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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DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom
Demirci, Sevgin ; Peters, Sander A. ; Ridder, Dick de; Dijk, Aalt D.J. van - \ 2018
The Plant Journal 95 (2018)4. - ISSN 0960-7412 - p. 686 - 699.
Arabidopsis thaliana - crossover - DNA shape - genome accessibility - machine learning - maize - meiotic recombination - prediction - rice - tomato

A better understanding of genomic features influencing the location of meiotic crossovers (COs) in plant species is both of fundamental importance and of practical relevance for plant breeding. Using CO positions with sufficiently high resolution from four plant species [Arabidopsis thaliana, Solanum lycopersicum (tomato), Zea mays (maize) and Oryza sativa (rice)] we have trained machine-learning models to predict the susceptibility to CO formation. Our results show that CO occurrence within various plant genomes can be predicted by DNA sequence and shape features. Several features related to genome content and to genomic accessibility were consistently either positively or negatively related to COs in all four species. Other features were found as predictive only in specific species. Gene annotation-related features were especially predictive for maize, whereas in tomato and Arabidopsis propeller twist and helical twist (DNA shape features) and AT/TA dinucleotides were found to be the most important. In rice, high roll (another DNA shape feature) and low CA dinucleotide frequency in particular were found to be associated with CO occurrence. The accuracy of our models was sufficient for Arabidopsis and rice (area under receiver operating characteristic curve, AUROC > 0.5), and was high for tomato and maize (AUROC ≫ 0.5), demonstrating that DNA sequence and shape are predictive for meiotic COs throughout the plant kingdom.

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.

Plant immunity and symbiosis signaling mediated by LysM receptors
Desaki, Yoshitake ; Miyata, Kana ; Suzuki, Maruya ; Shibuya, Naoto ; Kaku, Hanae - \ 2018
Innate Immunity 24 (2018)2. - ISSN 1753-4259 - p. 92 - 100.
Arabidopsis - CEBiP - CERK1 - chitin - LysM receptor - Plant immunity - rice - signal transduction - symbiosis
Plants possess the ability to recognize microbe-associated molecular patterns (MAMPs) and PAMPs through the PRRs, and initiate pattern-triggered immunity. MAMPs are derived from cell-envelope components, secreted materials and cytosolic proteins from bacteria, oomycetes or fungi, and some MAMPs play a similar function in the innate immunity in mammals. Chitin is a representative fungal MAMP and triggers defense signaling in a wide range of plant species. The chitin receptors CEBiP and CERK1 on the plasma membrane have LysM (lysin motif) in their ectodomains. These molecules play an important role for the defense responses in rice and Arabidopsis, strictly recognizing the size and acetylated form of chitin oligosaccharides. However, related LysM receptors also play major roles for the signaling in root nodule and arbuscular mycorrhizal symbiosis. This review summarizes current knowledge on the molecular mechanisms of the defense and symbiosis signaling mediated by LysM receptors, including the activation steps of chitin-induced defense signaling downstream of LysM receptors.
High day- and night-time temperatures affect grain growth dynamics in contrasting rice genotypes
Shi, Wanju ; Yin, Xinyou ; Struik, Paul C. ; Solis, Celymar ; Xie, Fangming ; Schmidt, Ralf C. ; Huang, Min ; Zou, Yingbin ; Ye, Changrong ; Jagadish, S.V.K. - \ 2017
Journal of Experimental Botany 68 (2017)18. - ISSN 0022-0957 - p. 5233 - 5245.
Chalkiness - grain filling - high day-time temperature - high night-time temperature - rice - starch metabolism enzymes - starch packaging
Rice grain yield and quality are predicted to be highly vulnerable to global warming. Five genotypes including heat-tolerant and susceptible checks, a heat-tolerant near-isogenic line and two hybrids were exposed to control (31 °C/23 °C, day/night), high night-time temperature (HNT; 31 °C/30 °C), high day-time temperature (HDT; 38 °C/23 °C) and high day- and night-time temperature (HNDT; 38 °C/30 °C) treatments for 20 consecutive days during the grain-filling stage. Grain-filling dynamics, starch metabolism enzymes, temporal starch accumulation patterns and the process of chalk formation were quantified. Compensation between the rate and duration of grain filling minimized the impact of HNT, but irreversible impacts on seed-set, grain filling and ultimately grain weight were recorded with HDT and HNDT. Scanning electron microscopy demonstrated irregular and smaller starch granule formation affecting amyloplast build-up with HDT and HNDT, while a quicker but normal amylopast build-up was recorded with HNT. Our findings revealed temporal variation in the starch metabolism enzymes in all three stress treatments. Changes in the enzymatic activity did not derail starch accumulation under HNT when assimilates were sufficiently available, while both sucrose supply and the conversion of sucrose into starch were affected by HDT and HNDT. The findings indicate differential mechanisms leading to high day and high night temperature stress-induced loss in yield and quality. Additional genetic improvement is needed to sustain rice productivity and quality under future climates.
Stomatal conductance, mesophyll conductance, and trans piration efficiency in relation to leaf anatomy in rice and wheat genotypes under drought
Ouyang, Wenjing ; Struik, Paul C. ; Yin, Xinyou ; Yang, Jianchang - \ 2017
Journal of Experimental Botany 68 (2017)18. - ISSN 0022-0957 - p. 5191 - 5205.
Drought - leaf anatomy - mesophyll conductance - rice - stomatal conductance - transpiration efficiency - wheat
Increasing leaf transpiration efficiency (TE) may provide leads for growing rice like dryland cereals such as wheat (Triticum aestivum). To explore avenues for improving TE in rice, variations in stomatal conductance (g s) and mesophyll conductance (g m) and their anatomical determinants were evaluated in two cultivars from each of lowland, aerobic, and upland groups of Oryza sativa, one cultivar of O. glaberrima, and two cultivars of T. aestivum, under three water regimes. The TE of upland rice, O. glaberrima, and wheat was more responsive to the g m /g s ratio than that of lowland and aerobic rice. Overall, the explanatory power of the particular anatomical trait varied among species. Low stomatal density mostly explained the low g s in drought-tolerant rice, whereas rice genotypes with smaller stomata generally responded more strongly to drought. Compared with rice, wheat had a higher g m, which was associated with thicker mesophyll tissue, mesophyll and chloroplasts more exposed to intercellular spaces, and thinner cell walls. Upland rice, O. glaberrima, and wheat cultivars minimized the decrease in g m under drought by maintaining high ratios of chloroplasts to exposed mesophyll cell walls. Rice TE could be improved by increasing the g m /g s ratio via modifying anatomical traits.
Physiological responses of rice to increased day and night temperatures
Shi, Wanju - \ 2017
Wageningen University. Promotor(en): Paul Struik, co-promotor(en): Xinyou Yin; K.S.V. Jagadisch. - Wageningen : Wageningen University - ISBN 9789463437110 - 202
crops - rice - oryza sativa - plant physiology - temperature - crop yield - grain - agronomy - gewassen - rijst - plantenfysiologie - temperatuur - gewasopbrengst - graan - agronomie

A more rapid increase in night-time temperature compared with day-time temperature and the increased frequency of heat waves associated with climate change present a serious threat to rice (Oryza sativa L.) production and food security. This thesis aims to understand the impact of high night-time temperature (HNT) and high day-time temperature (HDT) on rice grain yield and grain quality and to examine adaptation strategies to cope with high-temperature stresses.

Grain yield and quality of a susceptible indica genotype (Gharib) and all tested hybrids, when exposed to HNT in the field, were significantly reduced across seasons, with less average reduction in the dry season than in the wet season, indicating that other environmental factors under field conditions may contribute to impacts of HNT on yield. Among the different yield components, a reduced number of spikelets m−2 significantly contributed to yield loss under HNT followed by the consistently lower single-grain weight across all genotypes, while the impact of the decrease in percentage seed-set was less and season-specific. Lower grain yield and poorer grain quality in susceptible cultivar Gharib were associated with a significant reduction in non-structural carbohydrate translocation after flowering, resulting in reduced grain-filling duration. Increased total nitrogen application did not alleviate the negative impact of HNT. The proposed model approach showed that there were significant differences among cultivars in their changes in source-sink relationships in response to HNT. Given that rice grain yield and quality are challenged by a rise in HDT and HNT, in particular at flowering and during grain filling, differential impacts of HNT and HDT during these critical stages were observed. For the single-grain growth during grain filling, HDT either independently or in combination with HNT exerted greater influences than HNT on the grain filling dynamics, activities of starch metabolism enzymes, temporal starch accumulation patterns, and the process of chalk formation. During flowering, HDT increased spikelet sterility in tested hybrids and hybrids were less tolerant to high temperatures than high-yielding inbred varieties. Moreover, in contrast with HNT, HDT played a dominant role in determining spikelet fertility. Novel observations with a series of snapshots of dynamic fertilization processes demonstrated that disturbances in the pre-fertilization phase were the primary causes for heat-induced spikelet sterility, indicating the effectiveness of employing the early-morning flowering trait for mitigating the impact of heat stress at flowering on rice.

A comprehensive assessment of agriculture in lowlands of south Brazil: characterization and comparison of current and alternative concepts
Theisen, Giovani - \ 2017
Wageningen University. Promotor(en): Niels Anten, co-promotor(en): Lammert Bastiaans. - Wageningen : Wageningen University - ISBN 9789463436380 - 234
cropping systems - farming systems - crop management - lowland areas - wetlands - pampas - brazil - intensification - sustainability - productivity - indicators - soil management - rice - flooded rice - oryza sativa - maize - zea mays - glycine max - cover crops - livestock - rotation - mixed farming - seedbed preparation - farm machinery - teeltsystemen - bedrijfssystemen - gewasteelt - laaglandgebieden - pampa's - brazilië - intensivering - duurzaamheid (sustainability) - productiviteit - indicatoren - bodembeheer - rijst - natte rijst - maïs - dekgewassen - vee - rotatie - gemengde landbouw - zaaibedbereiding - landbouwwerktuigen

Agriculture in the lowlands of south Brazil is of strategic importance at the national level, since it supplies around 80% of the rice consumed by the Brazilian population. In Rio Grande do Sul, the southernmost state in Brazil, three million hectares of lowlands are ready for grain-based agriculture. Of this area, about half is fallow, partly used for cattle grazing, and irrigated rice is the predominant crop, cultivated annually on 1.1 million ha. The remaining area is used for soybean and other crops. The predominant cropping system is a combination of irrigated rice and cattle. Over the last decades, rice yields have steadily increased, but this rise in yield level has to a large extent been obtained at the expense of a continuously higher use of external inputs. The recent introduction of soybean in rotation with rice has partially improved the system, but in most areas the situation is becoming incompatible with the modern demands for sustainability. This thesis presents a long-term study (2006-2015) of five cropping systems for lowlands. Next to monocrop rice and two rice-soybean rotations conducted in either conventional or minimum tillage, the experiment contained two novel systems based on large ridges, on which soybean and maize were combined with either cover crops or crop-livestock integration in winter. In these last systems, 8-m-wide ridges were built to avoid flooding, thus allowing for diversification of cash crops and the cultivation of cover crops or pastures in winter time, as well as the use of no-tillage. All systems were evaluated at process-level, including soil preparation, seeding, plant nutrition, pest management, irrigation, harvesting, transport and cattle management, as well as regarding their performance for the different dimensions of sustainability, particularly environment, land productivity, economics, energy-use and labour. Next to system assessment, two additional experiments were conducted for the evaluation of two specific technologies for soil management in these areas. Crop livestock integration on the ridge-based system offered the best balance between food production, environmental impact and economics. This system is well suited to be used in fields that are kept fallow, thereby enlarging the agricultural productivity of the lowlands. The additional experiments revealed that a knife-roller can successfully substitute plough-and-harrow for soil preparation after rice harvest, and that germination of weed seeds can be reduced if crop seeding is conducted at a lower speed or using a no-tillage seeder equipped with an improved cutting mechanism. Overall the results show that by using alternative cropping systems that allow for diversification and new methods of field management it is possible to simultaneously attain a larger agricultural production and improved sustainability in the lowlands.

The role of strigolactones and the fungal microbiome in rice during drought adaptation
Andreo Jimenez, Beatriz - \ 2017
Wageningen University. Promotor(en): Harro Bouwmeester, co-promotor(en): Carolien Ruyter-Spira. - Wageningen : Wageningen University - ISBN 9789463437028 - 205
drought resistance - drought - abiotic injuries - rice - oryza sativa - plant-microbe interactions - nutrient uptake - defence mechanisms - hormones - fungi - genes - droogteresistentie - droogte - abiotische beschadigingen - rijst - plant-microbe interacties - voedingsstoffenopname (planten) - verdedigingsmechanismen - hormonen - schimmels - genen

Rice is the most important food crop in the world, feeding over half the world’s population. However, rice water use efficiency, defined by units of yield produced per unit of water used, is the lowest of all crops. The aim of this thesis was to study the effect of plant hormones and the root microbiome on drought tolerance in rice. The new plant hormone, strigolactone, was shown to be upregulated under drought and to regulate drought tolerance in interaction with the drought-hormone abscisic acid. Using a large collection of rice genotypes grown in the field, we showed that the composition of the root associated fungal microbiome is determined by the rice genotype and can contribute to drought tolerance.

Feeding Dar es Salaam: a symbiotic food system perspective
Wegerif, Marc C.A. - \ 2017
Wageningen University. Promotor(en): Han Wiskerke, co-promotor(en): Paul Hebinck. - Wageningen : Wageningen University - ISBN 9789463432061 - 291
agricultural society - rural society - farmers' markets - food products - agricultural products - supermarkets - rice - grain - tanzania - east africa - agrarische samenleving - plattelandssamenleving - boerenmarkten - voedselproducten - landbouwproducten - supermarkten - rijst - graan - oost-afrika

This thesis is a sociological analysis of the agri-food system that feeds most of the over four and a half million residents of the fast-growing city of Dar es Salaam in Tanzania. It is based on qualitative research that has generated a picture of the food system that supplies the important foods for the majority of residents of the city. The research took an actor orientated approach and started from urban eaters and then followed the food back through retailers, processors and transporters to the primary producers. Methodological lessons are derived from this process in particular the elaboration of the ‘ride-along’ as a research method. Foods followed include maize, rice, potatoes, green vegetables, eggs and milk. Other foods such as beef and chicken have also been touched on especially in relation to marketing and slaughtering operations.

Instead of dismissing what has been found as ‘informal’ or trying to fit it into structuralist paradigms, from orthodox economic or political economy perspectives, I have applied a grounded theory approach in seeking to understand the core ordering principles and rationality of this system that has shown a remarkable resilience over many years. Of particular interest, especially when looking at the functioning of market places and how new actors enter into the food system, is that more important to the food system than competition are various forms of collaboration.

This study comes at a time when global food production and distribution is dominated by powerful transnational corporations through an agro-industrial food system that is widely critiqued for its negative environmental and social impacts. Many argue that this industrial food system is unsustainable, yet its expansion can seem inevitable and alternatives are seen by many as incapable of feeding the world’s growing and increasingly urban population. ‘Value chain’ interventions have become popular among ‘development’ practitioners and policy makers seeking to integrate more producers into the global industrial food system rather than challenging that food system.

What I have found, and present in this thesis, is a ‘symbiotic food system’ made up of multitudes of small-scale and interdependent actors that produce the food and get it to urban eaters at a city feeding scale. They do this without any vertically - or horizontally -integrated corporate structures nor with government planning and organization of the food system. This food system responds well to the needs of urban eaters, especially those in poverty, and to the interests and circumstances of small scale food producers. It is a food system that outperforms value chain interventions in returns to producers and value to eaters and has social, economic and environmental advantages when compared to the agro-industrial and corporate dominated system. This challenges assumptions that corporate food chains are necessary, or desirable, to feed cities sustainably. The symbiotic food system that feeds Dar es Salaam is not perfect, but it is working and I believe worthy of further research and interventions to create a more enabling environment for such foods systems to flourish in Tanzania and elsewhere.

Agricultural intensification in Nepal, with particular reference to systems of rice intensification
Uprety, Rajendra - \ 2016
Wageningen University. Promotor(en): Thomas Kuijper, co-promotor(en): Harro Maat. - Wageningen : Wageningen University - ISBN 9789462579651 - 190
rice - oryza sativa - nepal - asia - south asia - intensification - livelihoods - livelihood strategies - farming systems - farming - crop management - fertilizers - nutrients - irrigation - varieties - rijst - azië - zuid-azië - intensivering - middelen van bestaan - strategieën voor levensonderhoud - bedrijfssystemen - landbouw bedrijven - gewasteelt - kunstmeststoffen - voedingsstoffen - irrigatie - rassen (planten)

This thesis deals with agricultural intensification in Nepal. The initial focus of the study was the System of Rice Intensification (SRI), as introduced in Nepal from 2001. The multiple factors affecting SRI adoption, modification and dissemination together with the option to apply SRI in different combinations of its components result in a variety of SRI applications. For the same reason the effect of SRI on overall agricultural and livelihood development of Nepalese farmers has to be evaluated within the variety of farming systems in which it is applied.

Despite government policies to promote rice cultivation, national rice production is declining. Farmer livelihood strategies, as reflected in rice farming systems, and field management strategies were influenced by several agro-ecological and socio-economic factors. Livelihood and field management strategies of rice farmers are interconnected. In the study presented here four livelihood strategies and three kinds of field management strategies are distinguished. Two livelihood strategies can be characterized as more intensive and more productive; the other two are less intensive and less productive. Livelihood strategies are more family resource-based strategies, while farmers’ field management strategies are more context-dependent. Field management strategies were characterized by forms of nutrient management. Intensive management strategies had most similarities with SRI. But rice intensification is not achievable as a general strategy.

Government policies (fertiliser subsidies) encourage increased fertiliser use. Study results didn't show any significant effect of volume of fertilisers on rice yield but the combined use of organic manure and mineral fertilisers resulted in the highest average rice yields. Irrigation management is another important factor for rice production. Field management is influenced by the reliability of water which was better in farmers' managed irrigation system. Choice of rice varieties influenced the overall rice farming system and cropping intensity and preference of varieties for rice cultivation by scientists and by farmers were different in eastern Nepal. Most popular varieties were those not recommended by science and policy and were disseminated farmer to farmer.

The introduction of SRI in Morang district resulted in several changes in rice farming, but only part of the farmers have adopted such technologies, and adoption has been only in part of their fields. Other farmers have incorporated some SRI practices in their conventional practices. After the introduction of SRI, farmers further tested, re-packaged or hybridized SRI methods to make SRI ideas suitable for their agro-ecological and socio-economic environments. In order to reform Nepalese rice farming, we need to recognize that different farmers, with different livelihood strategies, and with access to different kinds of fields, need different forms for agricultural intensification. High-intensive farmers prefer to use modified SRI methods where there is good irrigation and drainage facilities. There are many possibilities for improvement of the existing nutrient management practices of rice farmers in Nepal. Nutrient management will be useful to increase rice production because the majority of farmers currently use fertilisers non-judiciously. The SRI-recommended practices (younger seedlings, early weeding, use of organic manure, and alternate wetting and drying (AWD) irrigation) will be useful to improve the nutrient use efficiency of rice farmers. Cost-reduction strategies and less labour-intensive cultivation practices will be appropriate options to improve existing rice farming system of Nepal. Participatory cultivar selection and dissemination will be better strategies to introduce new, promising rice cultivars among rice farmers.

Seeds as biosocial commons : an analysis of various practices in India
Patnaik, Archana - \ 2016
Wageningen University. Promotor(en): Guido Ruivenkamp; Han Wiskerke, co-promotor(en): Joost Jongerden. - Wageningen : Wageningen University - ISBN 9789462578302 - 166
rice - seeds - plant genetic resources - plant genetics - seed production - seed storage - community development - gender - social environment - india - rural development - rijst - zaden - genetische bronnen van plantensoorten - plantengenetica - zaadproductie - opslag van zaden - gemeenschapsontwikkeling - geslacht (gender) - sociaal milieu - plattelandsontwikkeling

This research investigates and describes the conservation and use of Plant Genetic Resources (PGRs), especially seeds through processes of commonisation. Seeds form an important element for sustaining human life (through food production) and social relations (by maintaining agricultural socialities). Therefore, conservation and management of PGRs in the form of seeds are essential for plant breeding, agricultural production and to meet the growing food demand of the increasing population. However, the changed use of PGRs through enclosures and appropriation of the Intellectual Property Rights creates underutilisation of these resources, risking their important societal role. Thus, this research aimed at analysing how the processes of commonisation of PGRs, especially seeds as biosocial commons emerge in the Indian context.

The research applied an in-depth qualitative research approach using case study method. It focused on four distinct issues of disconnection, collective resistance, strategies of repossession and ability of stakeholders to provide insights broadly into the processes of commonisation of PGRs. Describing the different cases it also establishes whether and how opportunities for commonisation of PGRs as biosocial commons emerge within these contexts. The research analysed four cases where one case reflected on the intellectual commons produced through institutionalisation of PGRs and the other three cases reflected on the bottom-up perspective of commons produced through Non-Governmental Organisations (NGOs).

The research through its first case, the Central Rice Research Institute (CRRI), a public ex situ genebank, describes the disconnection of PGRs, while through the second case reflects on the collective activity of resistance through management of community seed banks (CSBs) by the Deccan Development Society (DDS). The third and fourth cases involved small, local initiatives; Loka Samabaya Pratisthan (LSP) and Sambhav that fostered collective action for repossession through in situ seed banks. The research used various techniques, such as interviews with respondents, focus group discussions (FGDs) and participant observation for primary sources of data, with published and unpublished documents, reports and official websites as secondary sources.

The second chapter of the thesis looks at the issue of disconnection and argues that storing seeds at genebanks disconnects the resources from their biosocial environment. Further, the evaluation of genetic traits within the stored seeds through the scientific intervention at the genebank creates the divide between the resources (seeds) and their informational content. Thus, this chapter concludes that disconnection of seeds from their biosocial environment leads to the creation of exclusive but positive intellectual commons.

The third chapter of the thesis looks at the issue of collective resistance and argues that disconnection of the community from their local food system can generate resistance and collective activity among the community. This chapter finds that the resistance and collective activity further brought in the interaction between the resource and the stakeholders through informal social relations and seed networks.

The fourth chapter of the thesis looks at the issue of strategies of repossession and argues that socio-political and ecological context play an important role in determining the strategy for repossession and commonisation of PGRs which further inhibits or facilitates the production of seeds as biosocial commons.

The fifth chapter of the thesis analyses the ability of stakeholders and finds that apart from institutional rights other factors like the social relations, ideology, negotiations and social identity of a stakeholder determines their ability in accessing the conserved resources.

The overall finding of the research suggests that the informal seed networks in the cases analysed stimulated in establishing the biosocial relations between the stakeholders and the resources. The biosocial relation further led seeds to function as biosocial commons. The research thus proposes that strengthening of these biosocial relations through informal seed networks can lead to the commonisation of the PGRs, especially seeds as biosocial commons in the Indian context.

Does Nilaparvata lugens gain tolerance to rice resistance genes through conspecifics at shared feeding sites?
Ferrater, Jedeliza B. ; Horgan, Finbarr G. - \ 2016
Entomologia Experimentalis et Applicata 160 (2016)1. - ISSN 0013-8703 - p. 77 - 82.
Bph3 gene - brown planthopper - contemporaneous feeding - Delphacidae - facilitation - Hemiptera - host plant resistance - oral secretions - Oryza sativa - Poaceae - rice - 016-3963

This study examines the possibility of horizontal and vertical transmission of virulence (the ability to tolerate a given resistant plant or resistance gene) between individuals from brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), populations with distinct feeding abilities when their populations share the same feeding sites (virulence acquisition hypothesis). We created optimal conditions for intraspecific interactions on the same rice, Oryza sativa L. (Poaceae), plants between planthoppers from populations with different feeding histories: an ‘avirulent’ population that was continually reared on a susceptible variety, and a ‘virulent’ population that had been selected over several generations on the resistant variety IR62, that possesses the Bph3 gene. We noted that planthoppers attained highest weights on rice plants that had previously been attacked by conspecifics from the IR62-selected population. We also tested the ability of planthoppers to feed on IR62 and the susceptible cv. Taichung Native 1 (TN1) after interacting with individuals from the IR62-selected population on a tolerant rice cultivar (Triveni). Feeding by avirulent planthoppers on both IR62 and TN1 improved after feeding on the same rice plants with virulent planthoppers. Furthermore, the effects were carried over to planthopper progenies. Our preliminary results indicate that feeding by mixed populations that include individuals adapted to feed on resistant varieties potentially accelerates adaptation by N. lugens to rice resistance.

Lubrication and perception of foods : tribological, rheological and sensory properties of particle-filled food system
Liu, K. - \ 2016
Wageningen University. Promotor(en): Erik van der Linden, co-promotor(en): Markus Stieger; Fred van de Velde. - Wageningen : Wageningen University - ISBN 9789462576803 - 236 p.
rheological properties - tribology - fat globules - particles - lubrication - sensory evaluation - simulation models - food - gels - rice - reologische eigenschappen - tribologie - vetbolletjes - deeltjes - smering - sensorische evaluatie - simulatiemodellen - voedsel - rijst

Background and aims

Food structure is determined by its composition and the interaction between the compositional or structural elements. Both food structure and the texture perception of foods undergo dynamic changes during different phases of oral processing. During oral processing, both rheological and tribological properties of foods are relevant for sensory perception. The general aim of this thesis was to understand the relationship between the structural properties, rheological and tribological properties during food breakdown, and the sensory perception of foods. More specifically, this thesis aimed to link the properties of food particles in liquid and semi-solid matrices to the tribological and rheological properties, and in this way, understand the sensory perception of these systems.

Methods

Fat droplets and micro-particle fat replacers based on protein and starch were investigated. These particles varied in size, morphology, deformability and stability, as well as their interaction with the surrounding matrix. These particles were dispersed in liquid or semi-solid gel phases, forming the food model systems under consideration. The friction and microstructural evolution of food model systems under shear was determined using a mouth-mimicking tribometer connected to a confocal laser scanning microscopy. The viscosities of liquid systems were analyzed using a rheometer, and the large deformation properties of semi-solid gel systems were determined during uniaxial compression tests. The sensory perception of the food model systems were measured using quantitative descriptive analysis. The release and deposition of fat droplets on the tongue were determined using in vivo fluorescence.

Results

Food structural elements could be manipulated to control the tribological properties of food model systems. Morphology, size, and deformability of food particles determine the lubrication behavior of the food systems. Spherical particles with micrometer size were able to reduce friction through a ball bearing mechanism, while irregularly shaped particles increased friction by increasing apparent surface asperity contacts. Deformable particles could flatten the surface by filling asperities, thus reduced friction. Coalescence of unstable droplets could plate-out on the surface and form film patches, thus reduced friction. Other structural elements, such as emulsifiers and sticky molecules, also influenced tribological properties of the systems. Interactions between the food structural elements could influence the rheological properties of liquid and semi-solid food systems. These properties as well as tribological properties were inter-related and all of them affect sensory perception. The inter-relations between physical and sensory properties of food systems were influenced by oral processing, such as oral processing duration and temperature. Furthermore, several fat reduction and replacement strategies were suggested, including increasing the availability of fat that is in contact with oral surfaces, improving the lubrication by ball bearing of particles, and reducing perception of negative attributes such as roughness.

Conclusions

This thesis showed the importance of food particle properties in both the tribological properties and sensory perception of foods, and emphasized the different lubrication mechanisms of different structure elements and their relation to perception. The differences in behavior of food particles between liquid and semi-solid gel systems were highlighted. These findings would enable a better understanding of relationship between food structure and their physical and sensory properties, and this would allow designing or modifying food products with targeted texture and sensory perception.

Network formation, learning and innovation in multi-stakeholder research projects : experiences with Adaptive Research and Learning Alliances in rice farming communities in Southeast Asia
Flor, R.J. - \ 2016
Wageningen University. Promotor(en): Cees Leeuwis, co-promotor(en): Harro Maat; Grant Singleton. - Wageningen : Wageningen University - ISBN 9789462576650 - 230 p.
learning activities - adult learning - learning - social networks - education - agricultural education - rice - farming - agricultural extension - south east asia - cambodia - leeractiviteiten - volwassenenstudie - leren - sociale netwerken - onderwijs - agrarisch onderwijs - rijst - landbouw bedrijven - landbouwvoorlichting - zuidoost-azië - cambodja

Mounting pressure on research organizations to achieve sustainable development outcomes from research has pushed them to use multi-stakeholder approaches. Insights are missing however, on how these influence social, technical, and institutional change, as well as what outcomes emerge from these. The thesis is an examination of the enactment of multi-stakeholder approaches, questioning how and to what extent Adaptive Research (AR) and Learning Alliance (LA) approaches influence socio-technical innovation in rice farming communities. Four case studies of research and development projects that employed the approaches in rice farming communities were elaborated in this thesis.

AR implementation in Indonesia (chapter 2), showed how AR fast-tracked technical adaptations and built upon the improvisational capacities of farmers. AR monitoring however, rendered invisible the adaptations required on the social aspect. Simultaneous social, technical, and institutional redesign was limited.

A case of LA implemented at national level engaged a network that changed and expanded after three years to include diverse actors (chapter 3). There were points where implementation (mis)aligned with assumptions from project implementers and from conceptual literature of the LA approach. The network influenced change at community level by engaging small groups that made reconfigurations on the technologies and the social arrangements for these (chapter 4). A community-level LA in Myanmar was also found to stimulate a self-organized learning process towards innovation for flatbed dryer technology (chapter 5).

A case where a project used AR only versus AR with LA in Myanmar (chapter 6), revealed differing networks, learning processes, and outcomes in terms of learning agenda. The involvement of a wider network resulted in a broader set of activities, which were initiatives outside the original plans of the project. The learning activities were not only about technologies but also included experimentations on supportive environment for access and use of the technologies.

This thesis therefore demonstrates that project actors implement AR and LA approaches through a range of translations in multiple contexts. These imply varied interactions in different types of networks. Such interactions triggered varied learning processes and thus influenced different planned or emergent outcomes. Both approaches have potential to catalyze innovation in farming communities; however, outcomes on adoption numbers provide a caveat that these approaches are not silver bullets that guarantee technology adoption. Instead, implementation that facilitates effective learning processes, and monitoring that flags where projects could support emergent outcomes, can help implementers improve their contributions to development in farming communities.

Interactions among rice-Xanthomonas-Rhizoctonia and biostimulans : Design of a framword to test the effect of a multiple species control of Xanthomonas and Rhizoctonia in rice
Wurff, A.W.G. van der; Streminska, M.A. ; Elings, A. - \ 2016
Bleiswijk : Wageningen UR Glastuinbouw (Report GTB 1390) - 26 p.
arable farming - rice - oryza - sustainable agriculture - plant protection - biological control - integrated control - xanthomonas - rhizoctonia - indonesia - akkerbouw - rijst - duurzame landbouw - gewasbescherming - biologische bestrijding - geïntegreerde bestrijding - indonesië
The Indonesian Ministry of Agriculture has the ambition to boast the sustainable production of rice in order to meet the increasing demand. Resource use efficiency can be improved if production loss owing to plant
pathogens is resolved. Knowledge on the role of biodiversity on system stability must be translated Agricultural practices. Species with overlap in function may constitute biological control measures to create a resilient system against pathogens. As species may counteract, the approach needs to take into account the diverse effects caused by different pathogens, both above-ground and below-ground. Above-ground as well as belowground biological control may benefit from a multiple species approach. Pest-enemy interactions are often embedded in rich communities of multiple interacting pathogens and natural enemies. Designing IPM for multiple pests requires understanding of all interactions among species, both pests and natural enemies. The goal of the research is to investigate which currently available biological control agents are compatible or even act synergistically in order to build a resilient and sustainable crop protection system against Xanthomonas and Rhizoctonia in rice in Indonesia.
Farmers, institutions and technology in agricultural change processes : outcomes from Adaptive Research on rice production in Sulawesi, Indonesia
Flor, Rica Joy ; Singleton, Grant ; Casimero, Madonna ; Abidin, Zainal ; Razak, Nasruddin ; Maat, Harro ; Leeuwis, Cees - \ 2016
International Journal of Agricultural Sustainability 14 (2016)2. - ISSN 1473-5903 - p. 166 - 186.
Adaptive Research - innovation systems perspective - monitoring - rice - socio-technical change - technology adoption

International agricultural research centres use approaches which aim to create effective linkages between the practices of farmers, introduced technologies and the wider environment that affects farming. This paper argues that such new approaches require a different type of monitoring as a complement to conventional approaches that tend to favour a quantitative assessment of adoption and impact at the farm level. In this context, we examined monitoring data from an Adaptive Research (AR) project highlighting complementary qualitative analysis. Our emphasis is to capture the improvisational capacities of farmers and to reveal social and institutional constraints and opportunities in a broader innovation system. Our approach provided clear insights into how rice farmers adjusted their practices and how actors involved linked (or not) with others in the innovation system. We also demonstrated how institutions such as policies, religious rituals or service provider arrangements pose conditions that establish or constrain practices aligned with introduced technologies. A broader perspective in monitoring AR therefore provides important additional insights into the factors which shape outcomes in farming communities. To expand outcomes, AR projects should also pay attention to designing and testing new institutional arrangements that create enabling conditions for agricultural innovation.

Adaptation of the brown planthopper, Nilaparvata lugens (Sta°l), to resistant rice varieties
Ferrater, J.B. - \ 2015
Wageningen University. Promotor(en): Marcel Dicke, co-promotor(en): F.G. Horgan; Peter de Jong. - Wageningen : Wageningen University - ISBN 9789462575592 - 200
insectenplagen - nilaparvata lugens - adaptatie - oryza sativa - rijst - cultivars - plaagresistentie - symbionten - gisten - endosymbionten - insect pests - adaptation - rice - pest resistance - symbionts - yeasts - endosymbionts

This thesis examines the three-way interaction between yeast-like symbionts, an insect herbivore [Nilaparvata lugens (Stål)] and its rice (Oryza sativa L.) host, during adaptation of the herbivore to resistant rice varieties. A long-term selection study (20 generations of continuous rearing, ca. 24 months) was conducted with N. lugens populations on four rice varieties (IR22, a susceptible variety and IR65482, IR62, and PTB33, three resistant varieties). Planthopper performance and the abundance of yeast-like symbionts (YLS) were monitored throughout the selection process. N. lugens populations adapted to the resistant varieties as noted by increasing body size and increased egglaying. Xylem feeding was observed as a possible behavioural adaptation of N. lugens: planthoppers on resistant plants had relatively high levels of xylem feeding compared with planthoppers on susceptible plants. Planthoppers selected on resistant varieties, had clear differences in YLS densities that were not related to fitness on the varieties and, therefore, did not support a YLS density-mediated adaptation hypothesis.

Furthermore, this study examined whether YLS density affected the capacity of planthoppers to switch between hosts on which they have been selected for several generations (natal plant) to new varieties (exposed plants) under normal YLS densities (symbiotic) and after reduction of YLS densities by heat treatment (aposymbiotic). The results suggested that YLS do not mediate host plant switching in planthoppers as removal of symbionts influenced body weight but not the relative capacity of nymphs to feed on different plants. This study also tested if virulence is acquired by shared feeding sites with virulent and avirulent planthoppers. In the study, planthoppers with varying levels of virulence affected the host plants differently: The most virulent hoppers appeared to suppress rice defences to a greater extent than non-virulent planthoppers. Planthoppers attained highest weights on those plants on which virulent planthoppers had previously fed which suggests that feeding by the virulent planthoppers facilitated subsequent planthopper feeding on the same plant. Our preliminary results indicate that feeding by mixed virulent-avirulent populations could potentially accelerate adaptation by N. lugens to resistant rice varieties.

The capacity of virulent and avirulent planthoppers to feed on a range of 24 resistant rice varieties was examined using a series of bioassays. Planthoppers were observed to feed and lay eggs on all the varieties tested, many of which have never been widely deployed in the field. Furthermore, planthoppers selected on resistant varieties often had increased fitness on other resistant varieties, even when these possess different resistance genes. However, there was no strong evidence that once planthoppers have adapted to a resistant variety, they will exhibit fitness costs on other varieties with dissimilar genes. The mechanisms underlying insect virulence are complex and further research on planthopper adaptation is necessary to help conserve genetic resources and prolong the durability of available resistant varieties.

How smallholder farmers in Uttarakhand reworked the system of rice intensification: innovations from sociotechnical interactions in fields and villages
Sen, D. - \ 2015
Wageningen University. Promotor(en): Paul Richards, co-promotor(en): Harro Maat; C. Shambu Prasad; Dominic Glover. - Wageningen : Wageningen University - ISBN 9789462575868 - 188
bedrijfssystemenonderzoek - rijst - uttarakhand - india - duurzame landbouw - farming systems research - rice - sustainable agriculture

The System of Rice Intensification (SRI) is presented in Asia and other parts of the world as an alternative ‘agro-ecological’ and ‘farm-based’ innovation in rice production. SRI calls for modifications in crop-management practices without relying on external inputs, which makes it different from innovations based on new rice varieties, which became dominant since the Green Revolution. SRI practices are therefore said to be appropriate for resource-poor smallholder farmers.

Previous studies on SRI have focused mainly on the yield effects in comparison with other crop management practices, overall costs and benefits of SRI or deviations from recommended practices. These studies have largely neglected farmers’ underlying strategies. This thesis provides an understanding of whether and how SRI can be called a ‘farm-based’ innovation. Rather than returning to earlier debates about SRI's adoption and disadoption, the study looks as how farm households and communities in Western Himalayan region of India responded to the introduction of SRI.

The main objective of this research was to understand how farmers respond to an intervention like SRI and what this tells us about SRI as a socio-technical system. The main research question addressed by this thesis is how SRI, conceived as a set of practices introduced from outside the communities, was incorporated into the local rice farming system. Specifically, the thesis examines how existing work groups were adjusted to accommodate the new method, how the SRI practices were interpreted and adjusted to fit with the local social and agro-ecological arrangements, and how the new method influenced existing rice farming practices in the locality.

The research was carried out in three contrasting villages of Uttarakhand, located in the Bhilangana sub-basin of the Western Himalayan region of India. SRI was introduced in this area in 2008. Fieldwork in the three villages was conducted throughout two rice seasons.

The theoretical resources drawn upon for this research include the concept of “socio-technical system”, “agriculture as performance”, and the culture of “task groups”. Together these concepts help to understand rice farming as a collective and mutually shaping social and technical performance rather than the activity of an individual farmer. The thesis shows how existing and new rice farming practices and task groups are reconfigured through socio-technical innovations within a given agro-ecological setting. SRI acted as a catalyst, initiating a process of readjustments in the socio-technical configurations of rice farming, varying according to the local context. Farm households, while incorporating SRI into the existing farming system, try to seek complementarity and synergy between various rice farming methods. This allows fluidity among task groups and leads to the extension and diversification of the repertoire of methods used, taking into account the dynamics of the larger socio-economic conditions. The thesis highlights farmers’ adaptive capacities to reconfigure practices, reorganize social formations, and reschedule routines in response to farming interventions, in order to maximize the exploitation of agro-ecological niches, minimize uncertainty in farm production and rationalize the employment of the available work force.

The study indicates a potential for task groups as units for effectively promoting new agricultural interventions. The groups performing farm operations are crucial in developing and adjusting farmers’ managerial skills to cater to the needs of the rice crop in light of the social and economic conditions of the community. For instance, elements of the set of SRI practices, like the use of younger seedlings, fewer seedlings per hill and wider spacing of hills were shown to have influenced practices in nominally ‘non-SRI’ plots. Changes in customary ritual like Din Bar announcing the date of rice transplanting, elevation in the status of Village Level Resource Persons (VLRPs), emergence of different forms of raised bed nurseries (RBNs), and inclusion of young women in transplanting groups reflect how introduction of SRI brought about changes in the social structure and institutions. This thesis thus highlights the role and importance of the human management component in farming activities and agricultural development. This provided insights into the integration of social and technical dimensions of crop cultivation, particularly the dynamics of rice farming using SRI but also for agronomy as a whole.

Keywords: Rice, smallholder farmers, System of Rice Intensification (SRI), socio-technical interactions, farm based innovations, task groups, technical practices, labour organization, mountain farms, Uttarakhand in India.

Investigations into the biosynthesis, regulation, and self-resistance of toxoflavin in Pseudomonas protegens Pf-5
Philmus, B. ; Shaffer, B.T. ; Kidarsa, T.A. ; Yan, Q. ; Raaijmakers, J.M. ; Begley, T.P. ; Loper, J.E. - \ 2015
ChemBioChem 16 (2015)12. - ISSN 1439-4227 - p. 1782 - 1790.
formylglycine-generating enzyme - fluorescens pf-5 - burkholderia-glumae - pyoluteorin - cocovenenans - expression - oxidation - system - rice - gaca
Pseudomonas spp. are prolific producers of natural products from many structural classes. Here we show that the soil bacterium Pseudomonas protegens Pf-5 is capable of producing trace levels of the triazine natural product toxoflavin (1) under microaerobic conditions. We evaluated toxoflavin production by derivatives of Pf-5 with deletions in specific biosynthesis genes, which led us to propose a revised biosynthetic pathway for toxoflavin that shares the first two steps with riboflavin biosynthesis. We also report that toxM, which is not present in the well-characterized cluster of Burkholderia glumae, encodes a monooxygenase that degrades toxoflavin. The toxoflavin degradation product of ToxM is identical to that of TflA, the toxoflavin lyase from Paenibacillus polymyxa. Toxoflavin production by P. protegens causes inhibition of several plant-pathogenic bacteria, and introduction of toxM into the toxoflavin-sensitive strain Pseudomonas syringae DC3000 results in resistance to toxoflavin.
African rice (Oryza glaberrima) cultivation in the Togo Hills: ecological and socio-cultural cues in farmer seed selection and development
Teeken, B.W.E. - \ 2015
Wageningen University. Promotor(en): Paul Richards; Paul Struik, co-promotor(en): Harro Maat; Edwin Nuijten. - Wageningen : Wageningen University - ISBN 9789462574359 - 306
oryza glaberrima - rijst - familiebedrijven, landbouw - veredelde rassen - sociale gebruiken - voedselzekerheid - afrika - rice - family farms - improved varieties - social customs - food security - africa
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