Removing the inefficiencies of 3-dimensional canopy photosynthesis by the alteration of leaf light-response dynamics and plant architecture

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences

Abstract

Photosynthesis in plants is the uptake of CO2 by leaves and its assimilation into carbohydrates within specialized organs (chloroplasts), a process that requires the absorption of light by chlorophyll. However the rate of photosynthesis over a given period of time varies according to environmental changes such as light intensity, leaf age, temperature and other factors.
This has consequences for productivity of crops which depend on high rates of photosynthesis for high yields. Productivity is the sum total of a large number of leaves in a canopy, many of which shade (or partly shading each other) and are usually different ages. We can calculate the potential productivity of whole canopies based on leaf photosynthetic attributes and other physical and physiological factors. When we do this the theoretical productivity tends to be much higher than the measured productivity. The reasons are unclear but a large part is thought to be due to the way leaves respond when re-constructed into a large 3D canopy. In this state, plants exist as a community which has emergent properties that we cannot necessarily predict from plants grown individually. If we can eliminate the gap between the theoretical and measured productivity we can achieve a step change in productivity.
Photosynthetic rate is very sensitive to light intensity. The difference in light intensities that exist within the canopy (an exponential decline from top to bottom) is significant and is affected by the precise architecture of the canopy i.e. the amount of leaf area per unit ground area, the angle, shape and size of leaves and their position within 3 dimensional space. This means that the light intensity has great variability in space and time within canopies e.g with frequent and transient appearance of 'light-flecks'. The movement of the canopy plays a major part in how fast or slow light flecks are generated, and where in the canopy they appear. Photosynthesis should be optimized to these rapidly changing conditions, but there are indications that it is not. The environment can cause a 'down-regulation' of photosynthesis in the field and this can be measured by comparing actual leaf photosynthesis against the maximum. It is not clear how this down-regulation interacts with canopy architecture and the responses of leaves.
One problem is that we do not have detailed images of crop canopies in 3 dimensions and we do not have sophisticated models that allow us to map the complex changes in light intensity to photosynthesis. Crop canopies perform a number of important agronomic roles, some photosynthetic , others not. Therefore we need to understand the problem 'in reverse' - i.e. to take good 3D images of crop canopies, both still and moving, calculate the typical changes in light intensity that occur in that canopy and then change photosynthetic dynamics so that it matches those changes.
We will grow canopies of productive crop plants, rice and wheat in a special glasshouse that will enable us to image crop canopies, when still, and produce 3D high resolution images using laser scanning and camera techniques. Novel techniques will be tested for detecting plant movement in wind and we will then distort these images to examine the effect of wind induced leaf 'flutter' and stem bending on light distribution. We will use these images in a mathematical ray-tracing program to finely map the changes in light that occur within the canopy. These changes will be used to predict which processes dominate the canopy-productivity process.
This is essentially a modelling and imaging project of plant canopies: we will begin the following phase by ordering rice mutants altered in key reactions identified from these models and grow these to test whole canopy productivity. If successful we can achieve a step change in productivity by eliminating any wasteful processes that occur within the canopy.

Technical Summary

Photosynthetic rate within plant canopies frequently fluctuates. However much of our understanding arises from steady state photosynthesis measurements. Solar movement and wind result in the formation of complex 3-dimensional plant canopy structures which induces large fluctuations in photosynthetic rate. In order to understand and improve the contribution of dynamic photosynthesis to plant productivity we must understand the relationship between canopy architecture, spatio-temporal kinetics in irradiance and biochemical regulation.
This project will utilize new glasshouses in which crop canopies of key species (rice and wheat) will be grown in which plants have full root and canopy interaction. The destructive and non - destructive imaging of these canopies in high resolution will be made using stereo cameras and laser scanners. In this environment plants will be kept motionless. Plant movement will be induced by fans and the frequency of movement assessed by novel techniques using newly available sensors.
Existing software packages will recreate full high resolution images of contrasting canopy structure that can be used in ray tracing analyses to generate complex spatio-temporal maps of light fluctuations according to solar position. Canopy movement data will be used to distort these images to investigate the impact of movement on the distribution of light..
Dynamic photosynthesis models will be used to predict the dominant processes that are likely to prevent photosynthesis from accurately tracking the changes in light. A model will be developed based on existing models of dynamic photosynthesis and parameterized using physiological data collected during this project.
The processes identified as likely to dominate for a given canopy structure will be tested using rice mutants ordered from existing collections. Canopies grown will be measured for key photosynthetic parameters and biomass production rate.

Planned Impact

Who will benefit from this research?

In addition to the academic beneficiaries described elsewhere :
1. Crop improvement. Those attempting to genetically improve crop plants for higher yields and resource use efficiency (such as commercial and government plant breeders) will be provided with a source of traits and gene combinations.
2. Food production. Rising global population and pressures upon land use caused by urbanization and erosion mean that higher productivity is essential to meet food security needs by 2050. If the gap between theoretical and actual production rates are closed then beneficiaries are universal because this would represent a sustainable improvement via inherent improvement in resource use efficiency. Most notable are those in poor areas and marginal environments.
3. Energy production. Sustainable (not competing with food) production of energy crops and secondary fuels which use the by products of food crops would increase production.
4. Agricultural businesses would benefit from increased productivity and resource use efficiency and may invest more in the area of modeling of basic plant processes.
5. The tools (software, hardware and techniques) produced by this project would be made available to the public and scientists and may provide those in technological research and development with the knowledge to innovate further.
6. These data may be used for prediction of vegetative productivity. They may be incorporated into predictive models of crop yield that are utilized by policy advice bodies such as the IPCC. The PI collaborates with individuals, applied consortia and institutes such as the Wheat Yield Consortium and the International Rice Research Institute which have programmes that could directly use the results in predictive models of crop yield.
7. Public sector may benefit if the tools prove useful for imaging of processes relevant to the quality of life and society in general, e.g. in the imaging of plant canopies to aid in the realistic recreation of landscapes for the construction amenity areas and recreation.
8. An improvement in crop yield or crop resource use efficiency results in the potential to reduce impact on the natural environment by reducing land cultivated and inputs of water and nitrogen (via the inherent improvement in photosynthesis).

How will they benefit ?

If successful it will result in a step change in resource use efficiency and yield for many scenarios. Almost a billion people in the world are defined by the FAO as 'hungry'. A step change in yield would instantly alleviate this whilst for poor farmers it would help them to generate extra cash to lift them out of poverty and improve health and wellbeing. For the rest of the world it may result in a lowering of food prices which would benefit economies and prevent surplus depletion allowing security. It would also reduce risky speculation on food prices.
The time taken would be restricted by the ability to introduce genes into crop plants by breeding, introgression and transformation. Possibly prototype plants could be available 3-5 years after the lifetime of this grant (allowing time to breed for stable mutant lines).
For plant breeders the improvement in productivity would allow a focus on areas that may be critical to specific crops such as diseases and pests.

Activities that will enhance impact of this project

A website dedicated to the project, updated regularly will be hosted and created by Nottingham.
A techniques workshop will take place in Nottingham in 2011 as part of the EU Harvest network of photosynthesis researchers, co-organized by the PI. The project will be exposed to about 60 academics, post-doctoral workers and Phd students by holding a special session on canopy imaging and measurement. The techniques used and the project objectives will be presented.

Publications

10 25 50
 
Description We have developed a low cost but high accuracy technique for the automated reconstruction of plant canopies using stereo imaging. This means you can use images from a standard camera to produce a 3D image of a plant with 2D leaf surfaces. This may have many applications in vision, ( including entertainment) but our application is to enable the accurate tracking of light within a plant canopy.
We have also developed modelling techniques for canopy photosynthesis so we can use the canopy architecture to predict how productive that particular canopy is, combined with simple leaf measurements of photosynthesis.
We have applied this new technique to reconstruct whole canopies of wheat from the field in high resolution 3D , something that has not been achieved before. We combined this with an empirical model for canopy photosynthesis and photo inhibition (stress in high light) in a large field experiment in Sutton Bonington. We concluded that there is a substantial impact of canopy architecture on canopy photosynthesis and this was published as a high impact article in the journal Plant Physiology. Following this we also examined how photosynthesis operates in lower regions of the wheat canopy and used our 3D model to predict that these shaded lower leaves have an excessive photosynthetic capacity and accumulate nitrogen in excess of requirements (this work is to be published later this year).
We have developed a new method for measuring canopy motion (the 4dimensional plant) and published this (see updated pubs list). We showed that canopy movement by wind has substantial impacts on productivity that has not yet been exploited. This has resulted in a BBSRC proposal in January 2017 round.
Exploitation Route Techniques developed so far (grant ends in 2015) will be used by plant and crop scientists who wish to rapidly produce low cost 3D representations of plant canopies to use for crop modelling, photosynthesis modelling, crop biology or phenotyping. In particular the wide applicability of using RGB in field situations means that it will be used within phenotyping platforms as a means of rapid high throughput plant measurement. Such systems exist in CIMMYT, Rothamsted, CSIRO and many other locations globally. Also, it is low cost so it can be used by developing countries on a low budget and who cannot afford laser-based techniques.
It may be used in entertainment or gaming industry for accurate light distribution.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment

URL https://www.cpib.ac.uk/tools-resources/software/canopy-reconstruction/
 
Description We have released reconstruction tools, instruction and software (https://www.cpib.ac.uk/tools-resources/). We have applied this technique to remodelling photosynthesis and photoinhibition in crop canopies (Burgess et al 2015), to solving the problem of wind induced movement in crop canopies for crop yield (Burgess et al 2016).
First Year Of Impact 2014
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment
Impact Types Economic

 
Description International Wheat Yield Partnership
Amount £1,002,229 (GBP)
Funding ID BB/N021061/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2016 
End 03/2019
 
Description TSB LED project
Amount £392,000 (GBP)
Organisation Technology Strategy Board (TSB) 
Sector Public
Country United Kingdom
Start 12/2013 
End 12/2016
 
Description Thailand workshop
Amount £15,000 (GBP)
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2014 
End 09/2014
 
Description The 4-dimensional plant: Enhanced mechanical canopy excitation for improved crop performance
Amount £806,919 (GBP)
Funding ID BBR004633/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 10/2020
 
Description Wolfson lab refurbishment Phenomics lab
Amount £217,000 (GBP)
Funding ID WL140052 
Organisation The Wolfson Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2014 
End 12/2016
 
Description iCASE DTP
Amount £71,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 10/2021
 
Title Mike Pound imaging method 
Description New technique for RGB stereo imaging of plant canopies and software reconstruction into a 2D plane 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2014 
Provided To Others? Yes  
Impact None yet 
URL https://www.cpib.ac.uk/tools-resources/software/canopy-reconstruction/
 
Title Photoinhibition 
Description Accurately measure photo inhibition in leaves using chlorophyll fluorescence, an advance on previous 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2012 
Provided To Others? Yes  
Impact non as yet but ccompanies interesteed in development include Walz 
URL http://www.ncbi.nlm.nih.gov/pubmed/22503831
 
Description Agrilamp / Greengage 
Organisation Greengage
Country United Kingdom 
Sector Private 
PI Contribution Provide academic research to aid lamp development
Collaborator Contribution Provide financial and technical support for plant growth lamp development
Impact TSB grant secured in 2012
Start Year 2011
 
Description International Rice Research Institute 
Organisation International Rice Research Institute
Country Philippines 
Sector Charity/Non Profit 
PI Contribution PhD students at Nottingham University carried out research in collaboration with this project. Papers published to aid the C4 rice project
Collaborator Contribution Supplied seed for analysis and resources for genetic analysis, field measurements.
Impact Papers (Feldman et al 2014, Smillie et al 2012) 3 PhD students have completed entire PhDs via this collaboration
 
Description Kasetsart 
Organisation Kasetsart University
Country Thailand 
Sector Academic/University 
PI Contribution Applied successfully to fund British Council run Researcher Links workshop in Thailand 23-26 September 2014
Collaborator Contribution Help secure funding and run workshop, possibilities for collaborations to screen rice lines.
Impact Links setup between UK and Thai researchers for future collaborations
Start Year 2012
 
Description NIAB 
Organisation National Institute of Agronomy and Botany (NIAB)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution academic research on transgenic wheat plants
Collaborator Contribution Provision of the transgenic wheat plants
Impact Non yet
Start Year 2013
 
Description Shanghai CAAS 
Organisation Chinese Academy of Agricultural Sciences
Country China 
Sector Academic/University 
PI Contribution Aided pre release with use of software and imaging techniques
Collaborator Contribution collaboration on use of ray tracing software and photosynthesis modelling. Support letter for research proposals.
Impact Aided securing current BBSRC grant with award letter
Start Year 2011
 
Title Mike Pound imaging software 
Description Software for reconstruction of 3d point cloud data into a 2D mesh for plant imaging analysis including ray tracing. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2014 
Impact non yet 
URL https://www.cpib.ac.uk/tools-resources/software/canopy-reconstruction/
 
Description Cereals 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Stand at UK cereals Event to share University research and teaching scope. Public outreach and student recruitment

UG recruitment in Agriculture degrees
Year(s) Of Engagement Activity 2010,2012
 
Description Chelsea Flower Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Co-oraginsed and attended a University stand on under-utilised crops at the Chelsea Flower show that won 'Best in group', mentioned on National TV .

TV mention, newspaper mention.
Year(s) Of Engagement Activity 2013
 
Description Public lecture in series 'whats it all about' held at Sutton Bonington 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Public lecture on research into improving crop photosynthesis and its wider importance and interest for society and food security . It was held at the University of Nottingham (Sutton Bonington) in April 2015 and open largely to the local public .
Year(s) Of Engagement Activity 2015
 
Description Public lecture on photosynthesis improvement in crops 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Public lecture on research into improving crop photosynthesis and its wider importance and interest for society and food security . It was held at the University of Nottingham (University Park) in August 2015 and open largely to the local public .
Year(s) Of Engagement Activity 2015
 
Description Teaching workshop -workshop on phenotyping photosynthetic phoneme at U. Wageningen 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Teaching undergraduates and postgraduates and industry representatives about techniques in photoprotection and canopy structure phenotyping.
This resulted in questions and discussions
Year(s) Of Engagement Activity 2014
 
Description Workshop on 3D imaging of crop plants, University of Nottingham UK 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact We organised and funded a small one day workshop at the University of Nottingham in May 2015 to disseminate and train people in the techniques for 3d Imaging of plant canopies that were developed during the project (Pound et al 2014, Burgess et al 2015). We invited all those who had shown in interest and supported the project form the beginning and extended the invitation beyond that to anyone in the UK who was interested in attendance.
The workshop was attended by approximately 5 people from outside the university and the rest (20 in total) were made up of local academic, PhD students and postdoctoral students.
Year(s) Of Engagement Activity 2015