainfilling = [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue

Progression through the EarlyGrainFilling phase is calculated daily and accumulated until the Target is reached. Progression = [Phenology].ThermalTime

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1.3.7 MidGrainFilling Phase

The MidGrainFilling phase goes from the EndCanopyDevelopment stage to the EndPodDevelopment stage. The Target for completion is calculated as

Target = FractionofMidToLateGrainfilling x MidToLateGrainfilling Where:

FractionofMidToLateGrainfilling = 0.5 (oD)

MidToLateGrainfilling = [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue - [Phenology].EarlyGrainFilling.Target EntireGrainfilling = [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue

EarlyGrainfilling = [Phenology].EarlyGrainFilling.Target

Progression through the MidGrainFilling phase is calculated daily and accumulated until the Target is reached. Progression = [Phenology].ThermalTime

1.3.8 LateGrainFilling Phase

The LateGrainFilling phase goes from the EndPodDevelopment stage to the EndGrainFill stage. The Target for completion is calculated as

Target = EntireGrainfillPeriod - [Phenology].EarlyGrainFilling.Target - [Phenology].MidGrainFilling.Target Where:

EntireGrainfillPeriod = 1020 (oD)

EarlyGrainFillingTarget = [Phenology].EarlyGrainFilling.Target MidGrainFillingTarget = [Phenology].MidGrainFilling.Target

Progression through the LateGrainFilling phase is calculated daily and accumulated until the Target is reached. Progression = [Phenology].ThermalTime

1.3.9 Maturing Phase

The Maturing phase goes from the EndGrainFill stage to the Maturity stage. The Target for completion is calculated as

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Progression through the Maturing phase is calculated daily and accumulated until the Target is reached. Progression = [Phenology].ThermalTime

1.3.10 Ripening Phase

The Ripening phase goes from the Maturity stage to the HarvestRipe stage. The Target for completion is calculated as

Target = 45 (oD)

Progression through the Ripening phase is calculated daily and accumulated until the Target is reached. Progression = [Phenology].ThermalTime

It is the end phase in phenology and the crop will sit, unchanging, in this phase until it is harvested or removed by other method ThermalTime = [Phenology].ThermalTime

These parameters are overridden by cultivar parameter descriptions to capture the difference between individual cultivars in terms of their phenological development. Responses shown here are only indicative. See cultivar descriptions for more information.

PreemergentThermalTime is calculated using linear interpolation.

X Y

13 0

25 12

50 0

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X Y

9 0

32 23

50 0

ReproductiveThermalTime is calculated using linear interpolation.

X Y

0 13

22 13

32 23

40 23

Returns the duration of the day, or photoperiod, in hours. This is calculated using the specified latitude (given in the weather file) and twilight sun angle threshold. If a variable called ClimateControl.PhotoPeriod is found in the simulation, it will be used instead.

Returns the a value depending on whether an event has occurred. A function is used to provide maturity date as days after sowing(DAS). PreEventValue = 0 ()

PostEventValue = [Plant].DaysAfterSowing

Returns the a value depending on whether an event has occurred. A function is used to provide flowering date as days after sowing(DAS). PreEventValue = 0 ()

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PostEventValue = [Plant].DaysAfterSowing

Returns the a value depending on whether an event has occurred. A function is used to provide maturity date as days after sowing(DAS). PreEventValue = 0 ()

PostEventValue = [Plant].DaysAfterSowing 1.3.11 DaysAfterEmergence

Accumulates OneDay between [Start] and [End] OneDay = 1 ()

1.4 Leaf

This organ is simulated using a SimpleLeaf organ type. It provides the core functions of intercepting radiation, producing biomass through photosynthesis, and determining the plant's transpiration demand. The model also calculates the growth, senescence, and detachment of leaves. SimpleLeaf does not distinguish leaf cohorts by age or position in the canopy.

Radiation interception and transpiration demand are computed by the MicroClimate model. This model takes into account competition between different plants when more than one is present in the simulation. The values of canopy Cover, LAI, and plant Height (as defined below) are passed daily by SimpleLeaf to the MicroClimate model. MicroClimate uses an implementation of the Beer-Lambert equation to compute light interception and the Penman-Monteith equation to calculate potential evapotranspiration. These values are then given back to SimpleLeaf which uses them to calculate photosynthesis and soil water demand.

InitialWt = MassPerPlant x [Peanut].SowingData.Population Where:

MassPerPlant = 0.06 (g/m2)

Population = [Peanut].SowingData.Population 1.4.1 Dry Matter Demand

The dry matter demand for the organ is calculated as defined in DMDemands, based on the DMDemandFunction and partition fractions for each biomass pool. 1.4.1.1 DMDemands

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = [Leaf].DeltaLAI / [Leaf].SpecificArea

DeltaLAI = [Leaf].DeltaLAI SLA = [Leaf].SpecificArea

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Growth in leaf area is used to calculate the leaf dry matter demand. Note that leaf biomass is assumed to consist of entirely structural dry matter. Storage = 0 (g/m2)

Metabolic = 0 (g/m2) 1.4.2 Nitrogen Demand

The N demand is calculated as defined in NDemands, based on DM demand the N concentration of each biomass pool. 1.4.2.1 NDemands

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = [Leaf].minimumNconc x [Leaf].potentialDMAllocation.Structural

MinNconc = [Leaf].minimumNconc

PotentialDMAllocation = [Leaf].potentialDMAllocation.Structural Metabolic = MetabolicNconc x [Leaf].potentialDMAllocation.Structural Where:

MetabolicNconc = [Leaf].criticalNConc - [Leaf].minimumNconc CritNconc = [Leaf].criticalNConc

MinNconc = [Leaf].minimumNconc

PotentialDMAllocation = [Leaf].potentialDMAllocation.Structural

1.4.2.1.1 Storage

The partitioning of daily N supply to storage N attempts to bring the organ's N content to the maximum concentration. Storage = [Leaf].maximumNconc × ([Leaf].Live.Wt + potentialAllocationWt) - [Leaf].Live.N

The demand for storage N is further reduced by a factor specified by the [Leaf].NitrogenDemandSwitch. MinimumNConc = 0.02 (g/g)

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X Y

3 0.06

4 0.05

9 0.03

MaximumNConc is calculated using linear interpolation.

X Y

3 0.06

4 0.05

9 0.03

The demand for N is reduced by a factor specified by the NitrogenDemandSwitch. 1.4.3 Dry Matter Supply

Leaf does not reallocate DM when senescence of the organ occurs. Leaf will retranslocate 50% of non-structural DM each day.

1.4.3.1 Photosynthesis

Biomass fixation is modelled as the product of intercepted radiation and its conversion efficiency, the radiation use efficiency (RUE) (Monteith et al., 1977). This approach simulates net photosynthesis rather than providing separate estimates of growth and respiration. The potential photosynthesis calculated using RUE is then adjusted according to stress factors, these account for plant nutrition (FN), air temperature (FT), vapour pressure deficit (FVPD), water supply (FW) and atmospheric CO2concentration (FCO2). NOTE: RUE in this model is expressed as g/MJ for a whole plant basis, including both above and below ground growth.

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This approach is based upon the value used inRobertson et al., 2002increased to account for partitioning to roots.

1.4.3.1.1 FT

FT is calculated as a function of daily min and max temperatures, these are weighted toward max temperature according to the specified MaximumTemperatureWeighting factor. A value equal to 1.0 means it will use max temperature, a value of 0.5 means average temperature. MaximumTemperatureWeighting = 0.75

This approach is based upon that used in Bell, WRight and Hammer (1992) Crop Sci

X Y

10 0

21 1

35 1

40 0

FVPD is calculated using linear interpolation.

X Y

0 1

10 1

50 1

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X Y

0 0

1 1

1.5 1

FW is calculated using linear interpolation.

X Y

0 0

1 1

1.4.3.1.2 FCO2

This model calculates the CO2impact on RUE using the approach ofReyenga et al., 1999.

For C3 plants,

FCO2= (CO2- CP) x (350 + 2 x CP)/(CO2+ 2 x CP) x (350 - CP)

where CP, is the compensation point calculated from daily average temperature (T) as CP = (163.0 - T) / (5.0 - 0.1 * T)

For C4 plants,

FCO2= 0.000143 * CO2+ 0.95

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1.4.4 Nitrogen Supply

Leaf can reallocate up to 100% of N that senesces each day if required by the plant arbitrator to meet N demands. Leaf can retranslocate up to 50% of non-structural N each day if required by the plant arbitrator to meet N demands. 1.4.5 Canopy Properties

Leaf has been defined with a LAIFunction, cover is calculated using the Beer-Lambert equation. Area = Initial + Change

Where:

Initial = AreaPerPlant x [Peanut].SowingData.Population Where:

AreaPerPlant = 0.005 ()

Population = [Peanut].SowingData.Population Change = AreaGrowth - AreaLoss

Where: 1.4.5.1 AreaGrowth

AreaGrowth is a daily accumulation of the values of functions listed below between the Emergence and EndCanopyDevelopment stages. Function values added to the accumulate total each day are:

DeltaArea = [Leaf].Allocated.StructuralWt x [Leaf].SpecificArea DeltaMass = [Leaf].Allocated.StructuralWt

SLA = [Leaf].SpecificArea 1.4.5.2 AreaLoss

AreaLoss is a daily accumulation of the values of functions listed below between the EndCanopyDevelopment and HarvestRipe stages. Function values added to the accumulate total each day are:

DeltaArea = [Leaf].Senesced.StructuralWt x [Leaf].SpecificAreaCanopy DeltaMass = [Leaf].Senesced.StructuralWt

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This approach is based upon that described byPorter, 2000to account for the impacts of population and row/plant spacing. Extinction coefficient is said to decrease with decreasing inter-plant spacing within the plant row.

ExtinctionCoefficient is calculated using linear interpolation.

X Y

0 0.214

335 0.7

Tallness is calculated using linear interpolation.

X Y 1 0 2 0 3 50 4 400 5 450 6 450 9 450 1.4.6 StomatalConductance

Stomatal Conductance (gs) is calculated for use within the micromet model by adjusting a value provided for an atmospheric CO2 concentration of 350 ppm. The impact of other stresses (e.g. Temperature, N) are captured through the modifier, Frgr.

gs = Gsmax350 x FRGR x stomatalConductanceCO2Modifier 1.4.6.1 StomatalConductanceCO2Modifier

This model calculates the CO2impact on stomatal conductance using the approach ofElli et al., 2020.

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where CP, is the compensation point calculated from daily average temperature (T) as CP = (163.0 - T) / (5.0 - 0.1 * T)

PhotosynthesisCO2Modifier = [Leaf].Photosynthesis.FCO2 1.4.7 Senescence and Detachment

The proportion of live biomass that senesces and moves into the dead pool each day is quantified by the SenescenceRate. 1.4.7.1 SenescenceRate

SenescenceRate is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below. Vegetative has a value between Emergence and EndPodDevelopment calculated as:

Rate = 0 (/d)

Reproductive has a value between EndPodDevelopment and Maturity calculated as: Leaf senescence rate is calculated to ensure that all leaves are senesced by crop maturity. Rate = [Phenology].ThermalTime / TTRemaining / Modifier

Where:

TTRemaining = TTRequired - TTComplete Where:

1.4.7.1.1 TTRequired

TTRequired = [Phenology].LateGrainFilling.Target + [Phenology].Maturing.Target + 1000

1.4.7.1.2 TTComplete

TTComplete = [Phenology].LateGrainFilling.ProgressThroughPhase + [Phenology].Maturing.ProgressThroughPhase Modifier = 1 (/d)

TT = [Phenology].ThermalTime

Senescent has a value between Maturity and HarvestRipe calculated as:

Leaf senescence rate is calculated to ensure that all leaves are senesced by crop maturity. Rate = 0.1 (/d)

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1.4.8 BiomassRemovalDefaults

This organ will respond to certain management actions by either removing some of its biomass from the system or transferring some of its biomass to the soil surface residues. The following table describes the default proportions of live and dead biomass that are transferred out of the simulation using "Removed" or to soil surface residue using "To Residue" for a range of management actions. The total percentage removed for live or dead must not exceed 100%. The difference between the total and 100% gives the biomass remaining on the plant. These can be changed during a simulation using a manager script.

Method % Live Removed % Dead Removed % Live To Residue % Dead To Residue

Harvest 0 0 100 100

Cut 0 0 100 100

Prune 0 0 0 0

Graze 0 0 0 0

1.5 Grain

This organ uses a generic model for plant reproductive components. Yield is calculated from its components in terms of organ number and size (for example, grain number and grain size).

FillingDuration = [Phenology].EarlyGrainFilling.Target + [Phenology].MidGrainFilling.Target + [Phenology].LateGrainFilling.Target EarlyGrainFillingDuration = [Phenology].EarlyGrainFilling.Target

MidGrainFillingDuration = [Phenology].MidGrainFilling.Target LateGrainFillingDuration = [Phenology].LateGrainFilling.Target 1.5.1 DMDemandFunction

DMDemandFunction is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below. GrainFilling has a value between StartGrainFilling and EndGrainFill calculated as:

HIGrainDemand = [AboveGround].Wt x HarvestIndexIncrease x [Phenology].ThermalTime Where:

HarvestIndexIncrease = OutstandingHarvestIndexIncrease / TTRemaining Where:

OutstandingHarvestIndexIncrease is calculated as the minimum of Increase and Zero Where:

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1.5.1.1 Increase

Increase = [Grain].PotentialHarvestIndex - [Grain].HarvestIndex Zero = 0 (g/m2/d)

TTRemaining = ReproductiveTT - ReproductiveTTComplete Where: 1.5.1.2 ReproductiveTT ReproductiveTT = [Phenology].EarlyGrainFilling.Target+[Phenology].MidGrainFilling.Target+[Phenology].LateGrainFilling.Target 1.5.1.3 ReproductiveTTComplete ReproductiveTTComplete = [Phenology].EarlyGrainFilling.ProgressThroughPhase+[Phenology].MidGrainFilling.ProgressThroughPhase+[Phenology].LateGrainFilling.ProgressThroughPhase AboveGroundWt = [AboveGround].Wt ThermalTime = [Phenology].ThermalTime MinimumNConc = 0.05 (g/g) MaximumNConc = 0.058 (g/g) WaterContent = 0.13 (g/g)

NFillingRate = [Grain].MaximumNConc x [Grain].DMDemandFunction x [Grain].DMConversionEfficiency NConc = [Grain].MaximumNConc

DMDemand = [Grain].DMDemandFunction

DMConversionEfficiency = [Grain].DMConversionEfficiency 1.5.2 BiomassRemovalDefaults

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Method % Live Removed % Dead Removed % Live To Residue % Dead To Residue Cut 0 0 100 100 Prune 0 0 0 0 Graze 0 0 0 0 DMConversionEfficiency = 0.89 (g/g) RemobilisationCost = 0 (g/g) CarbonConcentration = 0.4 (g/g)

HarvestIndex = [Grain].Wt / [AboveGround].Wt GrainWt = [Grain].Wt

AboveGroundWt = [AboveGround].Wt MaximumPotentialGrainSize = 0 ()

This parameter is not used. Grain growth is calculated from harvest index increase. NumberFunction = 0 (/m2)

Grain number is not estimated by this model.

PotentialHarvestIndex = [Pod].PotentialHarvestIndex x GrainFraction Where:

GrainFraction = 0.72 ()

PodHarvestIndex = [Pod].PotentialHarvestIndex

1.6 Root

The generic root model calculates root growth in terms of rooting depth, biomass accumulation and subsequent root length density in each soil layer. Root Growth

Roots grow downwards through the soil profile, with initial depth determined by sowing depth and the growth rate determined by RootFrontVelocity. The RootFrontVelocity is modified by multiplying it by the soil's XF value, which represents any resistance posed by the soil to root extension.

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where i is the index of the soil layer at the rooting front. Root depth is also constrained by a maximum root depth.

Root length growth is calculated using the daily DM partitioned to roots and a specific root length. Root proliferation in layers is calculated using an approach similar to the generalised equimarginal criterion used in economics. The uptake of water and N per unit root length is used to partition new root material into layers of higher 'return on investment'. For example, the Root Activity for water is calculated as

RAwi= -WaterUptakei/ LiveRootWtix LayerThicknessix ProportionThroughLayer

The amount of root mass partitioned to a layer is then proportional to root activity DMAllocatedi= TotalDMAllocated x RAwi/ TotalRAw

Dry Matter Demands

A daily DM demand is provided to the organ arbitrator and a DM supply returned. By default, 100% of the dry matter (DM) demanded from the root is structural. The daily loss of roots is calculated using a SenescenceRate function. All senesced material is automatically detached and added to the soil FOM.

Nitrogen Demands

The daily structural N demand from root is the product of total DM demand and the minimum N concentration. Any N above this is considered Storage and can be used for retranslocation and/or reallocation as the respective factors are set to values other then zero.

Nitrogen Uptake

Potential N uptake by the root system is calculated for each soil layer (i) that the roots have extended into. In each layer potential uptake is calculated as the product of the mineral nitrogen in the layer, a factor controlling the rate of extraction (kNO3 or kNH4), the concentration of N form (ppm), and a soil moisture factor

(NUptakeSWFactor) which typically decreases as the soil dries. NO3 uptake = NO3ix kNO3 x NO3ppm, ix NUptakeSWFactor

NH4 uptake = NH4ix kNH4 x NH4ppm, ix NUptakeSWFactor

As can be seen from the above equations, the values of kNO3 and kNH4 equate to the potential fraction of each mineral N pool which can be taken up per day for wet soil when that pool has a concentration of 1 ppm.

Nitrogen uptake demand is limited to the maximum daily potential uptake (MaxDailyNUptake) and the plant's N demand. The former provides a means to constrain N uptake to a maximum value observed in the field for the crop as a whole. The demand for soil N is then passed to the soil arbitrator which determines how much of the N uptake demand each plant instance will be allowed to take up.

Water Uptake

Potential water uptake by the root system is calculated for each soil layer that the roots have extended into. In each layer potential uptake is calculated as the product of the available water in the layer (water above LL limit) and a factor controlling the rate of extraction (KL). The values of both LL and KL are set in the soil interface and KL may be further modified by the crop via the KLModifier function.

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1.6.1 RootShape

KLModifier is calculated using linear interpolation.

X Y

0 1

3 1

TemperatureEffect is the Average of sub-daily values from a Models.Functions.XYPairs.

Firstly 3-hourly estimates of air temperature (Ta) are interpolated usig the method ofJones et al., 1986which assumes a sinusoidal temperature. pattern between Tmax and Tmin.

Each of the interpolated air temperatures are then passed into the following Response and the Average taken to give daily TemperatureEffect Response is calculated from an XY matrix (graphed below) which returns a value for Y interpolated from the Xvalue provided.

MaxDailyNUptake is calculated using linear interpolation.

X Y

0 1

5 3

SenescenceRate = 0.005 (/d)

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1.6.2 RootFrontVelocity

This approach is based upon that used inRobertson et al., 2002.

RootFrontVelocity is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below. PreEmergence has a value between Germination and Emergence calculated as:

Function = 15 (mm/d)

early has a value between Emergence and StartGrainFilling calculated as: Function = 35 (mm/d)

late has a value between StartGrainFilling and Maturity calculated as: Function = 0 (mm/d)

MaximumNConc = 0.01 (g/g) MinimumNConc = 0.005 (g/g)

NitrogenDemandSwitch has a value between Emergence and EndGrainFill calculated as: Constant = 1 ()

KNO3 is calculated using linear interpolation.

X Y

0 0.02

0.003 0.02

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X Y

0 0

0.003 0

1.6.3 BiomassRemovalDefaults

Harvest 0 0 20 0

Cut 0 0 20 0

Prune 0 0 0 0

Graze 0 0 0 0

NUptakeSWFactor is calculated using linear interpolation.

X Y

0 0

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SpecificRootLength = 60 (m/g)

This approach is based upon that used inRobertson et al., 2002. DMConversionEfficiency = 1 (g/g)

MaintenanceRespirationFunction = 1 (/d) RemobilisationCost = 0 ()

CarbonConcentration = 0.4 (g/g) 1.6.4 DMDemands

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = DMDemandFunction x StructuralFraction

Where:

1.6.4.1 DMDemandFunction

DMDemandFunction = PartitionFraction x [Arbitrator].DM.TotalFixationSupply Where:

1.6.4.1.1 PartitionFraction

PartitionFraction is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below.

Early has a value between Emergence and StartFlowering calculated as: Function = 0.2 (g/m2)

Middle has a value between StartFlowering and StartGrainFilling calculated as: Function = 0.2 (g/m2)

Late has a value between StartGrainFilling and Maturity calculated as: Function = 0.05 (g/m2)

StructuralFraction = 1 (g/m2) Metabolic = 0 (g/m2)

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1.6.4.2 Storage

The partitioning of daily growth to storage biomass is based on a storage fraction. StorageFraction = 1 - [Root].DMDemands.Structural.StructuralFraction

One = 1 (g/m2)

StructuralFraction = [Root].DMDemands.Structural.StructuralFraction 1.6.5 NDemands

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = [Root].minimumNconc x [Root].potentialDMAllocation.Structural

MinNconc = [Root].minimumNconc

PotentialDMAllocation = [Root].potentialDMAllocation.Structural Metabolic = MetabolicNconc x [Root].potentialDMAllocation.Structural Where:

MetabolicNconc = [Root].criticalNConc - [Root].minimumNconc CritNconc = [Root].criticalNConc

MinNconc = [Root].minimumNconc

PotentialDMAllocation = [Root].potentialDMAllocation.Structural 1.6.5.1 Storage

The partitioning of daily N supply to storage N attempts to bring the organ's N content to the maximum concentration. Storage = [Root].maximumNconc × ([Root].Live.Wt + potentialAllocationWt) - [Root].Live.N

The demand for storage N is further reduced by a factor specified by the [Root].NitrogenDemandSwitch. CriticalNConc = [Root].MinimumNConc

1.6.6 InitialWt

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = 0.1 (g/m2)

(27)

Storage = 0 (g/m2)

RootDepthStressFactor = 1 (0-1)

1.7 Nodule

This organ simulates the root structure associate with symbiotic N-fixing bacteria. It provides the core functions of determining N fixation supply and related costs. It also calculates the growth, senescence and detachment of nodules.

1.7.1 Dry Matter Demand

Where:

1.7.1.1.1 DMDemandFunction

DMDemandFunction = PartitionFraction x [Arbitrator].DM.TotalFixationSupply Where:

1.7.1.1.1.1 PartitionFraction

PartitionFraction is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below.

Early has a value between Emergence and StartFlowering calculated as: Function = 0.03 (g/m2)

Middle has a value between StartFlowering and StartGrainFilling calculated as: Function = 0.02 (g/m2)

Late has a value between StartGrainFilling and Maturity calculated as: Function = 0 (g/m2)

StructuralFraction = 1 (g/m2) Metabolic = 0 (g/m2)

(28)

1.7.1.1.2 Storage

The partitioning of daily growth to storage biomass is based on a storage fraction. StorageFraction = 1 - [Nodule].DMDemands.Structural.StructuralFraction

One = 1 (g/m2)

StructuralFraction = [Nodule].DMDemands.Structural.StructuralFraction 1.7.2 Nitrogen Demand

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = [Nodule].minimumNconc x [Nodule].potentialDMAllocation.Structural

MinNconc = [Nodule].minimumNconc

PotentialDMAllocation = [Nodule].potentialDMAllocation.Structural Metabolic = MetabolicNconc x [Nodule].potentialDMAllocation.Structural Where:

MetabolicNconc = [Nodule].criticalNConc - [Nodule].minimumNconc CritNconc = [Nodule].criticalNConc

MinNconc = [Nodule].minimumNconc

PotentialDMAllocation = [Nodule].potentialDMAllocation.Structural

1.7.2.1.1 Storage

The partitioning of daily N supply to storage N attempts to bring the organ's N content to the maximum concentration. Storage = [Nodule].maximumNconc × ([Nodule].Live.Wt + potentialAllocationWt) - [Nodule].Live.N

The demand for storage N is further reduced by a factor specified by the [Nodule].NitrogenDemandSwitch. MinimumNConc = 0.01 (g/g)

CriticalNConc = [Nodule].MinimumNConc MaximumNConc = 0.02 (g/g)

(29)

The demand for N is reduced by a factor specified by the NitrogenDemandSwitch. NitrogenDemandSwitch has a value between Emergence and EndGrainFill calculated as: Constant = 1 ()

1.7.3 Dry Matter Supply

Nodule does not reallocate DM when senescence of the organ occurs. Nodule does not retranslocate non-structural DM.

Nodule does not reallocate N when senescence of the organ occurs. Nodule does not retranslocate non-structural N.

1.7.5 FixationRate

FixationRate is the same as DailyPotentialFixationRate until it reaches StartGrainFilling stage when it fixes its value 1.7.5.1 DailyPotentialFixationRate

DailyPotentialFixationRate is calculated as the minimum of PotentialFixationRate and MaximumFixationRate Where:

PotentialFixationRate = [AboveGroundLive].Wt x SpecificFixationRate Where:

1.7.5.1.1 SpecificFixationRate

SpecificFixationRate is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below.

VegetativeGrowth has a value between Emergence and StartFlowering calculated as: Rate = 0.006 (g/m^2)

ReproductiveGrowth has a value between StartFlowering and EndGrainFill calculated as: Rate = 0.002 (g/m^2)

LiveBiomass = [AboveGroundLive].Wt MaximumFixationRate = 0.6 (g/m^2)

(30)

1.7.6 Senescence and Detachment

Nodule has senescence parameterised to zero so all biomass in this organ will remain alive.

Nodule has detachment parameterised to zero so all biomass in this organ will remain with the plant until a defoliation or harvest event occurs. 1.7.7 BiomassRemovalDefaults

Harvest 0 0 20 0

Cut 0 0 20 0

Prune 0 0 0 0

Graze 0 0 0 0

1.8 Shell

This organ is simulated using a GenericOrgan type. It is parameterised to calculate the growth, senescence, and detachment of any organ that does not have specific functions.

Where:

1.8.1.1.1 DMDemandFunction

DMDemandFunction is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below.

(31)

HIPodDemand = [AboveGround].Wt x HarvestIndexIncrease x [Phenology].ThermalTime Where:

HarvestIndexIncrease = OutstandingHarvestIndexIncrease / TTRemaining Where:

OutstandingHarvestIndexIncrease is calculated as the minimum of Increase and Zero Where:

1.8.1.1.1.1 Increase

Increase = [Shell].PotentialHarvestIndex - [Shell].HarvestIndex Zero = 0 (g/m2)

TTRemaining = ShellGrowthTT - ShellGrowthTTComplete Where: 1.8.1.1.1.2 ShellGrowthTT ShellGrowthTT = [Phenology].EarlyPodDevelopment.Target+[Phenology].EarlyGrainFilling.Target+[Phenology].MidGrainFilling.Target 1.8.1.1.1.3 ShellGrowthTTComplete ShellGrowthTTComplete = [Phenology].EarlyPodDevelopment.ProgressThroughPhase+[Phenology].EarlyGrainFilling.ProgressThroughPhase+[Phenology].MidGrainFilling.ProgressThroughPhase AboveGroundWt = [AboveGround].Wt ThermalTime = [Phenology].ThermalTime StructuralFraction = 1 (g/m2) Metabolic = 0 (g/m2) 1.8.1.1.2 Storage

The partitioning of daily growth to storage biomass is based on a storage fraction. StorageFraction = 1 - [Shell].DMDemands.Structural.StructuralFraction

One = 1 (g/m2)

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1.8.2 Nitrogen Demand

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = [Shell].minimumNconc x [Shell].potentialDMAllocation.Structural

MinNconc = [Shell].minimumNconc

PotentialDMAllocation = [Shell].potentialDMAllocation.Structural

1.8.2.1.1 Storage

The partitioning of daily N supply to storage N attempts to bring the organ's N content to the maximum concentration. Storage = [Shell].maximumNconc × ([Shell].Live.Wt + potentialAllocationWt) - [Shell].Live.N

The demand for storage N is further reduced by a factor specified by the [Shell].NitrogenDemandSwitch. Metabolic = 0 (g/m2)

MinimumNConc = 0.01 (g/g)

CriticalNConc = [Shell].MinimumNConc MaximumNConc = 0.045 (g/g)

The demand for N is reduced by a factor specified by the NitrogenDemandSwitch.

NitrogenDemandSwitch has a value between StartPodDevelopment and EndPodDevelopment calculated as: Constant = 1 ()

Shell does not reallocate DM when senescence of the organ occurs. Shell will retranslocate 10% of non-structural DM each day.

Shell can reallocate up to 100% of N that senesces each day if required by the plant arbitrator to meet N demands. Shell can retranslocate up to 50% of non-structural N each day if required by the plant arbitrator to meet N demands.

(33)

1.8.5 Senescence and Detachment

The proportion of live biomass that senesces and moves into the dead pool each day is quantified by the SenescenceRate. 1.8.5.1 SenescenceRate

SenescenceRate is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below. ReproductivePhase has a value between StartPodDevelopment and Maturity calculated as:

1.8.5.2 Rate

Rate is calculated as the minimum of Fraction and One Where:

Fraction = [Phenology].ThermalTime / TTRemaining Where:

TTRemaining = ReproductiveTT - ReproductiveTT1Complete Where: 1.8.5.2.1 ReproductiveTT ReproductiveTT = [Phenology].EarlyPodDevelopment.Target+[Phenology].EarlyGrainFilling.Target+[Phenology].MidGrainFilling.Target+[Phenology].LateGrainFilling.Target 1.8.5.2.2 ReproductiveTT1Complete ReproductiveTT1Complete = [Phenology].EarlyPodDevelopment.ProgressThroughPhase+[Phenology].EarlyGrainFilling.ProgressThroughPhase+[Phenology].MidGrainFilling.ProgressThroughPhase+[Phenology].LateGrainFilling.ProgressThroughPhase TT = [Phenology].ThermalTime One = 1 (/d)

Shell has detachment parameterised to zero so all biomass in this organ will remain with the plant until a defoliation or harvest event occurs. 1.8.6 BiomassRemovalDefaults

(34)

Method % Live Removed % Dead Removed % Live To Residue % Dead To Residue Harvest 0 0 100 100 Cut 0 0 100 100 Prune 0 0 0 0 Graze 0 0 0 0

1.9 Stem

This organ is simulated using a GenericOrgan type. It is parameterised to calculate the growth, senescence, and detachment of any organ that does not have specific functions.

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = Fraction x [Stem].PotentialGrowth

Where:

1.9.1.1.1 Fraction

Fraction is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below. StemGrowthPhase has a value between Emergence and EndCanopyDevelopment calculated as:

This approach is based upon that used inRobertson et al., 2002. Fraction = 0.9 (g/m2)

PodAndGrainGrowth has a value between EndCanopyDevelopment and EndGrainFill calculated as: Fraction = 0 (g/m2)

DMDemand = [Stem].PotentialGrowth Metabolic = 0 (g/m2)

(35)

Where: StorageFraction = 1 - [Stem].DMDemands.Structural.Fraction One = 1 (g/m2) StructuralFraction = [Stem].DMDemands.Structural.Fraction DMDemand = [Stem].PotentialGrowth 1.9.2 Nitrogen Demand

This is the collection of functions for calculating the demands for each of the biomass pools (Structural, Metabolic, and Storage). Structural = [Stem].minimumNconc x [Stem].potentialDMAllocation.Structural

MinNconc = [Stem].minimumNconc

PotentialDMAllocation = [Stem].potentialDMAllocation.Structural Metabolic = MetabolicNconc x [Stem].potentialDMAllocation.Structural Where:

MetabolicNconc = [Stem].criticalNConc - [Stem].minimumNconc CritNconc = [Stem].criticalNConc

MinNconc = [Stem].minimumNconc

PotentialDMAllocation = [Stem].potentialDMAllocation.Structural

1.9.2.1.1 Storage

The partitioning of daily N supply to storage N attempts to bring the organ's N content to the maximum concentration. Storage = [Stem].maximumNconc × ([Stem].Live.Wt + potentialAllocationWt) - [Stem].Live.N

The demand for storage N is further reduced by a factor specified by the [Stem].NitrogenDemandSwitch. MinimumNConc = 0.006 (g/g)

CriticalNConc = [Stem].MinimumNConc

(36)

X Y

3 0.025

4 0.02

5 0.015

The demand for N is reduced by a factor specified by the NitrogenDemandSwitch.

NitrogenDemandSwitch has a value between Emergence and StartGrainFilling calculated as: Constant = 1 ()

Stem does not reallocate DM when senescence of the organ occurs.

The proportion of non-structural DM that is allocated each day is quantified by the DMReallocationFactor. 1.9.3.1 DMRetranslocationFactor

DMRetranslocationFactor is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below. Vegetative has a value between Emergence and EndCanopyDevelopment calculated as:

RetranslocationFactor = 0 (/d)

GrainFilling has a value between EndCanopyDevelopment and EndGrainFill calculated as: RetranslocationFactor = 0.2 (/d)

Stem can reallocate up to 100% of N that senesces each day if required by the plant arbitrator to meet N demands. Stem can retranslocate up to 50% of non-structural N each day if required by the plant arbitrator to meet N demands. 1.9.5 Senescence and Detachment

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1.9.5.1 SenescenceRate

SenescenceRate is calculated using specific values or functions for various growth phases. The function will use a value of zero for phases not specified below. PostCanopyPhase has a value between EndCanopyDevelopment and Maturity calculated as:

1.9.5.2 Rate

Rate is calculated as the minimum of Fraction and One Where:

Fraction = [Phenology].ThermalTime / TTRemaining Where:

TTRemaining = PostCanopyTT - PostCanopyTTComplete Where: 1.9.5.2.1 PostCanopyTT PostCanopyTT = [Phenology].EarlyPodDevelopment.Target+[Phenology].EarlyGrainFilling.Target+[Phenology].MidGrainFilling.Target+[Phenology].LateGrainFilling.Target 1.9.5.2.2 PostCanopyTTComplete PostCanopyTTComplete = [Phenology].MidGrainFilling.ProgressThroughPhase+[Phenology].LateGrainFilling.ProgressThroughPhase TT = [Phenology].ThermalTime One = 1 (/d)

Stem has detachment parameterised to zero so all biomass in this organ will remain with the plant until a defoliation or harvest event occurs. 1.9.6 BiomassRemovalDefaults

Harvest 0 0 100 100

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Prune 0 0 0 0

Graze 0 0 0 0

1.10 AboveGround Biomass

This is a composite biomass class, representing the sum of 1 or more biomass objects. AboveGround summarises the following biomass objects:

· [Leaf].Live · [Leaf].Dead · [Stem].Live · [Stem].Dead · [Grain].Live · [Grain].Dead · [Shell].Live · [Shell].Dead

1.11 BelowGround Biomass

This is a composite biomass class, representing the sum of 1 or more biomass objects. BelowGround summarises the following biomass objects:

· [Root].Live · [Root].Dead · [Nodule].Live · [Nodule].Dead

1.12 AboveGroundLive Biomass

This is a composite biomass class, representing the sum of 1 or more biomass objects. AboveGroundLive summarises the following biomass objects:

· [Leaf].Live · [Stem].Live · [Grain].Live · [Shell].Live

(39)

1.13 Total Biomass

This is a composite biomass class, representing the sum of 1 or more biomass objects. Total summarises the following biomass objects:

· [Leaf].Live · [Leaf].Dead · [Stem].Live · [Stem].Dead · [Grain].Live · [Grain].Dead · [Shell].Live · [Shell].Dead · [Root].Live · [Root].Dead · [Nodule].Live · [Nodule].Dead

1.14 TotalLive Biomass

This is a composite biomass class, representing the sum of 1 or more biomass objects. TotalLive summarises the following biomass objects:

· [Leaf].Live · [Stem].Live · [Grain].Live · [Shell].Live · [Root].Live · [Nodule].Live

1.15 TotalDead Biomass

This is a composite biomass class, representing the sum of 1 or more biomass objects. TotalDead summarises the following biomass objects:

· [Leaf].Dead · [Stem].Dead · [Grain].Dead · [Shell].Dead · [Root].Dead · [Nodule].Dead

(40)

1.16 Pod Biomass

This is a composite biomass class, representing the sum of 1 or more biomass objects. HarvestIndex = [Pod].Wt / [AboveGround].Wt

PodWt = [Pod].Wt

AboveGroundWt = [AboveGround].Wt PotentialHarvestIndex = 0.5 ()

This approach is based upon that used inRobertson et al., 2002. Pod summarises the following biomass objects:

· [Shell].Live · [Shell].Dead · [Grain].Live · [Grain].Dead

1.17 AflotoxinRisk

AflotoxinRisk is the value of AccumulatedValue bound between a lower and upper bound where: 1.17.1 AccumulatedValue

Accumulates DailyIncrease between [Start] and [End]

DailyIncrease = TemperatureFactor x SoilWaterFactor x Constant Where:

(41)

X Y

22 0

30 1

35 0

SoilWaterFactor is calculated using linear interpolation.

X Y 0 1 0.2 1 0.21 0 1 0 Constant = 3 () Lower = 0 () Upper = 100 ()

1.18 Cultivars

EarlyBunch, Florunner, Holt, Redvale, Taabinga, Tapir, TMV2, VB97, VirginiaBunch 1.18.1 EarlyBunch

(42)

[Phenology].Vegetative.Target.FixedValue = 420 [Phenology].EarlyFlowering.Target.FixedValue = 160 [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 1050 [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.6 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.4 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.5 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,10,11 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,2.0,2.0,0.4 [Leaf].ExtinctionCoefficient.XYPairs.X = 0, 335 [Leaf].ExtinctionCoefficient.XYPairs.Y = 0.5, 0.5 1.18.2 VirginiaBunch

VirginiaBunch overrides the following properties: [Phenology].Vegetative.Target.FixedValue = 450 [Phenology].EarlyFlowering.Target.FixedValue = 160 [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 1020 [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.40 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.33 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.5 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,15,16 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,1.0,1.0,0 1.18.3 TMV2

TMV2 overrides the following properties:

(43)

[Phenology].EarlyFlowering.Target.FixedValue = 160 [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 1020 [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.40 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.33 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.5 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,15,16 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,1.0,1.0,0 1.18.4 Tapir

Tapir overrides the following properties:

[Phenology].Vegetative.Target.FixedValue = 390 [Phenology].EarlyFlowering.Target.FixedValue = 160 [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 1020 [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.40 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.33 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.5 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,15,16 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,1.0,1.0,0 1.18.5 VB97

VB97 overrides the following properties: [Phenology].Emerging.ShootLag=50

[Phenology].Vegetative.Target.FixedValue = 390 [Phenology].EarlyFlowering.Target.FixedValue = 100

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[Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 1020 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.33 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.5 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,15,16 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,2,2,0 [Leaf].ExtinctionCoefficient.XYPairs.X = 5, 335 [Leaf].ExtinctionCoefficient.XYPairs.Y = 0.2, 0.55 1.18.6 Florunner

Florunner overrides the following properties: [Phenology].Vegetative.Target.FixedValue = 400 [Phenology].EarlyFlowering.Target.FixedValue = 160 [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.7 [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 1020 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.20 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.33 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,15,16 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,2,2,0 [Leaf].ExtinctionCoefficient.XYPairs.X = 0, 335 [Leaf].ExtinctionCoefficient.XYPairs.Y = 0.6, 0.6 [Leaf].SpecificArea.XYPairs.X = 0, 17, 21, 35 [Leaf].SpecificArea.XYPairs.Y = .02, .02, .02, .02 [Leaf].SenescenceRate.Reproductive.Rate.Modifier.FixedValue = 100

(45)

1.18.7 Redvale

Redvale overrides the following properties: [Phenology].Vegetative.Target.FixedValue = 420 [Phenology].EarlyFlowering.Target.FixedValue = 200 [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 950 [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.5 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.2 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.5 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,15,16 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,2.0,1.0,0 1.18.8 Taabinga

Taabinga overrides the following properties: [Phenology].Vegetative.Target.FixedValue = 420 [Phenology].EarlyFlowering.Target.FixedValue = 200 [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 950 [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.5 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.20 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.5 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,15,16 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,2.0,1.0,0 1.18.9 Holt

Holt overrides the following properties:

(46)

[Phenology].EarlyFlowering.Target.FixedValue = 250 [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 1100 [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.5 [Phenology].MidGrainFilling.Target.FractionofMidToLateGrainfilling.FixedValue=0.2 [Grain].MaximumNConc.FixedValue = 0.067 [Stem].PotentialGrowth.PartitionFraction.StemGrowthPhase.StemFraction.FixedValue = 0.5 [Leaf].BranchingRate.XYPairs.X = 0,1,2,3,15,16 [Leaf].BranchingRate.XYPairs.Y = 0,1,2,2.0,1.0,0 MortalityRate = 0 () Properties (Outputs)

Name Description Units Type Settable?

AboveGround Above ground weight Biomass True

AboveGroundHarvestable Above ground weight Biomass False

AssimilateAvailable Amount of assimilate available to be damaged. double False

CoverGreen Total plant green cover from all organs - double False

CoverTotal Total plant cover from all organs - double False

CultivarNames Gets a list of cultivar names String False

DaysAfterEnding Counter for the number of days after corp being ended. USed to clean up data the day after an EndCrop, enabling some reporting.

d int32 True

DaysAfterSowing Number of days after sowing. d int32 False

IsAlive Return true if plant is alive and in the ground. boolean True

IsEmerged Return true if plant has emerged boolean False

IsEnding Returns true if the crop is being ended. Used to clean up data the day after an EndCrop, enabling some reporting.

(47)

Name Description Units Type Settable? IsReadyForHarvesting Returns true if the crop is ready for harvesting boolean False

LAI Leaf area index. m^2/m^2 double False

Organs Gets the organs. IOrgan True

PlantType Used by several organs to determine the type of crop. String True

Population Gets or sets the plant population. /m2 double True

SowingData The sowing data SowingParameters True

SowingDate Holds the date of sowing datetime True

Links (Dependencies)

Name Type IsOptional? Arbitrator IArbitrator True

clock IClock False

Leaf ICanopy True

mortalityRate IFunction False Phenology IPhenology False

Root IRoot True

structure IStructure True

summary ISummary False

Events published

Name Type

Cutting Void Cutting (Object sender, EventArgs e) Flowering Void Flowering (Object sender, EventArgs e)

(48)

Name Type Grazing Void Grazing (Object sender, EventArgs e) Harvesting Void Harvesting (Object sender, EventArgs e) LeafPlucking Void LeafPlucking (Object sender, EventArgs e) PlantEnding Void PlantEnding (Object sender, EventArgs e) PlantSowing Void PlantSowing (Object sender,

SowingParameters

e) Pruning Void Pruning (Object sender, EventArgs e) Sowing Void Sowing (Object sender, EventArgs e)

Methods (callable from manager)

Name Description

Document void Document(ITag tags, int32 headingLevel, int32 indent)

EndCrop void EndCrop()

Harvest void Harvest()

Harvest void Harvest(RemovalFractionsremovalData)

Harvest the crop.

ReduceCanopy void ReduceCanopy(double deltaLAI)

Set the plant leaf area index.

ReducePopulation void ReducePopulation(double newPlantPopulation)

Reduce the plant population. ReduceRootLengthDensity void ReduceRootLengthDensity(double rootLengthModifier) Set the plant root length density.

(49)

RemoveAssimilate void RemoveAssimilate(double deltaAssimilate)

Remove an amount of assimilate from the plant. RemoveBiomass void RemoveBiomass(String biomassRemoveType,RemovalFractionsremovalData) Harvest the crop.

RemoveBiomass BiomassRemoveBiomass(double amountToRemove)

Removes a given amount of biomass (and N) from the plant. RemoveBiomass void RemoveBiomass(String organName, String biomassRemoveType,

OrganBiomassRemovalTypebiomassToRemove) Remove biomass from an organ.

SetEmergenceDate void SetEmergenceDate(String emergencedate)

Force emergence on the date called if emergence has not occured already

SetGerminationDate void SetGerminationDate(String germinationdate)

Force germination on the date called if germination has not occured already Sow void Sow(String cultivar, double population, double depth, double rowSpacing, double maxCover, double budNumber, double rowConfig) Sow the crop with the specified parameters.

2 Peanut

Biomass of plant organs Properties (Outputs)

DMDOfStructural Dry matter digestibility. 0.7 for live, 0.4 for dead double True

MetabolicN Gets or sets the metabolic n. g/m^2 double True

(50)

MetabolicWt Gets or sets the metabolic wt. g/m^2 double True

N Gets the N amount. g/m^2 double False

NConc Gets the N concentration. g/g double False

StorageN Gets or sets the non structural n. g/m^2 double True StorageNConc Gets the non structural N concentration. g/g double False StorageWt Gets or sets the non structural wt. g/m^2 double True

StructuralN Gets or sets the structural n. g/m^2 double True

StructuralNConc Gets the structural N concentration. g/g double False StructuralWt Gets or sets the structural wt. g/m^2 double True

Wt Gets the wt. g/m^2 double False

Methods (callable from manager)

Add void Add(Biomassa) Adds the specified a.

Clear void Clear()

Multiply void Multiply(double scalar) Multiplies a biomass object by a given scalar SetTo void SetTo(Biomassa) Sets to. Subtract void Subtract(Biomassa) Subtracts the specified a.

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3 SowingParameters

Parameters which control how a plant is sown. Properties (Outputs)

BudNumber The bud number double True

Cultivar The cultivar to be sown. String True

Depth The depth mm double True

MaxCover The maximum cover double True

Population The population. /m2 double True

RowSpacing The row spacing mm double True

SkipDensityScale The skip plant seed density adjustment double True

SkipPlant The skip plant double True

SkipRow The skip row double True

SkipType The skip type double True

4 RemovalFractions

Data structure to hold removal and residue returns fractions for all plant organs Properties (Outputs)

NodesToRemove The nunber of Main-stem nodes to remove int32 True

SetPhenologyStage The Phenological stage that biomass removal resets phenology to. double True SetThinningProportion The Phenological stage that biomass removal resets phenology to. double True

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Name Description GetFractionsForOrgan OrganBiomassRemovalTypeGetFractionsForOrgan(String organName) Gets the removal fractions for the specified organ or null if not found. SetFractionToRemove void SetFractionToRemove(String organName, double fraction, String biomassType) Method to set the FractionToRemove for specified Organ SetFractionToResidue void SetFractionToResidue(String organName, double fraction, String biomassType) Method to set the FractionToResidue for specified Organ

5 OrganBiomassRemovalType

Data passed to each organ when a biomass remove event occurs. The proportion of biomass to be removed from each organ is the sum of the FractionToRemove and the FractionToRedidues

Properties (Outputs)

FractionDeadToRemove The amount of dead biomass taken from each organ and removeed from the zone on harvest, cut, graze or prune.

double True

FractionDeadToResidue The amount of dead biomass to removed from each organ and passed to residue pool on on harvest, cut, graze or prune

double True

FractionLiveToRemove The amount of live biomass taken from each organ and removeed from the zone on harvest,

cut, graze or prune. double True

FractionLiveToResidue The amount of live biomass to removed from each organ and passed to residue pool on on

harvest, cut, graze or prune double True

6 References

Elli, Elvis, Huth, Neil, Sentelhas, Paulo, Carneiro, Rafaela, Alcarde Alvares, Clayton, 2020. Global sensitivity-based modelling approach to identify suitable Eucalyptus traits for adaptation to climate variability and change. in silico plants 2.

Jones, C.A., Kiniry, J.R., Dyke, P.T., 1986. CERES-Maize: a simulation model of maize growth and development.

Monteith, J. L., Moss, C. J., 1977. Climate and the Efficiency of Crop Production in Britain [and Discussion]. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 281 (980), 277-294.

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Porter, Wade, 2000. Potential for peanut production in Southern Australia.

Reyenga, P.J., Howden, S. M., Meinke, H., McKeon, G.M., 1999. Modelling global change impacts on wheat cropping in south-east Queensland, Australia. Environmental Modelling & Software 14, 297-306.

Robertson, M. J., Carberry, P. S., Huth, N. I., Turpin, J. E., Probert, M. E., Poulton, P. L., Bell, M., Wright, G. C., Yeates, S. J., Brinsmead, R. B., 2002. Simulation of growth and development of diverse legume species in APSIM. Australian Journal of Agricultural Research 53 (4), 429-446.