Improving Maize Growth Processes in the Community Land Model:

Implementation and Evaluation

Bin Peng1*, Kaiyu Guan1*, Min Chen2, David M. Lawrence3, Yadu Pokhrel4,
Andrew Suyker5, Timothy Arkebauer6, and Yaqiong Lu3

1
Department of Natural Resources and Environmental Sciences and National Center for Supercomputing
Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
2
Joint Global Change Research Institute, Pacific Northwest National Laboratory, College Park, MD, USA
3
National Center for Atmospheric Research, Boulder, CO, USA
4
Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
5
School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
6
Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
*corresponding to: binpeng@illinois.edu, kaiyug@illinois.edu

© 2017. This manuscript version is made available under the Elsevier user license
http://www.elsevier.com/open-access/userlicense/1.0/
Abstract: Earth system models (ESMs) are essential tools to study the impacts of historical and future
climate on regional and global food production, as well as to assess the effectiveness of possible adaptations
and their potential feedback to climate. Several current ESMs have the capabilities to simulate crop growth.
However, some critical crop growth processes (e.g. flowering and other reproductive processes) and their
responses to environmental extremes (e.g. heat stress) are not yet represented in most of these models. In
this paper, an improved maize growth model was implemented in the Community Land Model version 4.5
(CLM4.5) by modifying the maize planting scheme, incorporating the phenology scheme adopted from the
APSIM model (Agricultural Production Systems sIMulator), adding a new carbon allocation scheme into
CLM4.5, and improving the estimation of canopy structure parameters including leaf area index (LAI) and
canopy height. Unique features of the new model (CLM-APSIM) include more detailed phenology stages,
an explicit implementation of the impacts of various abiotic environmental stresses (including nitrogen,
water, temperature and heat stresses) on maize phenology and carbon allocation, as well as an explicit
simulation of grain number and grain size. Evaluation of results at 7 AmeriFlux sites located in the US Corn
Belt show that the CLM-APSIM model performs better than the original CLM4.5 in simulating phenology
(LAI and canopy height), surface fluxes including gross primary production (GPP), net ecosystem exchange
(NEE), latent heat (LH), and sensible heat (SH), and especially in simulating the biomass partition and
maize yield. The CLM-APSIM model corrects a serious deficiency in CLM4.5-related to CLM4.5’s
underestimation of aboveground biomass (i.e. overestimation of belowground biomass) and overestimation
of Harvest Index, which lead to a reasonable yield estimation with wrong mechanisms. Moreover, 13-year
simulation results from 2001 to 2013 at the three Mead sites (US-Ne1, Ne2 and Ne3) show that the CLM-
APSIM model can more accurately reproduce maize yield responses to growing season climate
(temperature and precipitation) than the original CLM4.5 when benchmarked with the site-based
observations and USDA county-level survey statistics. The CLM-APSIM model is thus more suitable than
its predecessor models in terms of simulating abiotic environmental stresses on maize yield. This new
model provides an improved tool to attribute maize yield change to various processes under historical and
future climate, as well as to assess and design effective climate adaptation strategies for sustainable
agricultural production.
Key words: maize, Community Land Model, APSIM, phenology, carbon allocation, yield, stress

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1 Introduction
Global food security is under continuing pressure from increased population and climate change
(Rosenzweig et al. 2014). Maize (Zea mays L.) is the most important staple food and feed crop in the world
according to the total production. The Midwest Corn Belt of the United States produces more than 45% of
global maize production. However, maize yield in this area is projected to decrease with increasing vapor
pressure deficit (VPD) (Lobell et al. 2014), droughts (Ort and Long 2014, Lobell et al. 2014) and extreme
high temperatures (Schlenker and Roberts 2009) under climate change. For example, previous empirical
studies have shown that maize yield would be suppressed sharply when exposed to higher temperature
(Schauberger et al. 2017, Schlenker and Roberts 2009). However, the yield-to-temperature relationship is
an integral of the effects from several temperature-sensitive processes on crop growth and development
(Lobell et al. 2013). Therefore, parsing the overall temperature effects to crop yield into different processes
is of great value to understand and potentially mitigate the climate change impact on the global food
production (Peng, Guan and Chen 2016).
Process-based models are major tools to study the impacts of historical and future climate on regional and
global food production, to assess the effectiveness of possible adaptations and their potential feedback to
climate and to attribute different pathways through which climate can impact crop yields. There are two
main classes of process-based crop models currently used to study crop responses to climate: (1) agronomy
crop models and (2) crop models in the framework of earth system models (ESMs) (see Table 1 for an
example of the differences in specific models from these two classes). Agronomy crop models have been
developed by agronomists to simulate field-level crop growth and yield. Widely used agronomy crop
models include APSIM (Agricultural Production Systems sIMulator) (Keating et al. 2003, Holzworth et al.
2014), DSSAT (Decision Support System for Agrotechnology Transfer) (Jones et al. 2003), EPIC (Erosion
Productivity Impact Calculator or Environmental Policy Integrated Climate) (Williams et al. 1989), Hybrid-
Maize (Yang et al. 2017, Yang et al. 2004), CropSyst (cropping systems simulator) (Stöckle, Donatelli and
Nelson 2003, Stöckle et al. 2014), etc. They usually include detailed phenology development schemes with
many explicit stress terms and field management schemes. However, most of these models use empirical
light use efficiency (LUE) or radiation use efficiency (RUE) to simulate the net primary production (NPP),
which lumps the photosynthesis and respiration processes together. Thus, in these models, acclimation to
temperature for both photosynthesis and respiration and processes related to CO2 fertilization effect are not
mechanistically simulated. Moreover, most agronomy crop models do not solve the energy balance at the
soil-crop-atmosphere interface. Consequently, soil and leaf temperatures are not explicitly simulated;
instead, they use air temperature to drive crop phenology development and to quantify heat stress effects
on crop growth and yield. As recent studies have recognized the importance of canopy temperature in
assessing heat stress impact on crop yield (Stefan et al. 2014, Levis 2014, Webber et al. 2015), the lack of
simulated soil and leaf temperature in agronomy crop models significantly limits their utility for assessing
and attributing crop yield responses under climate change. Furthermore, agronomy crop models do not fully
simulate the surface flux exchanges at sub-daily time scale and are not coupled with climate models or earth
system models. Therefore they cannot be utilized to assess the feedback impact of agriculture management
on the broader climate system.
In contrast, crop models that are embedded in the land surface models (LSMs), the land component of
ESMs, numerically and explicitly solve the surface water, energy and carbon balances, and are ready to run
synchronously coupled to ESMs to simulate the two-way feedbacks between climate and agricultural
systems. Simple crop models and basic management practices were introduced into LSMs/ESMs relatively
recently (Kucharik 2003, Levis et al. 2012, Drewniak et al. 2013, Osborne et al. 2015, Liu et al. 2016, Song,
Jain and McIsaac 2013). However, the crop phenology representations in these LSM-based crop models

4
tend to be much simpler than in the agronomy crop models, and the phenology-stage-dependent stresses in
ESM crop models are largely missing. Due to these drawbacks, current ESM crop models tend to perform
not as well in simulating energy and carbon fluxes in agricultural ecosystems as in other ecosystems
(Lokupitiya et al. 2016), nor have similar performance in simulating crop yield as agronomy crop models.
Thus, combining the strengths of both agronomy crop models and ESM crop models can provide a direct
and promising way to improve crop modeling capabilities to study climate change impacts on crop yield
and the potential feedbacks.

Table 1. Strengths and weaknesses of CLM4.5 and APSIM models in crop growth simulation.

Model Strength Weakness

CLM4.5 x Sophisticated soil and canopy hydrology x Missing critical crop phenology stages
x Two-stream approximation of canopy (e.g. flowering) and reproductive
radiative transfer processes (e.g. grain number formation)
x Physical-based stomatal conductance, x Lack of stage-dependent stress
photosynthesis, and respiration simulation
x Explicit calculation of energy balance and x Linear accumulation of thermal time
canopy temperature
x More process-driven CO2 fertilization effects
x Can be coupled in climate model (CESM)

APSIM x More detailed crop phenology stages
x Stage-dependent stress simulation
x Piece-wise linear response of thermal time
x More detailed management practices
x RUE-based calculation of NPP and no
explicit simulation of photosynthesis
and respiration
x Lack of resolving energy balance
x Simplified soil hydrology

The Community Land Model (CLM) (Oleson et al. 2013, Lawrence et al. 2011) is the land component of
Community Earth System Model (CESM) (Hurrell et al. 2013). The original parameterization scheme for
cropping system management in CLM (Levis et al. 2012, Drewniak et al. 2013) is a heritage of the Agro-
IBIS ecosystem model (Kucharik 2003). The maize phenology in CLM is simulated through a 3-phase
algorithm (see section 2.1 for more detail) adopted from Agro-IBIS, which is a significant simplification of
the real maize growth stages. Previous studies found that the crop phenology scheme is critical for accurate
simulation of the agriculture ecosystem carbon exchange, and that the original maize module in CLM4.0
overestimates the leaf area index (LAI) and gross primary production (GPP) in the early growing season
due to earlier estimation of leaf emergence (Chen et al. 2015). In addition, except for water and nitrogen
stresses on photosynthetic capability, no other stresses are considered in the maize module of CLM. In
particular, the high temperature and drought stresses on phenological development and the reproductive
processes are not captured in current CLM and these processes have been found to have large impacts on
maize yield and the simulation of future maize production (Deryng et al. 2014).
Among many agronomy crop models, APSIM model (Keating et al. 2003, Brown et al. 2014, Holzworth et
al. 2014, McCown et al. 1996) is one of the most widely used and also one of the most advanced agronomy
crop models, with the capability to simulate growth and yield for a range of crop types including maize.
The maize module in APSIM (APSIM-Maize) was developed from a combination of the approaches used
in two derivatives of CERES-Maize model (Jones et al. 1986): the CM-KEN (CERES-Maize adapted in

5
Kenya) (Keating and Wafula 1992) and CM-SAT (CERES-Maize for semi-arid tropical environment)
(Carberry, Muchow and McCown 1989), with some additional features (such as the modified nonlinear
response of thermal time to temperature) from the maize model of Wilson, Muchow and Murgatroyd (1995).
In recent years, the APSIM crop model has been widely used in the United States (Archontoulis, Miguez
and Moore 2014, Jin et al. 2017, Jin et al. 2016b, Jin et al. 2016a, Lobell et al. 2013, Lobell et al. 2014,
Hammer et al. 2009), Australia (Song et al. 2010, Chauhan, Solomon and Rodriguez 2013), Asian (Gaydon
et al. 2017) and African countries (Sultan et al. 2014, Guan et al. 2015, Guan et al. 2017) and for global
scale applications (Elliott et al. 2014).
Here, we propose an improved maize modeling framework which combines the strengths of CLM and
APSIM with detailed description of its implementation. We also conduct a validation of the new crop model
and compare its performance with the original CLM crop model, benchmarked with multiple flux-tower
data, field biometric measurements and regional crop statistics. Since we primarily adopt the maize
phenology module from APSIM-Maize model along with some additional revisions and innovations, we
refer to our new crop model as “CLM-APSIM” hereafter.

2 Models, data and experiment design

2.1 The original maize module in CLM4.5
The interactive crop management scheme was initially implemented into CLM in version 4.0 (CLM4.0)
(Levis et al. 2012). Maize, soybean, and spring wheat (more generally temperate cereals) were represented
using their corresponding algorithms in the Agro-IBIS model (Kucharik 2003). Since then, the crop module
in CLM has been under continuous development. The standard calculation method of Vcmax,25 (maximum
carboxylation rate at the temperature of 25 °C, mol·m−2·s−1) for natural plant functional types (PFTs) in
CLM was applied to crops. The fertilizer and irrigation functionalities loosely follow the algorithm of
Ozdogan et al. (2010), and a nitrogen retranslocation scheme was included in CLM4.5 (Drewniak et al.
2013). Extra tropical crops including sugarcane, rice, cotton, tropical maize, and tropical soybean were also
added to post-4.5 version of CLM for the Benefits of Reducing Anthropogenic Climate changE project
(BRECE) (Levis et al. 2016) and AgMIP Global Gridded Crop Model Intercomparison (GGCMI) studies
(Elliott et al. 2015) with modified parameter values from Badger and Dirmeyer (2015). We utilize the
officially released CLM4.5 and focus on its maize module in this study.
In CLM4.5, the phenology of maize is simulated by a 3-phase algorithm (Fig. 1) based on linearly
accumulated Growing Degree Day (GDD) or Heat Unit Index (HUI). Phase 1 starts at planting and ends at
leaf emergence; Phase 2 covers from leaf emergence to the beginning of grain-filling, and represents the
vegetative stage; and Phase 3 starts from the beginning of grain-filling and ends at physiological maturity
and harvest, and it represents the reproductive stage. During phase 1, a maize planting event is triggered if
the following criteria are met (Eq. (A1)) during the planting window that spans April 1 to June 14 in the
northern hemisphere: (1) 10-day running mean air temperature becomes greater than 10 oC, (2) 10-day
running minimum air temperature gets higher than 6 oC, and (3) the 20-year running mean of accumulated
8 oC-based GDD ( ) between March and October is higher than 50 degree days. If these thresholds
are never reached during the planting window, then maize is planted at the end of the planting window. The
following phenological phases (leaf emergence, grain filling and maturity) are determined by certain
fractions of the maturity GDD ( ) which is derived as 0.85 and bounded from 950 to 1850
degree days (see Eq. (A3) and (A4)). Leaf emergence occurs once the accumulated soil starting from
the planting date reaches a fraction ( , = 3%) of . Similarly, the grain-filling phase is

6
triggered once the accumulated 2m air temperature from the planting date reaches another fraction
( , ) of the . , is estimated through a linear relationship with the Corn Relative
Maturity (CRM) rating for Pioneer-brand maize hybrids grown in the U.S. Corn Belt (Kucharik 2003) and
bounded from 55% to 65% (see Eq. (A7)). Maize maturity is reached once the accumulated 2m air
temperature from planting date reaches or the number of days from planting exceeds the
crop specific maximum growing days (165 days for maize). A harvest event is triggered immediately after
maturity in CLM4.5 crop model.
Once planted, the CLM4.5 crop model assigns 1g of seed carbon per m2 and an equivalent amount of seed
N given a leaf C:N ratio of 25:1 for maize. At leaf emergence, all seed C and N pools are transferred to the
leaf C and N pools. The net carbon assimilated from photosynthesis is allocated to fine roots, leaves, and
live stems during the vegetative stage with dynamic fractions (see Eq. (A9)). Once peak LAI is reached, all
carbon allocation goes to fine roots during the vegetative stage. During the grain-filling phase, the allocation
rules are changed to gradually reduce allocation to leaves and live stems with the residual fraction used for
filling the grain C and N pools (see Eq. (A10)). In CLM4.5, different organism C:N ratios are used for the
vegetative phase and the post grain-filling phase. At harvest, the root, leaf and live stem C and N pools are
all routed directly to the column litter pool, and the grain pool is harvested as crop yield with the dormant
crop pools all set to zero.
In CLM4.5, photosynthesis is simulated through a coupled leaf photosynthesis and stomatal conductance
model that is a variant of the Ball-Berry stomatal conductance model (Ball, Woodrow and Berry 1987, Ball
1988, Collatz et al. 1991), the Farquhar, von Caemmerer and Berry (1980) C3 photosynthesis model as
implemented by Collatz et al. (1991), and the Collatz, Ribas-Carbo and Berry (1992) C4 photosynthesis
model, and the C4 photosynthesis model is used for maize. Detailed implementation can be found in Bonan
et al. (2011). Photosynthesis scaling from leaf to canopy is achieved through a “two-big-leaf” approach, i.e.
differentiating sunlit and shaded leaves (Bonan et al. 2012). LAI is calculated from the leaf carbon storage
by using a constant specific leaf area during the entire growing season and is bounded with a maximum
LAI of 5.0 m2͑ m-2 for maize in CLM4.5. During the grain-filling period, LAI also declines in response to
the background litterfall rate in the same manner as simulated for natural PFTs in CLM4.5, but with a crop
specific turnover time. Canopy height is estimated from LAI and bounded with a maximum value of 2.5 m
for maize in CLM4.5. Further details about the maize growth parameterization in the CLM4.5 model can
be found in Appendix A.
2.2 Improved maize modeling in CLM-APSIM
In CLM-APSIM, we mainly revised or incorporated new features in sowing, phenology development,
carbon allocation, grain number and canopy structure estimation that will be described in detail below; all
other components including photosynthesis, respiration and nitrogen dynamics in the CLM-APSIM model
are the same as in CLM4.5. The unique features of CLM-APSIM are highlighted in Fig. 1 and the
environmental stresses included in the two models are summarized in Table 2.
Specifically, we adopt a more detailed phenology scheme from APSIM-Maize with 12 stages in the new
model (Fig. 1). Several important phenology stages are included during the vegetative phase, such as
germination, floral initiation and flowering. We also separate the end of grain-filling, physical maturity and
harvest stages during the reproductive phase though the harvest stage now is only a placeholder in CLM-
APSIM. Similar to CLM4.5 in which crop phenology is driven through GDD, the maize phenology
algorithm in APSIM is driven by an accumulated heat unit indicator, namely Thermal Time (TT). However,
instead of a simple linear GDD accumulation from daily mean air temperature as in CLM4.5, TT in APSIM
is calculated through a nonlinear (piece-wise linear) relationship from sub-daily air temperature (Wilson et

7
al. 1995) (also see Fig. B1). Recent comparison studies among different thermal functions (Kumudini et al.
2014) revealed that nonlinear thermal functions generally show better performance in simulating
phenological development prediction than empirical linear thermal functions, and may better represent the
phenological development response of maize to supra-optimal temperature conditions, which are expected
to occur more frequently under future climate change. The nonlinearity between the development rate and
temperature is actually rooted in the nonlinear response of enzyme dynamics to temperature (Bonhomme
2000, Kumudini et al. 2014). The adopted non-linear thermal function reflects the biological response of
maize development across the 0 °C to 44 °C range, a range that spans the temperatures encountered in most
environments in which maize is grown. It has four cardinal temperatures: 0 °C (minimum), 18 °C, 34 °C
(optimum), and 44 °C (ceiling) (Eq. (B4)). Daily TT accumulation was calculated from eight 3-hourly,
third-order polynomial interpolations between the minimum and maximum daily temperatures (Wilson et
al. 1995) in original APSIM model, while it is now derived from hourly temperature inputs in the CLM-
APSIM model.
The correct simulation of sowing date is a prerequisite for accurate simulation of maize phenology. Keeping
the original sowing scheme in CLM4.5 (see section 2.1) as an option in CLM-APSIM, we further implement
two new options for triggering the sowing event. The first new option, which is not from APSIM but newly
introduced, is that maize is sown once the following criteria are met (Eq. (B1)): (1) the 7-day running mean
air temperature is higher than 10°C ; (2) the 7-day running mean soil temperature is higher than 12°C; (3)
the 7-day running mean surface soil moisture is neither too low (< 0.25 ) nor too high (> 0.75 ) where
represents the mean saturated soil moisture of the sowing depth (0-9 cm); (4) the accumulated TT since
the earliest planting date gets larger than a threshold (500 °C day). If these criteria are not met during the
planting window, then maize is sown at the end of the window. Another new option is to use the observed
sowing date in CLM-APSIM when such information is available; this option allows more reliable
evaluation of post-sowing processes against observation. The first new option results in significant
improvements in simulating sowing dates when compared to the observed sowing data (see Results 3.1).
After sowing, the phenology stage is updated at a daily time step and fractional increments of the
phenological stages are calculated by the ratio of accumulated TT in a certain stage and target accumulated
TT for the next stage. The target TT values are set referencing those for different maize cultivars in APSIM
and previous calibration work for some maize hybrids planted in US Corn Belt (Archontoulis et al. 2014).
To account for non-optimal growth conditions, water and nitrogen stresses are applied to TT accumulation
for some phenological stages as in APSIM. Water stress is added to TT accumulation after sowing up
through the end of the flowering stage, while the nitrogen stress function is added from the end of juvenile
stage to the end of the flowering stage. Both water and nitrogen stresses are scaled between 0 (most stressed)
and 1 (no stress). From the end of juvenile stage to the end of the flowering stage, water and nitrogen
stresses coexist and the minimum term from these both stresses is applied and multiplied by TT
accumulation to get the actual TT accumulation. Water stress is calculated from the relative saturation
degree of soil moisture of the root zone (Eq. (B8)). Nitrogen stress is derived from specific leaf nitrogen
(SLN, gN͑ m-2) (Eq. (B9)). Both water and nitrogen stresses are bounded between 0.5 and 1.0 to account
for mitigation effects arising from management practices (Eq. (B7)). In addition, a threshold soil moisture
must be met for seed germination during the germination stage. The frozen stress which can lead to crop
failure is currently not implemented in the CLM-APSIM model as it has marginal effect on US maize
production.
The simulated grain number depends on the kernel number per plant (KNP) and the plant density. KNP is
the product of the number of ears per plant and the number of kernels per ear that achieve physiological
maturity. Previous agronomic studies have demonstrated that the grain number is most susceptible to

8
environmental stress at a critical period bracketing silking, and the plant growth rate (PGR) in this critical
period is a good indicator of kernel setting capability of maize plant under a wide range of environmental
and management practices (Andrade et al. 1999, Andrade et al. 2002). In CLM-APSIM, KNP is determined
in a short thermal time window (1-2 weeks, can be calibrated based on observations) around flowering
stage. The potential grain number (PGN) is firstly derived from PGR, which is represented as the mean dry
mass accumulation rate in the grain number determining window. A heat stress factor is explicitly
implemented to account for the negative impact of high temperature around silking on grain number. The
two cardinal temperatures for heat stress on grain number are set to be 36 °C and 40 °C and are the same
as those used in APSIM (Eq. (B19)).
Correct allocation of net carbon uptake into different organ pools is critical to simulate crop growth and
yield. In APSIM, carbon allocation to leaf and stem, as well as the change in leaf area, are all closely linked
with the node or leaf number (Hammer et al. 2010, Jones et al. 1986), and the dynamics of node number is
simulated through prescribed leaf appearance rates. Such a simulation scheme of leaf carbon and area was
primarily derived from limited field samples and contains complex and empirical parameterization, which
leads to challenges in extension to the broader scale due to the large number of unconstrained parameters.
Furthermore, this generic APSIM scheme does not consider the physical constraints of leaf carbon balance.
Thus, here we elect not to use the generic APSIM scheme, but adopt a different way to estimate the
allocation coefficients in CLM-APSIM. The potential allocation coefficients to different organs (root, stem,
leaf and grain) are phenology-stage dependent and are simulated through multi-nominal logistic functions
(Eq. (B20)) similar to those utilized in the JULES (Joint UK Land Environment Simulator) crop model
(JULES-Crop) (Osborne et al. 2015). The difference lies in that the JULES-Crop model uses the relative
crop development index (DVI) (Penning de Vries et al. 1989) to describe crop phenology and uses DVI as
an predictor for allocation coefficients (Osborne et al. 2015). We use the twelve ASPIM phenology stage
numbers to directly link with real maize phenology. These logistic relationships are calibrated against field
observations of aboveground biomass component fractions (leaf, stem and reproductive) at an irrigated
maize site in Mead, Nebraska (also see section 2.4 and Appendix B). The actual allocation coefficients (Eq.
(B21)) for non-reproductive organs are calculated from potential allocation coefficients after explicitly
accounting for light, water and nitrogen stresses as in the Integrated Science Assessment Model (ISAM)
crop model (ISAM-Crop) (Song et al. 2013). Following APSIM, the allocation coefficient for grain during
grain-filling stage is regulated by a demand-supply relationship. The carbon supply for grain-filling is the
residual carbon after allocation to other maintenance pools. The carbon demand for grain-filling is
calculated from actual kernel growth rate (KGR) and grain number. KGR is estimated from potential KGR
(pKGR), which is determined as the ratio of prescribed potential kernel weight to target TT during the
grain-filling period. A stress-free grain filling period can maximize the yield potential of a crop, while
severe stress during the grain-filling stage can cause kernel abortion or reduce grain weight, and may even
lead to the development of stalk rot. As non-optimal temperature, water and nitrogen conditions can slow
down the grain-filling rate, a stress factor ( , Eq. (B23)) is applied to reduce the pKGR under non-optimal
abiotic conditions. The temperature stress function for grain-filling has an optimum temperature from 22
o
C to 30 oC, and either too low or too high temperatures will lead to decreased kernel growth rate.
In CLM-APSIM, canopy structure parameters (canopy height and LAI) are directly estimated from organ
carbon pools. An exponential relationship is established between canopy height (Htop) and stem carbon
storage (Eq. (B25)). Instead of using a constant specific leaf area (SLA) for the entire growing season as in
CLM4.5, we establish an exponential relationship between SLA and crop stage (Eq. (B26)) to represent the
observed deceasing trend of SLA with crop phenological development (Danalatos et al. 1994). Canopy LAI
is then estimated from leaf carbon storage with this dynamic SLA. In this way, the maximum Htop and LAI
constraints used in CLM4.5 are no longer needed in CLM-APSIM model as both canopy height and LAI

9
are now constrained by the real carbon pools. Further details about the maize growth parameterization in
the CLM-APSIM model can be found in Appendix B.

Fig. 1. Conceptual diagram for phenological stages in the original CLM, APSIM and CLM-APSIM models.
Unique features in CLM-APSIM crop model are also highlighted. Note that the stage duration in this
diagram is not proportional to real stage length, and only presented for illustrative purpose.
2.3 Datasets
We use observations from seven AmeriFlux sites (see Table 3) that grow maize located in the US Corn Belt
for model evaluation. AmeriFlux (http://ameriflux.lbl.gov/) is a network of principal-investigator-managed
sites measuring ecosystem CO2, water, and energy fluxes in North, Central and South America. The seven
sites cover a relatively wide range of environmental (climate and soil) conditions in the maize planting area
in the Midwestern United States. The three sites (US-Ne1, Ne2 and Ne3) located at the University of
Nebraska-Lincoln’s (UNL) Agricultural Research and Development Center (ARDC) near Mead, NE are
the main sites used for our study due to their completeness of data collection – besides the eddy-covariance
flux and meteorological measurements, they also provide very detailed crop phenology and biomass
observations. Ne1 and Ne2 sites are irrigated sites equipped with center pivots, while Ne3 is a rainfed site.
Maize has been planted at Ne1 site continuously since 2001, while the other two Mead sites (Ne2 and Ne3)
are rotated maize-soybean cropping systems (Suyker et al. 2005, Verma et al. 2005, Suyker and Verma
2012). Maize was planted at Ne2 site in odd years during 2001 to 2009 and all years from 2010 to 2013,
while at Ne3 site in all odd years during 2001 to 2013. The gap-free hourly meteorological variables, i.e.
wind speed, surface air temperature, humidity, pressure, precipitation, downward shortwave and longwave
radiation, and surface fluxes including sensible and latent heat (SH and LH), gross primary productivity
(GPP) and net ecosystem exchange (NEE) during 2001 to 2013 are obtained from the FLUXNET2015 Tier
1 dataset (http://fluxnet.fluxdata.org/data/fluxnet2015-dataset/). The ground-based crop growth
observations at various stages during 2003 to 2013 maintained as part of the Carbon Sequestration Program
(CSP) at UNL ARDC (http://csp.unl.edu/Public/sites.htm) are also used in our study. The CSP dataset

10
contains crop phenological stages, seasonal variations of LAI and canopy height, as well as aboveground
biomass observations for green leaves, dead (yellow) leaves, stem and reproductive parts of maize (kernel,
cob, husk, ear shank, silk), which were made from destructive samples after drying to a constant temperature
of 105 oC. In the CSP observations, green leaves encompass all green leaf material from the collar to the
leaf tip, yellow leaves are defined as greater than 50% necrotic (or entirely yellow) leaf and the stem
includes stem, leaf sheaths, immature or undeveloped ears and unfurled leaves (see Law et al. (2008) for
further details). The observed sowing date information at the three Mead sites is also used here as an
additional model input.
The other four AmeriFlux sites used here are all maize-soybean rotation cropping systems: Bondville site
(US-Bo1) (Meyers and Hollinger 2004, Bernacchi, Hollinger and Meyers 2005) and Fermi lab agriculture
site (US-IB1) (Allison et al. 2005) in Illinois, the Brooks Field Site 10 (US-Br1) (Hernandez-Ramirez et al.
2011) in Iowa and the Rosemount-G21 site (US-Ro1) (Baker and Griffis 2005, Griffis et al. 2008) in
Minnesota. As these four sites are not included in the FLUXNET2015 Tier-1 dataset, we obtained the level-
2 dataset from the AmeriFlux website. A gap filling procedure for the meteorological variables was
conducted using the ERA-Interim dataset following the FLUXNET2015 gap filling method (Vuichard and
Papale 2015). LAI and canopy height measurement information for available years at these four sites are
also used in this study to evaluate the model performance in simulating phenology.
To further evaluate the simulated yield response to growing season temperature and precipitation variations
at the three Mead sites, the annual county-level maize yield statistics from the United States Department of
Agriculture (USDA) National Agricultural Statistics Service (NASS) and aggregated monthly
meteorological data (temperature and precipitation) from the Parameter-elevation Relationships on
Independent Slopes Model (PRISM) dataset (Daly et al. 2008) for Saunders county, Nebraska where the
three Mead sites are located are also used in this study. We assume the spatial scale mismatch here would
have little impact on the yield responses to environmental conditions.

11
Table 2. Environmental abiotic stresses accounted in the CLM4.5 and CLM-APSIM model. Model names in (out) of parentheses mean the specific
stress has been implicitly (explicitly) accounted for in that specific model. Implicit stresses are mainly implemented through temperature response
functions. Note that all stresses in CLM4.5 are also included in CLM-APSIM as the latter is built upon the former.
Process Temperature stress Heat stress Water stress Nitrogen stress Light stress
Photosynthesis CLM4.5, CLM-APSIM (CLM4.5), (CLM-APSIM) CLM4.5, CLM-APSIM CLM4.5, CLM-APSIM CLM4.5, CLM-APSIM
Respiration CLM4.5, CLM-APSIM -- CLM4.5, CLM-APSIM -- --
Phenology (CLM-APSIM) (CLM-APSIM) CLM-APSIM CLM-APSIM --
Carbon allocation -- -- CLM-APSIM CLM-APSIM CLM-APSIM
Grain number -- CLM-APSIM -- -- --
Grain filling CLM-APSIM (CLM-APSIM) CLM-APSIM CLM-APSIM --

Table 3. Information about the seven AmeriFlux sites used for model evaluation. MAT and MAP represent mean annual temperature and
precipitation (not including irrigation amounts for the US-Ne1 and Ne2 sites), respectively.
Altitude MAT MAP Available
Site Latitude Longitude Location Crop Types and Management References
(m) (oC) (mm) Years
US-Ne1 41.1651 -96.4766 361 Mead, NE 10.07 790 2001-2013 Irrigated, continuous maize (Verma et al. 2005, Suyker et
al. 2005, Suyker and Verma
2012)
US-Ne2 41.1649 -96.4701 362 Mead, NE 10.08 789 2001-2013 Irrigated, maize in odd years and (Verma et al. 2005, Suyker et
soybean in even years before 2009, al. 2005, Suyker and Verma
maize after 2009 2012)
US-Ne3 41.1697 -96.4397 363 Mead, NE 10.11 784 2001-2013 Rainfed, maize in odd years and (Verma et al. 2005, Suyker et
soybean in even years al. 2005, Suyker and Verma
2012)
US-Ro1 44.7143 -93.0898 290 Rosemount, MN 6.40 879 2004-2012 Rainfed, maize in odd years and (Baker and Griffis 2005,
soybean in even years Griffis et al. 2008)
US-Bo1 40.0062 -88.2904 219 Bondville, IL 11.02 991 1996-2008 Rainfed, maize in odd years and (Meyers and Hollinger 2004,
soybean in even years Bernacchi et al. 2005)
US-Br1 41.6915 -93.6914 313 Brooks, IA 8.95 842 2005-2011 Rainfed, maize in odd years and (Hernandez-Ramirez et al.
soybean in even years 2011)
US-IB1 41.8593 -88.2227 226 Batavia, IL 9.18 929 2005-2011 Rainfed, maize in even years and (Allison et al. 2005)
soybean in odd years

12
2.4 Experiment design
The model initial conditions have significant impacts on the subsequent estimation of C-N stages of
terrestrial ecosystem (Thornton and Rosenbloom 2005, Shi et al. 2013). Before full simulation experiments,
three-step spin-up experiments are conducted separately for all the seven sites to ensure steady-state initial
conditions in CLM4.5. Firstly, 1000-year accelerated decomposition spin-up experiments are conducted
using the C3 grass PFT, and with the atmospheric CO2 concentration set at 1860 levels, by repeatedly using
the CRU-NCEP climate reanalysis dataset during 1901 to 1920. We then continue with transient CO2
simulations with the C3 grass PFT from 1861 to 1920 by repeatedly using the 1901–1920 atmospheric
conditions and proceed with the remaining transient CO2 simulation from 1921 to 2010 with the rainfed
maize PFT. Standard for LSMs, the model state reaches equilibrium and a steady state when no temporal
drifts are observed in the slowest storage pools, such as total soil organic matter carbon, total ecosystem
carbon, and terrestrial water storage in CLM. As the studied crop sites have been long-term managed, the
steady state assumption may be not true but this uncertainty is not considered here in our study. After spin-
up experiments, we observe no significant trends in the total soil organic matter carbon and its absolute
values are within the range with previous studies done for agricultural ecosystems in the Corn Belt of United
States (Chen et al. 2015, Drewniak et al. 2015, Sus et al. 2013, Levis, Hartman and Bonan 2014). Both the
original CLM4.5 and CLM-APSIM are then run at the seven sites in the single-point mode with the same
initial conditions from the spin-up experiments and their respective observed forcing variables. Model-data
comparisons are conducted and three statistical metrics, including coefficient of determination (R2), root
mean square error (RMSE) and index of agreement (IOA) (see detailed definition in the note of Table 4),
are used to evaluate the model improvement.
We build the CLM-APSIM model with minimum parameter tuning. Only parameters in the potential carbon
allocation scheme to aboveground organs (see Eq. (B20)) and the dynamic SLA scheme (see Eq. (B26))
are calibrated using the observations at the Mead continuous irrigated maize site (Ne1 site). To ingest the
observed phenological stages which were recorded in Hanway scale (Ritchie, Hanway and Benson 1986),
we convert the observed stages into APSIM stages following the conversion method described in
Supporting Text S1. The ratios of differentiated organ biomass observations to differentiated total AGB
observations are used to constrain the allocation parameters to aboveground pools in Eq. (B20). Observed
SLA is derived as the ratio of observed LAI and leaf carbon and then used as constraint to parameters in
Eq. (B26). All other parameters in the CLM-APSIM model are either adopted directly from APSIM model
or empirically set without calibration (see Table B1). Thus, the model evaluation results at Ne1 site is partly
independent while the results at all other six sites are totally independent from the model calibration.

3. Results and analysis

3.1 Uncertainty in simulating sowing date
Fig. S1(a) shows the observed sowing dates at the three Mead sites. The observed sowing dates range from
early April to late May with considerable interannual variability. Fig. S1(a) also shows the starting/ending
dates of planting (dashed line) and the average planting date (solid line) that are extracted for the study sites
from a global crop calendar dataset with a spatial resolution of 5′ (Sacks et al. 2010); The planting date
range in this global crop calendar dataset can be as large as two months, equivalent to half of the maize
growing season length, indicating great spatial heterogeneity of sowing date. The differences between the
observed and simulated sowing dates by CLM4.5 and CLM-APSIM at the three Mead sites are shown in
Fig. S1(b) and S1(c), respectively. CLM4.5 consistently estimates earlier sowing dates, a known deficiency
of the CLM4.5 crop model, which causes overestimation of LAI in the early growing season and earlier

13
peak LAI when compared with observations (Levis et al. 2012, Drewniak et al. 2013). Sowing dates
estimated by the new scheme in CLM-APSIM are closer to the observations than those from original sowing
scheme in CLM4.5 which has an earlier bias of about 20 days, but we still see earlier bias of about 10 days
in CLM-APSIM. Due to the large uncertainties in estimated sowing dates by models, we force both the
CLM4.5 and CLM-APSIM models with observed sowing dates in subsequent model evaluations in order
to examine the other improvements to the model.
3.2 Phenology of LAI and canopy height
The simulated LAI and canopy height by CLM4.5 and CLM-APSIM for the IB1 site in 2008 and for other
six flux sites in 2007 are compared with observations in Fig. 2 and Fig. 3. CLM4.5 generally overestimates
LAI and canopy height during the vegetative stage at the seven sites. This is attributed to early leaf
emergence (Chen et al. 2015) estimated by CLM4.5. CLM4.5 also simulates earlier flag leaf development
than the observations, thus maintaining constant maximum LAI before leaf senescence, which happens
after the start of grain-filling, and also keeping canopy height unchanged for the rest of the growing season.
At the three Mead sites, the prescribed constraints for the maximum LAI and canopy height in CLM4.5 (a
maximum LAI at 5.0 m2͑ m-2, and a maximum canopy height at 2.5 m) seem unrealistic, as the observed
maximum LAI and canopy are a bit higher than these constraints. CLM-APSIM outperforms CLM4.5 in
simulating the phenology of LAI and canopy height. From the observations, compared with irrigated sites
(Ne1 and Ne2), maize at the rainfed sites has a lower LAI especially during the peak growing season. The
CLM4.5 fails to reproduce this difference, while CLM-APSIM shows a better ability to capture the impact
of irrigation on maize phenology. Comparison results for other years at the three mead sites shown in
supplementary Fig. S2 and S3 are also consistent with the results in Fig. 2 (a)-(c) and Fig. 3 (a)-(c). We
also notice that CLM-APSIM model slightly underestimates the LAI at Bo1 site and underestimates the
maximum canopy height at Ro1, Bo1 and IB1 sites.

14
Fig. 2. Comparison between simulated and observed leaf area index (LAI) at the seven AmeriFlux sites.
Results in 2008 at IB1 site and in 2007 for other six sites are shown here, while comparisons results for
other years for these sites can be found in the supplementary materials.

15
Fig. 3. Comparison between simulated and observed canopy height (Htop) at the seven AmeriFlux sites.
Results in 2008 at IB1 site and in 2007 for other six sites are shown here, while comparisons results for
other years for these sites can be found in the supplementary materials. Note that observations of canopy
height at Br1 site in 2007 are not available.

3.3 Surface energy and carbon fluxes

The surface flux parameterizations in CLM-APSIM are the same with those in CLM4.5, and thus any
performance changes in surface flux simulation between the two models are due to the improved
phenological development and carbon allocation schemes described in Section 2.2. Error statistics for
hourly gross primary production (GPP), net ecosystem exchange (NEE), latent heat flux (LH), and sensible
heat flux (SH) at the seven flux sites are summarized in Table 4. Time series comparison of simulated and
observed weekly fluxes are also shown in Fig. S4-S7 for the three Mead sites and Fig. S8-S11 for the other
four sites. Overall, CLM-APSIM improves the flux simulation with higher R2 and lower RMSE values than
CLM4.5 only with some minor exceptions. For example, the CLM-APSIM model simulated GPP matches

16
better with observations at the Ro1 site as the R2 increased from 0.37 to 0.66, RMSE decreased from 0.69
to 0.53 gC͑ m-2͑ h-1, and IOA increased from 0.74 to 0.86. We find that the flux simulation improvement
to happen mainly in GPP and NEE, and that these improvements are strongly tied to the improved crop
phenology. Improvements in LH and SH are also observed, but they are relatively marginal with smaller
improvements in R2 and RMSE compared with GPP and NEE.

17
 Table 4. Error statistics of hourly surface fluxes in the growing season (May to September) simulated by CLM4.5 and CLM-APSIM. GPP, NEE, LH and SH represent gross primary production,
net ecosystem exchange, latent heat and sensible heat fluxes, respectively. R2, RMSE and IOA stand for coefficient of determination, root mean square error and index of agreement, respectively.
Superior performance is marked in the bold font.

GPP NEE LH SH
RMSE RMSE RMSE RMSE
Site R2 IOA R2 IOA R2 IOA R2 IOA
(gC͑ m-2͑ h-1) (gC͑ m-2͑ h-1) (W͑ m-2) (W͑ m-2)
CLM- CLM- CLM- CLM- CLM- CLM- CLM- CLM- CLM- CLM- CLM- CLM-
CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM CLM
APSIM APSIM APSIM APSIM APSIM APSIM APSIM APSIM APSIM APSIM APSIM APSIM
Ne1 0.71 0.77 0.59 0.61 0.90 0.90 0.71 0.77 0.46 0.43 0.92 0.93 0.79 0.84 86 77 0.94 0.96 0.48 0.52 72 62 0.79 0.83
Ne2 0.58 0.66 0.72 0.78 0.83 0.83 0.58 0.66 0.55 0.55 0.86 0.88 0.76 0.80 91 86 0.93 0.94 0.42 0.42 75 67 0.78 0.79
Ne3 0.32 0.58 0.75 0.84 0.73 0.78 0.36 0.61 0.59 0.59 0.76 0.84 0.49 0.67 118 98 0.83 0.90 0.35 0.39 103 80 0.71 0.76
Ro1 0.37 0.66 0.69 0.53 0.74 0.86 0.43 0.66 0.50 0.39 0.80 0.89 0.58 0.58 95 96 0.84 0.84 0.36 0.33 65 66 0.74 0.70
Bo1 0.29 0.52 0.75 0.62 0.68 0.80 0.32 0.52 0.56 0.45 0.73 0.84 0.48 0.56 99 97 0.79 0.82 0.20 0.29 78 71 0.65 0.71
Br1 0.40 0.63 0.77 0.58 0.76 0.86 0.42 0.55 0.57 0.49 0.80 0.85 0.54 0.63 100 90 0.84 0.88 0.30 0.41 61 56 0.69 0.74
IB1 0.53 0.77 0.65 0.46 0.81 0.90 0.55 0.74 0.46 0.35 0.85 0.92 0.72 0.71 74 74 0.90 0.90 0.30 0.27 52 55 0.72 0.71
= 1.0 − ∑ − ∑ ( − ), = ∑ ( − ) ⁄ , = 1.0 − ∑ ( − ) ⁄∑ (| − | + | − |)
Where and represent the observations and model predictions, respectively. = + . The overbar ∙̅ represents expectation and |∙| represents absolute value.

18
3.4 Carbon allocation to organs
Fig. 4 compares the simulated above ground biomass (AGB) and below ground biomass (BGB) from the
two models at the three Mead sites in 2007, with the comparison results of other years shown in the
supplementary material. CLM4.5 consistently underestimates the AGB, in some years by a factor of two.
We also find an unrealistic “three-stage” increase in the CLM4.5 simulated AGB. The AGB increases fast
during the early period of growing season and then remains stable until the start of grain-filling, during
which the carbon allocation to grain begins in CLM4.5. In the CLM4.5, all available carbon is allocated to
root when the prescribed maximum LAI is reached before the grain-filling stage–this approach is used for
the convenience of simulation and has little theoretical basis. The CLM-APSIM estimated AGB better
matches the observations. The AGB comparison results for other years at the three Mead sites shown in
Fig. S12 also reveal superior performance of CLM-APSIM. BGB in CLM4.5 is consistently higher than
that from CLM-APSIM at the three Mead sites as shown in Fig. 4 (b), (d) and (f) for year 2007 and also in
Fig. S13 for other years. The BGB fraction in total biomass and the root-to-shoot ratio at the three Mead
sites are compared in Fig. S14 and Fig. S15. CLM4.5 simulates lower BGB fraction in total biomass and
root-to-shoot ratio than CLM-APSIM in the early growing season, indicating fast growth of leaf and stem
in CLM4.5 and this is consistent with the steep increase of LAI and canopy height shown in Fig. 2 and 3.
After that, the BGB fraction in total biomass and root-to-shoot ratio simulated by CLM4.5 suddenly
increase, since all the available carbon is allocated to the root after the flag leaf appears in CLM4.5. The
root-to-shoot ratio has unrealistically high values of up to 5.0 in CLM4.5, while the observed root-to-shoot
ratios for maize generally are below one and decrease throughout maize growth (Anderson 1988, Hébert,
Guingo and Loudet 2001, Amos and Walters 2006). The CLM-APSIM model well reproduces the observed
general range and the decreasing trend of root-to-shoot ratio with the phenological progression (see Fig.
S15) (Amos and Walters 2006).
The simulated fractions of leaf, stem and reproductive biomasses in AGB by CLM4.5 and CLM-APSIM
are compared with observations at the three Mead sites in 2007 shown in Fig. 5. Results for other years at
the three Mead sites are given in Fig. S16 to S18. Similar to the AGB shown in Fig. 4, the leaf and stem
fractions in AGB simulated by CLM4.5 also show the unrealistic “three-stage” dynamics. CLM4.5
overestimates the leaf fraction and underestimates the stem fraction in AGB after the flag leaf stage.
CLM4.5 also consistently overestimates the reproductive fraction in AGB during the entire reproductive
phase. CLM-APSIM generally reproduces the observed carbon allocation to different aboveground organs,
with some minor underestimation of the leaf carbon fraction and overestimation of stem carbon fraction
during the earlier vegetative phase.
The temporal dynamics of the carbon storage pools simulated by CLM4.5 and CLM-APSIM are averaged
and compared with observation averages over the three Mead sites in Fig. 6 and the results for each site are
shown in Fig. S19. CLM4.5’s overestimation of root biomass and underestimation of AGB pools (leaf,
stem, and grain) is clearly seen. CLM-APSIM corrects this deficiency and is able to reproduce the
observations.

19
Fig. 4. Simulated and observed aboveground biomass (AGB, left column) and belowground biomass (BGB,
right column) from CLM4.5 and CLM-APSIM at the three Mead sites (Ne1, Ne2, Ne3) in 2007. BGB
observations at the three Mead sites are not available. Comparisons results for other years for the three
Mead sites can be found in the supplementary materials.

20
Fig. 5. Simulated and observed leaf biomass fraction ( , left column), stem biomass fraction ( ,
middle column), and reproductive biomass fraction ( , right column) in AGB from CLM4.5 and CLM-
APSIM at the three Mead sites (Ne1, Ne2, Ne3) in 2007. Comparisons results for other years for the three
Mead sites can be found in the supplementary materials.

Fig. 6. Comparison between the observed biomass pools (b) and the simulated biomass pools from CLM4.5
(a) and CLM-APSIM (c) at the three Mead sites. Data are averaged over three sites and all available years.

21
Shaded areas represent ±1 confidence intervals obtained through 1000 times bootstrapping sampling.
Root biomass was not measured at the Mead sites.

3.5 Yield, grain number, grain size and their responses to climate variability
“Harvest index” (HI) is an important agronomic concept that describes the proportion of carbon from the
ABG that is converted to the final crop yield. HI essentially characterizes the carbon allocation between the
grain pool and other pools. Though process-based crop models usually do not explicitly simulate HI, HI
can be derived based on the model simulation results. We compute the HI from the grain carbon and above
ground carbon pools at harvest time simulated by both CLM4.5 and CLM-APSIM, and compare the model
estimations with field observations at the three Mead sites in Fig. 7. The observations show that the HI of
maize is around 0.65. The interannual variability at the rainfed sites is much larger than it is at the two
irrigated sites, which is expected. The CLM4.5 simulated HI is biased high, while the HI estimated from
CLM-APSIM better agrees with the observations with only slight underestimation. The CLM-APSIM
model also slightly underestimates the interannual variability of HI at the rainfed site.
The crop yields simulated by the two models are compared with the site observations in Fig. 8. The yield
simulated by CLM4.5 has a large negative bias, which is mainly caused by the underestimation of AGB,
though its negative impact on final yield is compensated by the overestimation of HI in CLM4.5. CLM-
APSIM not only improves the correlation between simulated and observed yield (R2 increased from 0.42
to 0.57) but also significantly reduces the negative bias compared with the simulated yield of CLM4.5. The
slight underestimation of yield in CLM-APSIM is related to the minor underestimation of HI, which is
determined by the carbon allocation process to the grain pool during the reproductive phase.

Fig. 7. Observed and simulated maize harvest index at the three Mead sites during 2003-2013. The lower
and upper boundary lines of the boxes represent the 25% (Q1) and 75% (Q3) percentiles while the
horizontal lines in the boxes represent the median values. Data values larger than Q3+1.5×(Q3-Q1) or
smaller than Q1-1.5×(Q3-Q1) are plotted as outliers with red plus symbols. The whiskers extend to the
adjacent values which are the most extreme data values not treated as outliers.

22
Fig. 8. Comparison between the simulated and observed maize yield at the three Mead sites during 2003-
2013. “Irrigated” maize includes Ne1 and Ne2 sites while “Rainfed” maize is for Ne3 site. Each dot in this
figure represents one site-year for maize. Black and purple colors refer to simulated results from CLM4.5
and CLM-APSIM models, respectively.

23
Fig. 9. Yield responses to mean temperature (left column) and total precipitation (right column) during
the growing season (June, July and August) at the three Mead sites from 2003 to 2013. The upper,
middle and lower panels are for site-based observation, NASS-based observation, and model
simulations (solid circles: CLM4.5 and open circles: CLM-APSIM), respectively. Blue and red colors
in this figure represent irrigated and rainfed maize years. Equations without p-values represent that the
linear regression is not significant at the 0.1 level (p>0.1). Note that at the county scale, the precipitation
amount doesn’t include the irrigation amount for irrigated maize (right column in middle panel) while
at the site scale, the precipitation amount includes the irrigation amount at the three Mead sites.

24
Fig. 10. The simulated responses of grain number (left column) and grain size (right column) to mean
temperature (upper panel) and total precipitation (lower panel) during the growing season (June, July and
August) from 2003 to 2013 at the three Mead sites by CLM-APSIM model. Blue and red colors in this
figure represent irrigated and rainfed maize years. Equations without p-value represent that the linear
regression is not significant at the 0.1 level.

The simulated yield responses to mean temperature and total precipitation during the most active portion
of the growing season (June, July and August) are compared with both site-level and county-level
observations in Fig. 9. Generally, the simulated results are as expected with climate variability having less
impact on irrigated maize yield than on rainfed maize yield. Rainfed maize yield decreases with increasing
mean temperature and increases with increasing growing season precipitation. These relationships are more
apparent in observations at the county scale than at the site scale, mostly due to the sample size, as we have
continuous reported county-level rainfed maize yield from NASS, while we have much smaller sample
sizes at the site level, i.e. rainfed maize were only grown for odd years at the rainfed Mead site (Ne3) during
2001 to 2013. Notably, the CLM4.5 simulated yield has a non-significant positive trend with increasing
temperature for both irrigated and rainfed maize, which is in contrary to the observations. While CLM-
APSIM successfully reproduces the negative response to temperature of maize yield in both irrigated
(significant at p<0.01) and rainfed (not significant) conditions. For precipitation, both CLM4.5 and CLM-
APSIM reproduce increased yield with increasing precipitation amount for rainfed maize. However, the
rainfed maize yield simulated by CLM-APSIM shows much higher sensitivity to precipitation than CLM4.5,
indicating CLM-APSIM may overestimate the impact of water stress on final maize yield.

25
The CLM-APSIM model has the capability to simulate grain number and grain size. The simulated grain
number and grain size show responses to temperature and precipitation during the growing season (June to
August) which combined determine the final crop yield, as shown in Fig. 10. For the grain number, there
is a statistically significant (p<0.01) relationship between grain number and increasing mean temperature
for irrigated maize, and a non-significant negative relationship with increasing mean temperature for rainfed
maize. The grain size significantly increases with increasing precipitation amount for both irrigated (p<0.05)
and rainfed (p<0.1) maize, and the slope for rainfed maize (2.02 ∙ ∙ ) is much larger than
that for irrigated maize (0.50 ∙ ∙ ). The simulated grain sizes for both irrigated and
rainfed sites decrease with increasing mean temperature, though the relationship for rainfed site is not as
significant as that at irrigated sites. The simulated grain size for rainfed site also increases significantly
(p<0.1) with increasing precipitation. The non-significant decreasing relationship with increasing
precipitation for grain size at the irrigated sites is mainly attributed to the increasing grain number at this
favorable condition.

Fig. 11 Correlation coefficients between harvested maize yield and monthly mean temperature (Tmean) (a)
and maximum temperature (Tmax) (b) in growing season (June, July and August) during 2003 to 2013 at
the rainfed Mead site.

We further diagnose the relationship between different periods of the growing season and the final yield,
by comparing the correlations between rainfed maize yield and monthly mean temperature in June, July
and August, respectively, from both observations and model simulations, as shown in Fig. 11. The final
yield is always negatively correlated with temperature in summer months at the site-scale and county-scale
observations, and this negative correlation is more prevalent in July when flowering occurs which affects
grain number. Both CLM4.5 and CLM-APSIM reproduce the negative correlation between final yield and
temperature in July and August, and the CLM-APSIM simulations are closer to the observations than
CLM4.5. However, both models underestimate the observed negative correlation in June.

26
4. Discussion
Advanced crop modeling capability is urgently needed to address short-term predictability of food
production and long-term projection and adaptation of agricultural systems under climate change. Two
major families of crop models are currently used in the community: one is the agronomy crop model and
the other one is LSM-based crop model, each with their strengths and weaknesses (see Table 1 for a
comparison between CLM4.5 and APSIM as an example of the differences in these two type of models).
Here we developed a model (i.e. CLM-APSIM) that largely integrates the strengths of both families of crop
models. Previous crop models in the ESM context were mostly used to provide a better surface flux
simulation for land-atmosphere interaction (Levis 2014), however recent and increasing interests of the
research community in food security and food-energy-water nexus have called for a much higher standard
in simulating crop yield itself. This trend motivates us to reconsider the details of crop growth
parameterization in ESMs, such as carbon allocation, Harvest Index, and their response to climate
variability. Our current work fills this gap by developing an advanced crop model that can be used in the
earth system modeling framework for regional and global assessment.
Specifically, we made two major contributions in this new model. Firstly, we have significantly improved
the representation of maize phenological development in CLM-APSIM. The 3-phase phenology scheme in
CLM4.5 was replaced by the 12-stage APSIM phenology scheme with only small increase of extra model
parameters (Fig. 1). The updated and more detailed phenology scheme enabled the simulation of specific
environmental stresses during different phenological stages. The importance of heat stress on flowering
stage (which determines the number of grain) and the grain filling stage (which determines the size of grain)
(Eyshi Rezaei et al. 2015, Rattalino Edreira, Mayer and Otegui 2014, Rattalino Edreira et al. 2011) has been
well documented. The original crop model in CLM4.5 considers little on these aspects, and thus its
simulated crop yield is much less sensitive to climate variability when benchmarking with the observations
(Fig. 9, 10 & 11). CLM-APSIM has significantly improved these sensitivities by adopting the APSIM’s
scheme as demonstrated by our results. Secondly, the CLM-APSIM model successfully corrects the
deficiencies in carbon allocation scheme of CLM4.5. Our results revealed that the carbon allocation scheme
in CLM4.5 is not realistic, as it largely underestimates above ground carbon pools and overestimates below
ground parts (Fig. 4 and 6). Also, the simulated Harvest Index in CLM4.5 is significantly higher than
observations (Fig. 7). These deficiencies in the original crop model of CLM4.5 lead to a reasonable range
of simulated crop yield (also note the significant negative bias in the simulated yield shown in Fig. 8), but
with the wrong intrinsic mechanisms, which would lead to possibly inaccurate results in future climate.
New model development always requires field-level data for calibration. The improvement reported here
would not be possible without the detailed and long-term biomass CSP data collected in the Nebraska Mead
sites (Verma et al. 2005, Suyker and Verma 2012), which is rarely seen elsewhere. This again highlights
the importance of high-quality field-level data for modeling development. We suggest the modeling
community to continue working with agronomists to further collect such detailed crop biomass data at
multiple locations to improve the crop modeling.
We notice that the CLM-APSIM model still could not fully capture the yield responses to climate in the
growing season, especially the yield responses to mean temperature in June (Fig. 11). We tentatively
attribute this deficiency to the original CLM4.5, as most of the CLM-APSIM improvements are in the
reproductive stage (i.e. post middle July in the US) and some processes in CLM4.5 require more validation
and improvements. For example, CLM4.5 may underestimate the impact of vapor pressure deficit (VPD)
on photosynthetic rate, and it may not simulate sufficient feedback between early growing season
evapotranspiration and later season soil water deficit which affects yield formation in the models. In reality,
higher temperature or VPD in early growing season would lead to increased water loss through

27
evapotranspiration, which can amplify water deficit in later growing season. Besides, currently pest and
weed impacts on crop yield have not been simulated in most crop models and it is also the case here.
Nevertheless, we argue that the CLM-APSIM model contains the most complete and comprehensive
processes for simulating crop responses to environmental stresses (see Table 2) among the current
generation of ESM-level crop models. With this capability, the CLM-APSIM model can be potentially used
to parse the overall temperature effects on crop yield into different processes, which is of great value to
choose potential adaptation strategies and to assess the potential climate change impact on global food
production.
We further highlight some opportunities here for future development. Firstly, more efforts are needed to
parameterize the sowing date from both climate and societal perspectives considering the importance of
sowing date in phenological development and its dependence on farmer’s decision. We made attempts to
account for the impact of soil temperature and soil moisture on sowing (Dobor et al. 2016) and obtained
some improvements in sowing date estimation though still with bias (see supplementary Fig. S1). Sowing
date information in global crop calendar dataset (Sacks et al. 2010) has been used as a benchmark for large
scale simulations and for calibration in some global crop models (Deryng et al. 2011); however, its
uncertainty is large and it cannot provide the interannual variability information for sowing date (see
supplementary Fig. S1). Using satellite data or other ancillary data to develop prognostic sowing date
scheme is not only necessary but also feasible (Urban, Guan and Jain in review). Secondly, we need more
experimental data to validate the model improvement and constrain the model parameters. Here we used
the CSP dataset from the three Mead sites which is, to our best knowledge, the longest observations of
maize phenological development and aboveground biomass, to support calibration and validation of CLM-
APSIM model. However, the simulated root biomass dynamics was still not fully validated due to lack of
belowground biomass observations. Another example is about heat stress parameterization. Though Stefan
et al. (2014) showed that the leaf temperature may be more appropriate to quantify the heat stress on crop
growth, more experimental studies are needed to establish a proper heat stress function for maize using
measured leaf temperature before transitioning to the use of the simulated leaf temperature in CLM-APSIM.
Thirdly, more biotic processes, such as pest and disease, and corresponding management practices should
be accounted in the future. Fourthly, more efforts should be devoted to explore the best representation of
various stresses in crop growth parameterization. Due to limited knowledge and experimental data, the
stress functions implemented in CLM-APSIM are empirical and largely unconstrained. Whether there is
double counting for water and nitrogen stresses in current implementation also deserves future exploration.
Last but not the least, more efforts are needed in model parameter estimation for further model performance
improvement. Some previous attempts have been made to calibrate the crop model in CLM (Bilionis,
Drewniak and Constantinescu 2015, Post et al. 2017). However, potentially due to model structural errors
as demonstrated in this study, parameter estimation for crop sites has been found to be less successful as
forest sites (Post et al. 2017). CLM-APSIM model, with its more complete physical processes, may provide
better opportunities for parameter calibration, especially if new remote sensing based phenology monitoring
product for maize (Viña et al. 2004, Gao et al. 2017) or sun-induced chlorophyll fluorescence (SIF) from
spaceborne observations (Zhang et al. 2014, Guan et al. 2016) are used as spatially explicit constraints.

5. Summary
In this study, we presented an updated maize model in the CLM framework, i.e. CLM-APSIM model.
Specifically, compared with the original CLM4.5 crop model, we adopted a more detailed phenology
scheme from APSIM model and incorporated a new carbon allocation scheme. The 12-stage crop
phenology scheme enables us to explicitly simulate the impact of environmental abiotic stresses on maize

28
growth at specific phenological stages in the CLM-APSIM. We found that CLM-APSIM outperforms the
original CLM4.5 at observed sites in simulating the phenology of LAI and canopy height, surface energy
and carbon fluxes, and yield. In particular, CLM-APSIM corrects the serious underestimation of
aboveground biomass (i.e. overestimation of belowground biomass) and overestimation of Harvest Index
in CLM4.5, which lays the foundation for more reasonable yield simulation with more correct underlying
mechanisms. Moreover, 13-year simulation results at the three Mead sites (US-Ne1, Ne2 and Ne3) show
that CLM-APSIM can better reproduce maize yield responses to growing season climate (temperature and
precipitation) than the original CLM4.5 when benchmarked with the site-based and USDA NASS county-
level observations. CLM-APSIM is thus more suitable than its predecessor models in terms of simulating
abiotic environmental stresses on maize yield. This new model provides an improved tool to attribute maize
yield change to various processes under historical and future climate, as well as to assess and design
effective climate adaptation strategies for sustainable agricultural production. Regional validation work of
this model over the US Corn Belt and development of its extension to other crop types (e.g. soybean, wheat,
and rice) are ongoing and will be presented in future studies.

Code and Data Availability

The CLM-APSIM model code and all data used in this study are available by request to Bin Peng
(binpeng@illinois.edu) or Kaiyu Guan (kaiyug@illinois.edu). The CESM/CLM model code can be freely
obtained through http://www.cesm.ucar.edu/.

Acknowledgement
BP and KG acknowledge the supports from the NASA New Investigator Award (NNX16AI56G), USDA
National Institute of Food and Agriculture (NIFA) Foundational Program award (2017-67013-26253), and
Blue Waters Professorship (National Center for Supercomputing Applications of University of Illinois at
Urbana Champaign) awarded to KG. DML acknowledges support from a USDA NIFA award 2015-67003-
23489. This research is part of the Blue Waters sustained-petascale computing project, which is supported
by the National Science Foundation (awards OCI-0725070 and ACI-1238993) and the state of Illinois. Blue
Waters is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for
Supercomputing Applications. We acknowledge the following AmeriFlux sites for their data records: US-
Ne1, US-Ne1, US-Ne3, US-Bo1, US-IB1, US-Br1, and US-Ro1. In addition, funding for AmeriFlux data
resources and core site data was provided by the U.S. Department of Energy’s Office of Science.

29
 Appendixes
Appendix A. Maize growth simulation in CLM4.5
A1. Maize planting in CLM4.5
In CLM4.5, maize is planted when the following criteria in the planting window are met:
>
> (A1)
>
Where and are the 10-day running means of surface air temperature and minimum air
temperature, respectively. and are the temperature thresholds for planting. represents the
minimum growing degree day (GDD) for maize growth. is the 20-year running mean of
accumulated 8 °C based growing degree days ( ) tracked from April through September in the northern
hemisphere and from October through March in the southern hemisphere with a maximum daily increment
of 30 °days:

= + − − 8, ℎ 0≤ − − 8 ≤ 30 · (A2)

Where and represent 2m surface air temperature and freezing temperature, respectively. The last
criterion in (A1) determines the suitable area for maize planting while the other two criteria determine the
planting date in each growing season. The planting window for maize is from April 1 st to June 15th in the
northern hemisphere and from October 1st to December 15th in the southern hemisphere. If the criteria are
not met during the planting window, maize is planted on the last day of the planting window.

A2. Phenological development for maize in CLM4.5

The 3-phase phenology development in CLM4.5 is determined by several heat unit thresholds related to
GDD requirement for maturity (GDDmat) which is defined as the following for maize:

= , , , (A3)

= , ( + , ) (A4)

Where , is a ratio parameter of GDDmat to . and represent the lower and

upper bounds of GDDmat. is maturity GDD requirement for a maize hybrid and is a delta
term for maturity GDD for maize. In CLM4.5, , = 0.85, = 950 · , =
1850 · , = 1700 · and = 150 · .

Leaves start to emerge when the accumulated growing degree days of soil temperature to 0.05 m depth
tracked since planting (GDDTsoil) reaches a heat unit threshold:

ℎ = , × (A5)

30
Where , is a parameter set to be 3% for maize. The heat unit threshold for beginning phase 2
(ℎ ) is estimated through a linear relationship with the Corn Relative Maturity (CRM) rating for
Pioneer-brand maize hybrids grown in the U.S. Corn Belt (Kucharik 2003):

= { [( + 53.683)⁄13.882 , 135.0], 73.0} (A6)

, = −0.002 × ( − 73.0) + , − 0.1 , (A7)

ℎ = , × (A8)

Where is a grain filling parameter and set to be 0.65 for maize.

A3. Carbon allocation for maize in CLM4.5

In CLM4.5, the carbon allocation coefficients are estimated separately for phase 2 and 3. During phase 2,
the allocation coefficients to each carbon pool are defined as:
=0
⎧
⎪
⎪ = − − × 1.0,
× ⁄ (A9)
⎨ −
⎪ = 1− ×
⎪ −1
⎩ = 1.0 − − −
Where , and represent the initial and final carbon allocation coefficients for fine root
and leaf, respectively. is a shape factor controlling the allocation coefficient for leaf during phase 2.
After LAI reaches a predefined maximum value ( ) in CLM4.5, the model stops carbon allocation
to leaf and stem ( =0 = 0) which means all available net carbon goes to root ( = 1)
after peak LAI during phase 2;
During phase 3, the allocation coefficients to each carbon pool are defined as:

⎧ = − − × 1.0,
⎪
⎪ −ℎ
⎪ = , × 1.0 − min 1.0,
× −ℎ
⎨ (A10)
−ℎ
⎪ = , × 1.0 − 1.0,
⎪ × −ℎ
⎪
⎩ = 1.0 − − −

Where represents the final allocation coefficients for live stem. , and are parameters
controlling the allocation coefficient for leaf and stem in phase 3.

A4. Canopy structure for maize in CLM4.5

31
 In CLM4.5, the LAI is calculated from the leaf carbon storage ( ) using a constant specific leaf area
(SLA) during the entire growing season and capped with a predefined maximum:

= × , (A11)

Canopy height is derived from the LAI phenology:

= , × ,1 (A12)
−1
Where = 5.0 ⁄ and , = 2.5 .

A5. Parameters for maize simulation in CLM4.5

Table A1. Main parameters and default values for maize growth simulation in CLM4.5 model

ID Parameter Physical meaning Default value

1 Threshold of 10-day running mean air temperature for planting 283.15
2 Threshold of 10-day running mean of minimum air temperature for planting 279.15
3 Lower bound of 20-year running mean of for planting 50
4 , Ratio of GDDmat to 0.85
5 GDD requirement for maize maturity 1700
6 Lower bound for 950
7 Upper bound for 1850
8 ∆ A delta term for maturity GDD for maize 150
9 , Fraction of heat unit index for leaf emergence 0.03
10 Grain filling parameter 0.65
11 Initial carbon allocation coefficient for fine root 0.4
12 Final carbon allocation coefficient for fine root 0.05

13 The b factor for leaf carbon allocation coefficient during phase 2 0.1
14 Final carbon allocation coefficient for leaf 0.0

15 Final carbon allocation coefficient for stem 0.05

16 Shape factor controlling carbon allocation to leaf in phase 3 5.0
17 Shape factor controlling carbon allocation to stem in phase 3 2.0
18 The decay factor for carbon allocation coefficient 1.05
19 SLA Specific leaf area 0.05
20 Maximum leaf area index for maize 5.0

32
21 , Maximum canopy height for maize 2.5

Appendix B. Maize growth simulation in CLM-APSIM

B1. Maize planting in CLM-APSIM
Providing an option to use the observed sowing date in CLM-APSIM, we also implemented a new planting
scheme considering the impact of soil temperature and moisture on sowing instead of only using air
temperature as in CLM4.5. Maize is planted in CLM-APSIM when the following criteria are met in the
same planting window as in CLM4.5:
>
⎧
⎪ >
(B1)
⎨ , < < ,
⎪ >
⎩ ,

Where , and represent the 7-day running mean of air temperature, averaged soil temperature
and saturation degree in the first three soil layer (0-9 cm) which covers the sowing depth of maize ranging
from 2.5 to 7.5 cm. The thresholds for maize planting are = 283.15 , = 285.15 , , = 0.25
and , =0.75. We considering the soil temperature condition as one of the criteria here as the seed will
absorb water but not initiate radicle (root) and coleoptile (shoot) growth, leading to seed rots and poor
emergence rate in cold soil temperature conditions. The soil moisture condition would also affect farmer’s
decision on sowing as either too low or too high soil moisture content after sowing would lead to poor
emergence rate and vehicle mobility would also be affected by high soil moisture conditions. We also set a
threshold ( , ) for the accumulated thermal time (ATT) since the earliest planting date (April 1st in
the northern hemisphere and October 1st in the southern hemisphere for maize) to trigger the sowing event.
The average soil temperature and saturation degree over the sowing layer are calculated as:

= , (B2)

∑ −∑ ,
= (B3)
∑ , −∑ ,

Where , represents the soil temperature of i-th layer with a thickness of . , , , and , represent
the volumetric soil moisture content, saturated, and residual soil moisture contents of i-th layer, respectively.

B2. Phenological development for maize in CLM-APSIM

Adopted from the APSIM model, there are 12 phenology stages in CLM-APSIM model: 1-sowing, 2-
germination, 3-emergence, 4-end of juvenile (endJuv), 5-floral initialization (fi), 6-flag, 7-flowering, 8-start
of grain filling (startGrainfill), 9-end of grain filling (endGrainfill), 10-muturity, 11-harvest and 12-end of
crop (endCrop) (also see Fig. 1). The phenology development after sowing is driven by the accumulation
of thermal time (TT) at a daily step. In contrast to GDD which has a linear response to air temperature, TT
is a piecewise linear function of air temperature:

33
 0, ℎ ≤ 0℃
⎧(10
⎪ − 0)⁄(18 − 0) × ( − 0), ℎ 0℃ < ≤ 18℃
⎪
10 + (18 − 10)⁄(26 − 18) × ( − 18), ℎ 18℃ < ≤ 26℃
= (B4)
⎨ 18 + (26 − 18) ⁄(34 − 26) × ( − 26), ℎ 26℃ < ≤ 34℃
⎪26 + (0 − 26)⁄(44 − 34) × (
⎪ − 34), ℎ 34℃ < ≤ 44℃
⎩0, ℎ > 44℃

Fig. B1 Comparison of temperature response functions for maize growth simulation in the CLM and CLM-
APSIM models
The temperature response functions for the CLM-APSIM and CLM models for maize growth are the same
when air temperature ranges from 18 to 34 ℃ but differs in both the low ( ≤ 18℃) and high ( >
34℃) temperature regimes (see Fig. B1). In original APSIM model, daily TT was calculated from eight 3-
hourly, third-order polynomial interpolations between the minimum and maximum daily temperatures
which are two input forcings to APSIM (Wilson et al. 1995). Here in CLM-APSIM, the daily TT ( )
is derived from the actual diel temperature cycle as:

= , ℎ = 24⁄ (B5)

Where is the model time step in hour and represents the thermal time at the i-th time step.
The phase change in a certain stage after sowing ( ≥ 2) is calculated from the TT accumulation in
that specific stage accounting for various environmental stresses:

∑ ×
ℎ = (B6)
,

When ℎ ≥ 1.0, the crop finishes the current stage and enters the next stage growth, i.e. =
+ 1. The target TT at each stage ( , ) is cultivar-dependent in the original APSIM.
Currently we set the target TT parameters referencing those for different cultivars in APSIM and with
calibrated modification for maize hybrids planted in US Corn Belt (Archontoulis et al. 2014) (see Fig. B2).

34
 Fig. B2 Target thermal time ( , ) for different phenological stages in CLM-APSIM model

Water and nitrogen stresses are considered in the phenology model of CLM-APSIM. The water stress
functions during the entire vegetative phase (from sowing to flowering) when water deficit occurs, while
nitrogen stress only functions from the end of juvenile stage to the flowering stage when nitrogen deficit
occurs. The stress factor for phenological development is derived as:

max , , , , ℎ ≤ ≤
= min( , , max( , , , )), ℎ < ≤ (B7)
1.0, ℎ
Where , and , are water and nitrogen stress factors, respectively and , and , are their
minimum values (currently set to be 0.5 in CLM-APSIM). The representations of water and nitrogen
stresses are as following (also see Fig. B3):

1.0, ℎ ⁄ ≥
, = (B8)
⁄( × ), ℎ ⁄ <

, = 1.0, 0, , × − , (B9)

Where is a threshold set to be 0.2 in CLM-APSIM. The actual evapotranspiration (ET), leaf nitrogen
content ( ) and green LAI are simulated in CLM and we use the daily average values for the stress
factor calculation here. The potential ET (PET) is calculated using the Priestley-Taylor approach in CLM-
APSIM. , and , are two constants taken from APSIM model.

35
Fig. B3 Response functions of water and nitrogen stress factors for phenology development in CLM-
APSIM model

B3. Grain number simulation for maize in CLM-APSIM

In CLM-APSIM, the potential grain number (PGN) is calculated from the plant growth rate (PGR) in a
short time window around the flowering stage:
, , ,
− , ≤ ≤ + , (B10)
, ,
Where and represent the accumulated target TT from sowing to the
flowering stage and accumulated TT from sowing to the current stage. , = 130 and , =
260 are the two parameters defining the window length. PGR in this window is then derived from dry
aboveground biomass accumulation:

−
= (B11)
, ×
Where and represent the dry aboveground biomass at the beginning of the window and the
current stage. , is the day number in the window. is a model input and represents the
planting density. PGN is then determined according to whether the cultivar is prolific or not:

, ,
= (B12)
,

= , × 1− − , × − , (B13)

= , × 1− − , × − , (B14)

36
 , , , and , are parameters for prolific cultivars while , ,
, and , are parameters for the base cultivars.

In order to account for the unfavorable high temperature impact on grain number, the actual grain number
(GN) in CLM-APSIM model is reduced through multiplying by a heat stress factor ( ):
,
= , × (B15)
100
Where GN is ramped from 0 when just entering the start of grain filling stage and the final grain number
,
when 100 degree days have passed since entering the start of grain filling stage. represents
the accumulated TT in the grain filling period.
The heat stress factor for grain number is calculated around the flag stage:

1.0 − , , ≤ ≤
= (B16)
1.0, ℎ
Where , is a daily temperature factor calculated when a high temperature event exists in a thermal
time window around the flag stage:

, = , ⁄ , − , × (B17)
Where , = −150 and , = 50 are two parameters determining the window
length for heat stress. The daily TT contribution ( , ) in this window is:

⎧
⎪ − , + , , ,
⎪
, =
⎨ (B18)
⎪
⎪min , − , ,
⎩

and the response function to high temperature ( ) is as following:

0, < ,
⎧
⎪ − ,
= , , ≤ ≤ ,
⎨ , − , (B19)
⎪1.0, >
⎩ ,

The two cardinal temperatures in are , = 36℃ and , = 40℃.

B4. Carbon allocation for maize in CLM-APSIM

In the CLM-APSIM model, the phenological stage dependent allocation parameters are simulated through
a two-step approach. In the first step, the potential allocation parameters are modeled with multinominal
logistic functions of crop stage which is similar to the JULES-crop model (Osborne et al. 2015). The

37
difference is that the JULES-crop model utilize a relative crop development index (DVI) (Penning de Vries
et al. 1989) as a predictor for allocation coefficients (Osborne et al. 2015) while we use the twelve ASPIM
phenology stage numbers. These logistic relationships are calibrated against 13-year field observations of
actual maize phenology which are converted into the APSIM stages (see Supplementary Text S1 for the
conversion method) and aboveground biomass component fractions (leaf, stem, and reproductive) at the
irrigated continuous maize site (US-Ne1) at Mead, Nebraska. The assumption here is that the condition at
this site is optimal for maize growth, but this assumption need to be reconsidered when more observations
are available in the future. The potential allocation parameters are:

, = + × ⁄∆
⎧
⎪ , = ( + × )⁄ ∆
(B20)
⎨ , = + × ⁄∆
⎪
⎩ , = 1⁄∆
Where , , , , , and , represent potential allocation coefficients for leaf, stem, fine
root and reproductive organs. and are fitted logistic parameters for different organs, and ∆=
∑ ( + × ) + 1, = , , .
In the second step, the potential allocation parameters for non-reproductive organs are revised by
accounting for the light, water and nitrogen stresses in the vegetative phase (Song et al. 2013) and a demand-
supply stress term accounting for the grain number impact on reproductive carbon allocation during the
grain filling phase is also applied:
= , ⁄[1 + (3 − − − )]
⎧
⎪
⎪ = , + (1 − ) ⁄[1 + (3 − − − )]
= , + (2 − − ) ⁄[1 + (3 − − − )] (B21)
⎨
⎪ × , , 2 × ,
⎪ = , when startGrainfill ≤ stage ≤ endGrainfill
⎩ × [1 + (3 − − − )]

Where = (− ), = , and = , represent the light, water and nitrogen stress factors
to carbon allocation, respectively. is the light extinction coefficient. is a scaling parameter for the
stresses. is the net available carbon for allocation. is a scaling parameter. The excess carbon
due to limited carbon demand during grain filling goes to the fine root carbon pool and thus the carbon
balance is guaranteed. The carbon demand for grain filling ( , ) is derived as:

, = × × (B22)
The actual kernel growth rate (KGR) is calculated from a potential kernel growth rate ( ) regulated
by a stress factor accounting for non-optimal water and temperature conditions during grain filling:

= × (B23)
where is the product of a water stress factor , = , and a temperature stress factor , . ,
is a multi-linear function of 3-hour air temperature with cardinal temperatures of [6.0,10,16,22,30,56.3] and
corresponding stress factor values of [0.0,0.40,0.75,1.0,1.0,0.0] which means the optimum temperature for
grain filling is from 22 to 30 oC and either too low or high temperatures will lead to decreased grain growth
rates.

38
The potential kernel growth rate is calculated by the ratio of potential kernel weight ( ) and total target
thermal time during the grain filling stage:

=
∑ (B24)

B5. Canopy structure for maize in CLM-APSIM

Like the APSIM and JULES-crop models, the canopy height in the CLM-APSIM model is estimated from
the stem carbon pool (Williams et al. 2017):

=κ (B25)
,

In the CLM-APSIM model, the specific leaf area (SLA) is dynamically estimated with a negative power
function of the crop stage:

= γ( ) (B26)
This relationship means that younger crops are able to produce thinner leaves and is consistent with the
observed decreasing trend of SLA along development stages (Danalatos et al. 1994). We also calibrate this
relationship at Ne1 site. This parameterization is different in CLM4.5 where the SLA is constant during the
entire growing season. The green leaf area index (LAI) is then estimated through the dynamic SLA and live
leaf carbon pool:

,
= × (B27)
,

It should be noted that we also removed the maximum canopy height ( , ) and LAI ( )
constraints which apply in original CLM4.5 in our revised CLM-APSIM model.

B6. Parameters for maize simulation in CLM-APSIM

Table B1. Main parameters and default values for maize growth simulation in CLM-APSIM model

ID Parameter Name Physical meaning Default value

1 0.20b
2 ,
3 ,
4 ,
5 ,
A critical point to trigger water stress for phenology
development
Minimum water stress for phenology development 0.50b
Slope parameter for nitrogen stress for phenology
1.79a
development
Interception parameter for nitrogen stress for
0.43a
phenology development
Minimum nitrogen stress for phenology development 0.50a

39
 Thermal time window parameter for determining
6 , 130a
grain number
Thermal time window parameter for determining
7 , 260a
grain number
8 , Maximum grain number for base cultivar 600a
9 , Coefficient for grain number for base cultivar 0.83a
10 , Critical plant growth rate for base cultivar 1.20a
Thermal time window parameter for heat stress to
11 , -150a
grain number
Thermal time window parameter for heat stress to
12 , 50a
grain number
The lower cardinal temperature for heat stress to
13 , 36a
grain number
The upper cardinal temperature for heat stress to
14 , 40a
grain number
, Accumulate target thermal time for reproductive
15 885a
phase
,
16 Accumulate target thermal time for vegetative phase 875a
Logistic parameter for potential leaf carbon
17 21.93c
allocation coefficient
Logistic parameter for potential leaf carbon
18 -2.72c
allocation coefficient
Logistic parameter for potential stem carbon
19 16.09c
allocation coefficient
Logistic parameter for potential stem carbon
20 -1.94c
allocation coefficient
Logistic parameter for potential fine root carbon
21 22.45c
allocation coefficient
Logistic parameter for potential fine root carbon
22 -2.68c
allocation coefficient
A scaling factor of stress terms to carbon allocation
23 0.5b
coefficient
Minimum stress factor to carbon allocation from
24 , 0.5b
grain filling demand
26 Potential kernel weight 300a
27 κ Scaling parameter for canopy height 3.2c
28 λ Scaling parameter for canopy height 0.35c
29 γ Fitted parameter for specific leaf area 0.25c
30 δ Fitted parameter for specific leaf area -0.93c

40
a
parameter values taken from APSIM model
b
parameter values set empirically
c
parameter values calibrated at Ne1 site

41
Appendix C. List of symbols

Symbol Physical meaning Unit

Carbon allocation coefficient for fine root -
,
Potential carbon allocation coefficient to fine root -
Final carbon allocation coefficient for fine root -
Initial carbon allocation coefficient for fine root -
Carbon allocation coefficient for leaf -
,
Potential carbon allocation coefficient to leaf -
Final carbon allocation coefficient for leaf -
Carbon allocation coefficient for reproductive organs -
,
Potential carbon allocation coefficient to reproductive organs -
Carbon allocation coefficient for stem -
,
Potential carbon allocation coefficient to stem -
Final carbon allocation coefficient for stem -
Shape factor controlling carbon allocation to leaf in phase 3 -
Shape factor controlling carbon allocation to stem in phase 3 -
The b factor for leaf carbon allocation coefficient during phase 2 -
The decay factor for carbon allocation coefficient -
Soil depth of the i-th layer m
Scale factor for carbon demand from grain filling -
,
Carbon fraction in dry leaf biomass -
,
Carbon fraction in dry stem biomass -
Stress factor to grain filling -
,
Water stress to grain filling -
,
Temperature stress to grain filling -
Stress response function to high temperature -
Heat stress factor for grain number -
, Fraction of heat unit index for leaf emergence -
, Fraction of heat unit index for the start of grain filling -
Stress factor for phenology development -
,
Nitrogen stress factor for phenology development -
, Minimum nitrogen stress for phenology development -
Interception parameter for nitrogen stress for phenology
, development -

Slope parameter for nitrogen stress for phenology development m2·g-1N

,

42
 ,
Water stress factor for phenology development -
, Minimum water stress for phenology development -
daily temperature factor when a high temperature event exists in
, a thermal time window around the flag stage -

grain filling parameter -

ℎ Heat unit index for the start of grain filling o
C·day
ℎ Heat unit index for leaf emergence o
C·day
Number of days in the thermal time window for determining
, grain number -

Total time step in a day -

Potential kernel growth rate mg·(oC·day) -1
Potential kernel weight mg/grain
A critical point to trigger water stress for phenology development -
,
Ratio of GDDmat to -
Accumulated thermal time since beginning of planting window o
for planting C·day
, Accumulated thermal time from sowing to present stage o
C·day
, Accumulated thermal time from start of grain filling to present o
C·day
, Accumulated target thermal time from sowing to flowering o
C·day
, Accumulated target thermal time for vegetative phase o
C·day
, Accumulated target thermal time for reproductive phase o
C·day
Net available carbon for allocation gC·m-2
,
Carbon demand for grain filling gC·m-2
Carbon pool of leaf gC·m-2
,
Carbon pool of live leaf gC·m-2
Carbon pool of stem gC·m-2
Dry above ground biomass at any time t g·m-2
Dry above ground biomass at the beginning of thermal time
window for determining grain number g·m-2

Actual evapotranspiration mm
o o
8 C-based growing degree day C·day
o
20-year running mean of C·day
o
Maturity GDD for maize hybrid C·day
o
GDD requirement for maize maturity C·day
o
Lower bound for C·day
o
Upper bound for C·day
Lower bound of 20-year running mean of for planting o
C·day

43
 8 oC-based growing degree day calculated from soil temperature o
at sowing depth C·day

Actual grain number -

,
Coefficient for grain number for base cultivar -
,
Coefficient for grain number for prolific cultivar -
,
Maximum grain number for base cultivar -
,
Maximum grain number for prolific cultivar -
Canopy height m
,
Maximum canopy height m
Kernel growth rate mg·(oC·day) -1
Leaf area index m2·m-2
Maximum leaf area index for maize m2·m-2
Light stress factor to carbon allocation -
Leaf nitrogen content gN·m-2
Nitrogen stress factor to carbon allocation -
Potential evapotranspiration mm
Potential grain number -
Potential grain number for base cultivar -
Potential grain number for prolific cultivar -
Plant growth date g·day-1
,
Critical plant growth rate for base cultivar g·day-1
,
Critical Plant growth rate for prolific cultivar g·day-1
7-day running mean of soil saturation degree over the sowing
depth -

,
Lower bound of soil saturation degree for planting -
,
Upper bound of soil saturation degree for planting -
Soil saturation degree of the sowing depth -
Specific leaf area m2·gC-1
Averaged soil temperature over the sowing depth K
Air temperature at 2m above surface K
7-day running mean of 2m air temperature K
7-day running mean of soil temperature over the sowing depth K
10-day running mean of 2m air temperature K
10-day running mean of 2m minimum air temperature K
Freezing temperature of water K
,
The lower cardinal temperature for heat stress to grain number K

44
,
The upper cardinal temperature for heat stress to grain number K
Soil temperature of the i-th layer K
Threshold of 10-day running mean air temperature for planting K
Threshold of 10-day running mean of minimum air temperature
for planting K

Threshold soil temperature for planting K

Thermal time o
C·day
Daily thermal time contribution to the total thermal time window o
, for heat stress C·day

Daily thermal time o

C·day
,
Thermal time window parameter for heat stress to grain number o
C·day
,
Thermal time window parameter for heat stress to grain number o
C·day
Thermal time of i-th sub-daily time step o
C·day
,
Thermal time window parameter for determining grain number o
C·day
,
Thermal time window parameter for determining grain number o
C·day
,
Target thermal time for flag stage o
C·day
,
Target thermal time for the i-th stage o
C·day
, maximum carboxylation rate at the temperature of 25 °C mol·m−2·s−1
Water stress factor to carbon allocation -
Logistic parameter for potential fine root carbon allocation
coefficient -

Logistic parameter for potential leaf carbon allocation coefficient -

Logistic parameter for potential stem carbon allocation
coefficient -

Logistic parameter for potential fine root carbon allocation

coefficient -

Logistic parameter for potential leaf carbon allocation coefficient -

Logistic parameter for potential stem carbon allocation
coefficient -

γ Fitted parameter for specific leaf area -

δ Fitted parameter for specific leaf area -
Model time step hour
ℎ Change of phenology phase in the i-th stage -
A delta term for maturity GDD for maize o
C·day
Soil moisture of the i-th layer m3·m-3
,
Residual soil moisture of the i-th layer m3·m-3
Mean saturated soil moisture for the sowing depth of maize m3·m-3

45
 ,
Saturated soil moisture of the i-th layer m3·m-3
κ Scaling parameter for canopy height -
λ Scaling parameter for canopy height -
Plant density m-2
A scaling factor of stress terms to carbon allocation coefficient -

Appendix D. List of acronyms

AGB Above Ground Biomass

AgMIP Agricultural Model Intercomparison and Improvement Project
Agro㻙IBIS Agricultural version of the Integrated Biosphere Simulator
APSIM Agricultural Production Systems sIMulator
ARDC Agricultural Research and Development Center
ATT Accumulated Thermal Time
BGB Below Ground Biomass
BRACE Benefits of Reducing Anthropogenic Climate changE project
CERES Crop-Environment Resource Synthesis model
CESM Community Earth System Model
CLM Community Land Model
CM-KEN CERES-Maize adapted in Kenya
CM-SAT CERES-Maize for semi-arid tropical environment
CRM Corn Relative Maturity
CropSyst Cropping Systems simulator
CRU Climate Research Unit
CSP Carbon Sequestration Program
DSSAT Decision Support System for Agrotechnology Transfer
DVI Development Index
EPIC Erosion Productivity Impact Calculator or Environmental Policy Integrated Climate
ESM Earth System Model
GDD Growing Degree Day
GGCMI Global Gridded Crop Model Intercomparison project
GPP Gross Primary Production
HI Harvest Index
HUI Heat Unit Index
IBIS Integrated Biosphere Simulator Model
IOA Index of Agreement
ISAM Integrated Science Assessment Model
JULES Joint UK Land Environment Simulator
KGR Kernel Growth Rate
KNP Kernel Number per Plant
LAI Leaf Area Index

46
LH Latent Heat flux
LSM Land Surface Model
LUE Light Use Efficiency
NASS National Agricultural Statistics Service
NCEP National Centers for Environmental Prediction
NEE Net Ecosystem Exchange
NPP Net Primary Production
PET Potential Evapotranspiration
PFT Plant Functional Type
PGN Potential Grain Number
PGR Plant Growth Rate
pKGR potential Kernel Growth Rate
PRISM Parameter-elevation Relationships on Independent Slopes Model
RMSE Root Mean Square Error
RUE Radiation Use Efficiency
SH Sensible Heat flux
SLA Specific Leaf Area
SLN Specific Leaf Nitrogen
TT Thermal Time
UNL University of Nebraska-Lincoln
USDA United States Department of Agriculture
VPD Vapor Pressure Deficit

47
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