Second International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications

Plant modeling and its applications to agriculture

Yan GUO
Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and
Environment, China Agricultural University, Beijing 100094, China
E-mail: yan.guo@cau.edu.cn

Abstract

from the improvement of crop management [1]. The

green revolution in the 1960s largely consisted in the
introduction of dwarf crop varieties e.g. wheat and rice
that can achieve high yield by their more efficient
architecture, and lower risk of lodging for high
chemical fertilizer inputs [2]. China, as an example,
has doubled the crop production in the past 40 years
[3].
On the other hand, the population in developing
countries is increasing rapidly. The Chinese population
is projected to reach 1.6 billion in 2030 [3], and it is
expected the world population will increase to about
10 billion in 2050 [4]. So the increase in food demand
is extremely high. Meanwhile, the arable land area of
the world is decreasing dramatically, because of rapid
urbanization, desertification, environmental pollution
and other factors. It is therefore a challenge to feed
such a large world population and this may result in a
serious problem of world food security. It is urgent to
augment the rate of increase in annual crop yields per
unit area. Therefore, a second green revolution [4] is
required, which is promoted by breeding super-high
yield crop varieties, and an optimized crop
management regime.
Plant growth modeling, which integrates
multidisciplinary knowledge including botany,
agronomy, plant physiology, meteorology, soil science,
mathematics and computer science, has been approved
to be a very useful tool for guiding agronomic
management, and has been used broadly such as in
decision support systems. Plant modeling has been
extended in the past decade by incorporating plant
architecture with plant functioning i.e. functionalstructural plant modeling (FSPM) [5], which can be
used to simulate the growth and development of a
plant quantitatively, including biomass and/or
architecture, the shoot part and/or root system, and the
interaction of the plant with its local environment.
FSPM can be used to provide guide for breeding new
crop varieties by optimizing plant architecture,
improve field management (e.g. planting density

While the world population is dramatically

increasing, arable land is decreasing significantly in
developing countries such as China. As a result, food
security is and will be a primary concern, especially
for developing countries with huge population and
limited arable land resources. To sustain food supplies,
it is urgent to conduct research towards a second
green revolution, which will build high crop yields by
means of developing super-high yield varieties and
optimizing management practices. The functionalstructural plant models have the potential to provide
robust tools for designing crop ideotype and best
management regimes.
A functional-structural plant model is built up by
integrating ecophysiological knowledge and plant
structural growth dynamics. It can be used to simulate
the resource acquisition, biomass production and
partitioning in plants at organ, plant, and plant stand
levels. Thus it can be used to design and optimize the
morphological traits for new crop varieties so that they
can capture resources (e.g. sunlight) more efficiently.
Developing countries, such as China, are facing the
problems of irrigation water shortage, low soil fertility,
and abuse of inorganic fertilizers, pesticides and
herbicides. Optimized field management regimes are
required to solve these troubles. And these
management regimes can be achieved with simulation
by plant models, which incorporate the function and
structure of plants aerial part and root system,
coupling with micro-environmental models e.g. soil
water and solute transportation models.

1. Introduction
World crop production increased dramatically in
the past century, especially after the World War Two.
The analysis of the reasons for the improvements in
world crop yield showed that half of crop yield
increase was due to the change in the genetic potential
of the crop, e.g. hybrid rice in China, and the other half

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arrangement, irrigation and fertilization scheduling). It

will take a key position in the second green revolution.
The present paper introduces the basic concepts of
plant growth modeling, mainly concentrates on
functional-structural plant modeling. Then the
agronomic applications of FSPM are discussed,
including designing the ideotype of a super-high yield
crop, and optimization of crop management. The
applications of FSPM in agricultural extension are also
discussed.

2. Modeling plant growth and

interactions with its environment

such as LIGNUM [17] and GREENLAB [18] were

presented to simulate plant morphogenesis on a
biomass basis, plant growth is computed incrementally
and the biomass acquired is distributed among organs
generated by the architectural model, which is at the
same time a phenological model. Final organ size is
variable depending on biomass budgets, and
constrained by allometric rules.

2.1 Plant modeling at organ, plant and canopy

level

the

Functional-structural plant models simulate

individual plant growth based on organ kinetics. Fig. 1
illustrates the simulation of maize plant growth
responding to its environmental conditions with the
GREENLAB model [19][20]. In this model, organ
initiation and expansion were monitored with thermal
time, the biomass production of maize plant was
computed according to the potential evapotranspiration
which connects with the climatic conditions, the green
leaf area of the maize plant, and the shading by
neighboring plants. The plant biomass produced was
then partitioned to the expanding organs according to
their relative sink strengths and expansion durations. It
can be seen from Fig. 1 that the model is capable of
simulating the organ e.g. cob growth in the early stage
which is not visible externally. Also shown in Fig. 1 is
a 3-D representation of maize plants at 18th and 33th
growth cycles (GCs) constructed by the model. Organ
expansion lasted several growth cycles, so the model is
helpful for analyzing the competition of the biomass
produced among competing sinks. The model can also
output the canopy heterogeneity under different
conditions e.g. plant density or sowing date.

A variety of models have been developed for

quantitatively describing plant growth based on a
description of ecophysiological processes [6][7], which
can be used to simulate synthetic and global variables
of plant growth under varied environmental conditions,
such as leaf area index, mass and number of organs,
total biomass of crops and/or crop yield. These models
have been very useful in farm production management,
particularly when combined with expert systems.
These ecophysiological models rarely treated plant
architecture in detail [8], and they were quite
insensitive to the morphological and architectural traits,
which plant breeders seek in order to improve crop
adaptation and productivity, and in particular to the
study of alternative plant type concepts that may guide
efforts to develop new crops. For example, Dingkuhn
et al. [9] proposed an alternative rice plant type
adapted to high population densities, based in part on
modified assimilate partitioning patterns among organs.
The model used in that study divided the leaf canopy
into horizontal strata, instead of successively appearing
leaves, because of the inability of the non-architectural
model in considering the demand functions generated
by organogenetic processes.
On the other hand, computer graphics scientists
developed models that represent plants very
realistically in three dimensions, for example using
software based on L-systems [10][11] or automata [12].
High degrees of architectural and geometric fit can be
achieved, and the resulting 3-D representation can be
used for different applications such as computing
spatial light distribution in plant canopy [13][14]. The
lack of environmental control of growth through the
plants physiological apparatus, however, limits the
biological and agronomic usefulness of such models.
Recently, functional-structural plant models were
built by incorporating ecophysiological knowledge and
morphology together, thus linking plant architecture
and functions in a whole system [8][15][16]. FSPM

2.2 Modeling the spatial light distribution

within the canopy
The spatial distribution of light interception in the
canopy was difficult to be determined experimentally.
Modeling is widely used as an efficient way to obtain
this information. Researchers often apply Beers law to
describe the light environment inside the plant canopy.
The applicability of Beers law depends on the basic
assumption of random arrangement of leaves.
Significant errors may occur when it is applied to
certain circumstances such as isolated trees [21] or row
crops at their early stage. Based on the output of the 3D canopy structure from the architectural plant model,
the transfer, reflection and transmittance of light in the
canopy can be simulated, thus accurately estimating
the interception by each organ e.g. leaf [14][22]. Fig. 2

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shows the simulated results of sunfleck distribution of

direct solar light in a 3-D maize canopy with the
parallel projection and Z-buffer algorithms. It is a
significant aid to ecophysiological crop modeling and
field mass and energy analysis.

distribution of root segments is also important, which

affect the volumes of soil to exploit, and the
competition from neighboring root systems [23]. Due
to the difficulty of directly observing and quantifying
the architecture of actual roots that are hidden in the
soil, limited information is available on 3-D root
architecture in soils.
Nevertheless, a few root models have been
developed to consider root 3-D architecture explicitly
and to generate information such as the position, and
orientation of root segments over time which are based
on field observations of the architecture and dynamics
of root systems [24][25]. Fig. 3 shows the simulated
root architecture of cotton using the GREENLAB
model.

Figure 1. Organ expansion kinetics (blade area, internode

length and cob biomass) and 3-D visualization of maize
plants at 18th and 33th growth cycles (GCs).

Figure 3. Simulated root architecture of cotton at 90th GC

using GREENLAB model.

Water transport in the soil-plant system can be

simulated based on simulated root architecture.
Clausnitzer and Hopmans [26] developed a spatially
explicit model that is capable of simulating dynamic
interactions between root growth and soil water status
by combining a 3-D root growth model with a transient
soil water flow model. This work has demonstrated the
potential utility of 3-D models in analyzing the
functional implication of root architecture. Lynch et al.
[27] developed a model that can simulate the radial
variation of root growth. This model was used to
estimate zones of P depletion in the surrounding soil
and to evaluate the resource acquisition efficiency of
different root architectures [28].
The growth of individual plants is based on the
whole plant, and it adjusts the shoot-root relation to
adapt itself to the constantly changed environment and

Figure 2. The simulated sunfleck distribution of direct

radiation on ground and plant surface at noon on Aug 08,
2002 in a maize canopy which seed was sown in rows in
north-south direction with a row spacing of 0.6 m and plant
spacing 0.6 m within the row. Fuscous color: low PAR
intensity; light-colored: high PAR intensity.

2.3 Root architecture modeling

Plant
architecture
modeling
has
mainly
concentrated on the aerial parts. Plants live on water
and nutrient uptake by their root system. To get these
resources efficiently, the total length and surface area
of roots must be large enough, and the spatial

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an architectural plant model, and the biomass

production and biomass partitioning in plant
architecture can be quantified. Evaluating the stability
of individual plants can be conducted with a
mechanical model [32] based on a 3-D plant model.
Thus systems aiding in the search of an ideotype of
super high-yield crop can be developed [7][33][34].
Plant breeders can search for the optimum crop
architecture by designing plants and simulating the
canopy interception features on computer and
determining the best. With the progress in
biotechnology [35][36], corresponding breeding or
genetically engineering methods for new varieties can
be carried out to match the computer designed plants
with the most desirable characteristics [37]. The model
can also be used for evaluating the risk of overheating
on designed crops which may result in susceptibility to
severe photoinhibition if plant architecture e.g. leaf
angles are changed [38].

environmental (biotic and abiotic) stress. Thus both

root and shoot should be considered in the same model
to simulate plant growth as a whole. As root systems
are major interfaces of plants for matter and energy
interchange with the environment they live in,
considering the root system is important to strengthen
the mechanism of plant-environment interactions in a
plant model. Now this work has started [29].

3. Applications of plant modeling to

agriculture
3.1 Designing the ideotype of super-high yield
crop with plant model
Crop yield has increased progressively with the
evolution of the cultivars in the past century. Yang et
al. [30] found that the architecture of rice plants in
China clearly changed in the past several decades (Fig.
4). The height of rice plants decreased greatly with
dwarf cultivar being used in the green revolution for
higher harvest index, and it increased again for more
plant biomass production, whereas the divergence
angle of the topmost three leaves decreased
dramatically. As it is known that improvement of crop
architecture can enhance canopy light interception, rice
breeders in China have now begun to breed new
varieties selectively with long, narrow, and very erect
top leaves [31] (Fig. 5). They believe this
configuration captures sunlight more effectively.

Figure 5. Rice cultivar of Peiai 64S/E32 having long,

narrow, and very erect top leaves.

3.2 Applications in agronomic management

Functional-structural plant modeling is very
valuable
for
understanding
competition
for
space/resources at the level of individual plants, thus to
be used for selecting an appropriate variety with
individual competitive ability suitable for improving
colony production in a given zone, and improving
planting and intercropping according to the colony
structural characteristics of crops.
The problems of irrigation water shortage affected
crop production dramatically in arid and semi-arid
areas such as Northern China. Plant models which
incorporate the function and structure of a plants
aerial part and root system, can be used for optimizing
the schedule of irrigation.
One of the main problems for optimizing field
water management in the past is to quantify field
evapotranspiration. Based on the simulated plant

Figure 4. Evolution of plant height and leaf angle of topmost

three leaves for mid-season indica rice cultivars in the past
60 years in Jiangsu province, China (Adapted from [30]). ET:
Early tall cultivars (1930-1950); IT: Improved tall cultivars
(1950s); DC: Dwarf cultivars (1960s); SDC: Semi-dwarf
cultivars (1970-1990); SDH: Semi-dwarf hybrid (1970-1990);
SR: Super rice (1990-2000)

As mentioned above, the spatial radiation

interception of plant canopy can be simulated based on

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architecture, the radiation energy reaching the soil

surface can be simulated, thus the soil evaporation can
be computed corresponding to soil water regime. With
the simulation of light interception of leaves, resistance
of plant water transportation, wind speed within the
canopy, spatial distribution of transpiration in the
canopy can be simulated accurately [39]. Soil
properties and the root system vary in both space and
time in small areas. These variations can have
significant impact on soil evaporation, plant water
uptake and transpiration. Functional-structural plant
modeling can be helpful for understanding the spatial
distribution of a root system. Dynamics of water
uptake can be simulated, with root growth
characteristics changing in response to local soil
conditions and the resulting difference in root pattern
can feed back on the spatial distribution of soil water.
With plant models which indicate the initiation and
growth of key organs of the crop for avoidance of
stress in its early stage [40], optimization of water and
fertilizer application rates and timing responses to soil
status can be achieved by coupling a plant model with
those for soil water and solute transport, thus improve
water use efficiency and to decrease soil and
groundwater contamination by reducing the loss of
fertilizers.
Functional-structural plant modeling is also
valuable for some special artificial production
environments, such as greenhouses where high
economic output is often sought for and the local
environmental conditions can be controlled
automatically. With the simulation results, optimum
environmental conditions such as temperature,
radiation intensity, CO2 concentrations, can be
determined and schedules for precision irrigation,
fertilization, and harvesting can be made accurately. It
can also be of help for the analysis of the
spatiotemporal dynamics of insect and disease
calamities in crop canopy, and simulating pathogen
dispersion by rain-splash [41], so as to optimizing
pesticide use and avoiding abuse of pesticides [42].

virtual crops on computers, observing crop growth

from any angles or roaming in the virtual canopy to see
how their plants will develop if alternative agronomic
or practices are applied, so as to optimizing crop
management. Plant models with interaction attributes
make farmers access to the new technology of field
management easier, more fun and efficient [8][42].

4. Concluding Remarks
Plant models, especially functional-structural
models which combine ecophysiological knowledge
and morphology, are very useful for guiding crop
management, and can provide useful tools for
designing ideotypes of super-high crop varieties. Thus
they should play a key part in the second green
revolution for world food security. However, there is
still a lot of work to do, such as improving the
mechanism of models interacting with environment,
parameterizing for real crops, combining model
parameters with quantitative trait loci [43][44][45], and
developing new algorithms to speed up computing
eco-physiological activities in canopies, which is very
complex and heavily demanding on computing power.
In addition, as models use mathematical equations to
mimic the physical world with a few assumptions, we
should use plant models under certain constraints in
order to ensure the reliability of their simulation.

ACKNOWLEDGEMENTS

This research was supported by the 863 program

of China (2006AA10Z231), the Program for
Changjiang Scholars and Innovative Research Team in
the University (IRT0412). Yuntao Ma, Xiping Wang,
Wuping Zhang and Bangyou Zheng provided Fig. 1,
Fig. 2, Fig. 3 and Fig. 5, respectively. Thanks also go
to the anonymous reviewers for their helpful comments
on the manuscript.

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