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Quality of fresh products is determined by genotype and environmental practices. Light intensity and spectrum are environmental factors which have significant effects on quality. Light can increase the content of metabolites, such as carbohydrates and antioxidants. To maintain shelf life of fresh products low temperature storage is often used during the postharvest phase as the water loss and metabolic rates slows down which will delay senescence. However, crops of tropical origin are sensitive to temperatures below 10-12 °C. One of such crops is basil (OcimumbasilicumL.). Basil suffers from chilling injury (CI) when stored at low temperature. CI is visible within a few days as dark spots on the leaves. Thus, there is a large potential to improve the chilling tolerance of basil. Chilling tolerance may be improved by an increase in carbohydrates and antioxidants such as phenolic compounds. They may scavenge the reactive oxygen species produced during chilling. In this thesis it was investigated if an increase in light intensity and modification of the light spectrum (i.e. an increase in percentage of blue light) could increase the content of carbohydrates and antioxidants resulting in improved chilling tolerance. Furthermore, it was investigated if the addition of far-red (FR) during cultivation would increase the levels of hormones related to chilling tolerance and in turn improve the postharvest chilling tolerance. Light also affects the morphology which is an important quality parameter. Thus, response of growth and morphology to light intensity and spectra was also studied. In a number of experiments basil was grown in a climate chamber in a vertical farming set-up and the effect of light intensity and spectra on at-harvest and postharvest quality were studied.

Because of chilling injury (CI), the benefit of low temperature storage to maintain freshness and quality along the chain cannot be maximized. Reducing CI will not only assure good performance of fruit and vegetable in the chain but also reduce postharvest loss and preserve nutritional sources for individuals, especially in developing countries. Therefore, efforts and studies are devoted to tackle CI in numerous fresh produce. Tackling CI problems needs synergistic approach that encompasses preharvest and postharvest factors. This thesis emphasis preharvest factors determining chilling sensitivity and postharvest factors that induce or alleviate CI. The state of the art with respect to the possible role of preharvest factors such as lighting and temperature in chilling sensitivity in tomato is described in Chapter 1. The possible interaction between the above mentioned preharvest factors and some postharvest factors on the development of CI in tomato were also elaborated. We reported that preharvest FR light induced cold tolerance in both MG and R tomatoes (Chapter 1). In MG tomatoes, additional FR light resulted in reduced weight loss, less pitting and faster red colour development during shelf life, and less softening after cold stored. Preharvest FR is likely protects the membrane integrity of MG tomatoes allowing uninterrupted lycopene synthesis. In R tomatoes, preharvest FR lead to firmer fruit at harvest lead to reduced weight loss and less decay during shelf life. The study showed that induced cold tolerance by FR light applied during cultivation, might be related to FR induced cuticle wax biosynthesis and the action of lycopene as an antioxidant during cold storage. Next to FR light we also showed that to some extent, preharvest blue LED lighting (BL) induces postharvest cold tolerance in ‘Foundation’ tomatoes. In this study CI indices and important quality properties such as colour, firmness, hydrogen peroxide, malondialdehyde, ascorbic acid and catalase activity were characterised during cold storage at 4 °C for different durations followed by shelf life of twenty days. Acquired cold tolerance of R fruits harvested from the 12B lighting conditions was related to its ability to loose red colour, presumably in favour of the scavenging of ROS. MG-tomatoes showed no CI symptoms, regardless of the preharvest lighting. No effects of light treatments were found on several antioxidant capacity indicators of both tomatoes. Because improved cold tolerance for R fruit was not due to differences in redox statues indicators (CAT activity, total ascorbic acid, H2O2 and MDA levels), the idea that lycopene in 12B tomatoes is a more efficient antioxidant compared to that of the other BL treatments is put forward (Chapter 3). Varying growth temperature (16, 22, 26 °C) effect quality properties and CI development in dwarf cultivars (Ponchi Re and Tarzan) tomatoes grown in climate chambers. The lowest growth temperature (16 °C ) performed better during shelf life and the effect of low growth temperature has a genetic component (Chapter 4). Low growth temperature delays the onset of red colour development during shelf life and the delay was more pronounced when fruit were first stored at low temperature. Cultivation at 16 °C resulted in fruit firmness retention during cold storage and shelf life which corroborated with lower weight loss. ‘Ponchi Re’ tomatoes showed less CI symptoms during after storage shelf life with higher growth temperatures, whereas the opposite was observed for ‘Tarzan’. We hypothesised that the delay in the start of the red colouration for ‘Ponchi Re‘ grown at 16 °C exposed the tomatoes to ROS without proper scavenging capacity provided by lycopene during cold storage. For ‘Tarzan’ tomatoes higher CI tolerance of tomatoes cultivated at 16 °C might be induced by higher firmness at harvest and lower weight loss during storage. The role of low oxygen storage in limiting CI development in tomatoes was also elucidated (Chapter 5). The effect of low oxygen on cold tolerance were consistent in different tomato types. Low oxygen (down to 0.5 kPa) during cold storage was beneficial for cold tolerance of MG stage of cherry type tomatoes. 5 kPa O2 showed the best results for both MG and R tomatoes in terms of delayed softening, less decay and full colouration (MG) during the after storage shelf life. Following this result, the combination of FR and low oxygen was tested. We investigated the role of low oxygen (0.5, 2.5 and 5 kPa O2) in limiting CI in round tomato cultivar for MG and R stage. Next we applied low oxygen (1 and 5 kPa O2) storage on tomato cultivated under additional FR. Low oxygen induced cold tolerance in MG and R tomatoes. We showed that decay, firmness loss and weight loss during were reduced under influence of low oxygen. Red colour degradation of R tomatoes (a CI symptom) was suppressed under low oxygen. The effect of low oxygen was greater on FR cultivated MG tomatoes due to a lower respiration rate that might resulted in low singlet oxygen formation. No clear relation was found between H2O2 level and the extent of CI. Therefore, we propose the idea that oxidative stress initiated by singlet oxygen and not superoxide anion plays a more pronounced role in inducing CI in tomato. Furthermore, we hypothesised that the formation of singlet oxygen was suppressed by low oxygen. The new understanding of the effect of pre- and postharvest conditions on tomato fruit postharvest CI development described in chapter 2-5 is discussed (Chapter 6). The possible role of the fruit’s physical properties in establishment of cold tolerance is explored. We proposed that the role of singlet oxygen as oxidative stress initiator and the ability of lycopene to scavenge singlet oxygen is important for cold tolerance in lycopene rich fruit like tomatoes. Furthermore, the limitation of the studies presented in this thesis as well as consequences of the main findings and further research recommendations are discussed.

High-tech greenhouses are major consumers of energy. This energy consumption is responsible for considerable carbon emissions and contributes to climate change and global warming. Light-emitting diodes (LEDs) have been promoted as a solution to the energy problem of illuminated greenhouses, due to their high efficacy in converting electricity to light. Current LEDs consume around 40% less electricity than the commonly used high-pressure sodium (HPS) lamps, while emitting equivalent light intensities.Despite their high efficacy, adoption of LEDs in greenhouses has been limited. High investment costs, lack of knowledge regarding the influence of LEDs on the greenhouse climate and crop, and low trust towards their claimed benefits, have all been cited as obstacles for adoption. Greenhouses with LEDs also require more heating than greenhouses with HPS lamps: due to their higher efficacy, LEDs contribute less heat to the greenhouse, which must be compensated by the heating system. Therefore, it has so far been unclear precisely how much energy can be saved by a transition to LEDs in greenhouses, and what factors contribute to this potential saving.This thesis explores how LEDs influence the energy consumption of greenhouses. It investigates the consequence of replacing HPS lamps by LEDs in terms of lighting demand, heating demand, and total energy use; analyzes how LEDs influence the greenhouse climate and energy balance; and examines further possibilities for energy saving by LEDs in future scenarios.Chapter 1 provides an overview of the greenhouse energy problem, using the Netherlands as an example. The chapter shows that the advent of LEDs in greenhouses has been accompanied by great expectations which have so far failed to materialize. The chapter suggests that a transparent and quantitative assessment of the potential benefits of LEDs will help adjust expectations towards this new lighting technology and promote the trust of growers. Process-based mathematical modelling is proposed as a method towards achieving these goals.Chapter 2 investigates the discipline of process-based greenhouse modelling. The chapter shows that a considerable number of greenhouse models are published, and sets out to understand the reasons for the existence of this multitude of models. In Section 2 of the chapter, substantial background on the concept of process-based greenhouse modelling is provided. Modelling studies published between 2018 and 2020 are categorized according to their objectives, types of greenhouse, and equipment they consider, and a model inheritance chart is presented, showing how current models are based on earlier works. Moreover, a comparison of modelling validation studies is performed.Based on this analysis, possible reasons for the abundance of greenhouse models are suggested, including a lack of model transparency and code availability, and a belief that model development is in itself a valuable research goal. The chapter ends with recommendations for the future advancement of the discipline. These include promoting model transparency and availability of source code, and establishing shared datasets and evaluation benchmarks.Chapter 3 presents GreenLight, a process-based model for a greenhouse with a tomato crop, which describes the influence of HPS and LED lamps on the climate, crop, and energy use. GreenLight’s performance is evaluated against data from a greenhouse with HPS and LED lamps. The model is found to perform reasonably well, with a relative error in the range of 1-12%. The model is offered in an open source format at https://github.com/davkat1/GreenLight, making it available for further inspection and extension by others.Chapter 4 uses GreenLight to predict the influence of replacing HPS lamps by LEDs in a greenhouse. A wide range scenarios is considered, including varying climates and multiple settings for indoor temperature, lamp intensity, and greenhouse insulation. In all scenarios, LEDs are found to reduce the energy demand for lighting by 40%, but to increase the demand for heating. This results in a total energy saving by transition to LEDs in the range of 10-25% for most scenarios. An important factor influencing how much energy can be saved by a transition to LEDs is be the ratio between the lighting and heating demand before the transition.Chapter 5 presents a novel concept for greenhouse climate control: heating by light. Since lamps provide heat as well as light, the chapter suggests that illuminating at high intensities could eliminate the need for heating. This approach could be very efficient, as it uses lighting both to enhance crop growth and to maintain the indoor temperature. LEDs offer new possibilities in this direction since they can be installed at very high intensities. The scenarios explored in this chapter show that heating a greenhouse exclusively by lamps is possible if sufficient lamp intensities are installed and a heat harvesting system is used to maintain indoor temperatures when the lamps are off. The chapter also shows that if no changes are made to the lamp control strategy, increasing the lamp intensity in the greenhouse typically results in a higher energy use, and a lower energy efficiency.Chapter 6 provides a general discussion, with further outlook described in Section 6: Section 6.1 points out that several reports predict that the energy use of greenhouses will greatly increase in the coming years, mainly due to lighting. It is suggested that the higher efficacy of LEDs might actually incentivize growers to illuminate. In this way, LEDs could contribute to an increase rather than a decrease of greenhouse energy use. Therefore, the rest of the section highlights possible avenues to reduce the energy use and carbon emissions of greenhouses, aside from LEDs. Finally, using some of the lessons learned in the current work, Section 7 provides a short discussion on a new type of growing system: sunless cultivation, also known as plant factories or vertical farms.Chapter 7 is an appendix, providing a user’s guide and a description of the GreenLight model, including a detailed description of the lamps, blackout screen, and heat harvesting sub-models. This description could serve as an aid for future researchers who wish to further use or extend the GreenLight model.

Crassulacean acid metabolism (CAM) is a photosynthetic adaption that has evolved in response to water stress and/ or high temperatures. CAM can be found in plants that grow in (semi)-arid habitats, but CAM also appears in plants in the humid tropics, for example, in epiphytes that have no direct access to soil. CAM plants are remarkable at conserving water, because they take up CO2 during the night, which allows them to keep their stomata closed during the hottest part of the day. The aim of this thesis was to increase understanding of CAM physiology by studying the economically important ornamental orchid Phalaenopsis. To reach this objective, Phalaenopsis plants were grown at several combinations of temperature and light. The response to these treatments was determined on different biological scales (from leaf to plant growth) and on different temporal scales (from seconds to the entire period of cultivation).Chapter 1 introduces CAM and describes how the diel cycle of CO2 uptake and CO2 refixation can be captured in four phases. CAM plants are often not considered when looking for future-proof solutions in agriculture, but one option that is being explored is the bio-engineering of CAM into C3 plants, which is also discussed here. The second half of this general introduction focuses on CAM in the orchid Phalaenopsis. The cultivation practice of the economically important Phalaenopsis pot plant is outlined, and the effects of temperature, light and CO2 on Phalaenopsis growth and development are summarized.Chapter 2 introduces a conceptual framework for CAM plants. A literature study revealed that currently no mechanistic models for CAM growth exist. Therefore, a conceptual framework was developed, which consists of three modules, covering 1) CAM photosynthesis, 2) allocation of assimilates among carbon pools, and 3) biomass accumulation among plant organs. The framework covers processes related to CAM physiology on different biological (from leaf to plant) and temporal (from hours to a full cultivation period) scales. It can function as the basis for development of a mechanistic crop growth model for CAM. Development of the framework also showed that Tt is still unclear how carbon is processed and allocated within CAM plants, when diel carbon fluxes are linked to plant growth.Chapter 3 demonstrates that genotypic variation is large between Phalaenopsis hybrids. In two experiments with 19 and 14 genotypes, the effects of temperature and light on vegetative growth traits were studied. Furthermore, the after-effects of these treatments on flowering traits were determined. Hierarchal component analysis provided insight in how traits correlated and how they contributed to growth and development of Phalaenopsis. Plants that were grown at 31°C showed a strong reduction of plant and root growth (biomass accumulation) compared to plants grown at 27°C, while leaf initiation rates increased. An increase in light intensity (from 60 µmol m-2 s-1 to 140 µmol m-2 s-1) accelerated both vegetative plant growth (biomass accumulation) and development (leaf initiation). Both an increase in light intensity, as well as an increase in temperature during the vegetative phase resulted in an increased number of flower spikes, and number of flowers and buds. In this chapter it is demonstrated that vegetative plant traits can be used to predict flowering quality despite genotypic and phenotypic variation. Traits like number of leaves and biomass of the vegetative plant are a good proxy for, respectively, number of inflorescences and inflorescence biomass.Chapter 4 describes physiological differences between genotypes that underpin plant growth and development of Phalaenopsis. Plants from two genotypes were exposed to light and temperature treatments comparable to those in chapter 3. Measurements on gas exchange and carbohydrate analysis within a diel CAM-cycle were combined with measurements of plant growth and development. Per genotype, principal component analysis (PCA) was used to identify which traits explained most of the variation that occurred. Genotypes were found to differ in processes related to all three modules of the framework described in chapter 2. This chapter elucidated that a correlation exists between cumulative diel CO2 uptake and vegetative plant dry weight of Phalaenopsis, but only when leaf area of the plant is considered, not when expressed on a m2 basis.Phase IV is considered important for its substantial contribution to CO2 uptake and to the productivity of CAM plants. Therefore, chapter 5 examines CO2 uptake via C3 and C4 carboxylation in phase IV in the CAM species Phalaenopsis ‘Sacramento’ and Kalanchoe blossfeldiana ‘Saja’. Short blackout periods, switching to 2% O2 and measurements of chlorophyll fluorescence during phase IV all indicated that in Phalaenopsis ‘Sacramento’, PEPC might be the main carboxylase. This is unlike what is known from other CAM species, where Rubisco is the main carboxylase in phase IV. Indeed, results of K. blossfeldiana ‘Saja’ confirmed that Rubisco was the main carboxylase. Additionally, carbohydrate analysis showed that starch accumulated in Phalaenopsis during phase IV which indicated that Rubisco also active as a carboxylase, alongside PEPC. This chapter discusses that having both carboxylases simultaneously active may lead to double carboxylation and futile cycling of CO2, but that it might also serve as a mechanism for photoprotection.Chapter 6 summarizes and reflects upon the concepts and conclusions of the previous chapters. This discussion focusses on how processes that are determined within diel cycles link to plant growth, which is determined over a longer period of time. The methodology that was used for gas exchange measurements is reflected upon. In this chapter, the effect of other environmental factors such as red: far-red and CO2 on Phalaenopsis cultivation are examined. This chapter furthermore described perspectives of the results of this thesis for commercial Phalaenopsis cultivation. Linking together the results of different chapters, it is demonstrated that diel CO2 uptake measured on a leaf can be used as a proxy for flowering quality, and could thus function as an early selection criterium when phenotyping in Phalaenopsis breeding. Additionally, some suggestions are given for future research, building on knowledge produced in this thesis, e.g. how to improve the conceptual framework.

L-ascorbate is a phytochemical essential for human health. Light regulates L-ascorbate (vitamin C; ASC) levels in plants with the vast majority of the evidence referring to leaves. In the present study the focus was on the effects of light on ASC levels in tomato fruits. The aim of this work as explained in Chapter 1, was to investigate which physiological processes and how do they mediate the effects of light on ASC levels in tomato fruits. Furthermore, the effects of light over the broader metabolome of the tomato fruit are investigated.In Chapter 2, a literature review is presented with the aim to highlight the physiological and biochemical network mediating the regulation of ASC by light. Respiration, photosynthesis and soluble carbohydrates are proposed to control ASC levels in plants. Possible interactions between these physiological components and their importance in light regulation of ASC in both leaves and fruits were discussed. Furthermore, a broad biochemical map for ASC biosynthesis, recycling and turnover was presented and the contribution of specific pathways to the ASC pool is discussed. It is concluded that the main biosynthetic pathway (D-man/L-gal) for ASC accounts for the vast majority of the ASC pool in leaves as well as in fruits.In Chapter 3, the effects of light intensity and spectrum on ASC levels in detached tomato fruits were investigated. ASC levels of fruits increased under light compared to darkness, as long as the fruits were green. Red fruits did not respond to the light treatments. Accumulation of ACS under light was not much affected by the light spectrum. The effect of light on ASC is proposed to be universal for tomato as several tested genotypes were found to be similarly responsive to the same light treatments. As only mature green fruits respond to the light treatments and the rate of photosynthesis correlated with ASC levels, it is put forward that the regulatory effect of light on ASC in tomato fruits is mediated through photosynthesis. No correlation between ASC levels and respiration rates was found.The precursor for ASC biosynthesis via the D-man/L-gal biosynthetic pathway is glucose. The hypothesis that the availability of soluble carbohydrates regulates ASC levels in tomato fruits was tested in a series of experiments presented in Chapter 4. The correlation between ASC and carbohydrates was tested in different settings: fruits with different ASC levels due to light intensity treatments, fruits with different carbohydrate levels due to fruit pruning treatments and fruits with different carbohydrate levels due to artificial feeding with carbohydrates. In all of the cases no correlation between the ASC levels and soluble carbohydrates was found. This suggests that soluble carbohydrates are not a limitation for ASC accumulation. Galacturonate, the precursor for the secondary/salvage biosynthetic pathway did not increase when ASC was upregulated by light. However, myo-inositol –a precursor of a pathway that was previously thought not to contribute in the ASC pool in non-genetically modified plants- increased when ASC was upregulated by light treatments.Apart from ASC, a variety of other fruit metabolites respond to the light environment. In two experiments presented in Chapter 5, light versus darkness and spectrum effects on the broad metabolic profile of tomato fruits were tested. Exposure of mature green fruits to light lead to acceleration of ripening as reflected in a more pronounced pigment and flavonoid accumulation and alkaloids reduction. Furthermore, presence of light positively influenced the levels of carotenoids, tocopherols and phenolic compounds. As these metabolites have been proposed to be beneficial for human health, the light treatment compared to darkness produces potentially fruits with improved nutritional value. The light treatment also affected flavour-related compounds such as malic acid, glutamate and GABA. Hence, light may improve the taste of fruits. These results should further be confirmed with sensory studies. Above mentioned results indicate that light treatments can be used to improve and/or fine tune certain quality traits of the tomato fruits.Chapter 6 summarizes and discusses the findings of Chapters 2 to 5 with the aim to present an overview of the physiological mechanism that mediates the regulation of ASC by light in tomato fruits. Practical concerns for the application of light aiming to improve tomato fruit quality are discussed. Furthermore, suggestions on approaches plant breeding may implement in improving ASC in plants are presented.

Variations in environment factors, e.g., light intensity, light spectrum, water and nutrient level, and crop structure manipulations may occur in the greenhouse. Changes in these factors could affect ornamental crop production in the greenhouse through affecting plant photosynthesis at different levels, e.g., leaf, plant and crop level. The aim of this thesis was to quantify photosynthesis responses to (i) combined changes in photosynthetically active radiation (PAR) and red to far-red ratio (R:FR), (ii) water and nitrogen stress combinations and (iii) crop structure manipulations at different levels for two ornamental crops: lily and rose. Using the photosynthesis model of Farquhar, von Caemmerer and Berry (the FvCB model) and the stomatal conductance model of Ball, Woodrow and Berry (the BWB model), leaf photosynthesis responses to water and nitrogen stress combinations were quantified for lily. The changes of the FvCB model parameters due to variations of water and nitrogen conditions were linearly correlated with the changes of leaf nitrogen per unit leaf area. Most of the BWB model parameters did not depend on the nitrogen level. Using a functional-structural plant model, photosynthesis responses to changes in PAR and R:FR, and the presence of bent shoots were quantified at plant and crop level for rose. At mild shade, plant responses to low R:FR were more important for plant photosynthesis, while with the increase of shade level, plant responses to low PAR became more important. Moreover, the consequences of responses to changes in PAR and R:FR for plant photosynthesis tended to mitigate each other. The presence of bent shoots increased flower shoots dry weight, which was entirely due to the contribution of extra photosynthesis by bent shoots. In addition, bent shoots reflected relatively more far-red than red light, which lowered the R:FR in light reflected upwards that can be received by flower shoots. The low R:FR from below was associated with a steeper leaf angle in flower shoots, which increased canopy photosynthesis by allowing more light to penetrate to the lower plant parts. Overall this thesis illustrates the importance of considering the interactions of multiple factors when quantifying photosynthesis responses to environmental variations. A functional-structural plant model is a useful tool to upscale photosynthesis responses from leaf to crop level.

Potato plants reproduce sexually through the formation of flowers, berries and seeds, and asexually through the formation of tubers. Environmental conditions can be used as a flexible switch to control reproduction in potato, steering it towards flowering when seeds are required for breeding or propagation, or towards tuberization when tubers are required for propagation or potato production. Light is a convenient environmental switch, as spectrum, photoperiod, light intensity and the daily light integral (DLI) can be manipulated. In this thesis the effect of light on tuberization and flowering time was quantified and the underlying molecular regulation was explored. Finally it was determined if tuberization and flowering compete and if so, how this is regulated. Tuberization is a short-day process. In long days, tuberization is delayed or even inhibited (depending on the genotype). In this thesis it was determined whether an external coincidence model can explain the photoperiodic effect on tuberization in potato. In the model plant Arabidopsis, photoperiodic flowering is controlled by coincidence of light and CONSTANS (CO) expression. In potato, a similar model was hypothesized to explain photoperiodic tuberization. Coincidence of the potato CO (StCOL1) expression and light in long days would induce StSP5G, which in turn would lead to the inhibition of StSP6A, the gene encoding for the tuberization signal StSP6A. Thus coincidence of StCOL1 and light is expected to repress tuberization. By using night breaks (30 minutes of light applied in the night) that coincided with StCOL1 expression in the night or not, it was demonstrated that coincidence between light and StCOL1 expression does not necessarily repress tuberization. In addition, it was shown that although flower bud appearance time is not affected by photoperiod, the number of leaves formed before the inflorescence in the genotype S. andigena decreases under shorter photoperiods, indicating an effect of photoperiod on potato flowering as well as tuberization. Not only day-length, but also light spectrum was found to affect the tuberization time. By applying far-red light throughout a long day, tuberization time was accelerated. However, far-red was not able to induce tuberization in genotypes that could not tuberize in long days. It was also demonstrated that the addition of blue light throughout a short day, delayed tuberization in some genotypes. However, when blue light was used to extend the day length to simulate a long day, tuberization was not as strongly repressed as in treatments where the day length was extended with white light. Neither far-red light, blue light nor day-length extension was found to affect the flower bud appearance time. Alternatively, a high DLI did accelerate flowering time in both short and long days. Under high DLI the number of the days until flower bud appearance was reduced, and less leaves were formed before the inflorescence. No correlation between high DLI-accelerated flowering and plant carbohydrate concentration was observed. Interestingly, it was found that accelerated flowering under high DLIs was controlled independently of the flowering time gene StSP3D. Finally it was tested if potato flowering and tuberization compete. Potato plants formed flower buds in both long and short days, but in short days where tuberization was strongly induced, the flower buds failed to develop. It was demonstrated that removing the tuber sink (by grafting or removing stolons) did not improve the flower development in tuber inducing conditions, while silencing the tuberization signal StSP6A did. It was also demonstrated that increasing StSP6A in long days impaired flower bud development, indicating that the tuberization signal StSP6A represses flower bud development rather than the competition for assimilates. This thesis discusses how potato flowering and tuberization are controlled by light on a molecular level and demonstrates how light can be used as a flexible regulator to manipulate potato reproduction.

Introduction The expansion of the market area of the European Union has caused a strong increase of supply and demand of fresh horticulture products of the Dutch glasshouse sector on the European market. Consequently there is increased competition with companies from new European member states, producing against lower prices, as well as changes in production and sales structure. In the Dutch food horticulture sector this led to a large horizontal and vertical merger between most of the auctions and a number of large exporters. From 1996 to 1998 VTN/The Greenery changed from a co-operative auction into a co-operative trade organisation. In the floriculture sector only horizontal mergers took place between co-operative auctions. The wholesalers/exporters remained independent. At present there are two Flower Auctions, FloraHolland te Naaldwijk (market share 98%) and Plantion in Ede (2%). Central research question This thesis explores the development of market structure, market strategy and market results in the horticulture glasshouse sector over the last thirty-five years. The central research question is whether the difference in market structure and market strategy in the Dutch sectors of glasshouse vegetables and glasshouse cut flowers and pot plants is a significant cause to explain the difference in market results for the growers and their co-operative organisations. The conceptual model A number of theories and models have been studied derived from the Industrial Organisation Theory. This theory focuses on the analysis of branches of industries, industry chains and markets involved. It examines the relation between market structure (S), market conduct (C) and market performance (P) through the SCP-model (in Dutch: SGR-model). A description and explanation is given of the static SCP-model of Bain, the dynamic SGR-model of De Jong and the branch-analysing models of Porter and Daems. The conceptual model of competition, concentration and performance (figure 1.1) has been constructed from these models to analyse the Dutch horticulture glasshouse sectors. Research of producers, sector research and research of auctions/sales organisations From 2006-2008 three research projects on producers were conducted amongst 40 growers of vegetables, 40 growers of cut flowers and 40 growers of pot plants, all under glass. Data and opinions of growers about their company, market strategy and performance were gathered. In the same period sector research of the development of total production, imports and exports took place in the three sectors of the glasshouse industry on sector level, on the level of sales organisations and the wholesalers/ exporters. The gathered data have been analysed and tested on selected variables. In three different chapters temporary conclusions have been drawn. The most important business and market characteristics and research outcomes are discussed in three separate tables at the end of these three chapters and the associated appendices. The research of producers was expanded in 2015/2016 on the basis of the data of the research 2006-2008 with econometric research and multiple analysis of a number of the most important variables of market structure and market conduct to explain the market results (Lerner Index). Results of sector research The three horticulture sectors under glass show a positive development in yearly production and export value over a period of thirty-five years, besides a small decrease in 2009 and 2011, as a result of the banking and EHEC crisis. In the Dutch floriculture sector the average growing figures are a bit higher than in the food horticulture sector because of a stronger yearly increase in the production of pot plants. In all three sectors the production and export values are increased almost every year until the banking crisis in 2009. After 2010/2011 the sectors have been recovering. Development of variables in Dutch horticulture glasshouse sector 1980-2016 The sector cut flowers under glass show a decrease of area and production (m2 glass) in The Netherlands. However, there is an increase of import and direct supply of cut flowers from foreign growers and Dutch companies from the southern part of Africa (roses, chrysanthemums etc.). All sectors profit from the growing import/re-export function of vegetables and fruit, cut flowers and pot plants from The Netherlands to neighbouring countries and trade partners in Europe. The high share of the sector variables domestic share and export share in all three sectors stimulate the development of production value, export value and prices. Results of research into auctions/sales organisations In the food horticulture and floriculture sectors there has been quite a difference in market strategy and market structure since 1998. In the sector vegetables under glass the degree of concentration of the four largest sales organisations (C4) has decreased to the level of before the merger (60%). In 1997 this figure was 96%. Also the share of growers of VTN/The Greenery in the area of Dutch vegetables under glass has decreased. VTN/The Greenery did not reach her target of 1996 with their strategy of horizontal and vertical concentration: organizing a larger bundling of the turnover of the Dutch auctions and wholesalers/exporters. The search for a good working integration of horticultural production and trade in one company with an efficient and effective structure has not been completed yet and started in 2016 with a new sales organisation. The financial position of VTN/The Greenery on the European market is not strong. Since 1996 the annual turnover has strongly fluctuated between 0.9 and 1.5 billion euros, with a variation range of 25 to 30 %. The supply of their own members halved, just like the income out of commission. The position on the Dutch market is stable, on the most important European markets difficult. The return on investment is low. In 2015 and 2016 a careful recovery started after the difficult years of crisis 2009, 2011 and 2013. Flower auctions FloraHolland and VBA showed a clear strategy and good results around the merger of 2007. The merger was a good example of a carefully implemented strategy of horizontal concentration, bringing together the interests of the flower auctions and their members. For FloraHolland the period of the crisis 2009-2011 was a test with success. There was an expansion of horizontal concentration across the borders: a new joint venture auction Rhein-Maas, founded together with the German organisation Landgard and there was an integration with the import auction TFA in Aalsmeer. Both organisations are important for the market position of FloraHolland. In the Dutch floriculture sector under glass there are hardly any examples of vertical concentration of producers or sales organisations with wholesalers/exporters. There are examples, though, of vertical co-operation between these organisations and international retail, especially with the larger growers of pot plants. The auction clock, physical and digital, is the most important sales method the flower auctions use daily. For most products there is a public pricing system. It provides a transparent process of supply and demand against sharp tariffs of the auction. For cut flowers as well as for pot and garden plants a large part of the product groups are sold by way of the auction clock, which mostly ensures a reliable reference price for mediation and personal selling and provides a good match of supply and demand and a ‘clean’ market. Attention to strengthen the position of the auction clock, especially with the selling of pot and garden plants, is important. The turnover of FloraHolland decreased in 2009 (bank crisis) and increased in 2010 and 2011 just above the level of 2008. Incomes out of services dropped. As costs decreased more than incomes, profits and solvency improved in this period. In 2012 FloraHolland realised a turnover increase of 3% compared to 2011. However, the incomes out of services decreased. In 2013 the sector performed reasonably. The turnover of FloraHolland increased slightly but costs were higher than incomes and FloraHolland had an exploitation loss. 2014 was a year of slight recovery, 2015 and 2016 ended with an increasing turnover of 3 and 4%. Profit after tax in these years are 12 and 3 million euros. For most of the growers and customers the results in 2015 and 2016 were positive. The decision of the wholesale/export (VGB) to contribute again in the promotion costs of Bloemenbureau Holland was welcomed very positively. Along with the new strategy of 2020 FloraHolland is working on the strengthening and expansion of the physical and digital market places. Research results of producers On producers level there is also quite a difference in market strategy, structure and results between growers in the sectors of glasshouse vegetables and glasshouse cut flowers and pot plants. At present there is a fierce struggle to survive in each sector. It seems that the small grower of cut flowers and pot plants stands a better chance than the small grower in vegetables. The most striking single relations between structure, conduct and result will be mentioned. Most striking single relations glasshouse vegetables - The small company has relatively higher costs than the larger types. If the sales organisation uses the principle of ‘the user pays the total costs made’ this burden is rather heavy for the smallest companies. - Auction growers mainly deliver round or grape tomatoes, the majority of independent growers choose for the special varieties. This influences the pricing process. - Small and large auction growers differ significantly in business size from independent growers, but realise comparable margins. Large-scale production does not always lead to lower average costs and a better margin, but it does entail a greater risk of too much supply and low prices. Growers with a larger business size are faced with larger financial problems in difficult years than smaller ones. - Horizontal concentration of the four largest growers of vegetables lies at a low level and their sales power is low. The concentration of the four largest sales organisations is about 60%. - Vertically integrated auction growers are smaller in business size and invest less than non- integrated independent growers. They realise comparable margins. - The importance of the sales organisation to realise good prices and margins for the members’ products seems rather small. Sharp purchase prices are of equal importance for the trade organisation and influence the margin of the members. - Higher investments don’t produce higher results (directly). More innovative investments are needed to improve prices and margins. Most striking single relations glasshouse cut flowers - The small auction grower realises an expected smaller turnover and pays higher commission than the larger auction grower, member of a growers organisation. Although there is no significant relation between grower type and realised margin, higher commission can lead to higher prices and margins. Besides the higher price level, smaller growers realise a higher solvency than larger growers. - Growers of roses under glass realise a higher margin than growers of chrysanthemums because of a wide and deep assortment. - Small growers of cut flowers show comparable or better results than the larger ones. - Horizontal concentration of the four largest growers of cut flowers lies, just like the sectors of vegetables and pot plants under glass, at a low level. The small auction grower has little market power and needs the sales organisation for reasonable prices and successful sales. - There are no significant relations between the organisation of sales and growers’ turnover, realised margin and the height of commission. It looks as if every grower uses his own mix of marketing and sales activities in a way that no significant differences in results arise. - Selling of cut flowers by means of the auction clock gives good results. Most striking single relations glasshouse pot plants - The smaller auction grower, with or without personal selling, realises an expected smaller turnover but a higher margin than the larger auction grower, member of a growers organisation. - Smaller growers (in m2 glass) get higher results or results comparable to those of the larger ones. Old and new companies get comparable margins. - Growers of green plants get a significant lower yearly turnover than growers of blooming pot plants. Green plants are often more unique than blooming plants. That is why growers of green plants get higher prices and margins. - Horizontal concentration of the growers of pot plants lies, just like in the other sectors, at a low level. The small auction grower has little market power and needs the sales organisation for realising reasonable prices and successful sales. - Like in the other sectors the small grower invests less in his business than the larger ones. Higher investments do not directly produce higher results. More innovative investments are needed to improve prices and margins. - There is a significant relation between the organisation of sales and the yearly realised turnover: larger growers use more personal selling besides the sales services of the auction, as their own business activity or as an activity of the growers organisation. Boarding out all sales activities to FloraHolland is effective especially for the small grower and enlarges the chance of realising a higher margin. Although he pays a higher commission, he realises a higher margin because of the positive relation between commission and margin. Producers results through econometric research Most striking multiple relations glasshouse vegetables The results of the econometric analysis show that in the sector glasshouse vegetables membership of a growers association produces better results on average than membership of a traditional marketing corporation. Especially young producers with new ideas about the organisation of the company and vertical co-operation with on average large and modern companies are booking the best results. Most striking multiple relations glasshouse cut flowers Auction growers using the auction clock exclusively to sell their products realise a higher margin on average than growers using other selling methods. The membership of a growers association produces higher results on average than no membership and smaller companies get higher margins than large ones. Senior growers get higher results than junior growers. The auction clock is the best guarantee for realising higher margins. It seems that in the sector cut flowers a larger scale has less effect on the margin than producing ‘niche’ product types. For the latter the selling method via the auction clock plays an important role. Companies with ‘niche’ products have higher fixed costs although a higher margin gives fewer problems when it comes to finance the production. Final conclusion The answer to the central question confirms the following: the difference in market structure and market strategy in the Dutch sectors of glasshouse vegetables and glasshouse cut flowers is a significant cause to explain the difference in market results. If we follow the position and the results of the small grower in the sector glasshouse vegetables, we are looking at a producer in a tight spot with lower average results for the grower and his co-operation in comparison with the independent grower and his grower association. In the sector glasshouse cut flowers the position and results of the small auction clock grower is better in comparison with the grower who sells on his own or via a growers association. The results of this research indicate that in the sector glasshouse vegetables the highest margins are obtained by the independent growers associations, working either cooperativly with the classical co-operations or independent there from but in any case with their own marketing strategy. In the sector glasshouse cut flowers it is the grower selling through the auction clock who gets the highest margins. In the sector glasshouse pot plants, where the type of the product clearly differs from the perishable vegetables and cut flowers, there are too few data to draw conclusions.

DNA-informed selection can strongly improve the process of plant breeding. It requires the detection of DNA polymorphisms, calculation of genetic linkage, access to reliable phenotypes and methods to detect genetic loci associated with phenotypic traits of interest. Cultivated chrysanthemum is an outcrossing hexaploid with an unknown mode of inheritance. This complicates the development of resources and methods that enable the detection of trait loci. Postharvest performance is an essential trait in chrysanthemum, but is difficult to measure. This makes it an interesting but challenging trait to phenotype and detect associated genetic loci. In this thesis I describe the development of resources and methods to enable phenotyping for postharvest performance, genetic linkage map construction and detection of quantitative trait loci in hexaploid chrysanthemum. Postharvest performance is a complicated trait because it is related to many different disorders that reduce quality. One of these disorders in chrysanthemum is disk floret degreening, which occurs after long storage. In chapter 2, we show that degreening can be prevented by feeding the flower heads with sucrose, suggesting carbohydrate starvation plays a role in the degreening process. To investigate the response to carbohydrate starvation of genotypes with different sensitivity to disk floret degreening, we investigated the metabolome of sugar-fed and carbohydrate-starved disk florets by 1H-NMR and HPAEC. We show that the metabolome is severely altered at carbohydrate starvation. In general, starvation results in an upregulation of amino acid and secondary metabolism. Underlying causes of genotypic differences explaining variation in disk floret degreening in the three investigated genotypes remained to be elucidated, but roles of regulation of respiration rate and camphor metabolism were posed as possible candidates. In chapter 3, disk floret degreening was found to be the most important postharvest disorder after 3 weeks of storage among 44 white chrysanthemum cultivars. To investigate the inheritance of disk floret degreening, we crossed two genotypes with opposite phenotypic values of both disk floret degreening and carbohydrate content to obtain a population segregating for disk floret degreening. To phenotype the cultivar panel and the bi-parental population precisely and in a high throughput manner, we developed a method that quantified colour of detached capitula over time. This method was validated with visual observations of disk floret degreening during vase life tests. In a subset of the bi-parental population we measured carbohydrate content of the disk florets at harvest. The amount of total carbohydrates co-segregated with sensitivity to degreening, which shows that the difference in disk floret degreening sensitivity between the parents could be explained by their difference in carbohydrate content. However, the correlation was rather weak, indicating carbohydrate content is not the only factor playing a role. In order to develop resources for DNA-informed breeding, one needs to be able to characterize DNA polymorphisms. In chapter 4, we describe the development of a genotyping array containing 183,000 single nucleotide polymorphisms (SNPs). These SNPs were acquired by sequencing the transcriptome of 13 chrysanthemum cultivars. By comparing the genomic dosage based on the SNP assay and the dosage as estimated by the read depth from the transcriptome sequencing data, we show that alleles are expressed conform the genomic dosage, which contradicts to what is often found in disomic polyploids. In line with this finding, we conclusively show that cultivated chrysanthemum exhibits genome-wide hexasomic inheritance, based on the segregation ratios of large numbers of different types of markers in two different populations. Tools for genetic analysis in diploids are widely available, but these have limited use for polyploids. In chapter 5, we present a modular software package that enables genetic linkage map construction in tetraploids and hexaploids. Because of the modularity, functionality for other ploidy levels can be easily added. The software is written in the programming language R and we named it polymapR. It can generate genetic linkage maps from marker dosage scores in an F1 population, while taking the following steps: data inspection and filtering, linkage analysis, linkage group assignment and marker ordering. It is the first software package that can handle polysomic hexaploid and partial polysomic tetraploid data, and has advantages over other polyploid mapping software because of its scalability and cross-platform applicability. With the marker dosage scores of the bi-parental F1 population from the genotyping array and the developed methods to perform linkage analysis we constructed an integrated genetic linkage map for the hexaploid bi-parental population described in chapter 3 and 4. We describe this process in chapter 6. With this integrated linkage map, we reconstructed the inheritance of parental haplotypes for each individual, and expressed this as identity-by-descent (IBD) probabilities. The phenotypic data on disk floret degreening sensitivity that was acquired as described in chapter 3, was used in addition to three other traits to detect quantitative trait loci (QTL). These QTL were detected based on the IBD probabilities of 1 centiMorgan intervals of each parental homologue. This enabled us to study genetic architecture by estimating the effects of each separate allele within a QTL on the trait. We showed that for many QTL the trait was affected by more than two alleles. In chapter 7, the findings in this thesis are discussed in the context of breeding for heterogeneous traits, the implications of the mode of inheritance for breeding and the advantages and disadvantages of polyploidy in crop breeding. In conclusion, this thesis provides in general a significant step for DNA-informed breeding in polysomic hexaploids, and for postharvest performance in chrysanthemum in particular.

(Semi-)closed greenhouses have been developed over the last decades to conserve energy. In a closed greenhouse, window ventilation is fully replaced by mechanical cooling while solar heat is temporarily stored in an aquifer. A semi-closed greenhouse has a smaller cooling capacity than a closed greenhouse and, in which mechanical cooling is combined with window ventilation. (Semi-)closed greenhouses create new climate conditions: high CO2 concentrations irrespective of the outdoor climate, and vertical gradients in temperature and vapour pressure deficit throughout the canopy. This thesis focuses on the crop physiology in (semi-)closed greenhouses, and investigates the effects of the new climate conditions on crop growth, development and underlying processes. Cumulative production in (semi) closed greenhouses increased by 6-14% compared to the open greenhouse, depending on the cooling capacity. The production increase in the (semi-)closed greenhouses was explained by the higher CO2 concentrations. In many species, feedback inhibition of photosynthesis occurs when plants are grown at high CO2. The results, however, suggest that high CO2 concentrations do not cause feedback inhibition in high producing crops, because the plants have sufficient sink organs (fruits) to utilise all assimilates. Pruning experiments showed that photosynthetic acclimation to elevated CO2 concentration only occurred when the number of fruits was considerably reduced. Cooling below the canopy induced vertical temperature and vapour pressure deficit gradients. These gradients correlated with outside radiation and outside temperature. Despite the occurrence of vertical temperature gradients, plant growth and fruit yield were mostly unaffected. Leaf and truss initiation rates did not differ in the presence or absence of a vertical temperature gradients, since air temperatures at the top of the canopy were kept comparable. The only observed response of plants to the vertical temperature gradient was the reduced rate of fruit development in the lower part of the canopy. This resulted in a longer period between anthesis and fruit harvest and an increase in the average fruit weight in summer. However, total fruit production over the whole season was not affected. The effects of the climate factors light, CO2 concentration, temperature, and humidity on leaf photosynthesis were investigated. The photosynthesis model of Farquhar, von Caemmerer and Berry (FvCB) was modified by adding a sub-model for Ribulose-1,5-bisphosphate carboxylase (Rubisco) activation. The photosynthetic parameters: the maximum carboxylation capacity (Vcmax) and the maximum electron transport rate (Jmax), α (the efficiency of light energy conversion), θ (the curvature of light response of electron transport), and Rd (the non-photorespiratory CO2 release) were estimated based on measurements under a wide range of environmental conditions in the semi-closed greenhouse. The simultaneous estimation method and the nonlinear mixed effects model were applied to ensure the accuracy of the parameter estimation. Observations and predictions matched well (R2=0.94). The yield increase in a closed greenhouse, compared to that in an open greenhouse was analyzed based on physiological and developmental processes. The yield increase in the (semi-)closed greenhouses was the result of an increase of net leaf photosynthesis. The (semi-)closed greenhouses have been applied commercially first in the Netherlands, and later in other countries. The knowledge obtained from (semi-)closed greenhouses is applied in conventional open greenhouse as well, which is called the next generation greenhouse cultivation. A number of innovations are being developed for greenhouse industry to reduce energy consumption while improving production and quality.

SUMMARY A large increase in agricultural production is needed to feed the increasing world population with their increasing demand per capita. However, growing competition for arable land, water, energy, and the degradation of the environment impose challenges to improve crop production. Hence agricultural production efficiency needs to increase. Greenhouses provide the possibility to create optimal growth conditions for crops, thereby improving production and product quality. Light is the driving force for plant photosynthesis and in greenhouse horticulture, light is often the most limiting factor for plant growth. Therefore, improving radiation use efficiency (RUE) in greenhouse production systems is imperative in order to improve plant growth and production. The objective of this thesis is to obtain insight in improving RUE in greenhouse production systems through better understanding of crop physiology. Three aspects related to RUE have been studied in this thesis, 1) improving light distribution in the crop canopy; 2) allowing more light in the greenhouse during summer; and 3) balancing the source and sink strength during plant growth. Light is heterogeneously distributed in the crop canopy. Due to the saturating response of leaf photosynthesis rate to light, a more homogeneous light distribution in the canopy will result in a higher crop photosynthesis. In Chapter 2, the effect of diffuse glass on spatial light distribution in a fully developed tomato canopy and its direct and indirect effects on crop photosynthesis were explored. Diffuse glass, which transforms a portion of direct solar light into diffuse light without influencing the light transmissivity of the glass, was applied as greenhouse cover. Under diffuse glass cover, light was more evenly distributed (in both horizontal and vertical direction) within the canopy compared with plants grown under conventional clear glass cover. Besides a more uniform light distribution, diffuse glass also resulted in higher leaf photosynthetic capacity in the middle of the crop canopy and in a higher leaf area index (LAI). The higher leaf photosynthetic capacity was positively correlated with a higher leaf total nitrogen and chlorophyll content. Moreover, lower leaf temperature and less photo-inhibition of top canopy leaves were observed under diffuse glass cover when global radiation was high. Total crop photosynthesis between 1st April and 1st October was enhanced by 7.2 % under diffuse glass. This enhancement mainly resulted from four factors (in order of decreasing importance): a more homogeneous horizontal light distribution, a higher leaf photosynthetic capacity, a more uniform vertical light distribution and a higher LAI. In summer growers of shade tolerant pot-plants often apply shading screens in the greenhouse or white wash on the greenhouse cover in order to avoid leaf or flower damage caused by high light. Shading carries a penalty on potential crop growth which is positively related to the amount of light that can be captured. Considering the advantageous properties of diffuse glass cover, i.e. a more homogeneous light distribution, a lower leaf temperature and less photo-inhibition when global radiation is high, in Chapter 3 we tested the feasibility of allowing more light (i.e. less shading) via diffuse glass cover for cultivation of shade tolerant pot-plants during summer. Two Anthurium andreanum cultivars (Pink Champion and Royal Champion) were grown in 3 greenhouse compartments. Under similar DLI [7.5 mol m-2 d-1 PAR (photosynthetic active radiation)], diffuse glass cover resulted in 8 % higher crop RUE (i.e. dry mass production per unit intercepted light) in ‘Royal Champion’ compared with clear glass cover treatment, which consequently resulted in higher total biomass production. This effect was not observed in ‘Pink Champion’. Under diffuse glass cover, high DLI (10 mol m-2 d-1 PAR) resulted in 20-23 % higher total biomass production in both cultivars compared with low DLI (7.5 mol m-2 d-1 PAR), this mainly resulted from the higher cumulative intercepted light. No flower or leaf damage was observed in these treatments. High DLI even resulted in more compact plants as indicated by a higher ratio of aboveground fresh mass to plant height. In Chapter 4, we addressed a question resulting from Chapter 3, i.e. why the stimulating effect of diffuse light on crop RUE in anthurium pot-plants is cultivar specific? We excluded the fraction of canopy light interception and steady-state leaf photosynthesis as potential explanations, and explained it from instantaneous leaf photosynthesis which closely correlates with the temporal light distribution. Diffuse glass cover smoothed the variation of temporal light distribution at a given point on a leaf during a clear day, which consequently resulted in less temporal variation of stomatal conductance in ‘Royal Champion’ which had stomata showing a fast-response to the variation in light intensity. As stomata are the gateway for CO2 uptake, less variation in stomatal conductance imposed less limitation for leaf photosynthesis under diffuse glass cover, thereby resulting in a higher crop RUE. For ‘Pink Champion’, however, stomata were less responding to variations in light intensity. Therefore, stomata imposed only a marginal limitation on leaf photosynthesis even under clear glass cover where the temporal incident light intensity varied substantially due to the shadow cast by the greenhouse construction parts and equipment. Application of supplementary assimilation light in greenhouses is rapidly increasing. The beneficial effect of supplementary assimilation light is determined by the balance between assimilate production in source leaves and the overall capacity of the plant to use these assimilates. Therefore, it is important to identify the source-sink balance during plant growth. In Chapter 5, three tomato cultivars with different potential fruit size [‘Komeett’ (large size); ‘Capricia’ (medium size); ‘Sunstream’ (small size, cherry tomato)] were grown under commercial crop management. We estimated the source-sink ratio from the early growth stage to fully fruiting stage through experimentation and model simulation. Carbohydrate content of leaves and stems were periodically determined. Tomato plants showed a period of sink limitation (‘Komeett’ and ‘Capricia’) or came close to sink limitation (‘Sunstream’) during the early growth stage under ample natural irradiance (early September) as indicated by a source-sink ratio higher than or close to 1. Fruiting tomato plants were source-limited as indicated by an extremely low source-sink ratio (average source-sink ratio from 50 days after planting onwards was 0.17, 0.22 and 0.33 for ‘Komeett’, ‘Capricia’ and ‘Sunstream’, respectively). During the fully fruiting stage, the source-sink ratio was negatively correlated with the potential fruit size when commercial fruit load was maintained. Carbohydrate content in tomato stems and leaves increased linearly with plant source-sink ratio. The experiments and results described in this thesis provide insights for improving RUE in greenhouse production systems. The main achievements and limitations as well as practical applications are discussed in Chapter 6.

Keywords: cell division, endoreduplication, cell expansion, cyclin, cyclin dependent kinase, growth theory, systems biology. Okello, R.C.O (2015) Multi-level analysis of the impact of temperature and light on tomato fruit growth. PhD thesis, Wageningen University, Wageningen, The Netherlands, 166 pp, with English and Dutch summaries. Tomato fruit growth commences with an increase in cell number followed by cell expansion. Upon cessation of cell division, a spectacular increase in nuclear DNA content without cell division (endoreduplication) occurs, which is positively correlated with cell size. Evaluation of the relative importance of each cellular process during fruit growth is important for attempts aimed at manipulating fruit size. In this thesis, the genetic and physiological basis for the differences in fruit size between cultivars and their response to fruit temperature was studied. In addition, the effects of darkness, white, blue, and red light around the fruits on tomato fruit growth were investigated. Temperature or light treatments were applied at the fruit level in all experiments in order to separate plant and fruit level responses. Fruit phenotype was assessed at whole fruit, cell and gene level. Expression patterns of 20 different genes encoding regulators of cell division, endoreduplication or cell expansion were analysed. Besides the experimental work, a literature review of the role of light in the regulatory networks of cell division, endoreduplication and cell expansion was conducted. Results from experiments were then placed into context of other studies in order to identify processes that drive fruit growth. Experiments showed that differences in fruit size between cultivars can result from differences in both cell number and cell size. Increased cell number in the larger fruited cultivar was corroborated by an increase in the expression of three cell division promoters (CDKB2, CycA1 and E2Fe) and a decrease in the expression of an inhibitor (fw2.2) of cell division. The observed smaller fruit size in heated compared with non-heated fruits appeared to stem from a reduction in cell size even when cell number tended to increase. The expression of three promoters (CDKB1, CDKB2, and CycA1) and one inhibitor (fw2.2) of cell division increased when fruits were heated. However, the expression of genes encoding proteins known to regulate endoreduplication and cell expansion did not corroborate observations on cell size in the temperature experiment. Fruits subjected to different light treatments did not differ in either fruit size or carbohydrate content. However, cell division was strongly stimulated at the expense of cell expansion by light. This thesis shows that cell division is stimulated by light irrespective of the organ under consideration while endoreduplication and cell expansion responses are organ specific. It is proposed that light effects on cell division, endoreduplication and cell expansion stem from either degradation of transcription factors or inhibitory competition between transcription factors for promoter regions of target genes. It is also argued here that the commonly observed positive correlation between cell number and fruit size does not imply a causal relationship. In addition, the thesis argues that fruit growth is dependent on cell-autonomous and non-cell-autonomous regulatory mechanisms as well as a global coordinator, the target-of-rapamycin and, consequently, the increase in fruit size follows the neo-cellular theory of fruit growth. This thesis provides clues on the link between gene expression and cell and fruit level observations. It also provides in depth knowledge on the role of environmental factors on the regulation of cell division, endoreduplication and cell expansion. Further studies at the level between genes and the cells will be necessary to quantify the relationship between gene expression and cell and fruit phenotype.

Oxygenic photosynthesis is the gateway of the sun’s energy into the biosphere, it is where light becomes life. Genetic variation is the fuel of evolution, without it natural selection is powerless and adaptation impossible. In this thesis I have set out to study a relatively unexplored field which sits at the intersection of these two topics, namely natural genetic variation in plant photosynthesis. To begin I reviewed the available literature (Chapter 2), from this it became clear that the main bottleneck restricting progress was the lack of high-throughput phenotyping platforms for photosynthesis. To address this an automated high-throughput chlorophyll fluorescence phenotyping system was developed, which could measure 1440 plants in less than an hour for ΦPSII, a measure of photosynthetic efficiency (Chapter 3). Using this phenotyping platform I screened five populations of Arabidopsis thaliana. Three of these populations resulted from bi-parental crosses and segregated for only two genomes, using these I conducted family mapping (Chapter 4). The final two populations were composed of natural, field collected, accessions and were analysed using a genome wide association approach (Chapter 5). The family mapping approach had greater statistical power due to within population replication and the genome wide association approach had higher mapping resolution due to historical recombination. Both approaches were used to identify genomic regions (loci) which were responsible for some of the variation in photosynthesis observed. The number and average effect of these loci was used to infer the genetic architecture of photosynthesis as a highly complex polygenic trait for which there are many loci of very small effect. In addition to screening these large populations a smaller subset of 18 lines was assayed for natural variation in phosphorylation of photosystem II (PSII) proteins in response to changing light (Chapter 6). This exploratory study indicated that this process shows considerable variation and may be important for adaptation of the photosynthetic apparatus to photosynthetic extremes. The genetic mapping studies just described, focus exclusively on genetic variation in the nuclear genome, whilst this contains the majority of the plants genetic information there is also a store of genetic information in the chloroplast and mitochondria. These genetic repositories contain genes which are essential for photosynthesis and energy metabolism. Any variation in these genes could have a large impact on photosynthesis. To study natural variation in these genomes I developed a new population of reciprocal nuclear-organellar hybrids (cybrids) which could be used to study the effect of genetic variation in organelles whilst controlling for nuclear genetic variation (Chapter 7). Preliminary results indicate that this resource will be of great use in disentangling natural genetic variation in nucleo-organelle interactions. Finally I looked at one chloroplast encoded photosynthetic mutation in more detail (Chapter 8). This mutation had evolved in response to herbicide application and had spread along British railways. When studying this population of resistant plants I found empirical evidence for organelle mediated nuclear genetic hitchhiking. This is a previously undescribed evolutionary phenomenon and is likely to be quite common. In conclusion there is an abundance of genetic variation in photosynthesis which can be used to improve the trait for agriculture and provide insights into novel evolutionary phenomena in the field.