Modelling and remote sensing of canopy light interception and plant stress in greenhouses

A greenhouse crop can be approached as an open system that can be affected by a number of parameters such as light, climate or nutrient supply. In the last decades efforts have been made to understand the functioning of this system and the interaction between the different parameters. The intensive nature of greenhouse cultivation combined with the economic necessity to enlarge the farm size makes the development of decision support systems (DSS) imperative to help the growers in managing their farms efficiently. The foundation of DSS are plant models and in order to work more efficiently they should be able to receive information in real time from sensors that measure different plant parameters such as light interception, leaf area index and photosynthetic stress in a non-destructive way. In order to develop functional DSS it is imperative to develop accurate models and monitoring techniques applied in the specific greenhouse environment. The aim of this thesis was to explore different techniques to simulate and monitor light interception and photosynthesis by a greenhouse grown tomato canopy. Since photosynthesis is directly linked to light absorption we opted to develop a three dimensional model that takes into account the explicit plant architecture. Different methodologies to monitor these physiological properties online by means of remote sensing were also explored. A number of physiological tomato models have been proposed the last decades, their main challenge being the correct simulation of fruit yield. For this, an accurate simulation of light interception, and thus photosynthesis, is of primary importance. At present most process-based models and the majority of three dimensional models, include simplifications of plant architecture that can compromise the accuracy of light interception simulations and, accordingly, canopy photosynthesis. In Chapter 2.1 the first steps towards the development of the model are presented. Light interception is highly dependent on the canopy structure, which is affected, among others, by the distance between plant rows, the distance of plants within the row, leaf pruning and crop variety. The model was used to test different crop planting scenarios on their effect on light interception. Light interception from the planting scenarios was then compared with results of a totally homogeneous canopy. Also analysis of differences between manual measurements of leaf length, width, elevation angle and leaf orientation was conducted. Changes of leaf elevation angles at two different times of the day were also measured. In tomato differences in leaf length, width and elevation angle of the leaves were mainly observed in the upper 90cm of the plant, in the still developing zone. Changes of the architectural characteristics of structural plant characteristics affected directly light interception by the crop canopy. Nevertheless even if plant structure stayed the same, light penetration could easily be manipulated by changing the row spacing in the crop, thus affecting light interception and potentially plant production. In Chapter 2.2 the development and calibration of a functional-structural tomato model is fully described. The model was used to investigate the canopy heterogeneity of an explicitly described tomato canopy in relation to temporal dynamics of horizontal and vertical light distribution and photosynthesis under direct and diffuse light conditions. The model consists of an architectural static virtual plant coupled with a nested radiosity model for light absorption and a leaf photosynthesis module. Different scenarios for horizontal and vertical distributions of light interception, incident light and photosynthesis were investigated under diffuse and direct light conditions. Simulated light interception showed a good correspondence to the measured values. Explicitly described leaf elevation angles resulted in higher light interception in the middle of the plant canopy compared to fixed and ellipsoidal leaf elevation angle distribution models, although the total light interception remained the same. The fraction of light intercepted at a north-south orientation of rows differed from an east-west orientation by 10% in winter and 23% on summer days. The horizontal distribution of photosynthesis differed significantly between the top, middle and lower canopy layer. Taking into account the vertical variation of leaf photosynthetic parameters in the canopy, led to ca. 8% increase on simulated canopy photosynthesis. Manipulation of plant structure can strongly affect light distribution in the canopy and photosynthesis. In Chapter 2.3 the idea of identifying different plant ideotypes for optimization of light absorption and photosynthesis was explored. Using the functional-structural tomato model presented in the previous chapters, a range of different plant architectural characteristics were tested for two different seasons in order to find the optimal architecture with respect to light absorption and photosynthesis. Sensitivity analyses were carried out for leaf elevation angle, leaf phyllotaxis, leaflet angle, leaf shape, leaflet arrangement and internode length. From the results of this analysis two possible ideotypes were proposed. Increasing light absorption in the top part of the canopy by 25 %, without changing light absorption of the canopy as a whole, augmented photosynthesis by 6 % in winter and decreased it by 7 % in summer. The measured plant structure was already optimal with respect to leaf elevation angle, leaflet angle and leaflet arrangement for both light absorption and photosynthesis while phyllotaxis had no effect. Increasing the length-to-width ratio of leaves by 1.5 or increasing internode length from 7 to 12 cm led to an increase of 7 – 10 % for light absorption and photosynthesis. The most important architectural traits found were the internode length and the leaf shape as they affect vertical light distribution in the canopy distinctly. A new plant ideotype with more spacious canopy architecture due to long internodes and long and narrow leaves led to an increase in photosynthesis of up to 10 %. In Chapter 3.1 ways to monitor on-line LAI and PAR interception of the canopy, under greenhouse conditions, through reflectance measurements, were explored. LAI and PAR interception were measured at the same moments as reflectance at six wavelengths in different developmental stages of tomato and sweet pepper plants. Normalized Difference Vegetation Index (NDVI) was calculated. Relationships between the measured parameters were established in experimental greenhouses and subsequently these were tested in commercial greenhouses. The best estimation for LAI and PAR interception was obtained from reflectance at 460nm for both tomato and sweet pepper. The goodness of the fit was validated with data from the commercial greenhouses and was also tested in this study. The divergence of the results from the ones reported from field experiments can be traced back to the special greenhouse environment, where more sources of reflectance are added due to construction parts and a white plastic covered background. Reflectance measurements offer a non- destructive way to estimate PAR interception and LAI (up to the value of 3) in greenhouse production systems. The relationship established between reflectance at 460 nm, PAR interception and LAI for both tomato and sweet pepper, can become a good tool for crop online monitoring in greenhouse conditions. Furthermore if information from reflectance sensors is used as input directly into the crop models, new opportunities for decision support systems in greenhouse production could be opened up. Photosynthetic stress induced by water deprivation in plants affects a number of physiological processes such as photosynthetic rate, stomatal conductance as well as the operating efficiency of PSII and non- photochemical quenching. Photochemical Reflectance Index (PRI) is reported to be sensitive to changes of xanthophyll cycle that occur during stress and could possibly be used to monitor changes in the physiological parameters mentioned before. In Chapter 3.2 the use of PRI as an early photosynthetic stress indicator was evaluated. A water stress treatment was imposed on a greenhouse tomato crop. CO2 assimilation, stomatal conductance, light and dark adapted fluorescence as well as PRI and relative water content of the rooting medium RWCs% where repeatedly measured. The same measurements were also performed on well-irrigated plants that acted as a reference. The experiment was repeated in four consecutive weeks. Results showed that PRI can be used as an early stress indicator only when light intensity at crop level was above 700μmol m-2 s-1. At lower values of light intensity the relationship of PRI to RWCs% was poor in comparison to photosynthesis or fluorescence parameters that showed a high correlation to RWCs%. For that reason we can conclude that PRI as water stress indicator cannot be independent of the ambient light conditions and its use can make sense only under conditions of high light. Finally in Chapter 4 the main achievements and limitations of this study are discussed and directions for future research are proposed. </p

A Prototype Sensor for Estimating Light Interception by Plants in a Greenhouse

Light interception is one of the most important factors for plant growth. The intercepted amount depends on the incoming radiation in the greenhouse and the percentage of interception by the crop and is directly related to the leaf area. Proper crop management requires the measurement of the most important growing factors. In case of application of crop growing models the simulation of the leaf area is one of the major uncertainties in the results of the models. Automatic calibration of the model based on radiation interception increases the accuracy of the model results. For the determination of the crop¿s light interception in a greenhouse, a radiation sensor was used which determines the ratio of the incoming radiation from the upper side and the reflection at a specific wavelength from the lower side. The ratio of reflected radiation versus intercepted radiation can be used to estimate light interception as well as leaf area. However, the measurement of this fraction can only be used after filtering out erroneous data due to technical errors, insufficient diffuseness, insufficient solar height, etc. This paper describes the boundary conditions to be taken into account for proper measurement of reflected radiation. Time series measurements of incoming, reflected and global radiation are used, to filter the data acquired by the sensor. The sensor functioned well during tests on a cucumber crop in a commercial greenhouse

Verbetering van de lichtonderschepping in een tomatengewas door aanpassing van de rijstructuur: Effecten van de rijstructuur op lichtverdeling, fotosynthese en productie

Doel van dit project was te onderzoeken wat het effect is van de rijstructuur op de lichtverdeling en fotosynthese van een tomatengewas, en de effecten daarvan op de productie. Ook werd gekeken of de bladstand en de fotosynthesecapaciteit van de bladeren zich aanpassen aan wijzigende lichtverdeling. Tevens werd de hypothese getest of alternatieve vormen van tussenplanten zouden leiden tot lagere verdamping en dus tot energiebesparing. Verder is gekeken naar het effect op productie van twee substraten, namelijk kokosmatten type ‘Profit’ van Van der Knaap, en steenwolmat type ‘Master Dry’ van Grodan

Measuring Leaf Motion of Tomato by Machine Vision

For a better understanding of growth and development of tomato plants in three dimensional space, tomato plants were monitored using a computer vision system. It is commonly known that leaves of tomato plants do not have a fixed position and orientation during the day; they move in response to changing environmental conditions such as the position of the sun. For better understanding, it was desired to quantify this motion. Using a stereovision concept, two cameras were mounted in an experimental greenhouse a short distance apart from each other to enable depth measurement. Markers were placed on strategic spots on the tomato plant branches and leaves in the field of view of both cameras. Images were taken every ten minutes during daytime on several consecutive days. In the greenhouse, a virtual 3D coordinate system was defined and camera and tomato plant position and orientation were defined in this coordinate system. Image processing techniques were used to trace the markers and the 3D position coordinate of each marker in each image was calculated to obtain the course of a marker during several days. Stems, branches, and leaf nerves were considered as kinematic mechanical, robot like, links and corresponding theory was used to model and calculate the motion of stems and leaves of a tomato plant. Analysis of the images showed both small (1-2 degrees) and large rotations (10 degrees or more) of the branches and the different leaves on a branch during the course of a day. Leaves on one side of a branch showed a parallel motion in the same direction; the leaves on the opposite side of the branch showed a mirrored motion. However, deviating patterns occurred too. The developed method proved to be able to precisely quantify the motion of stems, branches and leaves of tomato plants during several days

Towards a functional-structural plant model of cut-rose: simulation of light environment, light absorption, photosynthesis and interference with the plant structure

Background and Aims The production system of cut-rose (Rosa × hybrida) involves a complex combination of plant material, management practice and environment. Plant structure is determined by bud break and shoot development while having an effect on local light climate. The aim of the present study is to cover selected aspects of the cut-rose system using functional–structural plant modelling (FSPM), in order to better understand processes contributing to produce quality and quantity. Methods The model describes the production system in three dimensions, including a virtual greenhouse environment with the crop, light sources (diffuse and direct sun light and lamps) and photosynthetically active radiation (PAR) sensors. The crop model is designed as a multiscaled FSPM with plant organs (axillary buds, leaves, internodes, flowers) as basic units, and local light interception and photosynthesis within each leaf. A Monte-Carlo light model was used to compute the local light climate for leaf photosynthesis, the latter described using a biochemical rate model. Key Results The model was able to reproduce PAR measurements taken at different canopy positions, different times of the day and different light regimes. Simulated incident and absorbed PAR as well as net assimilation rate in upright and bent shoots showed characteristic spatial and diurnal dynamics for different common cultivation scenarios. Conclusions The model of cut-rose presented allowed the creation of a range of initial structures thanks to interactive rules for pruning, cutting and bending. These static structures can be regarded as departure points for the dynamic simulation of production of flower canes. Furthermore, the model was able to predict local (per leaf) light absorption and photosynthesis. It can be used to investigate the physiology of ornamental plants, and provide support for the decisions of growers and consultants.                    

Plants in silico:Why, why now and what? --- An integrative platform for plant systems biology research

A paradigm shift is needed and timely in moving plant modelling from largely isolated efforts to a connected community endeavour that can take full advantage of advances in computer science and in mechanistic understanding of plant processes. Plants in silico (Psi) envisions a digital representation of layered dynamic modules, linking from gene networks and metabolic pathways through to cellular organization, tissue, organ and whole plant development, together with resource capture and use efficiency in dynamic competitive environments, ultimately allowing a mechanistically rich simulation of the plant or of a community of plants in silico. The concept is to integrate models or modules from different layers of organization spanning from genome to phenome to ecosystem in a modular framework allowing the use of modules of varying mechanistic detail representing the same biological process. Developments in high-performance computing, functional knowledge of plants, the internet and open-source version controlled software make achieving the concept realistic. Open source will enhance collaboration and move towards testing and consensus on quantitative theoretical frameworks. Importantly, Psi provides a quantitative knowledge framework where the implications of a discovery at one level, for example, single gene function or developmental response, can be examined at the whole plant or even crop and natural ecosystem levels

Daily heliotropic movements assist gas exchange and productive responses in DREB1A soybean plants under drought stress in the greenhouse.

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