ArchiCrop: Casting light on the Architecture of Crop Yield
Crop yields are stagnating in many regions of the world requiring major changes in agricultural productivity. The increases needed to provide food security can be achieved by uncovering features limiting plant performance in contrasting environments but must also consider any future changes to climate. As the core driver of photosynthesis, light availability and the efficiency of its interception and conversion is critical to yield formation. Canopy architecture, the arrangement of plant material in 3-dimensions (3D), will determine how much light can be intercepted and so is a crucial component. However, architecture is determined by a complex number of traits and whilst the tools for its study have advanced, we still do not know enough about key features and it is known that it can be improved further.
Within this Leverhulme Fellowship, project ArchiCrop, I aim to identify the spatial and temporal differences in light composition and physiological processing to quantitatively predict crop performance under current conditions and those forecast due to climate change. Using climate change predictions, I will predict how current crop architectures will perform following changes in light composition; how the distribution of agricultural regions will alter globally and; identify key structural traits or alternative cropping practices that will aid crop performance in future environments. I will also, for the first time, identify the social and cultural preferences governing crop selection for architecture as they present a barrier to future changes in agricultural production.
Cells to Fields: crop movement characterisation across scales of order
Wind induced canopy movement alters the plant microenvironment and affects the distribution of key growth resources including light. This has consequences for photosynthesis and plant productivity and presents a critical knowledge gap. Whilst we have begun to understand the traits that may influence movement and potential impacts on biological processes at lower windspeeds, we are prohibited by the complexity of the interactions which combine biological and physical factors, and currently available analysis approaches. In the field of microbiology, recent advances in video analysis have been applied to study the movement of cilia (hairs that line the lungs and airways) on the microscopic scale. The multiDDM approach developed in PC’s lab (UoC) simplifies biological movement to a core set of parameters that represent motion across all length scales. Within this project, the multiDDM approach will be applied to large scale video capture of field-grown wheat plants. Parameters extracted from the pipeline will provide the first estimate of the impact of wind on crop productivity during critical periods of growth and provide the platform for future field phenotyping of crop genotypes. Simultaneously, the project will enable the improvement of methodologies to characterise biological motion from cell to field scale.
H2rObo: A semi-autonomous pipeline for the quantification of plant water use efficiency
Optimising water use efficiency (WUE) is a key target for agriculture with the need to reduce water inputs to our cropping systems (e.g. irrigation). WUE will become increasingly important as climate change leads to higher temperatures in many of Earth’s key agricultural regions. This can be linked to canopy architecture, whereby structural traits will determine the uptake and use of water. In this Royal Society funded project, I will use image capture via a robot-aided active vision system to accurately capture plant form and function.
The active vision system consists of a Universal Robots, UR5e, robotic arm, high precision turntable and RGB camera positioned in its own dedicated imaging studio on Sutton Bonington Campus.
PlanNet: Plant Networks for improving crop productivity in response to climate change
Canopy architecture, the arrangement of plant material in 3-dimensions (3D), determines resource capture and function through generation of the microclimate. However, architecture is determined by a complex number of traits and whilst the tools for its study have advanced, there are still a number of limitations preventing key breakthroughs. Within this Rank Prize funded project, I aim to develop new methodologies for the acquisition of plant architecture to quantitatively predict crop performance under current conditions and those forecast due to climate change. Project PlanNet will lead to the generation of a new, easy-to-use methodology using deep learning approached for the reconstruction of plants with automated quantification of architectural traits.
CropRay: A new improved ray tracer for analysing canopy light characteristics
Current manual characterisation of the in-canopy light environment relies on access to and use of costly equipment and the associated expertise to process and analyse results. In this Gatsby Charitable foundation funded project, we will be generating a new improved ray tracer to simulate the light dynamics within in silico 3-dimensional crop canopies. Taking advantage of latest improvement in hardware, CropRay will simulate both the quantity and quality (spectral composition) of light passing through leaves. This will provide the critical advancement needed to explore how features such as leaf density and geometry determine light penetration and composition, whilst also improving the realism of light modelling approaches, advancing on previous methods.
This work is being carried out by Dr Jonathon Gibbs, you can find more information on his website.
Crop growth in space
Future space missions to Mars will require astronauts to be away from Earth and resources for 3 years at a time. With each astronaut requiring approximately 1 tonne of food per year.
Joint with researchers including Professor Volker Hessel and Dr Matthew Knowling at the University of Adelaide plus Professor Dov Stekel and Dr Diriba Kumssa at the University of Nottingham we supervise a Nottingham-Adelaide sponsored PhD student, Shu Liang. Her project aims to model closed-loop agricultural systems to simulate potential growing conditions in space and identify crop species and growth requirements that will enable indefinite survival off-planet.
Phenotyping stomatal morphology
Stomata are integral to plant performance, enabling the exchange of gases between the atmosphere and the plant. The anatomy of stomata influences conductance properties with the maximal conductance rate, gsmax , calculated from their density and size. However, current calculations of stomatal dimensions are performed manually which are time-consuming and error prone. Here we show how automated morphometry from leaf impressions can predict a functional property: the anatomical gsmax.
Alternative cropping practices for sustainable agriculture
Improving the sustainability of agricultural systems will be critical to mitigate climate change and other adverse factors influencing crop yields. Adopting alternative cropping practices provides one way through this can be achieved. Intercropping refers to the cultivation of two crops simultaneously in close proximity and depending upon location and crop choice, can increase yields when calculated on a land area basis. Cultivating crops with trees in agroforestry systems can help buffer from adverse weather conditions. Vertical farming takes advantage of growth infrastructure and hardware to optimise plant growth, particularly in urban areas. Whilst urban agriculture, growth of vegetable and fruits in home gardens, allotments or on public streets, can provide an additional source of local produce. I am interested in these different systems, the components which make them productive and their benefits towards a sustainable future.
As part of this work I previously supervised an MSci student who is looking at the ease of using off the shelf hydroponic systems for herb production at home.
The Sutton Bonington Teaching and Medicinal Garden
The Sutton Bonington Teaching and Medicinal Garden was funded through the SB Development Committee, using generous donations from past alumni and members of the Old Kingstonian Association. The garden is split into two key focus areas; beds showcasing medicinal plants and a teaching kitchen garden to support students undertaking undergraduate degrees in Biosciences.
More details can be found on our dedicated garden website.
Past Research Projects
The 4-Dimensional Plant
Wind is a ubiquitous property of all field environments, yet how wind deforms a plant canopy and alters the distribution of light is rarely studied. As part of a BBSRC funded project, the 4-Dimensional plant developed visual tracking and enhanced 3D reconstruction methods needed to measure and model canopy movement and dynamic photosynthesis in rice and wheat populations. Joint with the Schools of Computer Science and Mathematics, this provided the first stages towards understanding how our crop canopies behave in the field and how this may influence their productivity.
Increasing crop yields will be integral to feeding an expanding population. This must be done sustainably and account for the transition from fossil fuels to more renewable resources, which may often compete for land. The increase in yields must also be achieved without a loss of nutritional quality whilst efficiently utilising scarce resources. CropBooster-P is part of an EU Horizon 2020 funded project across a consortium of European institutions to identify and prioritise opportunities for adapting and increasing crop yields within Europe and globally.
Molecular mechanisms of light energy utilisation
As part of a BBSRC funded grant to Professor Alexander Ruban at QMUL, I explored how the molecular composition of the photosynthetic antenna regulated light utilisation and how higher plants protect themselves against high light intensities. This included determination of the balance between photodamage and protoprotection in photosystem II and the role of components of the antenna in chlorophyll fluorescence quenching.
Key skills: chlorophyll fluorescence; spectroscopy and pigment analysis measurements including 77K emission and absorption and HPLC; chloroplast and thylakoids extraction; protein and chlorophyll quantification; running of gels, western blots and leaf clearing