Burgess, Alexandra Jacquelyn (2017) The variable light environment within complex 3D canopies ...

448 Pages·2017·17.42 MB·English

by  Christine Middleton

THE VARIABLE LIGHT ENVIRONMENT WITHIN
COMPLEX 3D CANOPIES
ALEXANDRA JACQUELYN BURGESS
BA (Hons) Oxon
Thesis submitted to the University of Nottingham for the degree of Doctor of
Philosophy
September 2016
Abstract
With an expanding population and uncertain consequences of climate
change, the need to both stabilise and increase crop yields is important. The
relationship between biomass production and radiation interception suggests
one target for improvement. Under optimal growing conditions, biomass
production is determined by the amount of light intercepted and the efficiency
with which this is converted into dry matter. The amount of light at a given
photosynthetic surface is dependent upon solar movement, weather patterns
and the structure of the plant, amongst others. Optimising canopy structure
provides a method by which we can improve and optimise both radiation
interception and also the distribution of light among canopy layers that
contribute to net photosynthesis. This requires knowledge of how canopy
structure determines light distribution and therefore photosynthetic capacity of
a given crop species.
The aim of this thesis was to assess the relationships between canopy
architecture, the light environment and photosynthesis. This focused on two
core areas: the effect of varietal selection and management practices on canopy
structure and the light environment and; the effect of variable light on select
photosynthetic processes (photoinhibition and acclimation). An image-based
reconstruction method based on stereocameras was employed with a forward
ray tracing algorithm in order to model canopy structure and light distributions
in high-resolution. Empirical models were then applied using parameterisation
from manually measured data to predict the effects of variable light on
photosynthesis.
The plasticity of plants means that the physical structure of the canopy is
dependent upon many different factors. Detailed descriptions of canopy
architecture are integral to predicting whole canopy photosynthesis due to the
spatial and temporal differences in light profiles between canopies. This
inherent complexity of the canopy means that previous methods for calculating
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light interception are often not suitable. 3-dimensional modelling can provide a
quick and easy method to retain this complexity by preserving small variations.
This provides a means to more accurately quantify light interception and
enable the scaling of cellular level processes up to the whole canopy.
Results indicate that a canopy with more upright leaves enables greater light
penetration to lower canopy layers, and thus higher photosynthetic
productivity. This structural characteristic can also limit radiation-induced
damage by preventing exposure to high light, particularly around midday.
Whilst these features may lead to higher photosynthetic rates per unit leaf area,
per unit ground area, photosynthesis is usually determined by total leaf area of
the canopies, and within this study, the erect canopies tended to have lower
total leaf areas than the more horizontal canopies. The structural arrangement
of plant material often led to low levels of light within the lower canopy layers
which were punctuated by infrequent, high light events. However, the slow
response of photosynthesis to a change in light levels meant that these sun
flecks cannot be used by the plant and thus the optimal strategy should be
geared towards light harvesting and efficient photosynthesis under low light
conditions.
The results of this study contribute to our understanding of photosynthetic
processes within the whole canopy and provide a foundation for future work in
this area.
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Publications
In Peer-reviewed Journals
Burgess AJ, Retkute R, Preston SP, Jensen OE, Pound MP, Pridmore TP, and
Murchie EH. The 4-dimensional plant: biological implications of wind-
induced movement. Frontiers in Plant Science 7: 1392
Burgess AJ*, Retkute R*, Pound MP, Preston SP, Pridmore TP, Foulkes MJ,
Jensen OE, and Murchie EH (2015) High-resolution 3D structural data
quantifies the impact of photoinhibition on long term carbon gain in wheat
canopies in the field. Plant Physiology, 169(2): 1192-1204
Retkute R, Smith-Unna SE, Smith RW, Burgess AJ, Jensen OE, Johnson GN,
Preston SP, and Murchie EH (2015) Exploiting heterogeneous environments:
does photosynthetic acclimation optimize carbon gain in fluctuating light?
Journal of Experimental Botany 66: 2437-2447
Burgess AJ, Retkute R, Pound MP, Mayes S, and Murchie EH. Applications
of image-based 3D reconstruction and modelling in assessing light
interception and productivity in multi-species intercrop systems. Annals of
Botany, in press
Pre-published or under review
Pound MP, Burgess AJ, Wilson MH, Atkinson JA, Griffiths M, Jackson AS,
Bulat A, Tzimiropoulos G, Wells DM, Murchie EH, Pridmore TP and French
AP (2016) Deep Machine Learning provides state-of-the-art performance in
image-based plant Phenotyping. Pre-published at bioRxiv doi:
http://dx.doi.org/10.1101/053033
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Burgess AJ, Retkute R, Chinnathambi K, Randall JWP, Smillie IRA, Carmo-
Silva E, and Murchie EH. Sub-optimal photosynthetic acclimation in wheat is
revealed by high resolution 3D canopy reconstruction. New Phytologist
Burgess AJ, Herman T, Retkute R and Murchie EH. Is there a consistent
relationship between canopy architecture, light distribution and
photosynthesis across diverse rice germplasm? Frontiers in Plant Science
Manuscripts
Burgess AJ, Herman T, and Murchie EH. The effect of nitrogen on rice
canopy architecture and photosynthesis; assessed using high-resolution
reconstruction and modelling.
Burgess AJ, Retkute R, Simpson C and Murchie EH. The effect of fluctuating
light on dynamic acclimation of Arabidopsis thaliana.
Book Chapters
Lin BB, Burgess AJ and Murchie EH (2015) Adaptation for climate sensitive
crops using agroforestry: case studies for coffee and rice. Chapter 11 in Ong
C, Black C and Wilson J. 2nd Eds Tree-Crop Interactions: Agroforestry in a
Changing Climate, CABI
Contributing author to Karunaratne, A.S. (2015) (eds) Proso Millet (Panicum
miliaceum L.)-Agronomy, Botany, Ecophysiology and Nutrition. Faculty of
Agricultural Sciences, Sabaragamuwa University of Sri Lanka, 70140,
Belihuloya, Sri Lanka.
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Acknowledgements
Firstly, I would like to thank my supervisors, Erik Murchie, Sean Mayes,
Debbie Sparkes and Festo Massawe, for tuition, support and guidance
throughout the course of my PhD.
I would also like to thank: Renata Retkute for helping me with the modelling
aspects of my project and assistance with figures; Michael Pound for help with
reconstructions and image analysis; John Alcock and Matt Tovey for running
the field trials; Jools Marquez for organising the laboratory; Tiara Herman,
Hayley Smith, Kannan Chinnathambi, Jamie Randall, CC Foo, Conor Simpson
and Lorna Mcausland for assistance with the laboratory and field work and; my
internal examiner, Kevin Pyke, for his invaluable advice.
My grateful thanks to my funders, Crops For the Future and the University of
Nottingham.
Finally, I would like to thank my family and my fiancé, Toby Townsend, for
supporting me throughout my studies and providing inspiration whilst I was
writing my thesis.
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Abbreviations
2D 2 Dimensional
3D 3 Dimensional
4D 4 Dimensional
AGDM Above ground dry matter
ANOVA Analysis of Variance
C Carbon
chl Chlorophyll
CL Constant Light
cLAI Cumulative leaf area index
CO Carbon dioxide
2
Col Columbia (Arabidopsis thaliana accession)
DAS Days after sowing
DAT Days after transplanting
F/ FI Fractional Interception
FL Flag leaf
FL Fluctuating Light
GM Gross margins
GS Growth stage
H O Water
2
HI Harvest Index
J Maximum rate of electron transport
max
K Potassium
LAD Leaf area duration
LAI Leaf area index
LCP Light compensation point
LEC Land equivalence coefficient
LED Light emitting diode
LER Land equivalence ratio
Ler Landsberg erecta (Arabidopsis thaliana accession)
LHC Light harvesting complex
LRC Light response curves
MAGIC Multi-parent advanced generation intercross
N Nitrogen
NUE Nutrient use efficiency
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O Oxygen
2
P Phosphorous
PAR Photosynthetically active radiation
P Maximum photosynthetic capacity
max
𝑃̅ Maximum photosynthetic capacity if the [fluctuating] light pattern
𝑚𝑎𝑥
was replaced by the average irradiance
𝑃𝑜𝑝𝑡 Optimal maximum photosynthetic capacity
𝑚𝑎𝑥
PNUE Photosynthetic nitrogen use efficiency
PPFD Photosynthetic photon flux density
PSI Photosystem I
PSII Photosystem II
R Dark respiration
d
RGB Red green blue
RH Relative humidity
ROS Reactive oxygen species
RUE Radiation use efficiency
SF Scaling factor
SF Scaling factor at 12:00 h
12
TPU Triose phosphate utilisation
TSP Total soluble protein
TVC Total variable costs
V Maximum rate of carboxylation
cmax
Ws Wassilewskija-4 (Arabidopsis thaliana accession)
WT Wild type
WUE Water use efficiency
θ Convexity
QUE) Quantum use efficiency/ quantum yield

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Table of Contents
Abstract………………………………………………………………………… i
Publications………………………………………………………………….…. iii
Acknowledgments……………………………………………………………… v
Abbreviations…………………………………………………………………... vi
List of Figures………………………………………………………………….. xv
List of Tables…………………………………………………………………… xx
Chapter 1: Introduction……………………………………………………….. 1
1.1 Research Context…………………………………………………… 1
1.2 Photosynthesis and Biomass Production…………………………… 3
1.3 The Canopy Light Environment and Architectural Characteristics... 13
1.3.1 Canopy Architecture……………………………………... 15
1.3.1.1 Architectural Features……………………………….. 16
Leaf Area……………………………………………… 16
Clumping……………………………………………… 17
Leaf Shape and Size…………………………………… 19
Leaf Inclination and Orientation………………………. 20
Leaf Movement………………………………………... 22
1.3.2 Direct versus Diffused Light…………………………….. 23
1.4 Linking Architecture, Photosynthesis and Biomass Production…… 24
1.5 Modelling…………………………………………………………... 26
1.5.1 Plant Structural Modelling……………………………….. 26
1.5.2 Light Modelling………………………………………….. 29
1.5.3 Plant Process Modelling: empirical versus mechanistic…. 31
1.6 Knowledge Gaps…………………………………………………… 33
Aims and Objectives……………………………………………………. 34
Hypotheses……………………………………………………………... 34
Thesis Layout…………………………………………………………... 35
Chapter 2: Core Methods and Method Development……………………….. 36
2.1 The Reconstruction Process………………………………………... 36
2.1.1 Imaging………………………………………………….. 38
Canopy Imaging: Imaging in situ……………………... 38
Single Plant Imaging………………………………….. 38
2.1.2 Reconstructions………………………………………….. 39
2.1.2.1 Point Cloud Reconstruction…………………… 40
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2.1.2.2 Surface Estimation…………………………….. 41
2.1.2.3 Canopy Formation…………………………….. 47
2.2 Reconstruction Method Development……………………………… 49
2.2.1 Reconstruction Optimisation…………………………….. 49
2.2.2 Optimisation on the Artificial Dataset…………………… 50
2.3 The Canopy Light Environment: Ray Tracing……………………... 57
PART I: THE EFFECT OF CROP CHOICE AND AGRONOMIC
PRACTICES ON CANOPY PHOTOSYNTHESIS…………………………. 59
Chapter 3: Methods for exploring the light environment within multi-
species cropping systems (intercropping)…………………………………….. 61
Paper Details……………………………………………………………. 61
Abstract…………………………………………………………………. 62
Introduction…………………………………………………………….. 63
Materials and Methods…………………………………………………. 69
Plant Material………………………………………………….. 69
Imaging and Ray Tracing……………………………………… 69
Gas Exchange………………………………………………….. 71
Ceptometer……………………………………………………... 72
Statistics………………………………………………………... 72
Modelling………………………………………………………. 72
Results………………………………………………………………….. 75
Validation of imaging and modelling...………………………... 75
The Light Environment………………………………………... 76
Assessing Productivity………………………………………… 80
Discussion………………………………………………………………. 84
High-resolution digital reconstruction as a method to explore
the intercrop light environment………………………………... 84
Studying light interception in heterogeneous canopies………... 90
Designing the optimal intercropping system…………………... 92
Concluding remarks……………………………………………. 94
Supplementary Material………………………………………………... 96
Chapter 4: The relationship between canopy architecture and
photosynthesis………….………………………………………………………. 102
Paper Details……………………………………………………………. 102
Abstract…………………………………………………………………. 103
Introduction…………………………………………………………….. 104
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