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Veel Afrikaanse boeren blijven verstoken van goed zaai- en pootgoed. Nationale overheden en bedrijven kunnen niet aan de vraag voldoen. Het Centre for Development Innovation in Wageningen werkt met boerengroepen om lokaal beter zaaizaad op de markt te brengen.

Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. Divers en Dichtbij Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Dit onderzoek is samen met Estafette Odin BV en de biologische dynamische telers GAOS in Swifterbant, De Groenen Hof in Esbeek en de Maatschap Dames en Heren Vos in Kraggenburg uitgevoerd. Het doel van dit project Divers en Dichtbij was de diversiteit op het veld en op het bord te vergroten. Daarmee bedoelen we niet alleen meer verschillende rassen, maar vooral andere type rassen of populaties die zelf meer genetische variatie bezitten. Dat kan door te kiezen voor zaadvaste rassen bij groentegewassen en populaties bij granen. Tot nu toe is populatieveredeling alleen toegepast bij granen en nog niet of nauwelijks bij groentegewassen (zie voor definities Box 1 op pagina 7). Dit betekent ook een keuze voor andere manieren van veredelen en selecteren. Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. En toch heeft ons brede speurwerk in dit project wel degelijk een aantal interessante zaadvaste rassen opgeleverd! Want gelukkig zijn er in Europa en Amerika diverse biologische veredelaars actief in het veredelen van zaadvaste rassen en populaties. De informatie in deze brochure is bedoeld voor telers en andere ketenpartijen om meer te leren over de mogelijkheden van zaadvaste rassen bij groenten en populaties bij tarwe.

One of the major bottlenecks limiting farmers’ access to good quality seed for food crops in Uganda is the shortage of early generation seed (EGS - breeder and foundation) to produce sufficient quantities of certified and/or quality declared) to satisfy the needs of farmers. A national study was conducted between October 2015 to March 2016 to analyse pathways for promoting commercial and sustainable production and delivery of EGS. Five crops (hybrid maize, rice, beans, sesame and finger millet) were selected. The analysis provides real examples of potential business models that could scale in a commercially sustainable manner. For areas that are best suited to public sector investment, opportunities for public-private collaboration and increased efficiencies in the sector are outlined. Generalizable principles and recommendations to guide key stakeholders as they pursue policies, investments, and interventions are proposed.

Het Strawberry latent ringspot virus (SLRSV, in het Nederlands Latent aardbeikringvlekkenvirus) komt in een groot aantal gewassen voor, waaronder o.a. aardbei, framboos, bessenstruiken, verschillende fruitbomen (kers, pruim, perzik), groenten en kruiden (asperge, selderij, peterselie) en siergewassen (roos, lelie en narcis). Binnen de EU is dit virus een quarantaine organisme in plantmateriaal van aardbei, braam en framboos. In andere delen van de wereld is SLRSV ook een quarantaine organisme in andere gewassen, voor de export van lelie naar o.a. China en de Verenigde Staten geldt een 0-tolerantie. SLRSV wordt overgebracht door een tweetal aaltjes-soorten: Xiphinema diversicaudatum en X. coxi. Er zijn echter vermoedens dat dit virus ook op andere manieren verspreid kan worden dan alleen door de twee genoemde Xiphinema-soorten. Er is namelijk overdracht waargenomen in teelten waarin geen Xiphinema is waargenomen. De vraag is dus op welke manieren SLRSV kan worden verspreid. In de literatuur is al gerapporteerd dat SLRSV in een hoog percentage (~70%) met zaad over kan gaan in bijvoorbeeld selderij, munt en braam. Van zaadoverdracht in het gewas lelie is tot op heden nog niets bekend. Bovendien kan het virus zeer algemeen voorkomende onkruiden als herderstasje en muur infecteren. Het doel van het onderzoek waarover in dit verslag wordt gerapporteerd was het nagaan of de verspreiding van SLRSV in lelie al dan niet via zaadoverdracht kan plaatsvinden. Hiervoor werden experimenten uitgevoerd met een vijftal leliecultivars die via zaad worden vermeerderd. SLRSV kon bij deze cultivars in het zaad, het stuifmeel en in nieuwe zaailingen worden aangetoond. SLRSV kon zo in hoge mate worden aangetoond in zaden afkomstig uit partijen met een zeker percentage SLRSV. Bij één cultivar werd een percentage van 30% infectie gevonden in zaailingen die waren gegroeid uit zaad uit een besmette partij. Het virus kon ook worden aangetoond in het stuifmeel van geïnfecteerde bloemen. De vraag of het virus ook via stuifmeel kan worden overgedragen van de ene plant naar de andere plant wordt op moment van deze rapportage nog onderzocht in een project gefinancierd door iBulb. Sommige zaad-overgedragen virussen verblijven voornamelijk aan de buitenkant van het zaad (op of in de zaadhuid) en infecteren het nageslacht pas wanneer de kiemplant door de zaadhuid heen breekt (bijvoorbeeld potexvirussen en tobamovirussen). Bij dit soort virussen is een zaadontsmetting nog een mogelijkheid om infectie van de jonge kiemplantjes te voorkomen. In het onderzoek waarover hier wordt gerapporteerd is naar voren gekomen dat SLRSV tot een andere categorie virussen behoort, namelijk de virussen die zaadoverdraagbaar zijn en daarbij al in het zaad in endosperm en zelfs het embryo aanwezig zijn. Voor deze groep virussen is zaadontsmetting geen remedie tegen zaadoverdracht. Samengevat heeft dit onderzoek de volgende nieuwe inzichten opgeleverd: • SLRSV is zaadoverdraagbaar in lelie • SLRSV is aantoonbaar in endosperm en embryo van leliezaad. Zaadontsmetting is geen optie om zaadoverdracht te voorkomen.

The programme on Integrated Seed Sector Development in Ethiopia aims to strengthen the development of a vibrant, market-oriented and pluralistic seed sector in the country, where quality seed of superior varieties is available and affordable for a larger number of farmers, thereby contributing to food security and economic development in Ethiopia. The programme is a joint effort of Bahir Dar University, Haramaya University, Hawassa University, Mekelle University, Oromia Seed Enterprise, the Ethiopian Seed Association and Centre for Development Innovation of Wageningen UR. Partners include governmental organizations at federal, regional and local level, non-governmental organizations, development organizations, and seed businesses operating at different scales. The programme is funded by the Directorate General for International Cooperation through the Embassy of the Kingdom of the Netherlands in Addis Ababa.

Het Strawberry latent ringspot virus (SLRSV, in het Nederlands Latent aardbeikringvlekkenvirus) komt in een groot aantal gewassen voor, waaronder o.a. aardbei, framboos, bessenstruiken, verschillende fruitbomen (kers, pruim, perzik), groenten en kruiden (asperge, selderij, peterselie) en siergewassen (roos, lelie en narcis). Binnen de EU is dit virus een quarantaine organisme in plantmateriaal van aardbei, braam en framboos. In andere delen van de wereld is SLRSV ook een quarantaine organisme in andere gewassen, voor de export van lelie naar o.a. China en de Verenigde Staten geldt een 0-tolerantie. SLRSV wordt overgebracht door een tweetal aaltjes-soorten: Xiphinema diversicaudatum en X. coxi. Er zijn echter vermoedens dat dit virus ook op andere manieren verspreid kan worden dan alleen door de twee genoemde Xiphinema-soorten. Er is namelijk overdracht waargenomen in teelten waarin geen Xiphinema is waargenomen. De vraag is dus op welke manieren SLRSV kan worden verspreid. In de literatuur is al gerapporteerd dat SLRSV in een hoog percentage (~70%) met zaad over kan gaan in bijvoorbeeld selderij, munt en braam. Van zaadoverdracht in het gewas lelie is tot op heden nog niets bekend. Bovendien kan het virus zeer algemeen voorkomende onkruiden als herderstasje en muur infecteren. Het doel van het onderzoek waarover in dit verslag wordt gerapporteerd was het nagaan of de verspreiding van SLRSV in lelie al dan niet via zaadoverdracht kan plaatsvinden. Hiervoor werden experimenten uitgevoerd met een vijftal leliecultivars die via zaad worden vermeerderd. SLRSV kon bij deze cultivars in het zaad, het stuifmeel en in nieuwe zaailingen worden aangetoond. SLRSV kon zo in hoge mate worden aangetoond in zaden afkomstig uit partijen met een zeker percentage SLRSV. Bij één cultivar werd een percentage van 30% infectie gevonden in zaailingen die waren gegroeid uit zaad uit een besmette partij. Het virus kon ook worden aangetoond in het stuifmeel van geïnfecteerde bloemen. De vraag of het virus ook via stuifmeel kan worden overgedragen van de ene plant naar de andere plant wordt op moment van deze rapportage nog onderzocht in een project gefinancierd door iBulb. Sommige zaad-overgedragen virussen verblijven voornamelijk aan de buitenkant van het zaad (op of in de zaadhuid) en infecteren het nageslacht pas wanneer de kiemplant door de zaadhuid heen breekt (bijvoorbeeld potexvirussen en tobamovirussen). Bij dit soort virussen is een zaadontsmetting nog een mogelijkheid om infectie van de jonge kiemplantjes te voorkomen. In het onderzoek waarover hier wordt gerapporteerd is naar voren gekomen dat SLRSV tot een andere categorie virussen behoort, namelijk de virussen die zaadoverdraagbaar zijn en daarbij al in het zaad in endosperm en zelfs het embryo aanwezig zijn. Voor deze groep virussen is zaadontsmetting geen remedie tegen zaadoverdracht. Samengevat heeft dit onderzoek de volgende nieuwe inzichten opgeleverd: • SLRSV is zaadoverdraagbaar in lelie • SLRSV is aantoonbaar in endosperm en embryo van leliezaad. Zaadontsmetting is geen optie om zaadoverdracht te voorkomen.

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.

The interest of research groups in desiccation tolerance (DT) has increased substantially over the last decades. The emergence of germinated orthodox seeds and resurrection plants as main research models has pushed the limits of our knowledge beyond boundaries. At the same time, new questions and new challenges were posed. The work presented in this thesis aims at shedding light on some of these questions, deepening our understanding of DT and providing relevant information to improve stress resistance in crops. Chapter 2 is a survey of the literature and discusses the ecological and evolutionary significance for seeds to be able to re-acquire DT after germination. This chapter also discusses recent progress in DT studies using developing and germinated seeds of the model plants Arabidopsis thaliana and Medicago truncatula. In Chapter 3 I used microarray data from a time series of DT re-acquisition, together with network analysis of gene expression, to gain temporal resolution and identify relevant genes involved in the re-acquisition of DT in germinated A. thaliana seeds by incubation in abscisic acid (ABA). Overall, genes related to protection, response to stresses, seed development and seed dormancy were up-regulated, whereas genes related to cell growth and photosynthesis were down-regulated with time. Genes that respond early to exogenous ABA were related to wax biosynthetic processes, lipid storage, seed development and response to ABA stimulus. Genes that respond late to exogenous ABA were related to syncytium formation and response to abiotic stimulus (mainly light stimulus). The robustness of the network was confirmed by the projection of sets of genes – related to the acquisition of DT, seed dormancy, drought responses of adult plants and re-induction of DT by polyethylene glycol – on this network. In Chapter 4 the relation between DT in germinated seeds and drought resistance in adult plants is analysed, using rice (Oryza sativa) as experimental model. Considering the predictions of a future with lower availability of fresh water, efforts to increase rice drought tolerance without reducing yield are increasingly important. The results presented in this chapter suggest that the intrinsic mechanisms of drought tolerance in adult plants are part of the mechanisms used by seeds to tolerate desiccation, but the molecular nature of these mechanisms remains elusive. Chapter 5 explores the relation between DT and longevity in germinated seeds of the Brazilian tree species Sesbania virgata as experimental model. DT and longevity are acquired by orthodox seeds during the maturation phase of development and lost upon germination. DT can be re-induced in germinated seeds by an osmotic and/or ABA treatment, but there is no information on how these treatments affect seed longevity. S. virgata seeds lose DT slowly upon radicle growth. The radicle appeared to be the most sensitive organ and the cotyledons the most resistant. The ability to produce lateral roots was key for whole seedling survival. An osmotic treatment improved DT in germinated S. virgata seeds, but not longevity. This implies that DT and seed longevity can be uncoupled. Xerophyta viscosa is one of the best studied resurrection species. Despite the fact that adult plants and mature seeds display DT, young X. viscosa seedlings are sensitive to fast drying. A treatment with ABA can induce DT early in shoots of these seedlings, but not in roots. Chapter 6 addresses the changes in the transcriptome and proteome of X. viscosa seedlings during induction of DT. A draft genome sequence of X. viscosa was used to improve transcript and protein identification and annotation. Differences in ABA signalling and the cross talk between ABA and ethylene were presented as determinant for shoot and root responses. Moreover, differences in the accumulation of late embryogenesis abundant proteins were also shown as being key for DT in shoots and roots. In Chapter 7, DT-transcriptomes of distantly related organisms are compared and surveyed for a core set of genes representing the signatures of critical adaptive DT mechanisms. A shortlist of 260 genes emerged, with a significant number of genes under the control of ABI3 and related to dormancy. The results reinforced the idea that core mechanisms and key regulators involved in DT developed early in the history of life and were carried forward by diverse species and life forms in a conserved manner and in conjunction with dormancy. In Chapter 8, the findings of this thesis are integrated, showing how they can contribute to future improvement of stress tolerance in crops. The ability of germinated seeds to re-acquire DT is discussed in combination with dormancy and longevity and related to seed survival under unfavourable environmental conditions. The relationship between drought- and desiccation tolerance and the role of ABA are presented briefly. Possible approaches to mine for new genes for crop improvement, such as searching for conserved genes and analysing new genome sequences, are addressed. Finally, a new perspective of the way to consider the evolution of DT is proposed.

Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. Divers en Dichtbij Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Dit onderzoek is samen met Estafette Odin BV en de biologische dynamische telers GAOS in Swifterbant, De Groenen Hof in Esbeek en de Maatschap Dames en Heren Vos in Kraggenburg uitgevoerd. Het doel van dit project Divers en Dichtbij was de diversiteit op het veld en op het bord te vergroten. Daarmee bedoelen we niet alleen meer verschillende rassen, maar vooral andere type rassen of populaties die zelf meer genetische variatie bezitten. Dat kan door te kiezen voor zaadvaste rassen bij groentegewassen en populaties bij granen. Tot nu toe is populatieveredeling alleen toegepast bij granen en nog niet of nauwelijks bij groentegewassen (zie voor definities Box 1 op pagina 7). Dit betekent ook een keuze voor andere manieren van veredelen en selecteren. Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. En toch heeft ons brede speurwerk in dit project wel degelijk een aantal interessante zaadvaste rassen opgeleverd! Want gelukkig zijn er in Europa en Amerika diverse biologische veredelaars actief in het veredelen van zaadvaste rassen en populaties. De informatie in deze brochure is bedoeld voor telers en andere ketenpartijen om meer te leren over de mogelijkheden van zaadvaste rassen bij groenten en populaties bij tarwe.

The programme on Integrated Seed Sector Development in Ethiopia aims to strengthen the development of a vibrant, market-oriented and pluralistic seed sector in the country, where quality seed of superior varieties is available and affordable for a larger number of farmers, thereby contributing to food security and economic development in Ethiopia. The programme is a joint effort of Bahir Dar University, Haramaya University, Hawassa University, Mekelle University, Oromia Seed Enterprise, the Ethiopian Seed Association and Centre for Development Innovation of Wageningen UR. Partners include governmental organizations at federal, regional and local level, non-governmental organizations, development organizations, and seed businesses operating at different scales. The programme is funded by the Directorate General for International Cooperation through the Embassy of the Kingdom of the Netherlands in Addis Ababa.

The interest of research groups in desiccation tolerance (DT) has increased substantially over the last decades. The emergence of germinated orthodox seeds and resurrection plants as main research models has pushed the limits of our knowledge beyond boundaries. At the same time, new questions and new challenges were posed. The work presented in this thesis aims at shedding light on some of these questions, deepening our understanding of DT and providing relevant information to improve stress resistance in crops. Chapter 2 is a survey of the literature and discusses the ecological and evolutionary significance for seeds to be able to re-acquire DT after germination. This chapter also discusses recent progress in DT studies using developing and germinated seeds of the model plants Arabidopsis thaliana and Medicago truncatula. In Chapter 3 I used microarray data from a time series of DT re-acquisition, together with network analysis of gene expression, to gain temporal resolution and identify relevant genes involved in the re-acquisition of DT in germinated A. thaliana seeds by incubation in abscisic acid (ABA). Overall, genes related to protection, response to stresses, seed development and seed dormancy were up-regulated, whereas genes related to cell growth and photosynthesis were down-regulated with time. Genes that respond early to exogenous ABA were related to wax biosynthetic processes, lipid storage, seed development and response to ABA stimulus. Genes that respond late to exogenous ABA were related to syncytium formation and response to abiotic stimulus (mainly light stimulus). The robustness of the network was confirmed by the projection of sets of genes – related to the acquisition of DT, seed dormancy, drought responses of adult plants and re-induction of DT by polyethylene glycol – on this network. In Chapter 4 the relation between DT in germinated seeds and drought resistance in adult plants is analysed, using rice (Oryza sativa) as experimental model. Considering the predictions of a future with lower availability of fresh water, efforts to increase rice drought tolerance without reducing yield are increasingly important. The results presented in this chapter suggest that the intrinsic mechanisms of drought tolerance in adult plants are part of the mechanisms used by seeds to tolerate desiccation, but the molecular nature of these mechanisms remains elusive. Chapter 5 explores the relation between DT and longevity in germinated seeds of the Brazilian tree species Sesbania virgata as experimental model. DT and longevity are acquired by orthodox seeds during the maturation phase of development and lost upon germination. DT can be re-induced in germinated seeds by an osmotic and/or ABA treatment, but there is no information on how these treatments affect seed longevity. S. virgata seeds lose DT slowly upon radicle growth. The radicle appeared to be the most sensitive organ and the cotyledons the most resistant. The ability to produce lateral roots was key for whole seedling survival. An osmotic treatment improved DT in germinated S. virgata seeds, but not longevity. This implies that DT and seed longevity can be uncoupled. Xerophyta viscosa is one of the best studied resurrection species. Despite the fact that adult plants and mature seeds display DT, young X. viscosa seedlings are sensitive to fast drying. A treatment with ABA can induce DT early in shoots of these seedlings, but not in roots. Chapter 6 addresses the changes in the transcriptome and proteome of X. viscosa seedlings during induction of DT. A draft genome sequence of X. viscosa was used to improve transcript and protein identification and annotation. Differences in ABA signalling and the cross talk between ABA and ethylene were presented as determinant for shoot and root responses. Moreover, differences in the accumulation of late embryogenesis abundant proteins were also shown as being key for DT in shoots and roots. In Chapter 7, DT-transcriptomes of distantly related organisms are compared and surveyed for a core set of genes representing the signatures of critical adaptive DT mechanisms. A shortlist of 260 genes emerged, with a significant number of genes under the control of ABI3 and related to dormancy. The results reinforced the idea that core mechanisms and key regulators involved in DT developed early in the history of life and were carried forward by diverse species and life forms in a conserved manner and in conjunction with dormancy. In Chapter 8, the findings of this thesis are integrated, showing how they can contribute to future improvement of stress tolerance in crops. The ability of germinated seeds to re-acquire DT is discussed in combination with dormancy and longevity and related to seed survival under unfavourable environmental conditions. The relationship between drought- and desiccation tolerance and the role of ABA are presented briefly. Possible approaches to mine for new genes for crop improvement, such as searching for conserved genes and analysing new genome sequences, are addressed. Finally, a new perspective of the way to consider the evolution of DT is proposed.

One of the major bottlenecks limiting farmers’ access to good quality seed for food crops in Uganda is the shortage of early generation seed (EGS - breeder and foundation) to produce sufficient quantities of certified and/or quality declared) to satisfy the needs of farmers. A national study was conducted between October 2015 to March 2016 to analyse pathways for promoting commercial and sustainable production and delivery of EGS. Five crops (hybrid maize, rice, beans, sesame and finger millet) were selected. The analysis provides real examples of potential business models that could scale in a commercially sustainable manner. For areas that are best suited to public sector investment, opportunities for public-private collaboration and increased efficiencies in the sector are outlined. Generalizable principles and recommendations to guide key stakeholders as they pursue policies, investments, and interventions are proposed.

Physical treatments of seeds to eradicate pathogens have the risk of reducing vitality of the seeds. Seed lots may differ in sensitivity to these treatments, therefore factors influencing this sensitivity, including the physiological condition of the seeds, should be identified. In this study priming was used to mimic the effect of pre-harvest onset of germination on the sensitivity to these treatments. The effect of humidification, by incubation for one day at 100% RH, followed by drying back, on the sensitivity was also analysed. Primed, humidified and control seeds were subjected to hot water, aerated steam or electron beam treatments at various levels. Two seed lots from Daucus carota (carrot), two seed lots from Brassica oleracea (kohlrabi) and one seed lot from Allium cepa (onion) were used in the tests. Primed seeds from all seed lots were more sensitive to the aerated steam treatment and the B. oleracea and A. cepa seed lots were also more sensitive to the hot water treatment after priming. Priming had no effect on the sensitivity towards the electron beam treatment. Humidification had no effect on the sensitivity towards the physical seed treatments, with the exception of the humidified onion seeds, which were clearly more tolerant towards the aerated steam treatment. It is concluded that seed companies should be aware that the onset seed germination processes prior to harvest may increase the sensitivity of the seeds towards aerated steam and hot water treatments.

Millipedes can cause considerable damage in the production of sweet potato and some other crops in East Africa. Quantitative information on intake of crop diets by and body weight gain of millipedes was collected in short-term no-choice feeding activity laboratory experiments conducted in north-eastern Uganda using female millipedes of the species Omopyge sudanica. Diets consisted of sweet potato and cassava storage root material, groundnut seeds, or maize grains. Differences in intake and body weight gain between diets were not statistically different. The consumption index, i.e., the ratio between intake and body weight gain, was significantly higher for sweet potato than for most other diets. The efficiency of conversion of ingested food, i.e., 100 × the ratio between body weight gain and intake, was significantly lower for the root crops — especially sweet potato — than for the grain crops. The research showed how difficult it is to obtain reliable, quantitative data on the feeding habits of millipedes, but also illustrated that O. sudanica can cause harm to crops in north-eastern Uganda and elsewhere in East Africa.

The opportunities for vegetable seed sales in Ethiopia are derived from the size and type of the product market. The product market for vegetables in Ethiopia has been growing rapidly, both in terms of crop portfolio, as well as size.

The opportunities for vegetable seed sales in Ethiopia are derived from the size and type of the product market. The product market for vegetables in Ethiopia has been growing rapidly, both in terms of crop portfolio, as well as size.

One of the most important developmental processes in the life-cycle of higher plants is the transition from a seed to a plant and from a generative to a vegetative developmental program. The major hallmark or end-point of the transition from seed to plant is the onset of photosynthesis and the concomitant shift from a heterotrophic to an autotrophic organism. It is advantageous for a species to keep the period of seedling establishment as short as possible since young seedlings are highly sensitive to biotic and abiotic stresses. This implies that the extreme stress tolerance of seeds to i.e. desiccation is lost upon germination. If the regulatory principles of the seed-to-seedling transition are better understood it may become feasible to maintain the seed’s stress tolerance well into the seedling stage. Despite the profound impact of seedling performance on crop establishment and yield, the seed-to-seedling transition has hardly been studied at the molecular level. This thesis aims at deciphering and understanding the molecular processes that govern this transition in Arabidopsis thaliana. A high-resolution study of the molecular events that occur during these successive transitional stages may provide clues as to the regulatory principles that drive this transition. It may also yield information about the factors that determine the (in)ability to revert to a developmental mode and which features are critical for the maintenance and loss of desiccation tolerance and other stress responses. In Chapter 1 important processes such as abscisic acid and their regulation are described and it is discussed in what way the seed-to-seedling transition may have links to a trait such as desiccation tolerance. An overview is presented of the current knowledge of the seed-to-seedling phase transition and the existence of a temporal developmental block that can be manipulated by osmotic treatment, the carbon/nitrogen balance and by abscisic acid which results in the re-establishment of desiccation tolerance. Chapter 2 focuses on comprehensive gene regulation by a detailed transcriptional analysis across seven developmental stages of the seed-to-seedling transition. It describes the inference of a gene co-expression network and several transcriptional modules. I show that such an approach highlights important molecular processes during seedling development, which would not likely be derived from comparative transcript profiling. Moreover, I show that a putative key regulator in one of the transcriptional modules affects late seedling establishment. In Chapter 3 it is shown how this phase transition is expressed in the primary metabolite profiles in correlation with gene expression. A metabolite-metabolite correlation analysis suggested two profiles, which point at the metabolic preparation of seed germination and of vigorous seedling establishment. Furthermore, a linear correlation between metabolite contents and transcript abundance (Chapter 2) provides a global view of the transcriptional and metabolic changes during the seed-to-seedling transition. It creates new perspectives of the regulatory complexes underlying the seed-to-seedling transition. Chapter 4 describes the development of a novel method to re-establish desiccation tolerance during the seed-to-seedling transition without adverse effects such as those caused by an osmotic treatment with polyethylene glycol. By using this method, named ‘Mild Air Drying Treatment’ (MADT), I show that the re-establishment of desiccation tolerance is not linked to a reduced ability to accumulate ABA in the desiccation sensitive seeds (germinated seeds at root hair stage). I also present a genetic interaction study of ABSCISIC ACID INSENSITIVE (ABI) genes in their germination response to ABA, and their response to the re-establishment of desiccation tolerance using the MADT. The interaction between ABI3 and ABI4, and between ABI4 and ABI5 act synergistically in the re-establishment of DT, as well as in the germination response to ABA. In a more in depth study in Chapter 5 I carried out an extensive transcript analysis to infer possible mechanisms of the re-establishment of desiccation tolerance using the MADT protocol. Possible mechanisms underlying the re-establishment of desiccation tolerance were inferred by employing a time-series comparison of germinated desiccation tolerant and -sensitive seeds. Early-response genes of the re-establishment of desiccation tolerance may play a role in events that promote the initial protection to dehydration stress, whereas the late-response genes may play a role in events that help seed to respond to the changes in water dynamics. Moreover, using a gene co-expression network and transcriptional module I concluded that a crosstalk between ABA-dependent and ABA-independent transcription factors regulate the re-establishment of desiccation tolerance. In Chapter 6 I discuss how the results presented in this thesis contribute to our knowledge of the molecular basis of the seed-to-seedling transition and the re-establishment of desiccation tolerance during its phase changes. Finally, new possibilities for further research are discussed, as well as the further use of the data sets to delineate the mechanisms underlying the seed-to-seedling transition and desiccation tolerance. Possible applications of the results for crop improvement are addressed. Thus, the generation of genetically modified plants that produce seeds with a stress tolerance that extends well into seedling stage may be feasible.

Summary Seed is the basic and most critical input for seed propagated agricultural crops: seed quality and seedling vigour determine plant establishment, growth and development in both natural and agricultural ecosystems. Seed quality and seedling vigour are mainly determined by the interactions of the following three components: genetic background, physiological quality and the environmental conditions during seed set, seed ripening, storage, seed germination and early seedling development. In the past, many efforts have been made to improve seed germination and seedling vigour by optimizing physiological and environmental factors (non-genetic factors); however, the paradigm has shifted to investigate genetic factors and to use these to improve crop performance by plant breeding. The aim of this thesis is to unravel the genetics of seed germination and seedling vigour under different conditions in Brassica rapa, using a systems genetics approach. Studies in many crop species have reported that seed germination and seedling vigour traits are governed by many genes and are strongly affected by environmental conditions. As salinity stress is becoming one of the most important abiotic stresses affecting crop growth and yield, we studied the genetics of seed germination and seedling vigour under neutral and salt stress conditions. For a number of crops, it has been established that larger seed size and higher seed weight indicate more reserve food and contribute positively to seedling establishment. Therefore, our hypothesis for this thesis is that transcriptional regulation of genes during seed development determines the composition and content of seed reserves, and that these seed reserves play a major role in seed germination and seedling growth, especially at the heterotrophic stage under optimal and sub-optimal conditions. B. rapa is an extremely diverse Brassica species which includes, besides many diverse leafy vegetable types and turnips, also oilseed crops. Brassica seeds are of high economic importance for several reasons. They are the starting point of the life cycle of the crop, but also they are directly used as sources of vegetable oil or condiments. At present, B. napus is the most important source of vegetable oil worldwide, but B. rapa is often used for introgression breeding to broaden its narrow genetic base resulting in genetic improvements. Therefore, the acquired knowledge is also useful for the scientific community and plant breeders working in B. napus and other Brassica species. In Chapter 2 we evaluated the genetic diversity of a B. rapa core collection of 168 accessions representing different crop types and geographic origins. Using the Bayesian cluster analysis software STRUCTURE, we identified four subpopulations: subpopulation 1 with accessions of Indian origin, spring oil, yellow sarson and rapid cycling; subpopulation 2 consisting of several types from Asian origins: pak choi, winter oil, mizuna, mibuna, komasuna, turnip green, oil rape and Asian turnip; subpopulation 3, which included mainly accessions of Chinese cabbage and subpopulation 4 with mostly vegetable turnip, fodder turnip and brocoletto accessions from European origin. The geographical distribution of the accessions was very much congruent with genetic, metabolic and morphological diversity. This initial study was followed by association studies for secondary metabolites from the tocopherol and carotenoids pathways, using the population structure of these four subpopulations as a correction term to control for spurious marker-trait associations (Chapter 2). Additionally, we used a machine learning approach, Random Forest (RF) regression, to find marker-trait associations. We chose the RF approach as it can handle large numbers of variables (markers, metabolites, transcript abundance) in combination with relatively small sample sets of accessions, to show its perspectives for application to the increasing amounts of data available through the different ~omics technologies. In our analysis, the markers showing significant association with metabolites identified by the RF approach overlapped with markers obtained from association mapping. Those markers could potentially be used for marker-assisted selection (MAS) in breeding for these secondary metabolites in different morphotypes or sub-populations. Knowledge of genetic distance as evaluated in this chapter allowed the choice of parents to create a segregating population for QTL analyses by maximizing genetic variation between the parents. In Chapter 4, a doubled haploid (DH) population from a cross of genetically diverse morphotypes of B. rapa, an oil-type yellow sarson (YS143) and a vegetable pak choi (PC175) (Chapter 2), was used to evaluate the genetic basis of seed germination and seedling vigour traits under both non-stress and salt stress conditions. The yellow sarson parent had larger seed size and higher thousand-seed weight than the pak choi parent, and displayed earlier onset, higher uniformity in germination, faster germination and maximum germination, and higher root- and shoot- lengths and biomass under both non-stress and salt stress conditions. Positive correlations of thousand-seed weight with earliness, speed and uniformity of germination and maximum germination percentage, supports that larger seeds germinate earlier, faster, more uniformly and to a higher maximum germination percentage than smaller seeds. Thus, we conclude that yellow sarson had higher seed quality and seedling vigour than pak choi. However yellow sarson also contributed negative alleles to seed germination, as illustrated by its allele of the QTL at A05 which decreases the uniformity of seed germination. In addition we also observed that yellow sarson seedling growth was more affected by salt stress than pak choi. All traits were scored over the DH population, and this clearly showed transgressive variation for most traits. Eight QTL hotspots were identified for seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 co-located with a homologue of the FLOWERING LOCUS C (BrFLC2) genes and its cis-acting expression QTL (cis-eQTL). FLC2 (BrFLC2 in B. rapa) is an important repressor of flowering time in both A. thaliana and B. rapa and recently, FLC2 was reported for its pleiotropic effect on seed germination in A. thaliana. A QTL hotspot on A05 with salt stress specific QTL co-located with the FATTY ACID DESATURASE 2 (BrFAD2) gene and its cis-eQTL. Besides the role of FAD2 in fatty acid desaturation, the up-regulation of this gene was associated with enhanced seed germination and hypocotyl elongation under salinity in B. napus (BnFAD2) and A. thaliana (FAD2). We observed epistatic interactions between the QTL hotspots at the BrFLC2 and BrFAD2 loci, and between other QTL hotspots. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. Therefore, morphological characteristics and the transcriptional signatures of developing seeds from yellow- and brown/black-seeded genotypes were studied to get to know the timing of key metabolic processes, to explore the major transcriptional differences and to identify the optimum stage for a genetical genomics study for B. rapa seed traits (Chapter 3). This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa. Most transcriptional changes occurred between 25 and 35 days after pollination (between the bent-cotyledon stage and the stage when the embryo fully fills the seed), which is later than in the related species B. napus. A weighted gene co-expression network analysis (WGCNA) identified 47 gene modules with different co-expression patterns, of which 17 showed a genotype effect, 4 modules a time effect during seed development and 6 modules both genotype and time effects. Based on the number of genes in gene modules, the predominant variation in gene expression was according to developmental stages rather than morphotype differences. We identified 17 putative cis-regulatory elements (motifs) for four co-regulated gene clusters of genes related to lipid metabolism. The identification of key physiological events, major expression patterns, and putative cis-regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of fatty acid composition and additional seed traits in Chapter 5. Since Brassica seeds are sources of vegetable oil, genetic studies of the gene regulatory mechanisms underlying lipid metabolism is of high importance, not only in relation to seed and seedling vigour, but also for Brassica oilseed breeding. In Chapter 5, an integrative approach of QTL mapping for fatty acids composition and for transcript abundance (eQTL) of genes related to lipid metabolism, together with gene co-expression networks was used to unravel the genetic regulation of seed fatty acid composition in the DH population of B. rapa. In this study, a confounding effect of flowering time variation was observed on fatty acid QTLs (metabolite level) at linkage group A02 and of seed colour variation on eQTLs (transcript level) at linkage group A09. At A02, fatty acid QTLs from 2009 seeds co-locate with the genetic position of a gene-targeted marker for BrFLC2, its cis-QTL, and a major flowering time QTL. Flowering time variation is very obvious in this DH population and the BrFLC2 gene at A02 (16.7 cM) is the major regulator of flowering time, with a non-functional allele in the yellow sarson parent. When QTL analysis was performed on seeds from 2011, from DH lines that flowered synchronously due to staggered sowing, this fatty acid QTL hotspot disappeared. The 2011 seed lot was used for further analysis combining fatty acid QTLs with eQTLs in this study. On A09, a large trans-eQTL hotspot was co-localized with a major seed colour QTL, in the region where the causal gene, the bHLH transcription factor BrTT8, was cloned. The role of this gene in seed colour development was functionally proven in B. rapa. As the yellow sarson and pak choi parents of this population have contrasting seed coat colour (Chapter 3) the DH lines segregated for seed colour. When seed colour variation was used as a co-variate in our statistical model, we could exclude its confounding effect on eQTL mapping. We compared the fatty acid QTL and eQTL results from the analyses before and after seed colour correction and later discuss the results from the analysis after correction. The distribution of major QTLs for fatty acids showed a relationship with the types of fatty acids: linkage group A03 contained major QTLs for monounsaturated fatty acids (MUFAs), A04 for saturated fatty acids (SFAs) and A05 for polyunsaturated fatty acids (PUFAs). Using a genetical genomics approach, eQTL hotspots were found at major fatty acid QTLs on A03, A04 and A05 and on A09. Finally, an eQTL-guided gene co-expression network of lipid metabolism related genes showed major hubs at the genes BrPLA2-ALPHA, BrWD-40, a number of seed storage protein genes and a transcription factor BrMD-2, suggesting essential roles of these genes in lipid metabolism. Several genes, such as BrFAE1, BrTAG1, BrFAD2, BrFAD5, BrFAD7, which were reported as important genes for fatty acid composition in seeds in other studies of related species, had relatively lower degrees of connection in the networks. However their cis-eQTLs co-localized with specific fatty acid QTLs, making them candidate genes for the observed variation. We hypothesize that these play a role in modifying fatty acid content or composition across genotypes, rather than playing essential roles in the pathway itself. These results suggest the need of a global study of lipid metabolism rather than a strict focus on the fatty acid biosynthesis pathway per se. This study gives a starting point for understanding the genetic regulation of lipid metabolism, by identification of a number of key regulatory genes, identified as major hub genes, and candidate genes for fatty acid QTLs. In the final chapter (Chapter 6) we summarize and critically discuss the relationships among phenotypic traits, metabolites and expression variation as well as the co-localization of QTLs from these different levels. In this thesis, we developed methodology to integrate transcriptomics and metabolomics data sets and to construct gene regulatory networks related to major fatty acids, and found a set of (possible) candidate genes involved in lipid metabolism. In the future, we recommend to integrate the genome-wide transcriptome data set with all major seed metabolites and phenotypic data on seed and seedling vigour to directly link all three components: transcriptome, metabolome and phenotypic traits, and ultimately expand the knowledge on the genetic regulation of seed metabolites, seed quality and seedling vigour in B. rapa to other Brassica species.

Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach by Paulo Roberto Ribeiro de Jesus The main objective of this thesis was to provide a detailed analysis of physiological, biochemical and molecular-genetic responses of Ricinus communis to temperature during seed germination and seedling establishment. In Chapter 2, I describe the assessment of 17 candidate reference genes across a diverse set of samples, including several tissues, various developmental stages and environmental conditions, encompassing seed germination and seedling growth in R. communis. These genes were tested by RT-qPCR and ranked according to the stability of their expression using two different approaches: GeNorm and NormFinder. Both GeNorm and Normfinder indicated that ACT, POB and PP2AA1 represent the optimal combination for normalization of gene expression data in inter-tissue studies. I also describe the optimal combination of reference genes for a subset of samples from root, endosperm and cotyledonary tissues. The selection of reference genes was validated by normalizing the expression levels of three target genes involved in energy metabolism with the identified optimal reference genes. This approach allowed me to identify stably expressed genes, and, thus, reference genes for use in RT-qPCR studies in seeds and seedlings of R. communis. In Chapter 3, a thermo-sensitive window is identified during seed germination in which high temperatures compromise subsequent seedling development. I assessed the biochemical and molecular requirements of R. communis germination for successful seedling establishment at varying temperatures. For that, I performed metabolite profiling (GC-TOF-MS) and measured transcript levels of key genes involved in several energy-generating pathways such as storage oil mobilization, β-oxidation of fatty acids and gluconeogenesis of seeds germinated at three different temperatures. Transient overexpression of genes encoding for malate synthase (MLS) and glycerol kinase (GK) resulted in higher starch levels in N. benthamiana leaves, which highlights the likely importance of these genes in energy-generating pathways for seedling establishment. Additionally, I showed that γ-aminobutyric acid (GABA), which is a stress-responsive metabolite, accumulated in response to the water content of the seeds during the initial phase of imbibition. In Chapter 4 I undertook a genomics approach using microarray analysis to determine transcriptome changes in three distinct developmental stages during seed germination at 20, 25 and 35ºC that could explain the thermo-sensitive window that is described in Chapter 3. Most of the differences in the R. communis transcriptome occurred between 6 hours of imbibition and the commencement of germination, i.e. radicle protrusion. This coincides with the thermo-sensitive window identified during seed germination in which high temperatures compromise seedling development. The transcriptome data was used to identify heat-stress responsive genes that might be involved in thermotolerance of R. communis during germination. Temperature had a major effect on genes involved in energy generating pathways, such as the Calvin-Benson-Bassham cycle, gluconeogenesis, and starch- and triacylglycerol degradation. Transcripts coding for ATP binding proteins, DNA binding proteins, RNA binding proteins, DNA-directed RNA polymerases I, II, and III, heat shock factor proteins, multiprotein-bridging factor proteins, and zinc finger proteins were also affected by temperature suggesting the whole transcriptional regulatory machinery was altered in response to temperature. Among the downregulated transcripts under high temperature, only three were shared by all three stages: an oxidation-related zinc finger 2, an F-box and wd40 domain protein, and a DNA binding protein/MYB-like transcription factor. Among the upregulated transcripts, nine were shared by all three stages: a BET1P/SFT1P-like protein, 14BB, a low-molecular-weight cysteine-rich protein LCR78, a WD-repeat protein, a GAST1 protein, an adenylate kinase 1/P-loop containing nucleoside triphosphate hydrolases superfamily protein, and four conserved hypothetical proteins. These genes constitute good candidates for further characterization of temperature-responsive genes in R. communis. In Chapter 5, I studied the genetic variation in the effect of temperature on growth of young R. communis seedlings and measured primary and secondary metabolites in roots and cotyledons of three R. communis genotypes, varying in stress tolerance. Seedling biomass was strongly affected by the temperature, with the lowest total biomass observed at 20ºC. The response in terms of biomass production for the genotype MPA11 was clearly different from the other two studied genotypes: genotype MPA11 produced heavier seedlings at all temperatures but the root biomass of this genotype decreased with increasing temperature, reaching the lowest value at 35ºC. In contrast, root biomass of genotypes MPB01 and IAC80 was not affected by temperature, suggesting that the roots of these genotypes are less sensitive to changes in temperature. A shift in carbon-nitrogen metabolism towards the accumulation of nitrogen-containing compounds seems to be the main biochemical response to support growth at higher temperatures. Carbohydrate content was reduced in response to increasing temperature in both roots and cotyledons, whereas amino acids accumulated to higher levels. The results in this chapter show that a specific balance between amino acids, carbohydrates and organic acids in the cotyledons and roots of genotype MPA11 seems to be an important trait for faster and more efficient growth of this genotype at higher temperatures. In Chapter 6, I decided to focus on the differential ability of genotypes MPA11 and IAC80 to sustain root biomass production at higher temperatures. Biomass allocation was assessed by measuring dry weight of roots, stems, and cotyledons of seedlings grown at three different temperatures. Seedlings grown at 25ºC and 35ºC showed greater biomass than seedlings grown at 20ºC. Cotyledon and stem dry weight increased for both genotypes with increasing temperature, whereas root biomass allocation showed a genotype-dependent behaviour. Genotype MPA11 showed a continuous increase in root dry weight with increasing temperature, while genotype IAC80 was not able to sustain further root growth at higher temperatures. Metabolite and gene expression profiles of genotype MPA11 demonstrated an increase in the levels of osmoprotectant molecules, such as galactinol and transcripts of genes encoding antioxidant enzymes and heat shock proteins, to a higher extent than in genotype IAC80. In Chapter 7 I raised the question whether carbohydrate accumulation in R. communis leaves, roots, and seeds, grown at low temperatures, as compared to higher temperatures, results from up-regulation of biosynthetic pathways, from down-regulation of catabolic pathways, or both. To answer this question, transcript levels were measured of genes encoding enzymes involved in starch biosynthesis, starch catabolism, and gluconeogenesis in leaves, roots, and seeds grown at 20ºC and 35ºC. Transcript levels of genes involved in starch catabolism were higher in leaves grown at 20ºC than at 35ºC, but up-regulation of genes involved in starch biosynthesis seems to compensate for this and, therefore, is the likely explanation for higher levels of starch in leaves grown at 20ºC. Higher levels of soluble carbohydrates in leaves grown at 20ºC may have been caused by a coordinated up-regulation of starch catabolism and gluconeogenesis pathways. In roots, starch catabolism and gluconeogenesis seem to be enhanced at elevated temperatures. Higher levels of starch in seeds germinated at low temperatures is associated with higher transcript levels of genes involved in starch biosynthesis. Similarly, higher transcript levels of RcPEPCK and RcFBPase are most likely causal for fructose and glucose accumulation in seeds germinated at 20ºC. This thesis provides important insights in the understanding of the plasticity of R. communis in response to temperature. The knowledge obtained may apply to other species as well. Additionally, based on the transcriptomics data, we selected several candidate genes that are potentially involved in, or required for, proper seed germination and seedling establishment under different temperatures, such as a number of transcription factors, a zinc finger protein, heat-shock proteins, malate synthase and glycerol kinase. Overexpressing Arabidopsis lines transformed with these R. communis genes, as well as Arabidopsis T-DNA lines, in which Arabidopsis homologs of these genes are knocked-out, are being generated for further phenotypical analysis. These overexpression and T-DNA lines should help us to understand the molecular requirements for vigorous seedling growth of R. communis under different environmental conditions. This work was performed at the Laboratory of Plant Physiology, Wageningen University. This research was financially supported by the Brazilian Government through the National Counsel of Technological and Scientific Development (CNPq grant number 200745/2011-5).

In this thesis I explore the ontological proposal of food sovereignty and I discuss the possibilities offered by studies like this one to the attempts of the social sciences to explain – in a symmetrical fashion - that develop between humans and other entities at the time of production, processing and consumption of food. In this effort I combine ethnography and history. I argue that in countries like Ecuador, food networks such as that of the lupine, Lupino mutabilis Sweet, since they do not establish ontological differences between nature and culture, promote the implementation of food sovereignty in practice, as long as agricultural and science and technology (S&T) policies enable the autonomous development of such networks. More specifically, food networks in the Andean highlands have functioned in a rhizomatic way, without establishing hierarchies between entities of different ontology: foods as goods or foods as gifts, society and nature, and have spread without discontinuities between town and country. This analysis enables me to show that these networks can promote food sovereignty, because in them is condensed an ontology distinct from that of modernity with regard to the cultivation, processing and consumption of food. Considering these findings I analyse the rationality of S&T policies and the current policies of the Ecuadorian State. I argue that such policies go against the logic of food networks. Food sovereignty is an achievable goal if Ecuadorian government policies contribute to the strengthening of food networks, creating new links so that they can sidestep the agribusiness model. The organisation of this thesis is unusual, as the object of study is a food network. This forced me to research and structure this dissertation in a particular way. So, I start with the ethnographic explanation of a food network. Here I analyse its operation, relationships and the paths it establishes. From this analysis it is possible to understand why S&T policies, specifically those related to plant breeding, created new social relations that affected the food networks of the highlands. I show here how the modern rationality on which agricultural policies are based inhibits the growth of food networks and works against food sovereignty. Then, from the analysis of the formation of the food sovereignty network, I examine the introduction of the food sovereignty proposal into the Ecuadorian Constitution and the changes made to the original proposal. I show how the translation of the Via Campesina proposal present in the constitution and the subsequent law is possible due to the intervention of actors linked with the big businesses of the food trade. All this enables me, finally, to discuss my contribution: the analysis of the ontological promise present in the food sovereignty proposal.

In this thesis I explore the ontological proposal of food sovereignty and I discuss the possibilities offered by studies like this one to the attempts of the social sciences to explain – in a symmetrical fashion - that develop between humans and other entities at the time of production, processing and consumption of food. In this effort I combine ethnography and history. I argue that in countries like Ecuador, food networks such as that of the lupine, Lupino mutabilis Sweet, since they do not establish ontological differences between nature and culture, promote the implementation of food sovereignty in practice, as long as agricultural and science and technology (S&T) policies enable the autonomous development of such networks. More specifically, food networks in the Andean highlands have functioned in a rhizomatic way, without establishing hierarchies between entities of different ontology: foods as goods or foods as gifts, society and nature, and have spread without discontinuities between town and country. This analysis enables me to show that these networks can promote food sovereignty, because in them is condensed an ontology distinct from that of modernity with regard to the cultivation, processing and consumption of food. Considering these findings I analyse the rationality of S&T policies and the current policies of the Ecuadorian State. I argue that such policies go against the logic of food networks. Food sovereignty is an achievable goal if Ecuadorian government policies contribute to the strengthening of food networks, creating new links so that they can sidestep the agribusiness model. The organisation of this thesis is unusual, as the object of study is a food network. This forced me to research and structure this dissertation in a particular way. So, I start with the ethnographic explanation of a food network. Here I analyse its operation, relationships and the paths it establishes. From this analysis it is possible to understand why S&T policies, specifically those related to plant breeding, created new social relations that affected the food networks of the highlands. I show here how the modern rationality on which agricultural policies are based inhibits the growth of food networks and works against food sovereignty. Then, from the analysis of the formation of the food sovereignty network, I examine the introduction of the food sovereignty proposal into the Ecuadorian Constitution and the changes made to the original proposal. I show how the translation of the Via Campesina proposal present in the constitution and the subsequent law is possible due to the intervention of actors linked with the big businesses of the food trade. All this enables me, finally, to discuss my contribution: the analysis of the ontological promise present in the food sovereignty proposal.

Summary Seed is the basic and most critical input for seed propagated agricultural crops: seed quality and seedling vigour determine plant establishment, growth and development in both natural and agricultural ecosystems. Seed quality and seedling vigour are mainly determined by the interactions of the following three components: genetic background, physiological quality and the environmental conditions during seed set, seed ripening, storage, seed germination and early seedling development. In the past, many efforts have been made to improve seed germination and seedling vigour by optimizing physiological and environmental factors (non-genetic factors); however, the paradigm has shifted to investigate genetic factors and to use these to improve crop performance by plant breeding. The aim of this thesis is to unravel the genetics of seed germination and seedling vigour under different conditions in Brassica rapa, using a systems genetics approach. Studies in many crop species have reported that seed germination and seedling vigour traits are governed by many genes and are strongly affected by environmental conditions. As salinity stress is becoming one of the most important abiotic stresses affecting crop growth and yield, we studied the genetics of seed germination and seedling vigour under neutral and salt stress conditions. For a number of crops, it has been established that larger seed size and higher seed weight indicate more reserve food and contribute positively to seedling establishment. Therefore, our hypothesis for this thesis is that transcriptional regulation of genes during seed development determines the composition and content of seed reserves, and that these seed reserves play a major role in seed germination and seedling growth, especially at the heterotrophic stage under optimal and sub-optimal conditions. B. rapa is an extremely diverse Brassica species which includes, besides many diverse leafy vegetable types and turnips, also oilseed crops. Brassica seeds are of high economic importance for several reasons. They are the starting point of the life cycle of the crop, but also they are directly used as sources of vegetable oil or condiments. At present, B. napus is the most important source of vegetable oil worldwide, but B. rapa is often used for introgression breeding to broaden its narrow genetic base resulting in genetic improvements. Therefore, the acquired knowledge is also useful for the scientific community and plant breeders working in B. napus and other Brassica species. In Chapter 2 we evaluated the genetic diversity of a B. rapa core collection of 168 accessions representing different crop types and geographic origins. Using the Bayesian cluster analysis software STRUCTURE, we identified four subpopulations: subpopulation 1 with accessions of Indian origin, spring oil, yellow sarson and rapid cycling; subpopulation 2 consisting of several types from Asian origins: pak choi, winter oil, mizuna, mibuna, komasuna, turnip green, oil rape and Asian turnip; subpopulation 3, which included mainly accessions of Chinese cabbage and subpopulation 4 with mostly vegetable turnip, fodder turnip and brocoletto accessions from European origin. The geographical distribution of the accessions was very much congruent with genetic, metabolic and morphological diversity. This initial study was followed by association studies for secondary metabolites from the tocopherol and carotenoids pathways, using the population structure of these four subpopulations as a correction term to control for spurious marker-trait associations (Chapter 2). Additionally, we used a machine learning approach, Random Forest (RF) regression, to find marker-trait associations. We chose the RF approach as it can handle large numbers of variables (markers, metabolites, transcript abundance) in combination with relatively small sample sets of accessions, to show its perspectives for application to the increasing amounts of data available through the different ~omics technologies. In our analysis, the markers showing significant association with metabolites identified by the RF approach overlapped with markers obtained from association mapping. Those markers could potentially be used for marker-assisted selection (MAS) in breeding for these secondary metabolites in different morphotypes or sub-populations. Knowledge of genetic distance as evaluated in this chapter allowed the choice of parents to create a segregating population for QTL analyses by maximizing genetic variation between the parents. In Chapter 4, a doubled haploid (DH) population from a cross of genetically diverse morphotypes of B. rapa, an oil-type yellow sarson (YS143) and a vegetable pak choi (PC175) (Chapter 2), was used to evaluate the genetic basis of seed germination and seedling vigour traits under both non-stress and salt stress conditions. The yellow sarson parent had larger seed size and higher thousand-seed weight than the pak choi parent, and displayed earlier onset, higher uniformity in germination, faster germination and maximum germination, and higher root- and shoot- lengths and biomass under both non-stress and salt stress conditions. Positive correlations of thousand-seed weight with earliness, speed and uniformity of germination and maximum germination percentage, supports that larger seeds germinate earlier, faster, more uniformly and to a higher maximum germination percentage than smaller seeds. Thus, we conclude that yellow sarson had higher seed quality and seedling vigour than pak choi. However yellow sarson also contributed negative alleles to seed germination, as illustrated by its allele of the QTL at A05 which decreases the uniformity of seed germination. In addition we also observed that yellow sarson seedling growth was more affected by salt stress than pak choi. All traits were scored over the DH population, and this clearly showed transgressive variation for most traits. Eight QTL hotspots were identified for seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 co-located with a homologue of the FLOWERING LOCUS C (BrFLC2) genes and its cis-acting expression QTL (cis-eQTL). FLC2 (BrFLC2 in B. rapa) is an important repressor of flowering time in both A. thaliana and B. rapa and recently, FLC2 was reported for its pleiotropic effect on seed germination in A. thaliana. A QTL hotspot on A05 with salt stress specific QTL co-located with the FATTY ACID DESATURASE 2 (BrFAD2) gene and its cis-eQTL. Besides the role of FAD2 in fatty acid desaturation, the up-regulation of this gene was associated with enhanced seed germination and hypocotyl elongation under salinity in B. napus (BnFAD2) and A. thaliana (FAD2). We observed epistatic interactions between the QTL hotspots at the BrFLC2 and BrFAD2 loci, and between other QTL hotspots. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. Therefore, morphological characteristics and the transcriptional signatures of developing seeds from yellow- and brown/black-seeded genotypes were studied to get to know the timing of key metabolic processes, to explore the major transcriptional differences and to identify the optimum stage for a genetical genomics study for B. rapa seed traits (Chapter 3). This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa. Most transcriptional changes occurred between 25 and 35 days after pollination (between the bent-cotyledon stage and the stage when the embryo fully fills the seed), which is later than in the related species B. napus. A weighted gene co-expression network analysis (WGCNA) identified 47 gene modules with different co-expression patterns, of which 17 showed a genotype effect, 4 modules a time effect during seed development and 6 modules both genotype and time effects. Based on the number of genes in gene modules, the predominant variation in gene expression was according to developmental stages rather than morphotype differences. We identified 17 putative cis-regulatory elements (motifs) for four co-regulated gene clusters of genes related to lipid metabolism. The identification of key physiological events, major expression patterns, and putative cis-regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of fatty acid composition and additional seed traits in Chapter 5. Since Brassica seeds are sources of vegetable oil, genetic studies of the gene regulatory mechanisms underlying lipid metabolism is of high importance, not only in relation to seed and seedling vigour, but also for Brassica oilseed breeding. In Chapter 5, an integrative approach of QTL mapping for fatty acids composition and for transcript abundance (eQTL) of genes related to lipid metabolism, together with gene co-expression networks was used to unravel the genetic regulation of seed fatty acid composition in the DH population of B. rapa. In this study, a confounding effect of flowering time variation was observed on fatty acid QTLs (metabolite level) at linkage group A02 and of seed colour variation on eQTLs (transcript level) at linkage group A09. At A02, fatty acid QTLs from 2009 seeds co-locate with the genetic position of a gene-targeted marker for BrFLC2, its cis-QTL, and a major flowering time QTL. Flowering time variation is very obvious in this DH population and the BrFLC2 gene at A02 (16.7 cM) is the major regulator of flowering time, with a non-functional allele in the yellow sarson parent. When QTL analysis was performed on seeds from 2011, from DH lines that flowered synchronously due to staggered sowing, this fatty acid QTL hotspot disappeared. The 2011 seed lot was used for further analysis combining fatty acid QTLs with eQTLs in this study. On A09, a large trans-eQTL hotspot was co-localized with a major seed colour QTL, in the region where the causal gene, the bHLH transcription factor BrTT8, was cloned. The role of this gene in seed colour development was functionally proven in B. rapa. As the yellow sarson and pak choi parents of this population have contrasting seed coat colour (Chapter 3) the DH lines segregated for seed colour. When seed colour variation was used as a co-variate in our statistical model, we could exclude its confounding effect on eQTL mapping. We compared the fatty acid QTL and eQTL results from the analyses before and after seed colour correction and later discuss the results from the analysis after correction. The distribution of major QTLs for fatty acids showed a relationship with the types of fatty acids: linkage group A03 contained major QTLs for monounsaturated fatty acids (MUFAs), A04 for saturated fatty acids (SFAs) and A05 for polyunsaturated fatty acids (PUFAs). Using a genetical genomics approach, eQTL hotspots were found at major fatty acid QTLs on A03, A04 and A05 and on A09. Finally, an eQTL-guided gene co-expression network of lipid metabolism related genes showed major hubs at the genes BrPLA2-ALPHA, BrWD-40, a number of seed storage protein genes and a transcription factor BrMD-2, suggesting essential roles of these genes in lipid metabolism. Several genes, such as BrFAE1, BrTAG1, BrFAD2, BrFAD5, BrFAD7, which were reported as important genes for fatty acid composition in seeds in other studies of related species, had relatively lower degrees of connection in the networks. However their cis-eQTLs co-localized with specific fatty acid QTLs, making them candidate genes for the observed variation. We hypothesize that these play a role in modifying fatty acid content or composition across genotypes, rather than playing essential roles in the pathway itself. These results suggest the need of a global study of lipid metabolism rather than a strict focus on the fatty acid biosynthesis pathway per se. This study gives a starting point for understanding the genetic regulation of lipid metabolism, by identification of a number of key regulatory genes, identified as major hub genes, and candidate genes for fatty acid QTLs. In the final chapter (Chapter 6) we summarize and critically discuss the relationships among phenotypic traits, metabolites and expression variation as well as the co-localization of QTLs from these different levels. In this thesis, we developed methodology to integrate transcriptomics and metabolomics data sets and to construct gene regulatory networks related to major fatty acids, and found a set of (possible) candidate genes involved in lipid metabolism. In the future, we recommend to integrate the genome-wide transcriptome data set with all major seed metabolites and phenotypic data on seed and seedling vigour to directly link all three components: transcriptome, metabolome and phenotypic traits, and ultimately expand the knowledge on the genetic regulation of seed metabolites, seed quality and seedling vigour in B. rapa to other Brassica species.

Keywords: Technography, Oryza glaberrima, Oryza sativa, farmer hybrids, sub-optimal agriculture, farmer adaptive management, plant genetic resources, peace and extreme (wartime) conditions, local seed channels, selection for robustness, Sierra Leone, West Africa. Abstract Mokuwa, G. A. (2015) Management of rice seed during insurgency: a case study in Sierra Leone. PhD Thesis, Wageningen University, 267 pp. In large parts of West Africa small scale farmers rely upon the cultivation of upland rice under low input conditions in a great diversity of micro-environments. It has been suggested that formal research should consider the context within which farmers address their food security issues. But these contexts need further clarification for poor and marginalized farm households facing many challenges, including dislocations associated with political and social unrest, and civil war. The research presented in this thesis builds on earlier findings concerning farmer management of rice genetic resources under farmer low-resource conditions. It starts with a regional focus, drawing on methods from the social and biological sciences, concerning the human, environmental and technical factors shaping the character and composition of rice varieties grown by small-scale farmers in coastal West Africa (seven countries from Senegal to Togo) and then focuses on specific in-depth field studies undertaken in Sierra Leone. Findings show that farmer rice genetic resources were persistently and enduringly adapted to local agro-ecologies via strong selection processes and local adaptation strategies, and that these adaptive processes were largely unaffected by the temporary contingencies of civil war. It is also shown that even under extreme (war-time) conditions success indicators in farmers’ local seed channels remain robust. Farmers continue to select and adapt their seed types to local contingencies, and war served as yet one more stimulus to further adaptation. This persistent human selective activity continues to make a significant contribution to the food security of poor and marginalized farm households in the region. The major finding of this thesis is that selection for robustness among varieties of the local staple, rice, helped to protect Sierra Leonean farmers against some of the worst effects of war-induced food insecurity. In this sense, therefore, war may have served to strengthen and prolong farmer preferences for robustness, but it was not the cause of this preference. The marked diversity farmers maintain in their rice varieties is understood to be part of a longer-term risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. In a world facing major climatic changes this local capacity for seed selection and innovation ought to be a valued resource for technological change. The present study provides a starting point for thinking about the improved effectiveness of institutional innovation strategies for farmer participatory innovation activities.

One of the most important developmental processes in the life-cycle of higher plants is the transition from a seed to a plant and from a generative to a vegetative developmental program. The major hallmark or end-point of the transition from seed to plant is the onset of photosynthesis and the concomitant shift from a heterotrophic to an autotrophic organism. It is advantageous for a species to keep the period of seedling establishment as short as possible since young seedlings are highly sensitive to biotic and abiotic stresses. This implies that the extreme stress tolerance of seeds to i.e. desiccation is lost upon germination. If the regulatory principles of the seed-to-seedling transition are better understood it may become feasible to maintain the seed’s stress tolerance well into the seedling stage. Despite the profound impact of seedling performance on crop establishment and yield, the seed-to-seedling transition has hardly been studied at the molecular level. This thesis aims at deciphering and understanding the molecular processes that govern this transition in Arabidopsis thaliana. A high-resolution study of the molecular events that occur during these successive transitional stages may provide clues as to the regulatory principles that drive this transition. It may also yield information about the factors that determine the (in)ability to revert to a developmental mode and which features are critical for the maintenance and loss of desiccation tolerance and other stress responses. In Chapter 1 important processes such as abscisic acid and their regulation are described and it is discussed in what way the seed-to-seedling transition may have links to a trait such as desiccation tolerance. An overview is presented of the current knowledge of the seed-to-seedling phase transition and the existence of a temporal developmental block that can be manipulated by osmotic treatment, the carbon/nitrogen balance and by abscisic acid which results in the re-establishment of desiccation tolerance. Chapter 2 focuses on comprehensive gene regulation by a detailed transcriptional analysis across seven developmental stages of the seed-to-seedling transition. It describes the inference of a gene co-expression network and several transcriptional modules. I show that such an approach highlights important molecular processes during seedling development, which would not likely be derived from comparative transcript profiling. Moreover, I show that a putative key regulator in one of the transcriptional modules affects late seedling establishment. In Chapter 3 it is shown how this phase transition is expressed in the primary metabolite profiles in correlation with gene expression. A metabolite-metabolite correlation analysis suggested two profiles, which point at the metabolic preparation of seed germination and of vigorous seedling establishment. Furthermore, a linear correlation between metabolite contents and transcript abundance (Chapter 2) provides a global view of the transcriptional and metabolic changes during the seed-to-seedling transition. It creates new perspectives of the regulatory complexes underlying the seed-to-seedling transition. Chapter 4 describes the development of a novel method to re-establish desiccation tolerance during the seed-to-seedling transition without adverse effects such as those caused by an osmotic treatment with polyethylene glycol. By using this method, named ‘Mild Air Drying Treatment’ (MADT), I show that the re-establishment of desiccation tolerance is not linked to a reduced ability to accumulate ABA in the desiccation sensitive seeds (germinated seeds at root hair stage). I also present a genetic interaction study of ABSCISIC ACID INSENSITIVE (ABI) genes in their germination response to ABA, and their response to the re-establishment of desiccation tolerance using the MADT. The interaction between ABI3 and ABI4, and between ABI4 and ABI5 act synergistically in the re-establishment of DT, as well as in the germination response to ABA. In a more in depth study in Chapter 5 I carried out an extensive transcript analysis to infer possible mechanisms of the re-establishment of desiccation tolerance using the MADT protocol. Possible mechanisms underlying the re-establishment of desiccation tolerance were inferred by employing a time-series comparison of germinated desiccation tolerant and -sensitive seeds. Early-response genes of the re-establishment of desiccation tolerance may play a role in events that promote the initial protection to dehydration stress, whereas the late-response genes may play a role in events that help seed to respond to the changes in water dynamics. Moreover, using a gene co-expression network and transcriptional module I concluded that a crosstalk between ABA-dependent and ABA-independent transcription factors regulate the re-establishment of desiccation tolerance. In Chapter 6 I discuss how the results presented in this thesis contribute to our knowledge of the molecular basis of the seed-to-seedling transition and the re-establishment of desiccation tolerance during its phase changes. Finally, new possibilities for further research are discussed, as well as the further use of the data sets to delineate the mechanisms underlying the seed-to-seedling transition and desiccation tolerance. Possible applications of the results for crop improvement are addressed. Thus, the generation of genetically modified plants that produce seeds with a stress tolerance that extends well into seedling stage may be feasible.

The study presents an integrated assessment of Myanmar’s seed sector. The study includes information and analyses on regulatory environment for seed production and sales, a characterization of Myanmar’s seed sector with its various seed systems, a landscape of current seed sector interventions; an analysis of three seed value-chains and Myanmar’s seed farm system; as well as business opportunities for the private sector. The report concludes with a number of pathways for developing a vibrant seed sector in which quality seed of superior varieties can be accessed by farmers.

The study presents an integrated assessment of Myanmar’s seed sector. The study includes information and analyses on regulatory environment for seed production and sales, a characterization of Myanmar’s seed sector with its various seed systems, a landscape of current seed sector interventions; an analysis of three seed value-chains and Myanmar’s seed farm system; as well as business opportunities for the private sector. The report concludes with a number of pathways for developing a vibrant seed sector in which quality seed of superior varieties can be accessed by farmers.

The recommendations focus on the need to increase the availability of and access to quality seeds; improve quality, varietal sustainability and resilience of the seed system; build capacities of key actors to improve on their production and business skills; and address issues of enabling environment in seed security.

Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach by Paulo Roberto Ribeiro de Jesus The main objective of this thesis was to provide a detailed analysis of physiological, biochemical and molecular-genetic responses of Ricinus communis to temperature during seed germination and seedling establishment. In Chapter 2, I describe the assessment of 17 candidate reference genes across a diverse set of samples, including several tissues, various developmental stages and environmental conditions, encompassing seed germination and seedling growth in R. communis. These genes were tested by RT-qPCR and ranked according to the stability of their expression using two different approaches: GeNorm and NormFinder. Both GeNorm and Normfinder indicated that ACT, POB and PP2AA1 represent the optimal combination for normalization of gene expression data in inter-tissue studies. I also describe the optimal combination of reference genes for a subset of samples from root, endosperm and cotyledonary tissues. The selection of reference genes was validated by normalizing the expression levels of three target genes involved in energy metabolism with the identified optimal reference genes. This approach allowed me to identify stably expressed genes, and, thus, reference genes for use in RT-qPCR studies in seeds and seedlings of R. communis. In Chapter 3, a thermo-sensitive window is identified during seed germination in which high temperatures compromise subsequent seedling development. I assessed the biochemical and molecular requirements of R. communis germination for successful seedling establishment at varying temperatures. For that, I performed metabolite profiling (GC-TOF-MS) and measured transcript levels of key genes involved in several energy-generating pathways such as storage oil mobilization, β-oxidation of fatty acids and gluconeogenesis of seeds germinated at three different temperatures. Transient overexpression of genes encoding for malate synthase (MLS) and glycerol kinase (GK) resulted in higher starch levels in N. benthamiana leaves, which highlights the likely importance of these genes in energy-generating pathways for seedling establishment. Additionally, I showed that γ-aminobutyric acid (GABA), which is a stress-responsive metabolite, accumulated in response to the water content of the seeds during the initial phase of imbibition. In Chapter 4 I undertook a genomics approach using microarray analysis to determine transcriptome changes in three distinct developmental stages during seed germination at 20, 25 and 35ºC that could explain the thermo-sensitive window that is described in Chapter 3. Most of the differences in the R. communis transcriptome occurred between 6 hours of imbibition and the commencement of germination, i.e. radicle protrusion. This coincides with the thermo-sensitive window identified during seed germination in which high temperatures compromise seedling development. The transcriptome data was used to identify heat-stress responsive genes that might be involved in thermotolerance of R. communis during germination. Temperature had a major effect on genes involved in energy generating pathways, such as the Calvin-Benson-Bassham cycle, gluconeogenesis, and starch- and triacylglycerol degradation. Transcripts coding for ATP binding proteins, DNA binding proteins, RNA binding proteins, DNA-directed RNA polymerases I, II, and III, heat shock factor proteins, multiprotein-bridging factor proteins, and zinc finger proteins were also affected by temperature suggesting the whole transcriptional regulatory machinery was altered in response to temperature. Among the downregulated transcripts under high temperature, only three were shared by all three stages: an oxidation-related zinc finger 2, an F-box and wd40 domain protein, and a DNA binding protein/MYB-like transcription factor. Among the upregulated transcripts, nine were shared by all three stages: a BET1P/SFT1P-like protein, 14BB, a low-molecular-weight cysteine-rich protein LCR78, a WD-repeat protein, a GAST1 protein, an adenylate kinase 1/P-loop containing nucleoside triphosphate hydrolases superfamily protein, and four conserved hypothetical proteins. These genes constitute good candidates for further characterization of temperature-responsive genes in R. communis. In Chapter 5, I studied the genetic variation in the effect of temperature on growth of young R. communis seedlings and measured primary and secondary metabolites in roots and cotyledons of three R. communis genotypes, varying in stress tolerance. Seedling biomass was strongly affected by the temperature, with the lowest total biomass observed at 20ºC. The response in terms of biomass production for the genotype MPA11 was clearly different from the other two studied genotypes: genotype MPA11 produced heavier seedlings at all temperatures but the root biomass of this genotype decreased with increasing temperature, reaching the lowest value at 35ºC. In contrast, root biomass of genotypes MPB01 and IAC80 was not affected by temperature, suggesting that the roots of these genotypes are less sensitive to changes in temperature. A shift in carbon-nitrogen metabolism towards the accumulation of nitrogen-containing compounds seems to be the main biochemical response to support growth at higher temperatures. Carbohydrate content was reduced in response to increasing temperature in both roots and cotyledons, whereas amino acids accumulated to higher levels. The results in this chapter show that a specific balance between amino acids, carbohydrates and organic acids in the cotyledons and roots of genotype MPA11 seems to be an important trait for faster and more efficient growth of this genotype at higher temperatures. In Chapter 6, I decided to focus on the differential ability of genotypes MPA11 and IAC80 to sustain root biomass production at higher temperatures. Biomass allocation was assessed by measuring dry weight of roots, stems, and cotyledons of seedlings grown at three different temperatures. Seedlings grown at 25ºC and 35ºC showed greater biomass than seedlings grown at 20ºC. Cotyledon and stem dry weight increased for both genotypes with increasing temperature, whereas root biomass allocation showed a genotype-dependent behaviour. Genotype MPA11 showed a continuous increase in root dry weight with increasing temperature, while genotype IAC80 was not able to sustain further root growth at higher temperatures. Metabolite and gene expression profiles of genotype MPA11 demonstrated an increase in the levels of osmoprotectant molecules, such as galactinol and transcripts of genes encoding antioxidant enzymes and heat shock proteins, to a higher extent than in genotype IAC80. In Chapter 7 I raised the question whether carbohydrate accumulation in R. communis leaves, roots, and seeds, grown at low temperatures, as compared to higher temperatures, results from up-regulation of biosynthetic pathways, from down-regulation of catabolic pathways, or both. To answer this question, transcript levels were measured of genes encoding enzymes involved in starch biosynthesis, starch catabolism, and gluconeogenesis in leaves, roots, and seeds grown at 20ºC and 35ºC. Transcript levels of genes involved in starch catabolism were higher in leaves grown at 20ºC than at 35ºC, but up-regulation of genes involved in starch biosynthesis seems to compensate for this and, therefore, is the likely explanation for higher levels of starch in leaves grown at 20ºC. Higher levels of soluble carbohydrates in leaves grown at 20ºC may have been caused by a coordinated up-regulation of starch catabolism and gluconeogenesis pathways. In roots, starch catabolism and gluconeogenesis seem to be enhanced at elevated temperatures. Higher levels of starch in seeds germinated at low temperatures is associated with higher transcript levels of genes involved in starch biosynthesis. Similarly, higher transcript levels of RcPEPCK and RcFBPase are most likely causal for fructose and glucose accumulation in seeds germinated at 20ºC. This thesis provides important insights in the understanding of the plasticity of R. communis in response to temperature. The knowledge obtained may apply to other species as well. Additionally, based on the transcriptomics data, we selected several candidate genes that are potentially involved in, or required for, proper seed germination and seedling establishment under different temperatures, such as a number of transcription factors, a zinc finger protein, heat-shock proteins, malate synthase and glycerol kinase. Overexpressing Arabidopsis lines transformed with these R. communis genes, as well as Arabidopsis T-DNA lines, in which Arabidopsis homologs of these genes are knocked-out, are being generated for further phenotypical analysis. These overexpression and T-DNA lines should help us to understand the molecular requirements for vigorous seedling growth of R. communis under different environmental conditions. This work was performed at the Laboratory of Plant Physiology, Wageningen University. This research was financially supported by the Brazilian Government through the National Counsel of Technological and Scientific Development (CNPq grant number 200745/2011-5).

In gangbare landbouwsystemen is, blijkens literatuuronderzoek, het risico van onkruidverspreiding via organische mest beperkt tot enige probleemsoorten. In dit artikel wordt aan de hand van verschillen in 'gangbare mest' en mest geproduceerd op biologische bedrijven duidelijk gemaakt, dat eerdere risico-schattingen niet volledig overdraagbaar zijn op biologische systemen. Er is experimenteel onderzoek gaande om de leemtes in kennis te vullen

Zaadbehandeling is doorgaans een uitgelezen kans om gebruik van gewasbeschermingsmiddelen fors terug te dringen. Coating van het zaad met insecticiden kan in een aantal situaties een effectieve bestrijdingsmethode zijn. Doordat de volvelds-, kweekplaat-, plantvoetbehandeling en soms een gewasbehandeling bij de start van de teelt kan vervallen, kan zo een grote besparing op het gebruik van middel verkregen worden. Bij coating wordt zaad voorzien van een dun laagje lijmstof. Dit voorkomt verstuiving van insecticiden, maar het vookomt ook dat de mens met het (giftige) middel in aanraking komt. Bij zaadbehandeling met insecticiden is coating dan ook verplicht. De voordelen van zaadcoating op een rij