The research seeks to understand the virus-host plant interactions for cassava brown streak disease (CBSD) caused by two viruses, Cassava brown streak virus (CBSV) and Ugandan Cassava brown streak virus (UCBSV) of the genus Ipomovirus, family Potyviridae. The diversity of six CBSD isolates from the endemic (Kenya, Malawi, Mozambique and Tanzania) and the recently developed epidemic areas (Uganda) of the disease in eastern Africa was studied. Five cassava varieties differing in virus resistance levels; Albert, Columbian, Ebwanateraka, TMS60444 (all susceptible) and Kiroba (tolerant) were graft-inoculated with the UCBSV and CBSV isolates. Based on a number of parameters, the isolates can be grouped into two main categories; severe and milder forms. Transmission of viruses using non-vector modes confirmed that CBSV was sap transmissible from cassava to cassava. Graft-inoculation of infected scions onto CBSD-free cassava plants was the most efficient mode of transmission which resulted in 80 and 100% rate for UCBSV and CBSV respectively. The two virus isolates were not transmitted through contaminated tools and hands. The effect of host-tolerance on virus was investigated in a long-term experiment where three cassava varieties Albert, Kiroba and Kaleso (field-resistant to CBSD) were graft-inoculated with UCBSV and CBSV. The three cassava varieties showed differences in virus movement, symptom development, severity and relative virus titres. The mechanisms of resistance to CBSD were investigated by making cuttings, from various parts of the plants, and a greater number of disease-free plants were generated from cuttings made from Kaleso than Kiroba and Albert. The fecundity of B. tabaci and its ability to transmit the virus were determined and results indicated no significant differences in the ability of the three cassava varieties to support whitefly development. Finally, thermal and chemical treatments of tissue cultured plants were conducted and the combinations of both treatments produced the greatest number of disease-free plants in all three varieties; Kaleso (50%), Kiroba (44%) and Albert (35%). The information generated in this thesis has greatly improved our understanding of the interactions between the three biotic factors; the host, virus and vector in the CBSD-pathosystem, which would be highly useful in designing effective disease management strategies.

This is an interdisciplinary research project on cassava (Manihot esculenta Crantz, Euphorbiaceae) ultimately working towards producing cassava roots which are long-lasting, free of post-harvest physiological deterioration (PPD). It aims to contribute to ensuring food security. In cassava, scopoletin and its -glycoside scopolin are considered phytoanticipants, not phytoalexins, due to their increasing accumulation during the PPD process compared to their barely detectable levels in fresh roots. Starting with a focussed literature review on the potential of cassava, contrasted with its limitations on harvesting due to PPD, and biosynthesis along the phenylpropanoid pathway of key hydroxycoumarins, e.g. scopoletin and esculetin, the associated gaps in our current knowledge have been set out. Whether scopoletin is biosynthesized de novo from L-phenylalanine in response to stress, or whether stress prompts its release from the corresponding glycoside is unknown. Therefore, assessing hydroxycoumarin biosynthesis and quantifying their accumulation patterns have been undertaken in wild-type and transgenic plants in order to elucidate the divergence in scopoletin biosynthetic pathways. The identification of key genes on each pathway leading to scopoletin in cassava, and then exploring their functional identities using the model plant A. thaliana and genetically engineered E. coli, where the genes were isolated, cloned, and expressed, were also undertaken. Transgenic A. thaliana lines with no activity of the key enzymes on the proposed pathway, namely F6ʹH1, CCoAOMT, and EOMT, were developed. Competition feeding experiments using stable isotopically labelled potential biosynthetic intermediates showed the incorporation of labelled ferulate into scopoletin in transgenic A.t-F6´H1 and M.e-F6´H. This confirmed the activity of other hydroxylase enzymes rather than F6´H1 in the ortho-hydroxylation steps. The hydroxycoumarins of interest were isolated, characterized, and quantified in the wild type and mutant lines using chromatographic and spectroscopic techniques, mainly NMR, HR-MS, and LC-MS. Taken together, a significant contribution to knowledge about hydroxycoumarin biosynthesis has been made.

Manioc (Manihot esculenta Crantz) is a staple food in the North and NE of Brazil and is the main crop and source of sustenance for many thousands of small-scale family farmers. It is native to Brazil and has been cultivated and adapted over thousands of years by indigenous peoples and small-scale farmers. Some 500 million people in the tropics of the Americas, Africa and the Far East currently rely on manioc as a staple crop for their daily energy needs. The study focuses both on farmers’ in situ maintenance of agrobiodiversity and on their management of change across the whole sequence of the production both of the manioc crop and manioc foods, and of the distribution, exchange and consumption of the foods (‘the Manioc Chain’). It further analyses the contrasting systems whereby manioc is classified and named by farmers and agronomists by reference to the manioc varieties cultivated in four case study sites. Much of the specialised literature on agrobiodiversity – along with global debates about food security and rural development – deals only with the specifically agricultural practice of growing food crops. This literature omits consideration of the other elements of the Manioc Chain and only rarely draws on the type of ethnographic and ethnobotanical literature that provides the historical and cultural framework for this research. Four case studies of manioc farming communities were conducted over a period of nine months – two in Pará and two in Bahia. The approach to this enquiry is farmer-centred and interdisciplinary. Empirical findings are based on interviews and visits with about 60 farmers, agricultural extension agents in the four sites and other agricultural professionals and numerous group and family discussions. The findings are complemented by a tabulation of the characteristics of around 214 varieties as a contribution to the ethnobotany of manioc. The findings demonstrate that the loss of genetic diversity in manioc tends to be in inverse proportion to the proximity of the community to large urban centres. There remain expert farmers who cultivate diversity for cultural and not just for economic reasons. The creativity of these farmers and of their families, as producers of manioc foods, arises within dynamic local food cultures. It is highly responsive to local market demand. Yet, even so, many aspects of the culture of these rural communities go unrecognised by professionals. A change of thinking will be necessary if the in situ conservation practised by many small farmers is to continue and not to be eroded. The economic preoccupations of agricultural professionals are rarely matched with any parallel interest in the on-farm conservation of agrobiodiversity. Farmers’ understanding, perceptions and management of manioc diversity exist in a separate realm. There is a disparity of outlook. The professionals want to help the farmers to adopt modern practices and to grow high yield varieties. Yet farmers’ motivations go wider than this. They manage many varieties of the crop for reasons that include minimising disease and pest infestations, ensuring soil quality, producing diverse manioc foods to satisfy different tastes and cultivating varieties that they find ‘pretty’ or unusual. The research analyses all stages of the Manioc Chain. This broad scope provides the conceptual basis for the finding that farmers adapt to externally induced change strategically by changing their practice in any one – or in a combination – of the several aspects of the Manioc Chain. In doing so, the farmers draw upon local knowledge which varies significantly between localities while also learning from external agents. The study concludes by arguing for a change in thinking of the professionals as to the framing of and the approach to the issue of retaining in situ, on-farm agrobiodiversity for the benefit of the farmers and for those whom they supply. Agrobiodiversity in manioc is a vital resource for future generations that once lost can never be replaced.

Cassava (Manihot esculenta Crantz) is an important tropical crop which provides a large portion of daily calories intake to hundreds of millions of people in Africa, Latin America, and tropical Asia. Cassava is grown for its starchy storage roots as staple food, as animal feed, and as industrial raw material. The utilisation of cassava is hindered by its characteristic physiological response, the post-harvest physiological deterioration (PPD). The inevitable wounding caused during harvesting and handling will trigger a series of physiological responses within 24 to 48 hours, which causes a blue-black discoloration in the storage roots, rendering these roots unmarketable and unpalatable in a few days. During the PPD response large amount of phenylpropanoid compounds, especially scopoletin and its glycoside, accumulate in the roots. Scopoletin may play an important role in PPD development but little work has been done on the possible relationship. Here we aim to examine the effects of altering scopoletin synthesis in cassava roots on the PPD response. In Arabidopsis thaliana, gene F6’H1 (feruloul CoA 6’-hydroxylase 1) is indispensable in the biosynthesis of scopoletin. Cassava F6’H1 candidate gene family involved in scopoletin synthesis were identified by their ability to functionally complement F6’H1 T-DNA insertion mutation in Arabidopsis thaliana that prevented synthesis of scopoletin. RNAi constructs targeting the identified cassava F6’H1 candidate gene family were designed, under the control of either constitutive CaMV 35S or root-specific StPAT promoters. These were used to transform wild-type cassava to down-regulate the expression of these scopoletin synthetic genes in F6’H1 gene family. The inhibition of cassava F6’H1 candidate gene expression and thus the scopoletin synthesis in transgenic cassava roots were confirmed by qRT-PCR and LC-MS, respectively. The RNAi transgenic cassava lines show less scopoletin accumulation and inhibited F6’H1 candidate genes expression during the PPD response. A reduced PPD discoloration development compared to that of the wild-type was also observed in the RNAi transgenic cassava lines.

More than 70% of Ghanaian farmers depend on cassava farming and processing as part of their livelihood activities. The study sought to identify the actors in the cassava value chains, how their livelihood features influence upgrading in the value chains and also, factors that farmers consider in deciding whether to sell fresh cassava roots to intermediate processors or to process the roots themselves and sell. The study was conducted in locations in six districts in Ghana. It combined the Value Chain Approach and the Sustainable Livelihoods Approach using qualitative and quantitative data. A stakeholder workshop was held to identify the main actors and their functions in the fufu, kokonte and cassava flour value chains. Livelihood analysis was conducted in two parts. First, it was carried out on eighty (80) households in the pounded fufu and kokonte value chains and the second aspect involved an intermediary flour processor – Amasa Agro Processing Company Limited and 43 individual farmers who supplied cassava roots to the Company. A cost benefit analysis was also carried out to determine whether selling of cassava roots is more profitable than processing the roots into shelf-stable products for sale. It was observed that farmers and processors, who are the main actors in the identified value chains, did not have adequate access to physical, social, natural, financial and human capital. Livelihood features that enhanced prospects for upgrading in the fufu value chain were increased access to energy, water and sanitation, group membership, access to information, and a vibrant enabling environment. Three livelihood constraints, poor access to credit, labour shortage and inadequate transport facilities have however, been found to create circumstances favourable to adoption of the new technology in the fufu value chain. In the kokonte value chain, it was observed that access to health facilities, improved transportation, group membership, access to information and an enabling environment enhanced prospects for upgrading. It was also observed that farmers made more profit when they processed their cassava and sold it than when they sell the cassava roots to the intermediary processor. Among the processed products, profits from grits were found to be the highest, followed by agbelima and gari. However, farmers indicated that they are more comfortable selling cassava roots and grits to the intermediary HQCF processor than middlemen and other buyers because in addition to bulk and prompt payment, they have their fields ploughed for them on credit basis and also get free cassava planting materials. To promote the adoption of new cassava-processing technologies in Ghana and elsewhere in Africa, strategies recommended were the provision of financial assistance, improving access to information through extension services, development of manual and cheaper kokonte slicing machines and legislation on the use of a percentage of High Quality Cassava Flour as a substitute to wheat flour in the baking industry.