Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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The evaluation of energy in fish feed
Haidar, Mahmoud - \ 2017
University. Promotor(en): Johan Verreth, co-promotor(en): Johan Schrama. - Wageningen : Wageningen University - ISBN 9789463438049 - 155
oreochromis niloticus - fish feeding - feed formulation - digestible energy - dietary protein - dietary fat - carbohydrates - growth - feed evaluation - fish culture - aquaculture - visvoeding - voersamenstelling - verteerbare energie - voedingseiwit - voedingsvet - koolhydraten - groei - voederwaardering - visteelt - aquacultuur

New and alternative plant ingredients are increasingly incorporated in fish feed due to the scarcity of captured fish and increased fishmeal and fish oil prices. As a result, current fish feeds are characterized by a highly variable ingredients composition, leading to a similar variability in the dietary macronutrients composition, especially the carbohydrates fraction. Appropriate formulation of the energy component in fish feeds requires information on nutrient digestibility, energy requirements for maintenance, and the efficiency of utilization of digestible energy for growth (kgDE). In fish feed formulation, the energy evaluation is based on digestible energy (DE) basis. The main assumptions of this DE system are that maintenance requirements and kgDE are independent of dietary factors. The main objective of this thesis was to evaluate and improve the DE system for Nile tilapia. Data showed that, opposite to what is assumed in literature and irrespective of the feeding level applied, an optimal digestible protein to digestible energy ratio (DP/DE) for young Nile tilapia could not be detected. In addition, it was expected that Nile tilapia would show a maximal protein deposition in relation to a wide range of DP/DE ratios, however, this was either observed. Further investigations showed that different body compartments/organs responded differently in terms of protein and fat composition as a result of changes in the dietary DP/DE ratio. In tilapia, viscera and the “rest” fraction (head, skin, fins and bones) were the main site for fat retention. In addition, protein content of fillets seems to be constant (about 17%) and not affected by dietary factors in Nile tilapia. In addition, the effect of using new plant ingredients in Nile tilapia diets was also investigated. The results showed that the ingredients composition had an effect on the maintenance requirements of Nile tilapia. Further, changes in the ratio of starch vs non starch carbohydrates revealed that energy retention was lower when more dietary fibers were included. In addition, the net energy retention differed also when the levels of digestible protein, fat and carbohydrates changed in the diets. The latter results proved that kgDE was not constant and was dependent on diet composition. All aforementioned results led us to calculate the energetic efficiencies of digestible protein, fat and carbohydrates for net energy retention. These estimated efficiencies were used to propose a net energy evaluation system being feasible for Nile tilapia.

Crop growth and development in closed and semi-closed greenhouses
Qian, Tian - \ 2017
University. Promotor(en): Leo Marcelis, co-promotor(en): Anja Dieleman; Anne Elings. - Wageningen : Wageningen University - ISBN 9789463430708 - 112
crops - crop production - growth - greenhouse crops - greenhouse horticulture - climate - semi-closed greenhouses - photosynthesis - temperature - gewassen - gewasproductie - groei - kasgewassen - glastuinbouw - klimaat - semi-gesloten kassen - fotosynthese - temperatuur

(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.

First week nutrition for broiler chickens : effects on growth, metabolic status, organ development, and carcass composition
Lamot, David - \ 2017
University. Promotor(en): Bas Kemp, co-promotor(en): Henry van den Brand; Peter Wijtten. - Wageningen : Wageningen University - ISBN 9789463430777 - 187
broilers - animal nutrition - poultry feeding - feeds - growth - metabolism - carcass composition - nutrition physiology - vleeskuikens - diervoeding - pluimveevoeding - voer - groei - metabolisme - karkassamenstelling - voedingsfysiologie

During the first week of life, broiler chickens undergo various developmental changes that are already initiated during incubation. Ongoing development of organs such as the gastro- intestinal tract and the immune system may affect the nutritional requirements during this age period. Despite the residual yolk that is available at hatch and that may provide nutritional support during the first days after hatch, the growth performance may be affected by the time in between hatch and first feed intake. Furthermore, it remains largely unknown to what extend nutritional composition of a pre-starter diet, as well as feed availability directly after hatch have an effect on physiological development directly after hatch, but also at later age. The aim of this thesis was to determine the impact of feed availability and feed composition provided during the first week of life on short-term physiological development, as well as potential long-term effects on growth performance of broiler chickens. Especially early hatched chickens were suggested to benefit more from direct feed access compared to midterm and late hatched chickens, as they tended to have a higher body weight gain during the first week after hatch. A delay in feed access for 48 h resulted in lowered body weight gain and feed intake when compared to direct feed access, but so did a short (13 to 26 h) delay in feed access after hatch. In the latter case, delayed feed access resulted in a lower weight to length ratio of the jejunum and ileum at 4 d of age compared with chickens with direct feed access. Although delayed feed access after hatch resulted in lower body weight gain during the first week after hatch and thereafter, it can be discussed whether this is truly an impairment of long-term growth or just a delayed onset of growth. With respect to feed composition, the inclusion of fish oil and medium chain fatty acids in a pre-starter diet had minor effects on humoral immune function. Inclusion of medium chain fatty acids did result in higher body weight gain and lowered feed efficiency during the first week of life, but only during the period it was provided. Feeding increased diet densities during the first week of life, obtained by formulating diets with different dietary fat levels, resulted in an increased gain to feed ratio, whereas body weight gain and feed intake decreased. Despite the shift in dietary energy supply from carbohydrates to fat and the perceived lower fat digestibility in young broiler chickens, nitrogen metabolizability and fat digestibility were not affected in the current study by feeding increased diet densities. The relative crop, liver and pancreas weights decreased when feeding increased diet densities, whereas the length of the entire intestinal tract increased. This suggests that broiler chickens repartition visceral organ development in response to feeding more concentrated diets during the first week of life. Interestingly, protein and fat accretion were not affected. Continued feeding of increased diet densities after 7 d of age resulted in increased BW gain, G:F ratio and metabolizable energy intake, but mainly during the periods that these diets were provided. In summary, even short durations of delayed feed access already impact intestinal development of young broiler chickens. However, a delayed feed access up to 48 h after hatch does not result in impaired growth, but only a delayed onset of growth. Even though digestibility of fats and oils may be suboptimal in young broiler chickens, feeding of these diets does not have to result in lowered performance per se. Young broiler chickens appear to adapt themselves towards high density diets with high fat inclusion levels in the first week of life, enabling them to digest and metabolize these diet types despite a suboptimal capacity for fat digestion. High density diets result in higher growth performance, but only for the period these diets are provided and thus carry-over effects at later age appear to be limited.

Monitoring mosselgroei Flakkeese spuisluis : resultaten T0 bemonstering 2016
Wijsman, J.W.M. ; Brummelhuis, E. ; Gool, A.C.M. van - \ 2016
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C126/16) - 33
mossels - mosselteelt - groei - monitoring - zuid-holland - mussels - mussel culture - growth
In de winter van 2016/2017 zal de Flakkeese spuisluis in de Grevelingendam weer in gebruik worden genomen. De spuisluis, bestaande uit een hevel, vormt een verbinding tussen het Grevelingenmeer en de Oosterschelde. Door het openen van de hevel zal als gevolg van het getij op de Oosterschelde water heen en weer worden getransporteerd tussen de Oosterschelde en het Grevelingenmeer. De verwachting is dat door de toename in waterbeweging de waterkwaliteit in het Grevelingenmeer zal verbeteren, met name nabij de bodem waar zuurstofloosheid optreedt. Om deze veranderingen te kunnen monitoren zijn er mosselen uitgezet in speciale mandjes op twee locaties in het Grevelingenmeer en twee locaties in de Oosterschelde. De groei en ontwikkeling van de mosselen kan worden gebruikt als een indicator voor de waterkwaliteit en -productiviteit. Doordat de mosselen gedurende een periode van enkele maanden zijn uitgezet, zijn de groeimetingen de resultante van de waterkwaliteit over die hele periode. Ook zijn in het Grevelingenmeer continue-metingen verricht voor zuurstofconcentratie (alleen bij de bodem) en temperatuur (nabij de bodem en het wateroppervlak). Dit rapport beschrijft de situatie in 2016 vóór de ingebruikname van de hevel.
Super-performance in a palm species
Jansen, Merel - \ 2016
University. Promotor(en): Niels Anten; Pieter Zuidema, co-promotor(en): Frans Bongers; M. Martínez-Ramos. - Wageningen : Wageningen University - ISBN 9789462579996 - 193
chamaedorea elegans - understorey - tropical forests - spatial variation - leaves - growth - population ecology - defoliation - genetic variation - onderlaag - tropische bossen - ruimtelijke variatie - bladeren - groei - populatie-ecologie - ontbladering - genetische variatie

The world is changing rapidly due to anthropogenic disturbance. Effects include: global warming, massive pollution, a changed global nitrogen cycle, high rates of land-use change, and exotic species spread. This has a tremendous impact on both natural and agricultural systems. To understand these impacts, good understanding of ecological systems and underlying drivers is necessary. Ecological systems can be studied at different levels of aggregation. Different levels of aggregation influence each other and are also influenced by external drivers like the environment. The population level is of particular interest, because many important ecological processes occur at the population level, like evolution, extinction, and invasion. Ecologists are increasingly recognizing that population processes are strongly influenced by one level of aggregation lower, the individual level. Individual heterogeneity (i.e. differences between individuals in performance), determines many population processes including population growth rate. However, the exact relations between individual heterogeneity, the external drivers of it, and the population level are not always well understood. Furthermore, methods to analyze these relations are not always available.

Individual heterogeneity occurs at different temporal scales, ranging from short- to long-term performance differences between individuals, where short- and long-term refer to the expected lifespan of the species in question. Short-term differences between individuals are relatively easily identifiable and are common in almost all species. But long-term differences are much harder to determine especially for long-lived organisms. Long-term differences between individuals in reproduction have been identified for several animal species, and in growth for several tree species, but less is known about the existence of such differences in other life forms (e.g. palms, lianas or clonal plants). Quantifying the extent to which individuals differ is essential for understanding the influence of individual heterogeneity on population processes. Super-performing individuals (i.e. individuals that persistently grow faster and reproduce more than others), probably contribute more to the growth of the population and therefore to future generations. Future populations will, therefore, have the genetic characteristics of the super-performers. Which characteristics this will be, depends on the genetic and environmental drivers of super-performance. Full understanding of the influence of individual heterogeneity on population processes, therefore, requires knowledge of the underlying causes of individual heterogeneity.

For many species, it is known that spatial variation in environmental conditions can cause short-term performance differences between individuals, but it is often not clear if the same environmental factors that cause short-term performance differences are also the environmental factors that cause long-term performance differences. Furthermore, genetic variation is known to cause performance differences, but to what extent is not well studied in natural long-lived plant populations. Within-population genetic variation can be maintained in habitats that are characterized by strong temporal or spatial heterogeneity in environmental conditions if the performance of a genotype relative to others depends on the environment it experiences.

Super-performing individuals possibly play an important role in the resistance and resilience of populations to disturbance (i.e. maintaining and recovering population growth rate under stress), because super-performers potentially contribute more to the recovery of the population. However, this depends on the relative tolerance to disturbance of super-performers compared to under-performers. A positive relation between performance and tolerance would make super-performers more important, while a negative relation would make them less important. Many types of disturbances entail leaf loss and tolerance to leaf loss is associated with performance being larger than what one would assume based on the amount of leaf area loss. Tolerance can be achieved by compensating for leaf loss in terms of growth rate, which entails either allocating more new assimilates to leaves, allocating new assimilates more efficiently to leaf area (i.e. by increasing specific leaf area), or growing faster with existing leaf area (i.e. by increasing net assimilation rate). Genetic variation in tolerance and compensatory responses would allow populations to adapt to changes in disturbance events that entail leaf loss.

Individual heterogeneity could also have implications for management. Plant and animal populations are managed at many different levels ranging from harvest from natural populations to modern agricultural practices. When harvesting from natural populations, it might be beneficial to spare the individuals that are most important for future production. Individuals could be spared, either because they contribute most to population growth, because they are tolerant to harvesting (which is relevant when only part of a plant is harvested), or when they start producing less or lower quality product. The productivity of natural populations could also be increased by actively promoting those environmental conditions and genotypes that allow for high productivity, which is the basis of agriculture and common practice in forest management. To determine how this can best be done, knowledge of the causes of individual heterogeneity is necessary.

The general aim of this thesis is to identify and quantify the mechanisms that determine individual heterogeneity and to determine how this heterogeneity, in turn, affects population level processes. This aim was divided into four main questions that I addressed: (1) To what extent do individuals differ in performance? (2) What causes individual heterogeneity in performance? (3) What are the demographic consequences of individual heterogeneity? (4) Can individual differences be used to improve the management of populations? To answer these questions, we used the tropical forest understorey palm Chamaedorea elegans as a study system, of which the leaves are an important non-timber forest product that is being used in the floral industry worldwide. We collected demographic data, measured spatial variation in environmental conditions, and applied a defoliation treatment to simulate leaf harvesting, in a natural population in Chiapas, Mexico. Furthermore, we grew seedlings from different mothers from our study population in the greenhouses of Wageningen University, where we also applied a defoliation treatment.

In Chapter 2 we quantified the extent to which individuals differ in long-term growth rate, and analyzed the importance of fast growers for population growth. We reconstructed growth histories from internodes and showed that growth differences between individuals are very large and persistent in our study population. This led to large variation in life growth trajectories, with individuals of the same age varying strongly in size. This shows that not only in canopy trees but also in species in the light limited understorey growth differences can be very large. Past growth rate was found to be a very good predictor of current performance (i.e. growth and reproduction). Using an Integral Projection Model (i.e. a type of demographic model) that was based on size and past growth rate, we showed that fast-growing individuals are much more important for population growth than others: the 50% fastest growing individuals contributed almost two times as much to population growth as the 50% slowest growing individuals.

In Chapter 3 we analyzed the extent to which observed long-term growth differences can be caused by environmental heterogeneity. Short-term variation in performance was mainly driven by light availability, while soil variables and leaf damage had smaller effects, and spatial heterogeneity in light availability and soil pH were autocorrelated over time. Using individual-based simulation models, we analyzed the extent to which spatial environmental heterogeneity could explain observed long-term variation in growth, and showed that this could largely be explained if the temporal persistence of light availability and soil pH was taken into account. We also estimated long-term inter-individual variation in reproduction to be very large. We further analyzed the importance of temporal persistence in environmental variation for long-term performance differences, by analyzing the whole range of values of environmental persistence, and the strength of the effect of the environmental heterogeneity on short-term performance. We showed that long-term performance differences become large when either the strength of the effect of the environmental factor on short-term performance is large, or when the spatial variation in the environmental factor is persistent over time. This shows that an environmental factor that in a short-term study might have been dismissed as unimportant for long-term performance variation, might, in reality, contribute strongly.

In Chapter 4 we tested for genetic variation in growth potential, tolerance to leaf loss, compensatory growth responses, and if growth potential and tolerance were genetically correlated in our study population. We quantified compensatory responses with an iterative growth model that takes into account the timing of leaf loss. Genetic variation in growth potential was large, and plants compensated strongly for leaf loss, but genetic variation in tolerance and compensatory growth responses was very limited. Growth performances in defoliated and undefoliated conditions were positively genetically correlated (i.e. the same genotypes perform relatively well compared to others, both with and without the stress of leaf loss). The high genetic variation in growth potential and the positive correlation between treatments suggests that the existence of super-performing individuals in our study population likely has (at least in part) a genetic basis. These super-performing individuals, that grow fast even under the stress of leaf loss, possibly contribute disproportionately to population resistance and resilience to disturbance. The low genetic variation in tolerance and compensatory responses, however, suggests that populations might have limited ability to adapt to changes in disturbance regimes that entail increases in leaf loss. Furthermore, the high genetic variation in growth potential could potentially be used in management practices like enrichment planting.

In Chapter 5 we explore the potential of using individual heterogeneity to design smarter harvest schemes, by sparing individuals that contribute most to future productivity. We tested if fast and slow growers, and small and large individuals, responded differently to leaf loss in terms of vital rates, but found only very limited evidence for this. Using Integral Projection Models that were based on stem length and past growth rate, we simulated leaf harvest over a period of 20 years, in several scenarios of sparing individuals, which we compared to “Business as usual” (i.e. no individuals being spared, BAU). Sparing individuals that are most important for population growth, was beneficial for population size (and could, therefore, reduce extinction risk), increased annual leaf harvest at the end of the simulation period, but cumulated leaf harvest over 20 years was much lower compared to BAU. Sparing individuals that produced leaves of non-commercial size (i.e. <25cm), therefore allowing them to recover, also resulted in a lower total leaf harvest over 20 years. However, a much higher harvest (a three-fold increase) was found when only leaves of commercial size were considered. These results show that it is possible to increase yield quality and sustainability (in terms of population size) of harvesting practices, by making use of individual heterogeneity. The analytical and modeling methods that we present are applicable to any natural system from which either whole individuals, or parts of individuals, are harvested, and provide an extra tool that could be considered by managers and harvest practitioners to optimize harvest practices.

In conclusion, in this thesis, I showed that in a long-lived understorey palm growth differences are very large and persistent (Chapter 2) and that it is likely that long-term differences in reproduction are also very large (Chapter 3). I also showed that spatial heterogeneity in environmental conditions can to a large extent explain these differences and that when evaluating the environmental drivers of individual heterogeneity, it is important to take the persistence of spatial variation into account (Chapter 3). Individual heterogeneity also is partly genetically determined. I showed that genetic variation in growth potential to be large (Chapter 4), and that fast growers keep on growing fast under the stress of leaf loss (Chapters 4,5). Therefore it is likely that genetic variation contributes to long-term differences between individuals. Genetic variation for tolerance and compensatory responses was estimated to be low (Chapter 4), suggesting that the adaptive potential of our study population to changes in disturbance events that entail leaf loss might be low. I also showed that super-performing individuals are much more important for the growth of the population (Chapter 2) and that individuals that are important for future production could be used to improve the management of natural populations (Chapter 5).

This study provides improved insight into the extent of individual heterogeneity in a long-lived plant species and its environmental and genetic drivers, and clearly shows the importance of individual heterogeneity and its drivers for population processes and management practices. It also presents methods on how persistent performance differences between individuals can be incorporated into demographic tools, how these can be used to analyze individual contributions to population dynamics, to extrapolate short-term to long–term environmental effects, and to analyze smart harvesting scenarios that take differences between individuals into account. These results indicate that individual heterogeneity, underlying environmental and genetic drivers, and population processes are all related. Therefore, when evaluating the effect of environmental change on population processes, and in the design of management schemes, it is important to keep these relations in mind. The methodological tools that we presented provide a means of doing this.

Simulation nitrogen-limited crop growth with SWAP/WOFOST : process descriptions and user manual
Groenendijk, Piet ; Boogaard, Hendrik ; Heinen, Marius ; Kroes, J.G. ; Supit, Iwan ; Wit, Allard de - \ 2016
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2721) - 59
crops - growth - soil - nitrogen - organic matter - mineralization - leaching - simulation models - nitrates - gewassen - groei - bodem - stikstof - organische stof - mineralisatie - uitspoelen - simulatiemodellen - nitraten
This report describes a soil nitrogen module (Soil-N), which is combined with the agro-hydrological model, SWAP, and the crop growth model, WOFOST. The core of the Soil-N module is a description of the nitrogen cycle, which is coupled to the organic matter cycle based upon the RothC-26.3 model. Nitrogen can be supplied to the soil as different types of fertilizer applications and through mineralisation of organic nitrogen. Ammonium and nitrate balances are calculated including uptake by plant roots, de-nitrification and leaching of nitrate. Data exchange is on a daily base. The partitioning of nitrogen within crops and the nitrogen contents of crop residues are calculated by WOFOST and passed to the Soil-N module. SWAP generates the data for establishing the water balance of the soil compartment for which the Soil-N perform the simulations. Nitrogen uptake by the crop is calculated as the minimum of the demand by the crop and the availability of nitrogen in the soil. The crop production rate is reduced when the mineral nitrogen stock is limited. Nitrogen-fixation is based on a simple approach. An improved sub-model for phenological stages of soybean was implemented. Increasing atmospheric CO2 concentrations can be accounted for. The innovated integrated model was tested using data sets from The Netherlands, China and Argentina, for which examples are given. This new model can be used as a tool in studies, in which both water and nitrogen can be limited for crop growth.
Examining growth, yield and bean quality of Ethiopian coffee trees : towards optimizing resources and tree management
Bote, Adugna - \ 2016
University. Promotor(en): Niels Anten, co-promotor(en): Jan Vos; F.L. Ocho. - Wageningen : Wageningen University - ISBN 9789462578319 - 138
coffea - coffea arabica - trees - growth - yields - quality - radiation - nitrogen - agroecosystems - bomen - groei - opbrengsten - kwaliteit - straling - stikstof - agro-ecosystemen

Coffee (Coffeaarabica L.)bean production and quality are determined by a diversity of interacting factors (e.g. shade, nitrogen, crop traits). Bean yield increases with increase in radiation, but adequate fertilizer suppliesare needed to sustain the productivity. This thesis analysed coffee tree growth, bean production and bean quality in relation to different degrees of exposure to radiation and nitrogen supply. Growth of leaves and branches and properties of leaves such as specific leaf area, nitrogen content per unit leaf area and light-saturated rate of photosynthesis were determined. Radiation interception and nitrogen uptake were also determined as were radiation use efficiency and apparent nitrogen recovery. Tree biomass and coffee bean yield responded positively to both radiation and nitrogen supply. Abundant bean yield to the detriment of vegetative growth, however, resultedin biennial bearing in coffee trees. Effects of fruit load on coffee treegrowth and productivity were studied for two consecutive years and the resultshowed that competition between fruit growth and vegetative growth predisposed the trees for biennial bearing. Reduced vegetative growth when fruit load is high reduces the number of flower bearing nodes and hence yields in the next season. Coffee quality is a sum of favourable characteristics that satisfies requirements of different actors in the coffee chain and is the factor determining the price on the coffee market. This study has also examined coffee quality attributes in relation to radiation and nitrogen, fruit load manipulation, and genotype by environment (different altitudes) interactions. The result indicated that factors and conditions that support non-limiting supply of resources for bean to grow and a sufficient long period of maturation promote coffee bean quality. Overall, the study gained further understanding of coffee tree growth, yield and bean quality responses to aforementioned factors and explored traits that underlie the patterns. Further works are required to use the traits and describe the behaviour of coffee trees in different agro-ecosystems.

Microalgae production in a biofilm photobioreactor
Blanken, Ward - \ 2016
University. Promotor(en): Rene Wijffels, co-promotor(en): Marcel Janssen. - Wageningen : Wageningen University - ISBN 9789462578425 - 234
algae - algae culture - biofilms - bioreactors - growth - production costs - biomass - artificial lighting - photosynthesis - carbon dioxide - algen - algenteelt - bioreactoren - groei - productiekosten - biomassa - kunstmatige verlichting - fotosynthese - kooldioxide

Microalgae can be used to produce high-value compounds, such as pigments or high value fatty acids, or as a feedstock for lower value products such as food and feed compounds, biochemicals, and biofuels. In order to produce these bulk products competitively, it is required to lower microalgae production cost. Production costs could be reduced by employing microalgae biofilms as a production platform. The main advantages of microalgae biofilms are a direct harvest of concentrated microalgae paste, and the uncoupling of the hydraulic retention time from the microalgal retention time. The latter allows to decrease the liquid volume or to employ dilute waste streams. To successfully employ biofilms, however, it is required that microalgal biofilms can be cultivated at high productivity and high photosynthetic efficiency. The aim of this thesis was to optimize the productivity of microalgal biofilms.

Light energy drives microalgal growth. Sunlight is free and abundant, but sunlight intensity varies over the day and the seasons. This makes it impossible to maintain optimal production conditions throughout the day. These fluctuations in irradiance can be prevented by applying artificial lighting. Although, artificial lighting will supply a constant light intensity and thus increase productivity and simplify process control, it will also increase microalgae production cost. A quantitative evaluation of lighting costs and energy requirement was still missing and this was the topic of Chapter 2. The costs related to artificial lighting were identified as 25.3 $ per kilogram of dry-weight biomass, with only 4% to 6% of the electrical energy required to power the lamps eventually stored as chemical energy in microalgal biomass. Energy loss and increased production cost may be acceptable for the production of high value products, but in general they should be avoided.

In Chapter 3, a photobioreactor design based on a rotating biological contactor (RBC) was introduced and used as a production platform for microalgal biomass cultivated in a biofilm. In the photobioreactor, referred to as the Algadisk, microalgae grow in biofilm on vertical rotating disks partially submerged in water with dissolved nutrients. The objective was to evaluate the potential of the Algadisk photobioreactor, and identify the window of operation of the process with respect to the effects of disk roughness, disk rotation speed and CO2 concentration. These parameters were evaluated in relation to biomass productivity, photosynthetic efficiency, and the long-term cultivation stability of the production process.

The mesophilic green microalga Chlorella sorokiniana was used as a model organism. In the lab-scale Algadisk reactor, a productivity of 20.1 ±0.7 gram per m2 disk surface per day and a biomass yield on light of 0.9 ±0.04 gram dry weight biomass per mol photons were obtained. This productivity could be retained over 21 weeks without re-inoculation. To obtain maximal and stable productivity it was important that the disk surface provides a structure that allows biomass retention on the disk after harvest. The retained biomass acts as inoculum for the new biofilm and is therefore essential for quick biofilm regrowth. Most important process parameters were CO2­ supply, temperature, and pH. Although deviations of these parameters from the optimal conditions resulted in productivity loss, the system quickly recovered when optimal conditions were restored. These results exhibit an apparent opportunity to employ the Algadisk photobioreactor and biofilm systems in general at large scale for microalgae biomass production provided CO2 supply is adequate.

In order to better understand the process conditions inside the biofilm a model was developed in the further chapters. These mathematical models were calibrated and validated with dedicated experiments. In Chapter 4 first a general applicable kinetic model was developed able to predict light limited microalgal growth. This model combines a mathematical description for photoautotrophic sugar production with a description for aerobic chemoheterotrophic biomass growth. The model is based on five measurable biological parameters which were obtained from literature for the purpose of this study. The model was validated on experiments described in literature for both Chlorella sorokiniana and Chlamydomonas reinhardtii. The specific growth rate was initially predicted with a low accuracy, which was most likely caused by simplifications in the light model and inaccurate parameter estimations. When optimizing the light model and input parameters the model accuracy was improved and validated. With this model a reliable engineering tool became available to predict microalgal growth in photobioreactors. This microalgal growth model was included in the biofilm growth models introduced in Chapters 5 and 6.

In Chapter 5 microalgal biofilms of Chlorella sorokiniana were grown under simulated day-night cycles at high productivity and high photosynthetic efficiency. The experimental data under day/night cycles were used to validate a microalgal biofilm growth model. For this purpose the light limited microalgal growth model from Chapter 4 was extended to include diurnal carbon-partitioning and maintenance under prolonged dark conditions. This new biofilm growth model was then calibrated and validated experimentally. Based on these experiments and model simulations no differences in the light utilization efficiency between diurnal and continuous light conditions were identified. Indirectly this shows that biomass lost overnight represents sugar consumption for synthesis of new functional biomass and maintenance related respiration. This is advantageous, as this result shows that it is possible to cultivate microalgae at high photosynthetic efficiencies on sunlight and that the night does not negatively impact overall daily productivity. Long periods of darkness resulted in reduced maintenance related respiration.

Based on simulations with the validated biofilm growth model it could be determined that the photosynthetic efficiency of biofilm growth is higher than that of suspension growth. This is related to the fact that the maintenance rate in the dark zones of the biofilm is lower compared to that in the dark zones of suspension cultures, which are continuously mixed with the photic zone.

In Chapter 3 it was identified that concentrated CO2 streams are required to obtain high productivities. However, over-supplying CO2 results into loss of CO2 to the environment and is undesirable for both environmental and economic reasons. In Chapter 6 the phototrophic biofilm growth model from Chapter 5 was extended to include CO2 and O2 consumption, production, and diffusion. The extended model was validated in growth experiments with CO2 as limiting substrate. Based on the validated model the CO2 utilization and productivity in biofilm photobioreactors were optimized by changing the gas flow rate, the number of biofilm reactors in series, and the gas composition. This resulted in a maximum CO2 utilization efficiency of 96% by employing flue gas, while the productivity only dropped 2% compared to non-CO2 limited growth. In order to achieve this 25 biofilm reactors units, or more, must be operated in series. Based on these results we conclude that concentrated CO2 streams and plug flow behaviour of the gaseous phase over the biofilm surface are essential for high CO2 utilization efficiencies and high biofilm productivity.

In Chapter 7 the implications of these studies for the further development of biofilm photobioreactors was discussed in the light of current biofilm photobioreactor designs. Design elements of state of the art biofilm photobioreactors, were combined into a new conceptual biofilm photobioreactor design. This new design combines all advantages of phototrophic biofilms minimizing the amount of material required. Further improvements by means of process control strategies were suggested that aim for maximal productivity and maximal nutrient utilization efficiency. These strategies include: control of the biofilm thickness, control of the temperature, and optimized nutrient supply strategies.

Aspects of bulblet growth of lily in vitro
Askari Rabori, N. - \ 2016
University. Promotor(en): Richard Visser, co-promotor(en): Geert-Jan de Klerk. - Wageningen : Wageningen University - ISBN 9789462577602 - 130 p.
lilium - in vitro - growth - in vitro regeneration - abiotic conditions - stress - bulbs - groei - in vitro regeneratie - abiotiek - bollen

Many geophytes have a high ornamental value. They are preferably propagated by micropropagation because in this way large quantities of uniform, disease-free starting material are produced in a short period of time. In comparison with shoots, bulblets have several clear advantages as starting material. Therefore, in vitro bulblet formation is an important target for improvement of tissue culture of geophytes. The research described in this thesis was carried out with the lily cultivars ‘Santander’ and ‘Stargazer’.

Commercially, lily is the second geophyte in the global flower industry. The size of lily bulblets regenerated in vitro has a direct effect on the performance in the field. After planting, large bulblets sprout with a stem and gain twice as much weight compared with small bulblets that sprout with a rosette. In the present study we studied basic and applied aspects of the following topics: (1) new methods for sterilization during initiation, (2) the effect of scale-related factors on bulblet growth, (3) growth enhancement by moderate abiotic stresses, and (4) the effect of CO2 removal from headspace of tissue culture containers on lily bulblet growth and as a control Arabidopsis thaliana seedling growth.

Contamination is an everlasting problem in tissue culture laboratories. Lily bulbs are underground organs and contain therefore more contaminants as compared with aerial organs. During initiation, operators cause additional contamination in two ways that have as yet not been recognized adequately. (1) Rinsing explants with sterile water after surface-sterilization is the generally advised method to remove the residues of decontaminants. However, when scales are heavily contaminated, the surface-sterilization does not kill microorganisms in all scales. Surface-sterilization is usually done with batches of 10 to 30 scales and the contaminated scales may cross-contaminate uninfected scales during rinsing in water. We have tested the rinsing water and found heavy bacterial contamination in the 2th and especially the 3rd rinse. The contaminated rinsing water resulted in a high incidence of cross-contamination. Cross contamination was reduced almost fully by rinsing in diluted NaClO solution (0.03%) instead of sterile water. There was no negative effect of diluted NaClO on growth. (2) A second way of introducing contamination by the operator is the entering of microorganisms during detachment from mother bulbs via the vascular bundles caused by negative hydrostatic pressure within the bulb tissue. By detaching scales from bulbs submerged in 0.03% NaClO, hydrostatic-pressure related contamination was strongly reduced. The growth of bulblets increased by 22% and 17% when cross contamination and negative-hydrostatic pressure related contamination were prevented.

Storage organ formation is controlled by interacting environmental, biochemical and genetic factors. We studied various aspects of the effect of the scale explant. We found that large explants produced larger bulblets than small explants. When bulblets were excised and cultured in vitro, growth was improved by 33% when a small piece of the original scale explant was left attached to the bulblet. The position in the scale from where the explant was excised affected the growth of the regenerating bulblets. Basal-scale explants improved bulblet growth by 40-50 % compared with apical-scale explants. This might be related to the physiological state of the tissues: there was more starch and there were more vascular bundles present in basal scale explants. Furthermore, excision of an explant from the middle of the scale improved bulblet growth by 40-50 % compared with explants excised from the edge of the scale. In general, the middle scale explants were heavier and contained wider vascular bundles.

Plants in stressful conditions tend to allocate a higher proportion of biomass to below-ground biomass (roots and storage organs) as compared to above ground biomass. We investigated the effect of moderate abiotic stresses on lily bulblets grown in vitro. In general, lily bulblets showed an increased growth after moderate stresses. Hot air increased growth by 30%, hot water by 40%. We also examined the effect of drought and anaerobiosis. Drought stress increased growth of bulblets by 40% in the cultivar ‘Stargazer’, but significantly decreased bulblet growth in cv ‘Santander’. Anaerobiosis increased growth in ‘Stargazer’ and ‘Santander’ by 32% and 65%, respectively. We also showed that a moderate stresses treatment protects lily bulblets against future severe abiotic stresses.

In general, the in vitro situation is not favorable for plants. Composition of the headspace (high humidity, strongly fluctuating CO2- and O2-levels and accumulation of gases like ethylene), low light, and wounding are unfavorable conditions that plants have to deal with. We examined the effect of CO2 starvation on growth in vitro with and without addition of 3% sucrose to the medium. A CO2-poor headspace reduced the growth of bulblets, leaves, roots and scale explants strongly, also in the presence of 3% sucrose. CO2 removal from the headspace decreased growth of Arabidopsis seedlings by 50 % on medium with 3% sucrose. It seems unlikely that the growth reduction on medium with 3% sucrose is caused solely by the lack of sucrose production in photosynthesis when CO2 is removed. Indeed, we found evidence that the low CO2 resulted in heavy stress that in turn may reduce growth. Fv/Fm in lily and Arabidopsis dropped when CO2 was removed. Occurrence of reactive oxygen radicals (ROS) was examined in Arabidopsis seedlings by staining with nitroblue tetrazolium (NBT). ROS was virtually absent in ex vitro growing seedlings and very abundant in seedlings grown under CO2 starvation. Seedlings grown under normal tissue culture conditions showed an intermediate presence of ROS. We hypothesize that low levels of CO2 may results in ROS in in vitro seedlings which reduces growth.

Recovery of nutrients from biogas digestate with biochar and clinoptilolite
Kocaturk, N.P. - \ 2016
University. Promotor(en): L. Stoumann Jensen; Lijbert Brussaard, co-promotor(en): S. Bruun; Kor Zwart. - Wageningen : Wageningen University - ISBN 9789462578234 - 130 p.
biochar - clinoptilolite - digestate - nutrients - waste management - fractionation - growth - clinoptiloliet - digestaat - voedingsstoffen - afvalbeheer - fractionering - groei

The liquid fraction of digestate contains nutrients which makes it a valuable fertiliser in agricultural crop production systems. However, direct application of digestate may raise practical and environmental problems. Therefore, processes to concentrate nutrients have been proposed aiming not only to treat the liquid fraction of digestate to overcome the problems related to direct application, but also to recover the nutrients of which natural reserves are being depleted such as phosphorus and potassium.

In this thesis, the focus was on the evaluation of the use of clinoptilolite and biochar for nutrient recovery from the liquid fraction of digestate; and to investigate the further use of these nutrient-enriched materials as fertiliser.

This thesis showed that sorption with clinoptilolite and biochar can be a promising technology to recover nutrients from liquid fraction of digestate. Using biochar and clinoptilolite provides concentration of nutrients and, thereby, volume reduction which allows for savings on storage, transport and application of the voluminous liquid fraction of digestate. The end-products are digestate-enriched clinoptilolite and enriched biochar can act as N fertilisers.

Grasgroei meten met de grashoogtemeter
Holshof, G. ; Stienezen, M.W.J. - \ 2016
Wageningen : Wageningen UR Livestock Research (Livestock Research rapport 925) - 23 p.
grassen - groei - meting - opbrengsten - graslandbeheer - grasses - growth - measurement - yields - grassland management
Het effect van een verhoogde ammoniak concentratie in het water op fysiologie, groei en voeropname van Europese paling (Anguilla anguilla)
Abbink, W. ; Blom, E. ; Pelgrim, Thamar ; Vries, P. de; Vis, J.W. van de; Schram, E. - \ 2015
Yerseke : IMARES (Rapport / IMARES C187/15) - 18 p.
european eels - ammoniak - dierfysiologie - groei - voeropname - visteelt - aquacultuur - dierenwelzijn - dierlijke productie - kweekvis - palingen - huisvesting, dieren - diergezondheid - ammonia - animal physiology - growth - feed intake - fish culture - aquaculture - animal welfare - animal production - farmed fish - eels - animal housing - animal health
Culturing soles on ragworms: growth and feeding behaviour
Ende, S.S.W. - \ 2015
University. Promotor(en): Johan Verreth, co-promotor(en): Johan Schrama. - Wageningen : Wageningen University - ISBN 9789462575622 - 128
solea - soleidae - kweekvis - voeropname - groei - prooi - wormen - foerageren - voedingsgedrag - prestatieniveau - vijverteelt - aquacultuur - farmed fish - feed intake - growth - prey - helminths - foraging - feeding behaviour - performance - pond culture - aquaculture

Ende, S.S.W. (2015). Culturing soles on ragworms: Growth and feeding behaviour. PhD thesis, Wageningen University, The Netherlands.

Despite the high market demand and intensive research efforts since the 1960s commercial culture of common sole (Solea solea L.) has been unsuccessful. Problems related to availability and price of suitable raw materials (invertebrates) and the low tolerance to crowding have hampered the development of intensive sole culture. Alternative extensive pond cultures systems are currently explored where common sole can graze on natural food. The general aim of this study was to get insight into which factors limit growth of common sole foraging on ragworms in ponds. The results did not show any nutritional effects that may hamper the growth of common sole. At non-limiting conditions, i.e. when fed chopped ragworms and when housed in sediment free tanks, common sole showed higher food intake, higher growth rates and higher nutrient utilization efficiencies than when fed mussels or a formulated diet. The results however suggest that growth in a pond with ragworms was limited by reduced foraging capabilities of common sole. To explore this hypothesis, the effect of prey size, predator size and prey density were tested. Overall, intake of buried ragworms was reduced by more than half in contrast to intake of unburied ragworms. Intake of buried ragworms was reduced regardless of ragworm size or common sole size. Increasing ragworm density only resulted in satiation intake values in smaller common sole. Our results additionally indicate that the presence of common sole hampers ragworm performance in a pond. Ragworms reduced their feeding activities when receiving water from tanks which contained common sole and ragworms, i.e. when common sole could graze on ragworms. Results from this PhD study suggest that the growth of common sole in ponds is not limited by nutritional but by their foraging abilities. However, the results of this study are too incomplete to fully predict growth performance of common sole in a pond. Factors such as temperature, oxygen supply or feeding activity need to be investigated to make comprehensive growth predictions.

Functional analyses of AtCHR12 and AtCHR23 : plant growth responses upon over-expression of chromatin remodeling ATPase genes
Folta, A. - \ 2015
University. Promotor(en): Ton Bisseling, co-promotor(en): Ludmila Mlynarova. - Wageningen : Wageningen University - ISBN 9789462575561 - 144
planten - groei - genexpressie - chromatine - atp - arabidopsis - solanum lycopersicum - zaadkieming - groeiregulatoren - plants - growth - gene expression - chromatin - seed germination - growth regulators

Living organisms have to deal with changing environmental conditions during their whole life cycle. In contrast to animals, plants are sessile organisms. Therefore they have evolved multiple regulatory mechanisms that help them to cope with changing conditions. One of the first responses to stress conditions is reduction or arrest of growth. Therefore regulation of growth and development is essential to successfully complete their life cycle. To correctly time their development, plants need to integrate various environmental signals with intrinsic developmental programs. In this integration, regulation of gene expression plays a major role.

The genetic information of an organism is stored in DNA sequence. DNA forms a complex with histones and other proteins, which is called chromatin. Chromatin is a highly dynamic complex and modification of the chromatin structure makes DNA more or less accessible to the transcriptional machinery and other regulatory proteins. The modification of chromatin organization is called chromatin remodeling and it involves both covalent modifications of DNA and histone tails, and non-covalent modification of chromatin structure by ATP-dependent chromatin remodeling complexes. ATP-dependent chromatin remodeling complexes comprise multiple protein subunits with SNF2 ATPase as a catalytic subunit. Depending on the subunit composition, the complexes can perform different tasks at various places of chromatin, and can be active at different developmental stages (Chapter 1).

The SNF2 ATPases are conserved from yeast to plants. In Arabidopsis, 41 SNF2 ATPases have been identified. The focus of this thesis is on two of those ATPases – AtCHR12 and AtCHR23. It has been shown previously that AtCHR12 is involved in growth responses to environmental cues. We have extended these studies to its paralog AtCHR23 (Chapter 2). In contrast to over-expression of AtCHR12, which affects growth only during reproductive stage of development, over-expression of AtCHR23 leads to smaller seedlings and reduced vegetative growth. Upon application of mild abiotic stress, the growth reduction is stronger than in wild-type plants. Moreover, the transgenic plants manifest increased variability of growth. The increased growth variability correlates with increased expression variability of genes associated with stress. The results indicate that accurate and controlled expression of AtCHR23 is required for stability and robustness of growth, as well as gene expression.

Regulation of growth is important not only during vegetative or reproductive stage of development, but also during embryo development. The growth of the embryo is interrupted during the embryo maturation phase and it was suggested that AtCHR12 may be involved in this temporary growth arrest. Here we have shown that both AtCHR12 and AtCHR23 are expressed during embryo development, and that over-expression of AtCHR12 or AtCHR23 affects the embryo maturation phase with consequences on two important developmental transitions in plant life – germination and transition to flowering.

Over-expression of AtCHR12 or AtCHR23 leads to reduced seed germination, which is more pronounced under stress conditions (Chapter 3). The reduced germination of over-expressing lines is associated with increased transcript levels of seed maturation genes and reduced degradation of their mRNAs in germinating seeds. The results indicate that repression of AtCHR12 and AtCHR23 in germinating seeds is required for full germination.

The connection between embryo development and flowering time control was observed in transgenic lines over-expressing AtCHR12 (Chapter 4). Over-expression of AtCHR12 results in early flowering under both long- and short-day conditions. The early flowering phenotype correlates with reduced expression of the main flowering repressor, FLC. The reduced FLC expression correlates with increased levels of repressive histone mark H3K27me3 on the FLC locus. Additionally, FLC expression was affected already during FLC reprogramming, which takes place during embryo development. This leads to reduced FLC expression in mature embryos. The results show that AtCHR12 over-expression affects flowering time by different mechanisms than other Snf2-subfamily ATPases. In contrast to AtCHR12, BRAHMA was shown to regulate flowering time via the photoperiod pathway, while SPLAYED affects flowering time by repressing FT expression.

We have observed that over-expression of AtCHR12 or AtCHR23 affects plant growth in response to stress, and play a role in germination and transition to flowering. These traits are also important for agriculture, and such genes are potentially interesting targets for breeding programs. To test, if such genes have a similar role in crops, we have studied the effect of the tomato ortholog of AtCHR12 and AtCHR23 on tomato growth.

Tomato (Solanum lycopersicum), as well as other crops, have only one ortholog of AtCHR12 and AtCHR23, which was suggested to possess a role of both ATPases. We have successfully cloned the tomato ortholog and over-expressed it in tomato plants (Chapter 5). The transgenic tomato plants have reduced vegetative growth and compacted reproductive structures, resembling the phenotype of AtCHR23 and AtCHR12 over-expression, respectively. However, in contrast to Arabidopsis, the tomato plants responded to abiotic stress similarly as wild-type, and they flowered later than wild-type plants. The results indicate that modification of expression of AtCHR12 and AtCHR23 orthologs could be used to develop novel methods to control plant growth.

Taken together, the research described in this thesis identifies AtCHR12 and AtCHR23 as regulators of plant growth, especially in response to environment, as well as of the seed maturation program with clear effects on seed germination and flowering time, and we show that such genes can be potentially interesting for agriculture and horticulture practice.

Natriumgevoeligheid en recirculatie bij Cymbidium. Tussenrapport na 1e teeltjaar : Behoud plantgezondheid en voorkomen groeiremming bij hergebruik drainwater
Kromwijk, J.A.M. ; Voogt, W. - \ 2015
Bleiswijk : Wageningen UR Glastuinbouw (Rapport GTB 1371) - 24
teelt onder bescherming - glastuinbouw - cymbidium - recirculatiesystemen - emissie - natrium - drainagewater - groei - kwaliteit - gewaskwaliteit - protected cultivation - greenhouse horticulture - recirculating systems - emission - sodium - drainage water - growth - quality - crop quality
In the Netherlands, the government and horticultural industry have agreed to lower the emission of nutrients to the environment. Until recently no drain water was reused in the cultivation of Cymbidium orchids as growers were allowed to discharge the drain water when a sodium level of more than 0 mmol/l was reached. As reusing drain water is a new phenomenon for Cymbidium, growers are now faced with a lack of knowledge on the effects of drain water reuse. Therefore a trial was started to investigate the effect of sodium accumulation on crop growth and flowering in two varieties of Cymbidium. Different sodium concentrations are given while maintaining the EC at 0.8. These sodium treatments have a lower “nutritional EC” than the control treatment without sodium. As of February 2015 unusual symptoms in the leaves emerged at the two highest levels of sodium resulting in dead leaf tips / leaves. This is potassium deficiency, induced by the lower potassium concentration in the nutritional solution and by inhibition of the potassium uptake by a high sodium concentration. In the first year of cultivation, sodium accumulation had no effect on production as the flower stalks were already induced before the start of the treatments. Cymbidium is a perennial crop in which negative effects on production and quality take a long time to become visible, so the experiment will be continued into a second year of cultivation. This research is funded by the Cymbidium growers in the Netherlands, Product Board for Horticulture and Top Sector Horticulture and Propagation Materials.
Microalgae diets for landbased aquaculture of the cockle Cerastoderma edule: impacts of dietary fatty acids on growth
Reis Batista, I.C. dos - \ 2015
University. Promotor(en): Aad Smaal, co-promotor(en): Johan Kamermans; Rene Wijffels. - Wageningen : Wageningen University - ISBN 9789462575875 - 132
schaaldieren - schaal- en schelpdierenteelt - algen - voedering - voersamenstelling - diëten - vetzuren - groei - tanks - plassen - aquacultuur - shellfish - shellfish culture - algae - feeding - feed formulation - diets - fatty acids - growth - ponds - aquaculture

Land-based shellfish culture as a part of a multi-trophic aquaculture systems has yet to be implemented in Europe. Recently the pilot project Zeeuwse Tong (The Netherlands) evaluated the feasibility of a system of fish (Dover sole), ragworms, phytoplankton and bivalves. This thesis focused on the dietary fatty acids impact on growth, survival and fatty acid composition of juveniles (shell length >5mm) of the common cockle Cerastoderma edule, for land-based culture.

Dietary fatty acids were chosen as the main nutritional research subject given the existing literature indicating their importance for reproduction, and growth and survival of larvae, post-larvae, spat and seed of most bivalves. However, since grow-out of juvenile cockles in land-based aquaculture is not common, no information is available on the dietary fatty acid requirements of juveniles. To determine if the presence of specific fatty acids is more important for growth and survival of juvenile cockles than the total amount of dietary fatty acids supplied, least cost linear programming was used to design live microalgae diets. Monocultures of indigenous algae were grown under controlled conditions and sampled to determine their quality in terms of dry weight, organic matter, lipid and fatty acids composition. These differences in biochemical composition of the microalgae were used in a least-cost programming software, and allowed the formulation of three diets with different fatty acid contents, but similar dry weight, organic matter, lipid and total fatty acid content. The formulated diets were then used to determine the importance of dietary fatty acids for growth, survival and fatty acid composition of juvenile cockles (Cerastoderma edule). Juvenile cockles (6.24±0.04 mm) were constantly fed live microalgal diets with similar lipid, organic matter and total fatty acid contents but different individual fatty acid concentrations: high-EPA, no-DHA and low-ARA diets. Growth was positively affected by high-EPA and low-ARA diets, whereas no significant growth was observed for the no-DHA diet. However, high mortality of cockles fed no-DHA diet and the low absorption efficiency and clearance rate of this diet indicate that this diet is unsuitable for juvenile cockles. In balanced diets with EPA and DHA, lower concentrations of ARA did not limit growth. The combination of EPA and DHA in a live microalgae diet was beneficial for the growth and survival of juvenile cockles, but no conclusion on the importance of supplying only EPA could be made. To address this, an additional growth experiment was designed. Growth and fatty acid profiles of juveniles cockles were determined after 28 days of feeding diets:1) with EPA 2) with DHA; 3) with EPA and DHA from a mixture of a diatom with a green algae; 4) with EPA and DHA from a mixture of the two green algae and 5) without long-chain (>C20) fatty acids. Significantly higher growth rate was observed with the treatment rich in EPA, while the lowest growth rates were found in without EPA. These results indicate that EPA is necessary for the short-term growth of cockles. Moreover, the fatty acid profile of the polar lipids confirmed that, like most marine invertebrates, juvenile C. edule are not able to biosynthesize EPA and DHA from 18:3n-3 but are capable of biosynthesizing diene and triene NMI fatty acids. The occurrence of the NMI fatty acids was diet related, thus refuting the possibility of production of NMI as replacement for EPA and DHA.

Furthermore, in order to develop land-based culture of cockles it is crucial to have a supply of high quality live microalgal diets produced with minimum effort. Therefore, the use of simplified microalgae media, with different nitrogen sources (nitrate or ammonium) and molar N:P ratio, phosphorus, silica, iron, manganese and vitamins were also investigated. Chaetoceros muelleri, a marine diatom that was chosen given its robustness and quality as food for juvenile cockles, reacted positively to all simplified media. At the exponential phase, all cultures had reached similar cellular concentrations and dry weight productions. Cultures grown on ammonium media had a longer cultivation period, 20 days. Considering dry-weight production, culture duration, nutrient efficiency and lipid composition, the simplified media containing ammonium, phosphorus, silica, iron, manganese and vitamins proved to be a viable choice for batch culture of C. muelleri. The choice between these two media depends on the final purpose of the microalgae cultures and whether lipid contents (NH49:1), dry weight biomass (NH425:1) or nitrogen input and output (NH49:1) are more important.

In this thesis it was demonstrated that mono-algal diets with high EPA, as well as mixed live microalgae diets with high EPA and DHA contents proved to be suitable diets for C. edule juveniles. In addition, a positive relation between growth and the amount fed was found. The growth rates of the cultured cockles in this thesis are in accordance with the rates observed under natural conditions. The use of the simplified microalgae culture medium tested represents a significant decrease in the cost and preparation of the medium, as well as longer production and harvest periods, while maintaining microalgae quality. These results indicate that land-based aquaculture of cockles and microalgae is therefore a promising venture, with potential for expansion.

Multi-level analysis of the impact of temperature and light on tomato fruit growth
Okello, R.C.O. - \ 2015
University. Promotor(en): Paul Struik; Leo Marcelis, co-promotor(en): Ep Heuvelink; Pieter de Visser. - Wageningen : Wageningen University - ISBN 9789462571648 - 166
solanum lycopersicum - tomaten - groei - temperatuur - licht - plantenfysiologie - celdeling - cyclinen - genexpressie - tomatoes - growth - temperature - light - plant physiology - cell division - cyclins - gene expression

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.

Minerals in fish: does the source matter?
Antony Jesu Prabhu, P. - \ 2015
University. Promotor(en): Johan Verreth, co-promotor(en): C. Mariojouls; S. Kaushik; Johan Schrama. - Wageningen : Wageningen University - ISBN 9789462574809 - 267
visvoeding - mineralen - voedingsstoffenbehoeften - mineraalmetabolisme - voer - minerale supplementen - groei - lichaamssamenstelling - visteelt - aquacultuur - fish feeding - minerals - nutrient requirements - mineral metabolism - feeds - mineral supplements - growth - body composition - fish culture - aquaculture
Investigation of a growth model incorporating density dependence for the mackerel management plan simulations
Brunel, T.P.A. - \ 2015
IJmuiden : IMARES (Report / IMARES Wageningen UR C134/15) - 12
trachurus - density dependence - growth - models - simulation models - fish culture - dichtheidsafhankelijkheid - groei - modellen - simulatiemodellen - visteelt
This report presents a framework to model density dependent growth for the North East Atlantic mackerel. The model used is the classical von Bertalanffy equation, but modified so that growth is reduced when stock size increases. The model developed was able to reproduce quite closely the trends in the observed historical weight-at-age data. This framework can therefore be incorporated in the simulation tool used for the mackerel management plan evaluation. But since the actual mechanisms through which stock size affects growth are not identified, density dependent growth should not be used as the base case scenario in simulations. However it can be used in sensitivity tests which can be conducted to assess the potential impact of density dependent growth on simulation output, such as Fmsy.
Using natural variation to unravel the dynamic regulation of plant performance in diverse environments
Molenaar, J.A. - \ 2015
University. Promotor(en): Harro Bouwmeester; Joost Keurentjes, co-promotor(en): Dick Vreugdenhil. - Wageningen : Wageningen University - ISBN 9789462573444 - 186
planten - genomen - loci voor kwantitatief kenmerk - warmtestress - genetische kartering - groei - droogte - plantengenetica - plantenfysiologie - plants - genomes - quantitative trait loci - heat stress - genetic mapping - growth - drought - plant genetics - plant physiology

Summary

All plants are able to respond to changes in their environment by adjusting their morphology and metabolism, but large differences are observed in the effectiveness of these responses in the light of plant fitness. Between and within species large differences are observed in plant responses to drought, heat and other abiotic stresses. This natural variation is partly due to variation in the genetic composition of individuals. Within-species variation can be used to identify and study genes involved in the genetic regulation of plant performance.

Growth of the world population will, in the coming years, lead to an increased demand for food, feed and other natural products. In addition, extreme weather conditions with, amongst others, more and prolonged periods of drought and heat are expected to occur due to climate change. Therefore breeders are challenged to produce stress tolerant cultivars with improved yield under sub-optimal conditions. Knowledge about the mechanisms and genes that underlie tolerance to drought, heat and other abiotic stresses will ease this challenge.

The aim of this thesis was to identify and study the role of genes that are underlying natural variation in plant performance under drought, salt and heat stress. To reach this goal a genome wide association (GWA) mapping approach was taken in the model species Arabidopsis thaliana. A population of 350 natural accessions of Arabidopsis, genotyped with 215k SNPs, was grown under control and several stress conditions and plant performance was evaluated by phenotyping one or several plant traits per environment. Genes located in the genomic regions that were significantly associated with plant performance, were studied in more detail.

Plant performance was first evaluated upon osmotic stress (Chapter 2). This treatment resulted not only in a reduced plant size, but also caused the colour of the rosette leaves to change from green to purple-red due to anthocyanin accumulation. The latter was visually quantified and subsequent GWA mapping revealed that a large part of the variation in anthocyanin accumulation could be explained by a small genomic region on chromosome 1. The analysis of re-sequence data allowed us to associate the second most frequent allele of MYB90 with higher anthocyanin accumulation and to identify the causal SNP. Interestingly MYB75, a close relative of MYB90, was not identified by GWA mapping, although causal sequence variation of this gene for anthocyanin accumulation was identified in the Cvi x Ler and Ler x Eri-1 RIL populations. Re-sequence data revealed that one allele of MYB75 was dominating the population and that the MYB75 alleles of Cvi and Ler were both rare, explaining the lack of association at this locus in GWA mapping. For MYB90, two alleles were present in a substantial part of the population, suggesting balancing selection between them.

Next, the natural population was exposed to short-term heat stress during flowering (Chapter 3). This short-term stress has a large impact on seed set, while it hardly affects the vegetative tissues. Natural variation for tolerance against the effect of heat on seed set was evaluated by measuring the length of all siliques along the inflorescence in both heat-treated and control plants. Because the flower that opened during the treatment was tagged, we could analyse the heat response for several developmental stages separately. GWA mapping revealed that the heat response before and after anthesis involved different genes. For the heat response before anthesis strong evidence was gained that FLC, a flowering time regulator and QUL2, a gene suggested to play a role in vascular tissue development, were causal for two strong associations.

Furthermore, the impact of moderate drought on plant performance was evaluated in the plant phenotyping platform PHENOPSIS. Homogeneous drought was assured by tight regulation of climate cell conditions and the robotic weighing and watering of the pots twice a day. Because plant growth is a dynamic trait it was monitored over time by top-view imaging under both moderate drought and control conditions (Chapter 4 and 5). To characterise growth it was modelled with an exponential function. GWA mapping of temporal growth data resulted in the detection of time-dependent QTLs whereas mapping of model parameters resulted in another set of QTLs related to the entire growth period. Most of these QTLs would not have been identified if plant size had only been determined on a single day. For the QTLs detected under control conditions eight candidate genes with a growth-related mutant or overexpression phenotype were identified (Chapter 4). Genes in the support window of the drought-QTLs were prioritized based on previously reported gene expression data (Chapter 5). Additional validation experiments are needed to confirm causality of the candidate genes.

Next, to search for genes that determine plant size across many environments, biomass accumulation in the natural population was determined in 25 different environments (Chapter 6). Joint analysis of these data by multi-environment GWA mapping resulted in the detection of 106 strongly associated SNPs with significant effects in 7 to 16 environments. Several genes involved in starch metabolism, leaf size control and flowering time determination were located in close proximity of the associated SNPs. Two genes, RPM1 and ACD6, were located in close proximity of SNPs with significant GxE effects. For both genes, alleles have been identified that increase resistance to bacterial infection, but that reduce biomass accumulation. The sign of the allelic effect is therefore dependent on the environmental conditions. Whole genome predictions revealed that most of the GxE interactions observed at the phenotypic level were not the consequence of strong associations with strong QxE effects, but of moderate and weak associations with weak QxE effects.

Finally, in Chapter 7 I discuss the usefulness of GWA mapping in the identification of genes underlying natural variation in plant performance under drought, heat stress and a number of other environments. Strong associations were observed for both environment-specific as well as common plant performance regulators. Some choices in phenotyping and experimental design were crucial for our success, like evaluation of plant performance over time and simplification of the quantification of the phenotype. It is suggested that follow-up work should focus on the functional characterization of the causal genes, because such analyses would be helpful to identify pathways in which the causal genes are involved and to understand why sequence variation results in changes at the phenotype level. Although translation of the findings to applications in crops is challenging, this thesis contributes to the understanding of the genetic regulation of stress response and therefore will likely contribute to the development of stress tolerant and stable yielding crops.

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