Articles

https://doi.org/10.1038/s41477-019-0398-8

Quantifying impacts of enhancing photosynthesis

on crop yield
Alex Wu   1*, Graeme L. Hammer1, Al Doherty1, Susanne von Caemmerer   2 and Graham D. Farquhar2

Enhancing photosynthesis is widely accepted as critical to advancing crop yield. However, yield consequences of photosyn-
thetic manipulation are confounded by feedback effects arising from interactions with crop growth, development dynamics and
the prevailing environment. Here, we developed a cross-scale modelling capability that connects leaf photosynthesis to crop
yield in a manner that addresses the confounding factors. The model was validated using data on crop biomass and yield for
wheat and sorghum from diverse field experiments. Consequences for yield were simulated for major photosynthetic enhance-
ment targets related to leaf CO2 and light energy capture efficiencies, and for combinations of these targets. Predicted impacts
showed marked variation and were dependent on the photosynthetic enhancement, crop type and environment, especially the
degree of water limitation. The importance of interdependencies operating across scales of biological organization was high-
lighted, as was the need to increase understanding and modelling of the photosynthesis–stomatal conductance link to better
quantify impacts of enhancing photosynthesis.

E
nhancing photosynthesis is widely accepted as critical to
advancing crop yield1,2 to meet growing food demand globally3.
Potential manipulation targets have been proposed for both C3
and C4 crop species4,5. It is argued that enhanced leaf photosynthe-
sis would lead to improved canopy photosynthesis, crop biomass
and yield. However, the connection between leaf photosynthesis
and crop yield is not necessarily straightforward, owing to feedback
effects arising from interactions with crop growth, development
dynamics and the prevailing environment. For example, effects
of photosynthetic manipulation can be diminished when scaled
to the canopy due to complexities associated with canopy light
interception6. Some modelling studies7 have suggested that a large
enhancement of the primary CO2-fixing enzyme translates to little
improvement in grain yield. The current inability to quantify these
cross-scale interactions hampers the ability to rigorously assess the
potential impact of photosynthetic manipulation on crop yield.
Modelling tools that connect prediction of leaf photosynthesis
and field crop performance have the potential to assess and guide
photosynthetic manipulation efforts. Such cross-scale modelling
tools can be developed by connecting robust leaf-level photosyn-
thesis to crop growth and development models via effective canopy-
modelling approaches8. The connections incorporate, for example,
the dynamics of canopy light interception as leaves appear, expand,
shade one another and senesce. Further, canopy leaf nitrogen status,
which can determine photosynthetic physiology at leaf level9, arises
as an emergent consequence of crop nitrogen uptake and allocation
to the competing demands of organs growing at different stages of
the crop life cycle10–12. In turn, photosynthesis at leaf level can drive
canopy biomass accumulation, which is then allocated to growing
organs within the plant in crop models. The ‘two-way’ nature of
such cross-scale modelling (Fig. 1) is necessary for advancing model
development in the integrated manner required for assessing likely
impacts of photosynthetic manipulation6.
In addition to light and nitrogen, the importance of water in
dryland cropping systems cannot be overstated. Crop water status
and the link to stomatal conductance are critical considerations in
cross-scale modelling connecting leaf photosynthesis and field crop
performance. Crop water status can be quantified from the balance
of potential canopy transpiration (demand) and the capacity to
extract water from the soil (supply)12,13. Leaf-level conductance of
CO2 and water from photosynthesis modelling can be integrated to
determine canopy transpiration demand. This is contrasted with the
potential supply derived from crop growth and development mod-
els14 to indicate crop water status and when feedback is required to
limit canopy transpiration, and hence leaf photosynthesis, using the
restriction on stomatal conductance required to meet the shortfall
in water demand. Use of such a ‘two-way’ modelling framework
ensures crop water status effects are effectively integrated across
scales of biological organization.
In this study, a cross-scale model connecting leaf photosynthesis
and field crop performance was developed to provide the capacity to
assess and guide photosynthetic manipulation efforts targeting crop
yield improvement. The model connects biochemical models of C3
and C4 photosynthesis15,16 with wheat and sorghum crop growth and
development models of the agricultural production system simula-
tor (APSIM v.7.8) software platform (http://www.apsim.info/)12,17,18.
Introducing the biochemical photosynthesis models, which are not
part of the daily crop growth calculation in the standard version of
APSIM, provided the capacity to increase the resolution of the two-
way modelling approach. This also incorporated effects of the three
major environmental drivers—light, nitrogen and water—across the
scales of modelling. The model was tested qualitatively using simu-
lated diurnal canopy responses and validated using seasonal data on
crop biomass and yield for wheat and sorghum from a diverse set of
field experiments. Photosynthetic manipulation targets have been
proposed for enhancing C3 and C4 photosynthesis for crop yield
improvement4,5,19. These included three major targets related to leaf
CO2 capture and light-energy efficiencies: maximum carboxylation
rate of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco),
electron transport capacity and mesophyll conductance for CO2.

1
ARC Centre of Excellence for Translational Photosynthesis, Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The
University of Queensland, Brisbane, Queensland, Australia. 2ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences,
Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia. *e-mail: c.wu1@uq.edu.au

380 Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants

NaTurE PlanTs Articles
Weather

Temperature Radiation
VPD Temperature
CO2 VPD
O2 Precipitation

Absorbed radiation Diurnal sun angle LAI

SLN (solar geometry) SLN
Transpiration supply Diurnal radiation Transpiration
/leaf fraction (direct and diffuse) supply
Light
CO2 Radiation
NADPH assimilation
ATP rate Growth
Thylakoids Precipitation Development
Sunlit fraction
60 Potential
PCO Rubisco PCR Respiration
40 photosynthesis
Transpiration
20
A (µmol m−2 s−1)
CH2O allocation

Acanopy
CO2 Mes(C )
3 Leaf area
0
or BS(C4) Water ΔCH2O
limited N fertilization
Mes C4 Shaded fraction
60 Irrigation

10 0
12 0
14 0
0
0
cycle

0
:0
:0
:0
:0
6:

18
C3 path 40 Transpiration Evaporation
ATP PEP demand
CO2 20

Tcanopy,hr
Intercellular Supply Transpiration
CO2 airspace 0
demand and
0 200 400 Actual actual
Ci (µbar) transpiration Drainage Leaching
Leaf epidermis Stomata Soil

10 0
12 0
14 0
0
0
0
:0
:0
:0
:0
6:

18
Time of day
H2O CO2 Phenology
Photosynthetic biochemistry Canopy architecture and leaf optical Canopy development
properties (sunlit and shaded leaf area) N dynamics
Stomatal conductance
Canopy nitrogen distribution Root growth, water and N uptake
CO2 diffusion
Canopy photosynthesis and transpiration Crop management
Temperature response
Crop growth,
Leaf photosynthesis Canopy photosynthesis development and yield

Fig. 1 | Cross-scale modelling framework connecting the diurnal canopy photosynthesis–stomatal conductance module with crop growth and
development models. Processes that are modelled at each scale are driven by the environment and two-way interactions between the scales. The crop
models determine canopy LAI, SLN and potential transpiration supply for the day; the sun–shade leaves model partitions captured radiation and leaf
nitrogen to the two leaf fractions; and the leaf-level biochemical models of photosynthesis estimate potential CO2 assimilation rate of the two fractions
in response to captured radiation and leaf nitrogen. The resultant daily integral of potential canopy CO2 assimilation and canopy transpiration demand
generate the potential daily biomass increment and soil water usage through transpiration for the crop model. In the case when the transpiration supply
for the day is less than the transpiration demand, transpiration is reduced to the supply level, and canopy CO2 assimilation is recalculated based on the
reduced conductance. Once biomass increment is determined, using transpiration supply and demand, the crop models allocate it to growing organs
within the plant depending on the stage of crop development and environment-dependent allocation rules. The realized transpiration, together with
evaporation and drainage from soil, is deducted from soil water content. This establishes the state of the cross-scale system for the subsequent diurnal
calculation using the two-way modelling framework. A detailed schematic of the framework connecting leaf photosynthesis with the crop model is given in
Supplementary Fig. 1. BS, bundle sheath; Mes, mesophyll; PCR, photosynthetic carbon reduction cycle; PCO, photosynthetic carbon oxidation; VPD, vapour
pressure deficit.

While these targets are all feasible for improving photosynthetic at approximately 75 μmol CO2 m−2 s−1 for the C3 wheat and, as
efficiency, achieving them involves a range of difficulties1. In this expected, at a higher level (around 90 μmol CO2 m−2 s−1) for the C4
study, consequences on crop yield of enhancement of these three sorghum, on a ground area basis (Fig. 2a,c). These estimates were
targets and their combinations were simulated for C3 wheat and comparable to results measured in similarly sized maize canopies20.
C4 sorghum crops in a typical Australian production environment. In both C3 and C4 canopies, Acan consisted of contributions from
Implications of the modelling capability for crop improvement the sunlit (Asun) and shaded (Ash) leaf fractions, but the contribu-
through photosynthetic manipulation are discussed. tion from Asun dominated. In the example shown in Fig. 2, Asun and
Ash were mostly limited by the electron transport-limited rate (Aj)
Canopy photosynthesis–stomatal conductance model as opposed to the Rubisco activity-limited rate (Ac), which is the
The diurnal canopy photosynthesis–stomatal conductance model other major limitation of photosynthesis16. Even though the shaded
(DCaPST) developed here (see Methods and Fig. 1) was analysed leaf fraction had much higher Ac because of the larger number of
for its response to levels of water availability for C3 wheat and C4 sor- shaded leaves in the canopy, it was not realized due to the much
ghum grown in a typical Australian cropping region during a day in lower Aj. The simulated canopy photosynthesis, with the prescribed
the spring and summer, respectively. CO2 assimilation rate (A), tran- daily environment and canopy photosynthesis parameterization
spiration rate (T) and stomatal conductance to water vapour (gsH2O) (Supplementary Tables 5 and 6) indicated that Aj was limiting in
per unit of ground area were simulated for the sunlit and shaded leaf both the sunlit and shaded leaf fractions (Fig. 2a,c). As expected, the
fractions of the canopy having a canopy leaf area index (LAI) of 6 m2 sunlit leaf fraction, with higher A, required higher gsH2O to supply
leaf per m2 ground area (Fig. 2 and Supplementary Table 5). Model sufficient CO2 for photosynthesis; however, this was lower for the
parameterization was based on generic values reported for C3 wheat C4 canopy (Fig. 2i,k), reflecting its enhanced efficiency. The diurnal
and C4 sorghum (Supplementary Table 6). pattern for Tcan resembled that of Acan, but was skewed towards the
Simulated diurnal patterns of A, Thr and gsH2O were consistent afternoon due to a higher air vapour-pressure deficit (Fig. 2e,g). The
with expectations and known effects. Under non-limiting water higher Acan for the C4 canopy was also associated with a reduced Tcan,
conditions, simulated C3 wheat and C4 sorghum canopy photosyn- indicating that the model generated the known higher radiation-
thesis (Acan) with a LAI of 6 m2 leaf per m2 ground area (the mature use efficiency and higher transpiration efficiency of the C4 sorghum
canopy size under good growth conditions) peaked around midday compared with the C3 wheat21 as an emergent property.

Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants 381

Articles NaTurE PlanTs

C3 wheat C4 sorghum

Water non-limiting Water limited Water non-limiting Water limited

120
a b c d
A (µmol m–2 s–1)
90

60

30

0
1.5 e f g h
1.2
Thr (mm h–1)

0.9

0.6

0.3

0
1.2 i j k l
1.0
gsH2O (mol m–2 s–1)

0.8
0.6
0.4
0.2
0
00

00

0
00

00

0
00

00

0
00

00

0
:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0

:0
6:

8:

6:

8:

6:

8:

6:

8:
10

12

14

16

18

10

12

14

16

18

10

12

14

16

18

10

12

14

16

18
Time of day

Fig. 2 | Simulated diurnal responses of C3 and C4 CO2 assimilation (A), hourly transpiration (Thr) rates and stomatal conductance for water vapour
(gsH2O) for non-limiting and limiting water situations. a–l, Diurnal responses of C3 wheat (a, b, e, f, i and j) and C4 sorghum (c, d, g, h, k and l). a–d, Canopy
photosynthesis (solid curves) is the sum of the contributions from the sunlit (grey area) and shaded (patterned area) leaf fractions from 6:00 to 18:00.
Sunlit leaf A is shown as dashed lines; the shaded leaf fraction is shown as dotted lines. A for an individual leaf fraction is given by the minimum of the
Rubisco-activity-limited rate (Ac) (grey) and the electron transport-limited rate (Aj) (black). The limiting factor is highlighted by grey or patterned shading.
e–h, Thr of the sunlit (dashed line) and shaded (dotted line) leaf fractions, and the sum for the canopy (solid line). i–l, gsH2O of the sunlit (dashed) and
shaded (dotted) leaf fractions. In water-limited simulations (b, f, j, d, h and l) total diurnal canopy transpiration is limited to half of that used in the water
non-limiting case (a, e, i, c, g and k); that is, area under the solid curve in f and h is half of that in e and g. Parameter values for the simulation are given in
Supplementary Fig. 3 and Supplementary Tables 5 and 6.

Under water-limited conditions, daily Tcan demand may not be
met. When this occurs, the model reduces Tcan to a level commen-
surate with soil water uptake. This was modelled with the expected
midday ‘transpiration plateau’22 (Fig. 2f,h), which resulted in asso-
ciated stomatal closure (Fig. 2j,l and Methods). With only half of
daily Tcan allowed in the water-limited simulation, this limited CO2
availability inside leaves and reduced A (Fig. 2b,d). In this situation,
the reduction in Ac was significant and became the limiting factor
in both C3 wheat and C4 sorghum, as opposed to Aj as the limiting
factor in the non-limiting-water conditions (Fig. 2a–d). The model
also generated a higher photosynthesis:transpiration ratio over the
simulated diurnal cycle, which is consistent with known effects23,24.
Hence, the testing of the model at diurnal level indicates that the
DCaPST modelling framework is capable of faithfully capturing
the expected interplay between canopy A, gsH2O and Thr for both
C3 and C4 systems.
Cross-scale model validation
The integrated cross-scale model (see Methods and Fig. 1) gener-
ated predictions of total biomass and grain yield for the diverse vali-
dation set of detailed field experiments for wheat and sorghum that
showed little difference from the standard APSIM crop model vali-
dations (Fig. 3). For C3 wheat, there was little to no loss in precision
and predictive capability for total biomass (Fig. 3a,b) and a slight
reduction in the bias of predictions of grain yield (Fig. 3c,d) when
the DCaPST module was used in the APSIM framework. For C4
sorghum, use of the DCaPST module improved the biomass predic-
tion, with less overestimation at low biomass levels (Fig. 3e,f), but
had little consequence for grain yield (Fig. 3g,h).
The general adequacy of relationships between predicted and
observed values of biomass at maturity and grain yield across a wide
range of conditions for both the C3 and C4 crop species indicated
a robust predictive capability for the cross-scale model. The range
in observed biomass and yield was mostly ascribed to variation in
water limitation and nitrogen treatments12,18 and was reproduced
well by the effects of water limitation and nitrogen treatments on
the modelled leaf- and canopy-level A, gsH2O and T. The assumptions
in the model of canopy–atmosphere coupling did not introduce any
bias in model validation across the diverse environments employed.
Given the choice of robust biochemical models of photosynthesis
and effective connection with crop growth, development and envi-
ronmental factors6, the cross-scale model is appropriate for testing
the consequences of photosynthetic manipulation on yield at crop
scale in field production.
Yield consequences of photosynthetic manipulation
Multi-year crop-simulation studies were conducted for C3 wheat
and C4 sorghum crops to assess the likely yield impact of three
major photosynthetic manipulation targets: Rubisco carboxylation
rate, electron transport rate and mesophyll conductance for CO2,

382 Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants

NaTurE PlanTs Articles
C3 wheat C4 sorghum (Supplementary Fig. 4) and yield (Fig. 4) than C3 wheat. When sim-
30 a e ulated results were categorized into three environment types: water
y = 1.02x + 0.79 y = 0.97x + 0.21 non-limiting, above-average-yielding and below-average-yielding
R 2 = 0.90 R 2 = 0.88 rainfed cropping seasons, it was apparent that water limitation was
n = 107 n = 38
a dominating feature in this production environment. There were
20
very few instances for either species where the simulated rainfed
crop yield matched that of irrigated production.
The predicted yield response to 20% enhancement of the three
10 photosynthetic manipulation targets and combinations of the tar-
Predicted biomass (t ha–1)

Biomass Biomass gets ranged markedly from −1.9 to +12.1%, depending on the
C3 DCaPST C4 DCaPST photosynthetic enhancement, crop type and environment (Table 1).
0 The current simulation assumed that photosynthetic enhance-
30 b f ments were feasible without changes to plant nitrogen dynamics
y = 1.04x + 0.66 y = 0.84x + 2.25 and leaf nitrogen allocation to the photosynthetic apparatus. The
2
R = 0.91 R 2 = 0.89 positive responses occurred mostly when water was non-limiting.
n = 107 n = 38
20
The magnitude of responses declined progressively as water became
more limiting. Negative values were predicted for sorghum in rain-
fed low-yielding seasons, but were not seen for wheat. When water
was non-limiting, enhanced photosynthesis resulted in higher Acan,
10
T and gsH2O; this was ascribed to the coupling of A and gs (ref. 25),
Biomass Biomass leading to improved daily crop biomass increment (Supplementary
APSIM 7.8 wheat APSIM 7.8 sorghum Fig. 5a), biomass (Supplementary Table 8) and yield (Table 1). This
0 higher biomass trend in non-limiting water situations was consistent
0 10 20 30 0 10 20 30
with previous findings26 in which increased biomass was associated
Oberved biomass (t ha–1)
with photosynthetic enhancement in rice using the GECROS crop
15 c g modelling platform. However, in water-limited situations, enhanced
y = 1.00x + 0.06 y = 0.96x + 0.74
photosynthesis and coupled A–gs caused more rapid depletion of
R 2 = 0.91 R 2 = 0.88
n = 146 n = 38 soil water, restricting daily crop biomass increment, especially late in
10 the growing season during grain filling (Supplementary Fig. 5b,d).
The consequences of these critical dynamics captured in this model
generated the negative yield changes in these situations (Table 1).
5
Such effects of the pattern of water use on growth and yield across
the crop life cycle in water-limited environments are well known12,27.
Predicted yeild (t ha–1)

Yield Yield The enhancement of maximum electron transport rate at

C3 DCaPST C4 DCaPST 25 °C (Jmax25) had the greatest impact on yield for both C3 wheat
0
and C4 sorghum, compared with the other single-target photo-
15 d
y = 0.93x + 0.33
h
y = 0.96x + 0.68
synthetic manipulations (Table 1) under the simulated conditions
2
R = 0.92 R 2 = 0.88 (Supplementary Figs. 6 and 7). This trend is in line with the simu-
n = 146 n = 38 lated diurnal canopy photosynthesis, which showed that both wheat
10 and sorghum canopy photosynthesis were strongly limited by the
rate (Aj) allowed by electron transport capacity as shown in Fig. 2a,c.
When crops experienced water limitation, Acan was limited by sto-
5 mata conductance, which resulted in both Aj and Ac reduction, as
shown in Fig. 2b,d, and reduced yield impact of Jmax25 enhancement
Yield Yield (Table 1). Single-target enhancement in the maximum Rubisco-
APSIM 7.8 wheat APSIM 7.8 sorghum
carboxylation rate at 25 °C (Vcmax25) generated negligible impact on
0
0 5 10 15 0 5 10 15
average yield for both wheat and sorghum (Table 1), in line with
Oberved yield (t ha–1) the simulated diurnal canopy photosynthesis showing strong Aj
limitation (for example, Fig. 2a,c). Simulated diurnal canopy pho-
Fig. 3 | Predicted crop biomass and yield for C3 wheat and C4 sorghum tosynthesis at a lower canopy LAI also showed limitation by Aj for
plotted against field-observed data from a diverse validation set of both sunlit and shaded fractions, supporting the lack of impact
detailed field experiments12,18. a–h, Predicted crop biomass for wheat (a–d) of Vcmax enhancement (data not shown). Some yield response was
and sorghum (e–h). Biomass at maturity is predicted using APSIM with simulated with enhanced mesophyll conductance at 25 °C (gm25) in
the DCaPST model (a,e) or the APSIM standard biomass increment model C3 wheat in non-limiting water conditions, but there was little or
(b,f) for daily canopy biomass increment. Similarly, yield is predicted using no response in C4 sorghum. This is in line with the limitation asso-
APSIM with the DCaPST model (c,g) or the APSIM standard biomass ciated with CO2 drawdown from the intercellular air space to the
increment model (d,h) for daily canopy biomass increment. In each panel, Rubisco-carboxylation site in C3 leaves, whereas C4 photosynthe-
the solid line is the 1:1 line, the dashed line is the fitted linear regression sis minimizes this limitation via its carbon-concentrating mecha-
given by the equation fitting to the indicated sample size n. Parameter nisms. Simulation of simultaneous enhancement of Jmax25 and Vcmax25
values for the simulation are shown in Supplementary Table 6. resulted in additional yield gains in both wheat and sorghum com-
pared with enhancement of Jmax25 only. This is likely to have occurred
as a result of probable Ac limitation caused by the Jmax25 enhance-
ment. Simultaneous Vcmax25–Jmax25–gm25 enhancement had the great-
and combinations of these targets (see Methods). The baseline est impact on yield for C3 wheat compared with the other scenarios
simulation for a typical Australian crop production environment in the simulated environment, whereas yield gains in C4 sorghum
showed that C4 sorghum had higher average biomass at maturity were comparable to the Vcmax25–Jmax25 scenario; this was also likely

Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants 383

Articles
C3 wheat C4 sorghum
12
a b
n = 116
10
n = 54
8 n = 116
Yield (t ha–1)
n = 47
6 photosynthesis with crop growth and development, and integrated
n = 62
4
n = 69
2 (Fig. 3). This was facilitated by the recent development of a diurnal
0 effects in a framework that supports cross-scale modelling6. Here,
H
L
d
d
n_
n_
te
te
n_
n_
ga
ga
ai
ai
ai
ai
R
R
i
i
R
R
Irr
Irr
Fig. 4 | Baseline simulation of C3 wheat and C4 sorghum yield using 116
years of available weather data. a,b, Results of predicted yield distribution
for wheat (a) and sorghum (b) associated with three environment types:
irrigated, non-limiting water supply with full irrigation; rainfed cropping for
years with above-average yield (rain_H); and rainfed cropping for years
with below-average yield (rain_L). Parameter values for the simulation are
shown in Supplementary Tables 6 and 7. In the box plots, horizontal lines
indicate the first quartile, median and third quartile of the yield distribution,
whiskers indicate the 10th and 90th percentile, and dash-dot lines indicate
the mean, which are also shown in Table 1 (n = the number of years of
simulation in the different environment types).
to be a result of non-limiting mesophyll conductance (Table 1).
Overall, the trends predicted in the multi-year crop-simulation
studies were emergent consequences generated by the dynamics in
the leaf-level responses, diurnal canopy photosynthesis responses
and environmental context of the crop.
The effects of photosynthetic enhancements were also exam-
ined with decoupling of the A–gs link, as evidence from photo-
synthetic manipulation studies support this possibility28. However,
this remains an active area of research in which possible mecha-
nisms are being examined29,30. In the decoupled case, Ci/Ca (frac-
tion of intercellular CO2 partial pressure to that of the ambient air)
was reduced to maintain gsH2O at the level simulated in the coupled
A–gs case, despite the increase in A. Photosynthetic enhancement
with a decoupled A–gs link reversed the negative yield impacts pre-
dicted with Jmax enhancement (Ci/Ca reduced from 0.45 to 0.4) and
the Vcmax25–Jmax25 and Vcmax25–Jmax25–gm25 scenarios (both with Ci/Ca
reduced from 0.45 to 0.39) in the simulated low-yielding seasons
for C4 sorghum (Table 1). This was associated with the potential to
accumulate more biomass with the enhancements, while maintain-
ing similar levels of gsH2O and T as in the baseline simulation, due to
the reduced Ci/Ca. Hence, the negative consequences of crop water-
use patterns throughout the season associated with the coupled sce-
nario were avoided (Supplementary Fig. 5b). In non-limiting water
conditions (full irrigation), however, the decoupled scenario slightly
reduced the benefit of photosynthetic enhancement; this can be
ascribed to stomatal limitation of photosynthesis (Supplementary
Fig. 5a), which has slightly more effect in C3 wheat (Ci/Ca was reduced
from 0.7 to 0.69, 0.68 and 0.68, for Jmax25, Vcmax25–Jmax25 and Vcmax25–
Jmax25–gm25 scenarios, respectively). In some cases, there was no dif-
ference between the coupled and decoupled scenarios (Table 1),
because the enhancement did not alter A sufficiently to change gsH2O
and the level of Ci/Ca, as used in the coupled scenario (that is, in the
case of increasing Vcmax25 and gm25 in both C3 wheat and C4 sorghum),
and/or increase in A did not require higher stomatal conductance to
384
NaTurE PlanTs
maintain Ci/Ca at the same level (that is, in the case of gm25 enhance-
ment in C3 wheat). The simulated stomatal effects on photosynthetic
manipulation and yield indicate clearly that increased understand-
ing of the nature of the A–gs link is required.
The cross-scale model reproduces field observations
The two-way modelling approach developed for the cross-scale
model presented here has reliably connected models of C3 and C4 leaf
the major environmental drivers (that is, light, nitrogen and water)
across scales. As validated, the cross-scale models reproduced field-
observed biomass and yield of C3 wheat and C4 sorghum across
diverse environments as well as the standard APSIM crop models
canopy photosynthesis model that incorporated light and nitrogen
extending this work, we have integrated a dynamic crop water bal-
ance with leaf-level photosynthesis and stomatal conductance as
a significant step in the capability for simulating crop production
associated with photosynthetic enhancements under realistic pro-
duction environments. This was achieved by developing a canopy-
level photosynthesis–stomatal conductance model that facilitated
connection between leaf-level processes and the consequent crop
status (that is, LAI, specific leaf nitrogen (SLN, in g N per m2 leaf)
and crop water supply), which was dependent on the dynamics of
crop growth and resource capture over the crop life cycle12. This
model extends the capability of crop modelling by spanning scales
from a biochemical representation of instantaneous photosynthesis
to seasonal crop yield without any loss in predictive capacity relative
to simpler models.
A critical emergent effect of the cross-scale modelling system
operating through the crop life cycle was that enhanced photosyn-
thesis improved biomass accumulated early in the season when soil
water was more abundant, but in doing so, depleted soil water at a
faster rate, leaving less for later in the season if enhanced photosyn-
thesis is coupled to increased stomatal conductance and transpira-
tion (Supplementary Fig. 5). In situations of terminal water shortage,
which occur frequently in rainfed cropping, this results in restricted
stomatal conductance, photosynthesis and biomass increment dur-
ing the critical grain-filling period with a resultant negative impact
on biomass and yield (Table 1 and Supplementary Table 8). These
critical dynamics of crop water status and interactions across scales
associated with assessing impacts of photosynthetic enhancement
have not previously been accounted for in a rigorous manner26,31.
The results of this study highlight the importance of effective two-
way connections between photosynthesis- and crop-level processes
for prediction of effects on crop growth, development and yield.
Quantifying consequences of photosynthetic manipulation
The simultaneous increase in Rubisco activity, electron transport
and mesophyll conductance is likely to generate the greatest yield
gains in wheat, whereas the combination of Rubisco activity and
electron transport is most effective for sorghum (Table 1). Notably,
we have shown here that the interplay with dynamic crop water bal-
ance and the nature of the photosynthesis–stomatal conductance
(A–gs) link affect the predicted consequences on yield of photo-
synthetic manipulation. The findings in relation to the coupling
and decoupling of the A–gs link highlight the importance of main-
taining gsH2O as a strategy for translating photosynthetic enhance-
ment into yield improvement in water-limited situations. This
notion resonates with efforts targeting improved crop transpira-
tion efficiency32 and leaf-level water use efficiency33. However, this
also poses a challenge as current knowledge on the nature of the
A–gs link, with respect to photosynthetic manipulation, is incom-
plete. One study has shown that reducing the amount of Rubisco
did not change gsH2O (ref. 28), suggesting that the decoupled A–gs
Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants
NaTurE PlanTs Articles
Table 1 | Simulated percentage change in average yield relative to the baseline case with different photosynthetic manipulation
targets in different environments
C3 wheat C4 sorghum
Yield A–gs 120% 120% 120% 120% 120% Yield A–gs 120% 120% 120% 120% 120%
(t ha−1) coupling Vcmax25 Jmax25 gm25 Vcmax25 Vcmax25, (t ha−1) coupling Vcmax25 Jmax25 gm25 Vcmax25 Vcmax25,
(%) (%) (%) and 120% (%) (%) (%) and 120%
120% Jmax25 120% Jmax25
Jmax25 and Jmax25 and
(%) 120% (%) 120%
gm25 gm25
(%) (%)
Full irrigation 6.3 Yes 0.0 7.2 1.2 10.6 12.1 9.4 Yes 0.4 8.0 0.0 9.2 9.3
No 0.0 6.3 1.2 9.5 11.0 No 0.4 7.9 0.0 9.2 9.2
Rainfed 4.4 Yes 0.0 3.7 0.3 4.6 5.3 6.6 Yes 0.5 2.3 0.1 3.0 3.1
above- No 0.0 5.6 0.3 8.5 9.2 No 0.5 5.1 0.1 6.7 6.8
average-
yielding
seasons
Rainfed 1.7 Yes 0.0 3.5 0.5 4.7 5.4 2.7 Yes 0.4 −1.1 0.1 −0.6 −0.9
below- No 0.0 5.2 0.5 8.2 8.9 No 0.4 1.9 0.1 3.2 3.3
average-
yielding
seasons
Scenarios also include results for both coupled and decoupled photosynthesis–stomatal conductance (A–gs) situations. Manipulations include 20% enhancement in the maximum rate of Rubisco activity
at 25 °C (Vcmax25), maximum rate of electron transport at 25 °C (Jmax25), mesophyll conductance at 25 °C (gm25) and simultaneous Vcmax25–Jmax25 and Vcmax25–Jmax25–gm25 enhancements, while other parameters
are kept at their default values (Supplementary Tables 6 and 7).

scenario may apply to changes in Rubisco content. However, it is
not clear whether this can be generalized for any manipulation of
Rubisco content. Although this would not affect interpretation of
the current simulation of enhanced Vcmax (Table 1), it will need to
be clarified for crop species or situations that are more limited by
Rubisco activity. For mesophyll conductance (gm), current evidence
obtained by manipulation of aquaporins suggests that A–gs cou-
pling33 may not be an issue in water-limiting growing conditions,
as gm25 enhancement did not alter A sufficiently to change gsH2O
(Table 1); however, if an enhanced A response is achieved by increas-
ing gm, the nature of the A–gs link may become important. Other
approaches, such as leaf morphological manipulation, could pro-
vide the possibility of achieving a decoupled A–gs link33. The results
reported here indicate the importance of including enhancement
of the electron transport chain in both C3 wheat and C4 sorghum
(Table 1). However, it is currently not clear whether the associated
decoupled A–gs scenario is possible. Given this uncertainty, there
is a possibility of negative yield change in low-yielding conditions
(that is, dry seasons). Understanding the mechanistic basis of this
link is indicated as a critical area of research need. The value of
manipulating photosynthesis is as dependent on effects on the A–gs
link as it is on direct effects on A in most field production environ-
ments. Our findings highlight the need to appropriately model the
nature of the A–gs link.
The cross-scale modelling framework developed here bridges
the prediction gap between C3 and C4 leaf photosynthesis and crop
yield by addressing connections with crop growth and development
dynamics, and their interactions with the prevailing environment
throughout the crop life cycle. This modelling framework provides
a capability to assess likely yield impacts in C3 and C4 crop types
in field production environments and to identify the manipula-
tions that are likely to be of greatest value. This generates testable
hypotheses that would require appropriately bioengineered plants
for experimental validation. The model also offers the capacity to
identify previously less-highlighted critical issues associated with
photosynthetic manipulation in water-limited cropping situations,
such as the importance of the A–gs link, which require increased
understanding to support effective modelling. When combined
with reliable climate predictions, the modelling framework also
provides the scope to evaluate photosynthetic manipulations in
future climate conditions.
Methods
Overview of the cross-scale model connecting leaf photosynthesis, stomatal
conductance and crop growth and development. DCaPST modules were
developed and connected with the wheat and sorghum crop models of APSIM
v.7.8 on the basis of a cross-scale modelling framework that facilitates two-
way connection between the levels of modelling8 (Fig. 1). DCaPST builds
substantially on a previous canopy-photosynthesis model6 by incorporating
stomatal conductance, thus enabling prediction of canopy-level transpiration.
This connection was facilitated by the partitioning of the crop canopy into sunlit
and shade leaf fractions. The cross-scale model involved (1) the crop model
determining relevant crop attributes such as LAI, SLN (in g N per m2 leaf) and
extent of soil water uptake for transpiration supply, and (2) leaf and canopy
photosynthesis models determining potential daily canopy biomass increment and
transpiration demand. The dynamic interplay (Fig. 1) of these components with the
prevailing environment enabled the simulation of crop growth and development
through the crop life cycle.
In summary, the procedures involved converting daily environmental variables
to hourly values over the diurnal period (from sunrise to sunset) and partitioning
canopy leaf area, simulated using the crop models, into sunlit and shaded leaf
fractions on the basis of solar geometry and canopy architecture using a sun-
and-shade leaves approach34–36. The light absorption of the two leaf fractions
was calculated on the basis of incident direct and diffuse radiation and optical
properties of the leaves. Daily canopy-leaf nitrogen status was predicted with the
crop model12 and used to determine photosynthetic physiology of the leaf fractions.
To account for the effects of crop water status on A and T, the concept of water
supply and demand interplay used in the crop models12,37 was adopted. Crop
demand for water was established via the leaf stomatal conductance required for
the potential level of photosynthesis possible in the absence of water limitation.
The potential was obtained by solving the combined photosynthesis–conductance
model (Supplementary equation (22)), assuming a prescribed equilibrium Ci/Ca.
The resultant transpiration influenced leaf temperature (Tl) (Supplementary
equation (42)), which also influenced A. For any hour of the day, when crop
water supply fell short of the demand, stomatal conductance was restricted, and
leaf temperature was consequently elevated, both of which influenced A. Given
the level of absorbed light, canopy leaf nitrogen status and the interplay of water
supply and demand, canopy A and T were estimated for each leaf fraction on an

Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants 385

Articles
hourly basis. The resultant integrated daily values were returned to the crop models
to drive canopy growth and contribute to subsequent changes in soil water. The
soil-evaporation component of the water balance was calculated independently of
canopy T, on the basis of the fraction of incident energy reaching the soil surface
and surface wetness38. The crop model allocated the available biomass increment
to growing organs within the plant, depending on the stage of crop development
and environment-dependent rules for allocation12. The consequent state of the
crop regulated the subsequent diurnal canopy-photosynthesis state and potential,
providing the interaction from the two-way modelling framework required for
effective simulation across scales of biological organization.
Potential photosynthesis drives stomatal conductance and transpiration
demand when water supply is non-limiting. A was calculated using models
that combine C3 and C4 photosynthesis models16 and CO2 diffusion models
based on Fick’s law of diffusion (Supplementary equation (22)). This reflected
the interdependency of A and CO2 diffusion and availability inside leaves. For
calculating potential A and T demand when water supply was non-limiting, the
CO2 diffusion model shown below assumes that the intercellular CO2 partial
pressure (Ci) is a constant fraction of the CO2 partial pressure of the ambient air
(that is, constant Ci/Ca), and that there is a drawdown of CO2 across mesophyll cells
resulting in chloroplastic CO2 partial pressure (Cc) in C3 conditions or mesophyll
CO2 partial pressure (Cm) in C4 simulations:
Ci A calculated previously, was used to partition the revised Tcan to sunlit and shade
CcorCm = × Ca− (1)
Ca gm
where gm (mol m−2 s−1 bar−1) is mesophyll conductance to CO2. The constant Ci/Ca
was used to simulate the effect of the coupled A–gs regardless of A (refs. 39,40).
Parameterizing Ci/Ca is important to the modelling of A–gs (ref. 41). The default
Ci/Ca was set to 0.7 and 0.45 for C3 wheat and C4 sorghum, respectively40,42,43.
To calculate T demand, equation (1) was expanded to include the contribution
from the leaf boundary layer and stomatal conductance for CO2 and the effect of
a ternary system of gases (water vapour, CO2 and air)44 to better reflect the A/Ci
measurement from the portable gas exchange system (LI-COR) (Supplementary
equation (29)). The calculation of T assumed an allowance for leaf boundary layer
conductance associated with decreasing wind speed deeper in the canopy, and that
the atmosphere and canopy were coupled. The resultant gs was multiplied by 1.6, as
derived by McPherson and Slatyer45 from earlier studies, to obtain gsH2O, converted
to stomatal resistance to water (rsw, s m−1) (Supplementary equation (13)) and
input into the Penman–Monteith combination equation (Supplementary equation
(38)). Leaf temperature (Tl) was calculated with the saturation heat equation
(Supplementary equation (42)). Tl was then used to determine photosynthesis
model parameter values using temperature-response functions (Supplementary
equations (10) and (11)). The dependencies formed between A, gs, T and Tl can
only be solved iteratively. Even though Cc was the target required to obtain A in the
combined A–gs model, setting Tl as the iterative solution target was a more efficient
approach to obtaining solutions for all the components. Due to the complexity of
the C4 model, it was also required to iteratively solve for Cm (Supplementary Table 2).
Altogether, this formed the loop for estimating leaf potential A and T demand.
Two-way connection of leaf and crop scales. Connecting the leaf-level A–gs
models with the APSIM wheat and sorghum crop models was facilitated by
partitioning the canopy LAI (LAIcan), derived in the crop growth models, into
sunlit and shaded leaf fractions on the basis of canopy architecture34–36. For
each fraction, the absorbed photosynthetically active radiation from both
direct and diffuse solar radiation was estimated, given absorption, reflection
and transmittance properties of the leaves (Supplementary equations (3)–(5)).
SLN, dynamically simulated in the crop growth models, was used to determine
photosynthetic physiology and conductance parameters in the photosynthesis
models: Vcmax25, Jmax25, gm25 and the maximum phosphoenol pyruvate carboxylation
rate at 25 °C (Vpmax25) for C4 photosynthesis (Supplementary equations (6)–(9))9,46,47.
Calculated T for the two leaf fractions was summed to obtain the canopy total,
which was determined hourly and summed over the diurnal period to obtain daily
canopy transpiration demand (Tcan,D,DAY). The ratio of the contribution to T by
the sunlit and shaded leaf fractions at each hour (Tsun,D:Tsh,D) was also calculated.
Actual daily canopy transpiration (Tcan,A,DAY) was given by the minimum of crop
water supply and demand so that under water non-limiting conditions, Tcan,A,DAY
was given by Tcan,D,DAY, which was then used to update the soil-water balance in
the crop model. Calculated potential A for the two leaf fractions was summed
and integrated to obtain diurnal canopy photosynthesis (Acan,DAY). Daily above-
ground (shoot) biomass increment (BIOshoot,DAY) was calculated from Acan,DAY using
a conversion ratio (B) to obtain daily whole-plant biomass growth (BIOtotal,DAY).
The conversion ratio combined factors allowing for biochemical conversion of CO2
to biomass and CO2 loss due to maintenance respiration48, which was consistent
with the conservative respiration:photosynthesis ratio approach49. In order to
use this approach, the photosynthesis models were modified by setting leaf-level
respiration (Rd) to 0 (Supplementary equation (22))6. Subsequently, a portion of
BIOtotal,DAY was allocated for root growth. The root:shoot ratio was used to obtain
BIOshoot,DAY (Supplementary equation (1)). This ratio depends on growth stage
386
NaTurE PlanTs
as parameterized in the APSIM crop models. Typically, the ratio is high in the
early stages of crop development and decreases towards flowering. The value for
BIOshoot,DAY was returned to the crop models for allocation among active organs and
calculation of crop attributes for the next diurnal cycle.
Crop water supply estimation. The potential for water supply to the canopy from
soil water uptake was calculated on a daily basis (Tcan,S,DAY, mm H2O per day) in the
crop models. Tcan,S,DAY depends on the effective rooting depth of the crop and the
rate at which soil water can be extracted from the soil layers occupied by roots12.
The APSIM crop models include contribution from rainfall, irrigation (if applied),
crop uptake, soil evaporation and drainage for determining soil water content17,50.
The extraction rate depends on the soil water content in relation to the lower limit
of extractable water content for the given soil layer and an extraction capacity
factor that incorporates the effects of both soil hydraulic conductivity and root
length density on water uptake12. Possible soil water extraction was derived by
summing over soil layers to give Tcan,S,DAY (Supplementary equation (2)).
Limited transpiration restricts stomatal conductance and photosynthesis when
crop water supply is limited. When estimated Tcan,D,DAY from the leaf-level A–gs
model was not met by Tcan,S,DAY, as would occur under water-limited conditions,
Tcan,A,DAY was given by Tcan,S,DAY and involved changes in the diurnal pattern of
Tcan. The new diurnal pattern was simulated by iteratively reducing a maximum
threshold of Tcan so that Tcan,A,DAY was reduced to the level of Tcan,S,DAY. Tsun:D:Tsh,D, as
leaf fractions. This produces a diurnal pattern with a flat-topped hourly profile
or ‘transpiration plateau’ (Fig. 2f,h), in line with observations by Olioso et al22.
This is also consistent with the field observation of plants wilting in the middle
of the day when crop water supply becomes limiting relative to demand. Once
actual transpiration was defined, gs was calculated using the Penman–Monteith
combination equation (Supplementary equation (38)) and converted to the
appropriate units (Supplementary equation (13)). The calculated gs would also
exhibit reduction during hours when Tcan is reduced (Fig. 2j,l). Tl was then
calculated from the saturation heat equation (Supplementary equation (42)). The
revised gs and Tl values were then input into the A–gs model to calculate water-
limited photosynthesis, which was converted to daily crop biomass increment and
connected with crop models as described above.
Model testing and validation simulations. The DCaPST module was analysed
for its response to levels of water availability on typical days during wheat and
sorghum crop growth (Supplementary Table 5) using default DCaPST parameter
values (Supplementary Table 6) to determine whether simulated results reflected
behaviour expected from known responses. Simulated leaf-level A/Ci curves,
generated using the same default DCaPST parameter values, followed wheat and
maize leaf gas-exchange measurements closely (Supplementary Fig. 3). Diurnal
patterns simulated for a full-size canopy (LAI of 6 m2 leaf per m2 ground area) were
generated for well-watered and water-limited situations.
In addition, extensive detailed field experimental datasets have been used for
validating the sorghum and wheat crop models in the APSIM platform12,18. Here
we used the same datasets to conduct validation simulations with the APSIM–
DCaPST integrated cross-scale modelling system. The results for simulated
biomass and yield were also compared with results using the standard APSIM crop
growth model in the absence of the DCaPST module (Fig. 3).
Baseline simulation of wheat and sorghum crops grown in a typical Australian
production environment. To examine effects of manipulating photosynthesis on
crop growth and yield in field production environments, a long-term simulation
was conducted using default DCaPST parameter values (Supplementary Table 6)
and necessary crop model parameter values (Supplementary Table 7) to provide a
baseline for comparison. Simulated C3 wheat and C4 sorghum crops were sown on
15 May and 15 October, respectively, every year between 1900 and 2016 at Dalby,
Queensland. Daily weather data for the period were sourced from http://apsrunet.
apsim.info/ for Dalby Post Office (station number: 041023). Soil information from
a local cropping vertosol soil was obtained from the APSOIL database (APSOIL
number: 14). Soil N at sowing was fixed at 50 kg NO3 ha−1 and 5 kg NH4 ha−1 and
one application of 360 kg NO3 ha−1 at sowing was added to simulate non-limiting N
conditions. Soil water at sowing was fixed at 100 mm plant-available water. Crops
were simulated with either water non-limiting (full irrigation) or under rainfed
cropping conditions, which generated varying levels of water limitation depending
on the season.
Photosynthetic manipulation targets and modelling scenarios. Experimental
approaches for enhancing Rubisco carboxylation rate, electron transport
capacity and mesophyll conductance for CO2 and design of the corresponding
model scenarios by adjusting the associated DCaPST parameters are described
below. These parameter adjustments were applied to the baseline simulation
for assessment of their effects. The current simulation assumed that that
photosynthetic enhancements were feasible without changes to plant nitrogen
dynamics and leaf nitrogen allocation to photosynthetic apparatus. All
photosynthesis parameter values were kept constant except for those targeted in
Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants
NaTurE PlanTs
the manipulation scenario simulations. Simulations were conducted with Ci/Ca
either kept constant or allowed to vary, to test the coupled or decoupled A–gs link.
The APSIM crop model parameters associated with plant growth, development
and yield were not altered.
Rubisco catalyses the first major step of CO2 assimilation in photosynthesis.
Manipulation of the Rubisco carboxylation rate is possible by replacing its large and
small subunits with subunits from other species having faster rates51. Simulating an
increased carboxylation rate was parameterized by a 20% increase in χVc, the slope
of the linear relationship between Vcmax at 25 °C and SLN (Supplementary equations
(6)–(9)). Assumptions for defining the default Vcmax and PEP regeneration in C4
photosynthesis (Supplementary Table 6) are shown in Supplementary Fig. 3, where
the parameters were inferred from fitting an ACi curve for maize.
The chloroplast electron transport chain is the energy provider of
photosynthesis. Enhancing the maximum rate of electron transport has been
proposed to increase the electron transport-limited rate of photosynthesis (Aj).
This is feasible via an increase in activity of the cytochrome b6f complex, which
participates in both linear and cyclic electron transport, through overexpression of
one of its subunits, Rieske FeS52. An increase of nearly 20% in Jmax can be achieved52.
Simulating overexpression of Rieske FeS for electron transport chain enhancement
was parameterized by a 20% increase in χJ, the slope of the linear relationship
between Jmax at 25 °C and SLN.
Mesophyll conductance (gm) for CO2 determines the drawdown of CO2
from the intercellular air space to the sites of Rubisco carboxylation in C3 or
phosphoenol pyruvate carboxylation in C4 in the mesophyll cell. There is wide
natural variation in gm in both C3 and C4 species53,54, ranging two-to-threefold and
contributed to by anatomical characteristics of leaves55. Despite the potential for
doubling gm by exploiting natural variation via plant breeding, the feasibility of this
approach has yet to be demonstrated. One promising approach to enhancing gm is
by increasing expression of aquaporins in mesophyll membranes56, which has been
shown to enhance gm by 20% in C3 tobacco plants57. Simulating overexpression of
aquaporins for gm enhancement was parameterized by a 20% increase in χgm, the
slope of the linear relationship between gm at 25 °C and SLN.
Reporting Summary. Further information on research design is available in the
Nature Research Reporting Summary linked to this article.
Data availability
The data that support the findings of this study can be found in the related cited
articles and/or from the corresponding author upon reasonable request.
Code availability
The compiled code and files used in the validation, baseline and photosynthetic
manipulation simulations are freely available for download at https://github.com/
QAAFI/DCaPST.
Received: 24 September 2018; Accepted: 4 March 2019;
Published online: 8 April 2019
References
1. Long, S. P., Marshall-Colon, A. & Zhu, X.-G. Meeting the global food
demand of the future by engineering crop photosynthesis and yield potential.
Cell 161, 56–66 (2015).
2. Parry, M. A. J. et al. Raising yield potential of wheat. II. Increasing
photosynthetic capacity and efficiency. J. Exp. Bot. 62, 453–467 (2011).
3. Ray, D. K., Mueller, N. D., West, P. C. & Foley, J. A. Yield trends are
insufficient to double global crop production by 2050. PLoS ONE 8,
e66428 (2013).
4. von Caemmerer, S. & Evans, J. R. Enhancing C3 photosynthesis. Plant
Physiol. 154, 589–592 (2010).
5. von Caemmerer, S. & Furbank, R. T. Strategies for improving C4
photosynthesis. Curr. Opin. Plant Biol. 31, 125–134 (2016).
6. Wu, A., Doherty, A., Farquhar, G. D. & Hammer, G. L. Simulating daily field
crop canopy photosynthesis: an integrated software package. Funct. Plant Biol.
45, 362–377 (2018).
7. Sinclair, T. R., Purcell, L. C. & Sneller, C. H. Crop transformation and the
challenge to increase yield potential. Trends Plant Sci. 9, 70–75 (2004).
8. Wu, A., Song, Y., van Oosterom, E. J. & Hammer, G. L. Connecting
biochemical photosynthesis models with crop models to support crop
improvement. Front. Plant Sci. 7, 1518 (2016).
9. Evans, J. R. Nitrogen and photosynthesis in the flag leaf of wheat (Triticum
aestivum L.). Plant Physiol. 72, 297–302 (1983).
10. van Oosterom, E. J., Borrell, A. K., Chapman, S. C., Broad, I. J. & Hammer,
G. L. Functional dynamics of the nitrogen balance of sorghum: I. N demand
of vegetative plant parts. Field Crops Res. 115, 19–28 (2010).
11. van Oosterom, E. J., Chapman, S. C., Borrell, A. K., Broad, I. J. & Hammer,
G. L. Functional dynamics of the nitrogen balance of sorghum. II. Grain
filling period. Field Crops Res. 115, 29–38 (2010).
Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants
Articles
12. Hammer, G. L. et al. Adapting APSIM to model the physiology and genetics
of complex adaptive traits in field crops. J. Exp. Bot. 61, 2185–2202 (2010).
13. Robertson, M. J., Fukai, S., Ludlow, M. M. & Hammer, G. L. Water extraction
by grain sorghum in a sub-humid environment. I. Analysis of the water
extraction pattern. Field Crops Res. 33, 81–97 (1993).
14. Hammer, G. L. et al. Can changes in canopy and/or root system architecture
explain historical maize yield trends in the U.S. corn belt? Crop Sci. 49,
299–312 (2009).
15. Farquhar, G. D., von Caemmerer, S. & Berry, J. A. A biochemical
model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149,
78–90 (1980).
16. von Caemmerer, S. Biochemical Models of Leaf Photosynthesis Vol. 2 (CSIRO
Publishing, 2000).
17. Holzworth, D. P. et al. APSIM—evolution towards a new generation of
agricultural systems simulation. Environ. Model. Softw. 62, 327–350 (2014).
18. Brown, H. E. et al. Plant modelling framework: software for building and
running crop models on the APSIM platform. Env. Model. Softw. 62,
385–398 (2014).
19. Evans, J. R. Improving photosynthesis. Plant Physiol. 162, 1780–1793 (2013).
20. Grant, R. F., Peters, D. B., Larson, E. M. & Huck, M. G. Simulation of canopy
photosynthesis in maize and soybean. Agric. For. Meteorol. 48, 75–92 (1989).
21. Sinclair, T. R. & Muchow, R. C. Radiation use efficiency. Adv. Agron. 65,
215–265 (1999).
22. Olioso, A., Carlson, T. N. & Brisson, N. Simulation of diurnal transpiration
and photosynthesis of a water stressed soybean crop. Agric. For. Meteorol. 81,
41–59 (1996).
23. Ghannoum, O. C4 photosynthesis and water stress. Ann. Bot. 103,
635–644 (2009).
24. Ghannoum, O., Evans, J. R. & von Caemmerer, S. in C4 Photosynthesis and
Related CO2 Concentrating Mechanisms (eds Raghavendra, A. S. & Sage, R. F.)
129–146 (Springer, 2011).
25. Ball, J. T., Woodrow, I. & Berry, J. in Progress in Photosynthesis Research (ed.
Biggins, J.) Ch. 48 (Martinus Nijhoff Publishers, 1987).
26. Yin, X. & Struik, P. C. Can increased leaf photosynthesis be converted into
higher crop mass production? A simulation study for rice using the crop
model GECROS. J. Exp. Bot. 68, 2345–2360 (2017).
27. Amir, J. & Sinclair, T. R. A model of water limitation on spring wheat growth
and yield. Field Crops Res. 28, 59–69 (1991).
28. von Caemmerer, S. et al. Stomatal conductance does not correlate with
photosynthetic capacity in transgenic tobacco with reduced amounts of
Rubisco. J. Exp. Bot. 55, 1157–1166 (2004).
29. Fujita, T., Noguchi, K. & Terashima, I. Apoplastic mesophyll signals induce
rapid stomatal responses to CO2 in Commelina communis. New Phytol. 199,
395–406 (2013).
30. Mott, K. A. & Peak, D. Effects of the mesophyll on stomatal responses in
amphistomatous leaves. Plant Cell Environ. 41, 2835–2843 (2018).
31. McGrath, J. M. & Long, S. P. Can the cyanobacterial carbon-concentrating
mechanism increase photosynthesis in crop species? A theoretical analysis.
Plant Physiol. 164, 2247 (2014).
32. Sinclair, T. R. Is transpiration efficiency a viable plant trait in breeding for
crop improvement? Funct. Plant Biol. 39, 359–365 (2012).
33. Flexas, J. et al. Mesophyll conductance to CO2 and Rubisco as targets for
improving intrinsic water use efficiency in C3 plants. Plant Cell Environ. 39,
965–982 (2016).
34. Hammer, G. L. & Wright, G. C. A theoretical-analysis of nitrogen and
radiation effects on radiation use efficiency in peanut. Aust. J. Agric. Res. 45,
575–589 (1994).
35. de Pury, D. G. G. & Farquhar, G. D. Simple scaling of photosynthesis from
leaves to canopies without the errors of big-leaf models. Plant Cell Environ.
20, 537–557 (1997).
36. Duncan, W. G., Loomis, R. S., Williams, W. A. & Hanau, R. A model for
simulating photosynthesis in plant communities. Hilgardia 38, 181–205
(1967).
37. Messina, C., Hammer, G., Dong, Z. S., Podlich, D. & Cooper, M. in Crop
Physiology: Applications for Genetic Improvement and Agronomy (eds Sadras,
V. & Calderini, D.) 235–265 (Elsevier, 2009).
38. Ritchie, J. T. Model for predicting evaporation from a row crop with
incomplete cover. Water Resour. Res. 8, 1204–1213 (1972).
39. Wong, S. C., Cowan, I. R. & Farquhar, G. D. Leaf conductance in relation to
assimilation in Eucalyptus pauciflora Sieb. ex Spreng—influence of irradiance
and partial pressure of carbon dioxide. Plant Physiol. 62, 670–674 (1978).
40. Wong, S. C., Cowan, I. R. & Farquhar, G. D. Stomatal conductance correlates
with photosynthetic capacity. Nature 282, 424–426 (1979).
41. Wolz, K. J., Wertin, T. M., Abordo, M., Wang, D. & Leakey, A. D. B. Diversity
in stomatal function is integral to modelling plant carbon and water fluxes.
Nat. Ecol. Evol. 1, 1292–1298 (2017).
42. Leakey, A. D. B. et al. Photosynthesis, productivity, and yield of maize are not
affected by open-air elevation of CO2 concentration in the absence of
drought. Plant Physiol. 140, 779–790 (2006).
387
Articles
43. Pengelly, J. J. L. et al. Functional analysis of corn husk photosynthesis. Plant
Physiol. 156, 503 (2011).
44. von Caemmerer, S. & Farquhar, G. D. Some relationships between the
biochemistry of photosynthesis and the gas exchange of leaves. Planta 153,
376–387 (1981).
45. McPherson, H. & Slatyer, R. Mechanisms regulating photosynthesis in
Pennisetum typhoides. Aust. J. Biol. Sci. 26, 329–340 (1973).
46. Yamori, W., Nagai, T. & Makino, A. The rate-limiting step for CO2
assimilation at different temperatures is influenced by the leaf nitrogen
content in several C3 crop species. Plant Cell Environ. 34, 764–777 (2011).
47. Braune, H., Mueller, J. & Diepenbrock, W. Integrating effects of leaf nitrogen,
age, rank, and growth temperature into the photosynthesis-stomatal
conductance model LEAFC3-N parameterised for barley (Hordeum vulgare L.).
Ecol. Model. 220, 1599–1612 (2009).
48. Sinclair, T. R. & Horie, T. Leaf nitrogen, photosynthesis, and crop radiation
use efficiency—a review. Crop Sci. 29, 90–98 (1989).
49. Gifford, R. M. Plant respiration in productivity models: conceptualisation,
representation and issues for global terrestrial carbon-cycle research. Funct.
Plant Biol. 30, 171–186 (2003).
50. Probert, M. E., Dimes, J. P., Keating, B. A., Dalal, R. C. & Strong, W. M.
APSIM’s water and nitrogen modules and simulation of the dynamics of
water and nitrogen in fallow systems. Agric. Syst. 56, 1–28 (1998).
51. Lin, M. T., Occhialini, A., Andralojc, P. J., Parry, M. A. J. & Hanson, M. R. A
faster Rubisco with potential to increase photosynthesis in crops. Nature 513,
547–550 (2014).
52. Simkin, A. J., McAusland, L., Lawson, T. & Raines, C. A. Overexpression of
the RieskeFeS protein increases electron transport rates and biomass yield.
Plant Physiol. 175, 134–145 (2017).
53. Jahan, E., Amthor, J. S., Farquhar, G. D., Trethowan, R. & Barbour, M. M.
Variation in mesophyll conductance among Australian wheat genotypes.
Funct. Plant Biol. 41, 568–580 (2014).
54. Ubierna, N., Gandin, A., Boyd, R. A. & Cousins, A. B. Temperature response
of mesophyll conductance in three C4 species calculated with two methods:
18
O discrimination and in vitro Vpmax. New Phytol. 214, 66–80 (2017).
388
NaTurE PlanTs
55. von Caemmerer, S. & Evans, J. R. Temperature responses of mesophyll
conductance differ greatly between species. Plant Cell Environ. 38,
629–637 (2015).
56. Flexas, J. et al. Mesophyll diffusion conductance to CO2: an unappreciated
central player in photosynthesis. Plant Sci. 193, 70–84 (2012).
57. Flexas, J. et al. Tobacco aquaporin NtAQP1 is involved in mesophyll
conductance to CO2 in vivo. Plant J. 48, 427–439 (2006).
Acknowledgements
This research was conducted by the Australian Research Council Centre of Excellence
for Translational Photosynthesis (CE1401000015) and funded by the Australian
Government.
Author contributions
A.W., G.L.H., S.v.C. and G.D.F. designed the study and contributed to the development
of the cross-scale model, A.W. constructed the model and A.D. engineered the software.
A.W. undertook model testing and refinement. A.W., G.L.H., S.v.C. and G.D.F. undertook
analysis of simulation results and contributed to writing and revising the paper.
Competing interests
The authors declare no competing interests.
Additional information
Supplementary information is available for this paper at https://doi.org/10.1038/
s41477-019-0398-8.
Reprints and permissions information is available at www.nature.com/reprints.
Correspondence and requests for materials should be addressed to A.W.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations.
© The Author(s), under exclusive licence to Springer Nature Limited 2019
Nature Plants | VOL 5 | APRIL 2019 | 380–388 | www.nature.com/natureplants
 nature research | reporting summary
Corresponding author(s): Alex Wu

Reporting Summary
Nature Research wishes to improve the reproducibility of the work that we publish. This form provides structure for consistency and transparency
in reporting. For further information on Nature Research policies, see Authors & Referees and the Editorial Policy Checklist.

Statistical parameters
When statistical analyses are reported, confirm that the following items are present in the relevant location (e.g. figure legend, table legend, main
text, or Methods section).
n/a Confirmed
The exact sample size (n) for each experimental group/condition, given as a discrete number and unit of measurement
An indication of whether measurements were taken from distinct samples or whether the same sample was measured repeatedly
The statistical test(s) used AND whether they are one- or two-sided
Only common tests should be described solely by name; describe more complex techniques in the Methods section.

A description of all covariates tested

A description of any assumptions or corrections, such as tests of normality and adjustment for multiple comparisons
A full description of the statistics including central tendency (e.g. means) or other basic estimates (e.g. regression coefficient) AND
variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals)

For null hypothesis testing, the test statistic (e.g. F, t, r) with confidence intervals, effect sizes, degrees of freedom and P value noted
Give P values as exact values whenever suitable.

For Bayesian analysis, information on the choice of priors and Markov chain Monte Carlo settings
For hierarchical and complex designs, identification of the appropriate level for tests and full reporting of outcomes
Estimates of effect sizes (e.g. Cohen's d, Pearson's r), indicating how they were calculated

Clearly defined error bars

State explicitly what error bars represent (e.g. SD, SE, CI)

Our web collection on statistics for biologists may be useful.

Software and code

Policy information about availability of computer code
Data collection Agricultural Production Systems sIMulator v7.8 (http://www.apsim.info/Products/Downloads.aspx)
Diurnal Canopy Photosynthesis-stomatal conductance module v1.0 (https://github.com/QAAFI/DCaPST)

Data analysis SigmaPlot for Windows Version 13.0. Build 13.0.0.83

Excel 2016 for Windows
For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors/reviewers
upon request. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research guidelines for submitting code & software for further information.

Data
April 2018

Policy information about availability of data

All manuscripts must include a data availability statement. This statement should provide the following information, where applicable:
- Accession codes, unique identifiers, or web links for publicly available datasets
- A list of figures that have associated raw data
- A description of any restrictions on data availability
The data that support the findings of this study can be found in the related cited articles and/or from the corresponding author upon reasonable request.

1
 nature research | reporting summary
Field-specific reporting
Please select the best fit for your research. If you are not sure, read the appropriate sections before making your selection.
Life sciences Behavioural & social sciences Ecological, evolutionary & environmental sciences
For a reference copy of the document with all sections, see nature.com/authors/policies/ReportingSummary-flat.pdf

Life sciences study design

All studies must disclose on these points even when the disclosure is negative.
Sample size The available number of crop biomass and yield observations collected in previous studies were used. This represent a wide range of
conditions in which C3 wheat and C4 sorghum were grown given yield range between less than 1 t/ha to 10 t/ha.

Data exclusions No data were excluded from the analyses.

Replication Reproducibility of model simulations was ensured by following the comprehensively documented instructions to install and run the simulation
software developed in this study (see https://github.com/QAAFI/DCaPST). All attempts at model simulation were successful and generated
identical results.

Randomization Field observed crop attributes (biomass and grain yield) for wheat and sorghum were analysed separately because of differences in species.

Blinding Not relevant because we were analysing crop attributes of the two species separately.

Reporting for specific materials, systems and methods

Materials & experimental systems Methods

n/a Involved in the study n/a Involved in the study
Unique biological materials ChIP-seq
Antibodies Flow cytometry
Eukaryotic cell lines MRI-based neuroimaging
Palaeontology
Animals and other organisms
Human research participants

April 2018