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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Perspectives of children orphaned by HIV/AIDS on ecology and gathering of wild orchids in Tanzania
Challe, Joyce F.X. ; Struik, Paul C. ; Price, Lisa L. - \ 2018
- p. 223 - 243.
children orphaned by HIV/AIDS - edible orchids - gathering knowledge acquisition - local ecological knowledge - orchid conservation

Orchid gathering in the Southern Highlands of Tanzania became an income generating strategy for HIV/AIDS-affected households, particularly for children orphaned by HIV/AIDS. Being orphaned might have implications for children's local ecological knowledge leading to indiscriminate harvesting of both preferred and non-preferred orchids. Using qualitative and quantitative mixed methods, we assessed the knowledge of wild orchid species among gatherers in four categories: Children orphaned by HIV/AIDS, children not affected by HIV/AIDS, HIV/AIDS-affected adults, and non-HIV/AIDS-affected adults. Data collection took place from February 2006 until February 2007. More than 70% of the children orphaned by HIV/AIDS relied on tuber taste and texture to distinguish preferred and non-preferred species. HIV/AIDS-affected adults were competent at using orchid morphology to distinguish preferred from non-preferred orchid species. Gatherers stated preferred orchid species were primarily found in restricted areas, and non-preferred species were widespread. Cramer's V analysis revealed an association between the HIV/AIDS status of a gatherer and the gatherer's views on the conservation status of preferred and non-preferred species. Gatherers perceived non-preferred species as having higher natural regeneration potential than preferred species. Cramer's V analysis also showed a difference in gathering knowledge acquisition between HIV/AIDS-affected double orphans who emigrated from urban settings, and those residing in their natal rural village under guardian care. Both types of orphans relied primarily on other children for gathering knowledge, but those with guardians also gleaned knowledge from guardians. Across categories, children also gained knowledge from middlemen, who buy and resell the preferred orchids.

Reducing damping-off problems in eggplant (Solanum melongena L.) : A participatory testing of nursery management in Bangladesh
Nahar, Naznin ; Islam, Md Rashidul ; Uddin, Mohammad Mahir ; Jong, Peter de; Struik, Paul C. ; Stomph, Tjeerd Jan - \ 2018
Crop Protection 112 (2018). - ISSN 0261-2194 - p. 177 - 186.
Damping-off - Healthy seedlings - Integrated pest management - Seed treatment - Soil treatment - Source of pathogens

Eggplant seedling production in homestead nurseries of farmers in Jamalpur (Bangladesh) is greatly compromised by damping-off. Therefore, farmers often do not have enough seedlings to transplant. Effective treatments of soil and seed to reduce disease pressure in the nurseries are available but little is known on the relative contributions of soil-borne and seed-borne pathogens to damping-off and on how nursery management can integrate management options under farmers’ conditions. A 2-year nursery study was conducted in consecutive seasons, jointly with farmers and using farmers’ preserved seed and farmers’ nurseries subject to damping-off problems. Year 1 involved a single nursery, Year 2 nine nurseries. The following treatments were tested: Trichoderma harzianum as soil amendment combined with seed treatment using either hot water or Carbendazim and farmers’ conventional practice: curative spraying after appearance of damping-off. In Year 1, a control (no intervention) treatment was also included. Emergence of seedlings, incidence of damping-off, seedling performance variables and farmers’ appreciation of seedling vigour were recorded. Soil treatment with T. harzianum combined with seed treatment with hot water increased seedling emergence and produced 25–64 percentage points more healthy seedlings than farmers’ conventional practice. This combined treatment also improved seedling performance (height, root length, lateral root development), and reduced stem girdling, a symptom associated with disease infection of transplants. To determine the contributions of nursery soil and farmers’ seed to damping-off, blotter and in vitro studies in the laboratory and tray studies in a screen house were performed. Soil proved to be the major pathogen source and treating nursery soil with T. harzianum had the largest positive effect on seedling performance, both reducing damping-off and enhancing seedling growth.

Roles of nitrogen and cytokinin signals in root and shoot communications in maximizing of plant productivity and their agronomic applications
Gu, Junfei ; Li, Zhikang ; Mao, Yiqi ; Struik, Paul C. ; Zhang, Hao ; Liu, Lijun ; Wang, Zhiqin ; Yang, Jianchang - \ 2018
Plant Science 274 (2018). - ISSN 0168-9452 - p. 320 - 331.
Cytokinin transport - Long-distance signaling - Nitrogen status - Root - shoot relationship - Source-sink relationship

Nitrogen is an essential, often limiting, factor in plant growth and development. To regulate growth under limited nitrogen supply, plants sense the internal and external nitrogen status, and coordinate various metabolic processes and developmental programs accordingly. This coordination requires the transmission of various signaling molecules that move across the entire plant. Cytokinins, phytohormones derived from adenine and synthesized in various parts of the plant, are considered major local and long-distance messengers. Cytokinin metabolism and signaling are closely associated with nitrogen availability. They are systemically transported via the vasculature from plant roots to shoots, and vice versa, thereby coordinating shoot and root development. Tight linkage exists between the nitrogen signaling network and cytokinins during diverse developmental and physiological processes. However, the cytokinin-nitrogen interactions and the communication systems involved in sensing rhizospheric nitrogen status and in regulating canopy development remain obscure. We review current knowledge on cytokinin biosynthesis, transport and signaling, nitrogen acquisition, metabolism and signaling, and their interactive roles in regulating root-shoot morphological and physiological characteristics. We also discuss the role of spatio-temporal regulation of cytokinins in enhancing beneficial crop traits of yield and nitrogen use efficiency.

Calibration and validation of the AquaCrop model for repeatedly harvested leafy vegetables grown under different irrigation regimes
Nyathi, M.K. ; Halsema, G.E. van; Annandale, J.G. ; Struik, P.C. - \ 2018
Agricultural Water Management 208 (2018). - ISSN 0378-3774 - p. 107 - 119.
Biomass - Crop modelling - Evapotranspiration, indigenous leafy vegetables - Water productivity

Traditional leafy vegetables (TLVs’) are vegetables that were introduced in an area a long time ago, where they adapted to local conditions and became part of the local culture. In Sub-Saharan Africa, the use of TLVs’ as a nutrient dense alternative food source to combat micronutrient deficiency of rural resource-poor households (RRPHs), has gained attention in debates on food and nutrition security. However, TLVs’ are underutilised because of lack of information on their yield response to water and fertiliser. To better assess TLVs’ yield response to water stress, the AquaCrop model was calibrated (using 2013/14 data) and validated (using 2014/15 data) for three repeatedly harvested leafy vegetables [Amaranthus cruentus (Amaranth), Cleome gynandra (Spider flower), and Beta vulgaris (Swiss chard)] in Pretoria, South Africa. Experiments were conducted during two consecutive seasons, in which the selected leafy vegetables were subjected to two irrigation regimes; well-watered (I30) and severe water stress (I80). Measured parameters were canopy cover (CC), soil water content (SWC), aboveground biomass (AGB), actual evapotranspiration (ETa), and water productivity (WP). Statistical indicators [root mean square error (RMSE), RMSE-standard deviation ratio (RSR), R2, and relative deviation] showed good fit between measured and simulated (0.60 < R2 < 0.99, 0.94 < RMSE < 5.44, and 0.04 < RSR < 0.79) values for the well-watered treatment. However, the fit was not as good for the water-stressed treatment for CC, SWC, ETa and WP. Nevertheless, the model simulated the selected parameters satisfactorily. These results revealed that there was a clear difference between transpiration water productivity (WPTr) for C4 crops (Amaranth and Spider flower) and a C3 crop (Swiss chard); WPTr for the C4 crops ranged from 4.61 to 6.86 kg m−3, whereas for the C3 crop, WPTr ranged from 3.11 to 4.43 kg m−3. It is a challenge to simulate yield response of repeatedly harvested leafy vegetables because the model cannot run sequential harvests at one time; therefore, each harvest needs to be simulated separately, making it cumbersome. To design sustainable food production systems that are health-driven and inclusive of RRPHs, we recommend that more vegetables (including traditional vegetables) should be included in the model database, and that sequential harvesting be facilitated.

Plant responses to elevated CO2 and the need to go deeper
Struik, Paul - \ 2018
RE: Unexpected results of a long-term experiment do not challenge the current paradigm of C3 vs C4 response to CO2
Struik, Paul - \ 2018
Pollen germination and in vivo fertilization in response to high-temperature during flowering in hybrid and inbred rice
Shi, Wanju ; Li, Xiang ; Schmidt, Ralf C. ; Struik, Paul C. ; Yin, Xinyou ; Jagadish, S.V.K. - \ 2018
Plant, Cell & Environment 41 (2018)6. - ISSN 0140-7791 - p. 1287 - 1297.
fertilization - flowering - high day-time temperature - high night-time temperature - in vivo pollen germination - rice

High-temperature during flowering in rice causes spikelet sterility and is a major threat to rice productivity in tropical and subtropical regions, where hybrid rice development is increasingly contributing to sustain food security. However, the sensitivity of hybrids to increasing temperature and physiological responses in terms of dynamic fertilization processes is unknown. To address these questions, several promising hybrids and inbreds were exposed to control temperature and high day-time temperature (HDT) in Experiment 1, and hybrids having contrasting heat tolerance were selected for Experiment 2 for further physiological investigation under HDT and high-night-time-temperature treatments. The day-time temperature played a dominant role in determining spikelet fertility compared with the night-time temperature. HDT significantly induced spikelet sterility in tested hybrids, and hybrids had higher heat susceptibility than the high-yielding inbred varieties. Poor pollen germination was strongly associated with sterility under high-temperature. Our novel observations capturing the series of dynamic fertilization processes demonstrated that pollen tubes not reaching the viable embryo sac was the major cause for spikelet sterility under heat exposure. Our findings highlight the urgent need to improve heat tolerance in hybrids and incorporating early-morning flowering as a promising trait for mitigating HDT stress impact at flowering.

Planten reageren onverwacht op extra kooldioxide
Struik, Paul - \ 2018

Planten groeien beter als de hoeveelheid koolstofdioxide in de atmosfeer stijgt, zo is de gedachte. Maar op lange termijn reageert het merendeel van de planten niet op extra CO2, blijkt nu uit onderzoek aan de universiteit van Minnesota.

Planten groeien beter als de hoeveelheid koolstofdioxide in de atmosfeer stijgt, zo is de gedachte. Maar op lange termijn reageert het merendeel van de planten niet op extra CO2, blijkt nu uit onderzoek aan de universiteit van Minnesota.

Hap rijst wordt straks een slappe hap door toename van CO2 in atmosfeer
Struik, Paul - \ 2018

De voedingswaarde van rijst, een belangrijke voedingsbron voor ruim 2 miljard mensen in de wereld, zal in de loop van deze eeuw minder worden door het toenemen van de concentraties CO2 in de atmosfeer. Dat kan nadelige gevolgen hebben voor de gezondheid van degenen die voor hun voeding afhankelijk zijn van dit gewas, schrijven onderzoekers in Science Advances.

The energy budget in C4 photosynthesis : insights from a cell-type-specific electron transport model
Yin, Xinyou ; Struik, Paul C. - \ 2018
New Phytologist 218 (2018)3. - ISSN 0028-646X - p. 986 - 998.
bioenergetics - C modelling - C photosynthesis - cell type - cyclic electron transport - energy balance - mixed decarboxylation - quantum yield
Extra ATP required in C4 photosynthesis for the CO2-concentrating mechanism probably comes from cyclic electron transport (CET). As metabolic ATP : NADPH requirements in mesophyll (M) and bundle-sheath (BS) cells differ among C4 subtypes, the subtypes may differ in the extent to which CET operates in these cells. We present an analytical model for cell-type-specific CET and linear electron transport. Modelled NADPH and ATP production were compared with requirements. For malic-enzyme (ME) subtypes, c. 50% of electron flux is CET, occurring predominantly in BS cells for standard NADP-ME species, but in a ratio of c. 6 : 4 in BS : M cells for NAD-ME species. Some C4 acids follow a secondary decarboxylation route, which is obligatory, in the form of ‘aspartate-malate’, for the NADP-ME subtype, but facultative, in the form of phosphoenolpyruvate-carboxykinase (PEP-CK), for the NAD-ME subtype. The percentage for secondary decarboxylation is c. 25% and that for 3-phosphoglycerate reduction in BS cells is c. 40%; but these values vary with species. The ‘pure’ PEP-CK type is unrealistic because its is impossible to fulfil ATP : NADPH requirements in BS cells. The standard PEP-CK subtype requires negligible CET, and thus has the highest intrinsic quantum yields and deserves further studies in the context of improving canopy productivity.
Bringing genetics and biochemistry to crop modelling, and vice versa
Yin, Xinyou ; Linden, Gerard van der; Struik, Paul C. - \ 2018
European Journal of Agronomy (2018). - ISSN 1161-0301
Complex phenotype - Crop improvement - G×E - Interdisciplinary approach - Systems modelling
Genetics, biochemistry, and crop modelling are independently evolving disciplines; however, they complement each other in addressing some of the important challenges that crop science faces. One of these challenges is to improve our understanding of crop genotype-to-phenotype relationships in order to assist the development of high-yielding and resource-use efficient genotypes that can adapt to particular (future) target environments. Crop models are successful in predicting the impact of environmental changes on crop productivity. However, when critically tested against real experimental data, crop models have been shown to be less successful in predicting the impact of genotypic variation and genotype-by-environment interactions exhibited in genetic populations. In order to better model gene-trait-crop performance relationships in support of breeding and genetic engineering programmes, crop models need to be improved in terms of both model parameters and model structure. We argue that integration of quantitative genetics and photosynthesis biochemistry with modelling is a first step towards a new generation of improved crop models. With genetic information and biochemical understanding incorporated, crop modelling also generates new insights and concepts that can in turn be used to improve genetic analysis and biochemical modelling of complex traits. This modelling-genetics-biochemistry framework (the MGB triangle framework) stresses the synergy among the three disciplines, and may best serve as a step to achieve the ultimate goal of the more broadly framed "Crop Systems Biology" approach to improve efficiency of both classical breeding and genetic engineering programmes.
Diagnosis of management of bacterial wilt and late blight in potato in Ethiopia : A systems thinking perspective
Damtew, E. ; Tafesse, Shiferaw ; Lie, R. ; Mierlo, B. van; Lemaga, B. ; Sharma, K. ; Struik, P.C. ; Leeuwis, C. - \ 2018
NJAS Wageningen Journal of Life Sciences (2018). - ISSN 1573-5214
Bacterial wilt - Complex problems - Disease management - Late blight - Potato - Systems thinking
Potato is one of the most important food crops for smallholder farmers in the Ethiopian highlands. Diseases, particularly bacterial wilt (caused by Ralstonia solanacearum) and late blight (caused by Phytophthora infestans), are among the major constraints of potato production, despite continuous efforts to control them. Bacterial wilt and late blight are complex problems with multiple technical and institutional features, involving multiple actors with different perceptions and understanding, not only of the problem but also of possible solutions. Appreciating such complexity, this study adopted a systems thinking perspective. It aimed to explore actors’ understanding of the complex problem situation and its implication for the management of the diseases at a collective level. Using a multi-stakeholder workshop and in-depth interviews, a qualitative study was conducted with actors that are directly or indirectly involved in the management of the two diseases. Results showed that actors essentially overlooked key systemic problems in the management of the two diseases. This is mainly reflected in actors’ tendency to give event-level responses, shift responsibilities and engage in a mutual blaming to the problem of bacterial wilt and late blight. Lack of a preventive disease management culture, limited recognition of interdependencies among activities of actors, power inequalities, and top-down and linear approaches in information and knowledge sharing are identified as key structural problems that are underrated by the actors. We contend that the most appropriate way forward towards the management of both diseases is designing and implementing management strategies that, on the one hand, are preventive of disease epidemics, and, on the other hand, foster horizontal information sharing, learning and collective action among the local actors in the system. Digital platforms, particularly mobile-based technologies, can play a role in catalyzing new forms of information sharing, broader learning, and collaboration among farmers and local actors.
Farmers’ knowledge and practices of potato disease management in Ethiopia
Tafesse, Shiferaw ; Damtew, E. ; Mierlo, B. van; Lie, R. ; Lemaga, B. ; Sharma, K. ; Leeuwis, C. ; Struik, P.C. - \ 2018
NJAS Wageningen Journal of Life Sciences (2018). - ISSN 1573-5214
Bacterial wilt - Disease management - Farmers’ knowledge - Farmers’ practices - Late blight - Phytophthora infestans - Potato diseases - Ralstonia solanacearum
Effective management of potato diseases such as bacterial wilt and late blight depends to a large extent on farmers’ knowledge of the diseases as well as on the integration of recommended management methods in their daily practices. Late blight has continued to be a dominant potato disease for many decades in Ethiopia, whereas bacterial wilt has emerged more recently with a devastating impact on the country's potato production systems. A survey of 261 randomly selected farmers was carried out in three major potato growing districts in the central highlands of Ethiopia to examine farmers’ knowledge and management practices of the two diseases, and to analyze the role of relevant knowledge in their practices. Considering their different characteristics, three groups of farmers were distinguished: producers of quality declared seed, producers of normal seed and producers of ware. The study shed light on the vital role the lack of knowledge about the diseases plays in shaping farmers’ daily potato production practices. Most farmers could recognize symptoms of the diseases on infected leaves and stems. However, they had very limited knowledge of the diseases including their causal agents, spreading mechanisms, and effective management methods, although they knew a little bit more about late blight than about bacterial wilt. Therefore, to effectively manage the diseases, farmers need to learn about the diseases and how to manage them in their local context applying a feasible combination of management options through a community-based approach. The effectivity of such an approach could be enhanced by stipulating operational standards in bylaws and through continuous monitoring of changes in farmers’ practices and environmental monitoring for disease occurrence by leveraging an interactive mobile-based platform.
Agronomy and photosynthesis physiology of hemp (Cannabis sativa L.)
Tang, Kailei - \ 2018
University. Promotor(en): Paul Struik, co-promotor(en): Xinyou Yin; S. Amaducci. - Wageningen : Wageningen University - ISBN 9789463438841 - 174

Hemp (Cannabis sativa L.) is a sustainable high-yielding crop that delivers valuable fibres, seeds and psychoactive substances. However, there is a lack of field experimental data on the cultivation of hemp because its production was largely abandoned in the last century. Hemp is now considered as an ideal crop to produce innovative biomaterials, and in particular, the dual-purpose hemp production (fibre + seed) is now the norm in European countries, driven by the shift of a rapidly expanding market for hemp seeds coupled with lower quality fibre requirements for innovative biomaterials. This study brought new information on the agronomy and photosynthesis physiology for the resurging production of hemp, particularly for dual-purpose production in Europe.

The effects of important agronomic factors, i.e. cultivar, planting density, and nitrogen fertilization, on the performance of the hemp crop were investigated under contrasting European environments. Based on the experimental data, for dual-purpose hemp production, a planting density of 90–150 plants m-2 is recommended for a monoecious cultivar that gives a long vegetative phase while leaving enough time for seed growth. A nitrogen fertilization rate of 60 kg N ha-1 was generally sufficient in the tested environments whereas further optimization of nitrogen fertilization requires accurate and precise assessment of plant nutritional status. To facilitate assessing plant nutritional status, a critical nitrogen dilution curve was determined for hemp.

The responses of leaf photosynthesis to nitrogen content and temperature were quantified using a biochemical model of C3 leaf photosynthesis, based on a complete set of photosynthetic measurements for hemp leaves. Then, by combining measurements and modelling, an upscaling was made from the leaf to the canopy level to analyse hemp’s photosynthetic nitrogen-use efficiency (NUE) and water-use efficiency (WUE) in response to water and nitrogen supply. The effect of nitrogen supply level on hemp’s NUE and WUE was largely determined by its effect on canopy size or leaf area index (LAI). The effect of short-term water stress on WUE and NUE was reflected in the stomatal regulation, whereas long-term water stress enhanced leaf senescence, reduced LAI but retained total canopy nitrogen content, and thus resulted in a further increase in WUE.

Findings in this thesis provided an improved understanding of the agronomy and photosynthesis physiology of hemp, particularly in relation to the dual-purpose production of hemp in Europe. Such understanding not only provides additional evidence that hemp can be grown as a sustainable crop over a wide range of climatic and agronomic conditions, but also provides essential information for parameterizing crop growth models. Prospects for further research were discussed in view of using the findings in this thesis in combination with a crop growth model to develop strategies for optimization of hemp cultivation and breeding.

Carbon footprinting of potato (Solanum tuberosum L.) production systems in Zimbabwe
Svubure, O. ; Struik, P.C. ; Haverkort, A.J. ; Steyn, J.M. - \ 2018
Outlook on Agriculture 47 (2018)1. - ISSN 0030-7270 - p. 3 - 10.
benchmarking - climate change mitigation - Cool Farm Tool-Potato - Greenhouse gas emission
Agriculture contributes significantly to the global greenhouse gas (GHG) emissions. Farmers need to fine-tune agricultural practices to balance the trade-offs between increasing productivity in order to feed a growing population and lowering GHG emissions to mitigate climate change and its impact on agriculture. We conducted a survey on the major cultural practices in four potato production systems in Zimbabwe, namely large-scale commercial, communal area, A1 and A2 resettlement production systems. The resettlement production systems were formed from the radical Fast Track Land Reform Programme initiated in 2000, which changed the landscape of commercial agriculture in Zimbabwe. We used survey data as an input into the ‘Cool Farm Tool – Potato’ model. The model calculates the contributions of various production operations to total GHG emission. Experienced growers were targeted. The average carbon footprint calculated was 251 kg CO2 eq./t potato harvested, ranging from 216 kg CO2 eq./t to 286 kg CO2 eq./t in the communal area and A2 resettlement production systems, respectively. The major drivers of the GHG emissions were fertilizer production and soil-related field emissions, which together accounted for on average 56% of the total emissions across all production systems. Although mitigation options were not assessed, the model outputs the factors/farm operations and their respective emission estimates allowing growers to choose the inputs and operations to reduce their carbon footprint. Opportunities for benchmarking as an incentive to improve performance exist given the large variation in GHG emission between individual growers.
Physiological and genetic dissection of rice tolerance to water-deficit stress
Kadam, Niteen Narharirao - \ 2018
University. Promotor(en): Paul Struik, co-promotor(en): Xinyou Yin. - Wageningen : Wageningen University - ISBN 9789463437400 - 242

Rice (Oryza sativa L.) is the world's most important staple food crop, especially in Asia. As a semi-aquatic crop species, water-scarcity and increasing severity of water-deficit stress owing to climate change, are a major threat to sustaining irrigated rice production. Improving the rice adaptation to water-deficit is, therefore, a primary breeding target. The main goal of this dissertation is to study the morphological, anatomical, physiological and genetic basis for responses of a rice plant to water-deficit stress.

To give leads into how water-deficit tolerant rice should behave, a comparative study were conducted, whereby representative rice genotypes was compared at the same moisture stress during the vegetative stage with genotypes of wheat, a dryland cereal wheat (Triticum aestivum L.) known to be more tolerant to water-deficit than rice. Under-water-deficit, rice genotypes (IR64 & Apo) developed thinner roots allowing rapid water-acquisition, whereas wheat followed a water-conserving strategy through developing thicker leaves and roots, and moderate tillering. Root anatomy such as root diameter, xylem and stele diameter and xylem number were more plastic in wheat than in rice under-water-deficit.

The methodology and findings from those representative genotypes were then projected to a diverse panel of nearly 300 rice genotypes. Such a panel was previously constructed by the International Rice Research Institute as a potential means of discovery of novel beneficial alleles for diverse phenotypic traits and their plasticity, with 46K high-quality single nucleotide polymorphisms (SNPs). A genome-wide association study (GWAS) was undertaken to identify the genomic regions regulating the morphological, physiological and root anatomical traits in rice, based on a large-scale greenhouse phenotyping of these traits. The genetic basis of these traits was different in control and water-deficit stress (strong quantitative trait loci [QTL] × environment interaction), in line with novel loci detected for the plasticity of traits. Key a priori candidate genes near to these genetic loci were also identified.

Rice grain yield is strongly affected by water-deficit stress coinciding with sensitive reproductive stage. Strong genotypic variability for grain yield as well as yield components and related traits were observed in the same rice indica diversity panel, under control and reproductive stage water-deficit stress in field conditions across two years. The GWAS analysis identified the core loci of rice genome governing the grain yield and related traits. Most of the genomic loci were specific to treatment and year, indicating strong QTL × environment interactions.

To enable GWAS findings to be used for better designing of genotypes by breeding, an existing process-based crop model GECROS was used in a case study, where grain yield of the same indica diversity panel (267 rice genotypes) from the control treatment in one season was dissected into eight physiological parameters. Some parameters had a stronger effect on grain yield than other parameters. Using these parameters, the model showed the ability to predict the genotypic variation of rice diversity panel for grain yield under different field conditions. Further, the GWAS analysis was extended to model-input parameters on randomly chosen 213 genotypes as a training dataset. The SNP-based estimates of parameter values calculated from the additive allelic effect of the loci were used as input to the crop model GECROS. Although the SNP-based modelling approach demonstrated the ability to predict the genotypic variation in training datasets under different environments, the prediction accuracy was lower in the remaining 54 genotypes used as a testing dataset. In addition, the prediction accuracy of grain yield was also lower using either parameter or SNP-based GECROS model in completely new season. However, the model-based sensitivity analysis effectively identified the different SNPs between control and water-deficit environments. Virtual ideotypes designed based on pyramiding the SNPs identified by modelling had a higher yield than those based on SNPs for yield per se.

In silico analysis of the regulation of the photosynthetic electron transport chain in C3 plants
Morales Sierra, A. ; Yin, Xinyou ; Harbinson, Jeremy ; Driever, Steven Michiel ; Molenaar, Jaap ; Kramer, David M. ; Struik, Paul - \ 2018
Plant Physiology 176 (2018)2. - ISSN 0032-0889 - p. 1247 - 1261.
We present a new simulation model of the reactions in the photosynthetic electron transport chain of C3 species. We show that including recent insights about the regulation of the thylakoid proton motive force, ATP/NADPH balancing mechanisms (cyclic and non-cyclic alternative electron transport), and regulation of Rubisco activity, leads to emergent behaviors that may affect the operation and regulation of photosynthesis under different dynamic environmental conditions. The model was parameterized with experimental results in the literature, with a focus on Arabidopsis thaliana. A dataset was constructed from multiple sources, including measurements of steady-state and dynamic gas exchange, chlorophyll fluorescence and absorbance spectroscopy under different light intensities and CO2. This dataset was used to test predictions of the model under different experimental conditions. Simulations suggested that there are strong interactions between cyclic and non-cyclic alternative electron transport and that an excess capacity for alternative electron transport is required to ensure adequate redox state and lumen pH. Furthermore, the model predicted that, under specific conditions, reduction of ferredoxin by plastoquinol was possible, especially after a rapid increase in light intensity. Further analysis also revealed that the relationship between ATP synthesis and proton motive force was highly regulated by the concentrations of ATP and ADP, and this facilitated an increase in non-photochemical quenching under conditions where metabolism was limiting, such as low CO2 or high light intensity. The model may be used as an in silico platform for future research on the regulation of photosynthetic electron transport.
Dynamic modelling of limitations on improving leaf CO2 assimilation under fluctuating irradiance
Morales, Alejandro ; Kaiser, Elias ; Yin, Xinyou ; Harbinson, Jeremy ; Molenaar, Jaap ; Driever, Steven M. ; Struik, Paul C. - \ 2018
Plant, Cell & Environment 41 (2018)3. - ISSN 0140-7791 - p. 589 - 604.
Arabidopsis - Lightflecks - Photosynthesis - Rubisco - Rubisco activase - Stomatal conductance - Sunflecks
A dynamic model of leaf CO2 assimilation was developed as an extension of the canonical steady-state model, by adding the effects of energy-dependent non-photochemical quenching (qE), chloroplast movement, photoinhibition, regulation of enzyme activity in the Calvin cycle, metabolite concentrations, and dynamic CO2 diffusion. The model was calibrated and tested successfully using published measurements of gas exchange and chlorophyll fluorescence on Arabidopsis thaliana ecotype Col-0 and several photosynthetic mutants and transformants affecting the regulation of Rubisco activity (rca-2 and rwt43), non-photochemical quenching (npq4-1 and npq1-2), and sucrose synthesis (spsa1). The potential improvements on CO2 assimilation under fluctuating irradiance that can be achieved by removing the kinetic limitations on the regulation of enzyme activities, electron transport, and stomatal conductance were calculated in silico for different scenarios. The model predicted that the rates of activation of enzymes in the Calvin cycle and stomatal opening were the most limiting (up to 17% improvement) and that effects varied with the frequency of fluctuations. On the other hand, relaxation of qE and chloroplast movement had a strong effect on average low-irradiance CO2 assimilation (up to 10% improvement). Strong synergies among processes were found, such that removing all kinetic limitations simultaneously resulted in improvements of up to 32%.
Effect of exogenous application of methyl jasmonate on physiological and biochemical characteristics of Brassica napus L. cv. Talaye under salinity stress
Ahmadi, F.I. ; Karimi, K. ; Struik, P.C. - \ 2018
South African Journal of Botany 115 (2018). - ISSN 0254-6299 - p. 5 - 11.
Growth and biological criteria - Methyl jasmonate - NaCl stress - Rapeseed - Stress alleviation
Salt stress caused by high soil salinity is one of the most serious limiting factors threatening crop production in many parts of the world. To alleviate stressful conditions such as salinity, various plant growth regulators, such as jasmonates, are involved. In the present study, the effect of exogenously applied methyl jasmonate (MeJA) on physiological and biochemical characteristics of rapeseed (Brassica napus L. cv. Talaye) was studied in combination with different concentrations of NaCl under greenhouse conditions. Plants treated only with NaCl stress showed a significant decrease in growth parameters and photosynthesis rate and a significant increase in CO2 compensation point, respiration rate, soluble sugar content, malondialdehyde content, proline content and antioxidant enzymes activities when compared with the control. Exogenously applied MeJA mitigated the inhibitory effect of salt stress on these variables at all NaCl levels. Exogenously applied MeJA counteracted the inhibitory effects of NaCl by increasing relative water content, soluble sugar content and photosynthesis rate.
Do all leaf photosynthesis parameters of rice acclimate to elevated CO2, elevated temperature, and their combination, in FACE environments?
Cai, Chuang ; Li, Gang ; Yang, Hailong ; Yang, Jiaheng ; Liu, Hong ; Struik, Paul C. ; Luo, Weihong ; Yin, Xinyou ; Di, Lijun ; Guo, Xuanhe ; Jiang, Wenyu ; Si, Chuanfei ; Pan, Genxing ; Zhu, Jianguo - \ 2018
Global Change Biology 24 (2018)4. - ISSN 1354-1013 - p. 1685 - 1707.
Climate change - Free-air CO enrichment - Leaf nitrogen content - Mesophyll conductance - Oryza sativa L. - Photosynthesis model - Stomatal conductance
Leaf photosynthesis of crops acclimates to elevated CO2 and temperature, but studies quantifying responses of leaf photosynthetic parameters to combined CO2 and temperature increases under field conditions are scarce. We measured leaf photosynthesis of rice cultivars Changyou 5 and Nanjing 9108 grown in two free-air CO2 enrichment (FACE) systems, respectively, installed in paddy fields. Each FACE system had four combinations of two levels of CO2 (ambient and enriched) and two levels of canopy temperature (no warming and warmed by 1.0-2.0°C). Parameters of the C3 photosynthesis model of Farquhar, von Caemmerer and Berry (the FvCB model), and of a stomatal conductance (gs) model were estimated for the four conditions. Most photosynthetic parameters acclimated to elevated CO2, elevated temperature, and their combination. The combination of elevated CO2 and temperature changed the functional relationships between biochemical parameters and leaf nitrogen content for Changyou 5. The gs model significantly underestimated gs under the combination of elevated CO2 and temperature by 19% for Changyou 5 and by 10% for Nanjing 9108 if no acclimation was assumed. However, our further analysis applying the coupled gs-FvCB model to an independent, previously published FACE experiment showed that including such an acclimation response of gs hardly improved prediction of leaf photosynthesis under the four combinations of CO2 and temperature. Therefore, the typical procedure that crop models using the FvCB and gs models are parameterized from plants grown under current ambient conditions may not result in critical errors in projecting productivity of paddy rice under future global change.
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