Identification and development of cassava brown streak disease resistant and early storage root bulking varieties in Malawi.

Doctor of Philosophy in Plant Breeding. University of KwaZulu-Natal, Pietermaritzburg 2016.Cassava (Manihot esculenta Crantz) production in Malawi, like in most of the East African countries, has suffered from cassava brown streak disease (CBSD), a disease that affects both the quality and yield of storage roots. The incidence of CBSD in Malawi has increased in recent years causing yield loss of up to 25%. Currently there is no information that indicates the availability of resistant cassava varieties in Malawi. In addition, most cassava varieties grown in Malawi are late bulking (12-18 months), and this contributes to high CBSD incidences, which increase with plant age. Therefore, there is need to develop CBSD resistant and early storage root bulking varieties, which can be harvested before the disease (storage root necrosis) becomes severe. Early storage root bulking, CBSD resistant varieties will not only provide good storage root quality and productivity per unit area of land, but will also facilitate the release of land for other farming activities. The main objective of the study was to develop cassava varieties that are resistant to CBSD and early storage root bulking, in order to improve the yield and quality of cassava in Malawi. The specific objectives of the study were (1) to assess farmers’ knowledge of CBSD and its management, (2) to identify early storage root bulking cassava genotypes as well as traits associated with early storage root bulking, (3) to assess the effect of harvest time on cassava genotype performance, stability and adaptability, (4) to evaluate cassava genotypes for resistance to CBSD and its associated yield losses and (5) to determine the mode of gene action and the importance of combining ability effects in the inheritance of CBSD resistance and early storage root bulking traits. Assessment of farmers’ knowledge of CBSD indicated that the majority of the farmers did not know the disease through foliar symptoms and only 10.1% of the farmers were able to identify CBSD. The study established that CBSD is a continuing threat to the cassava industry, where high incidence levels were observed. On average, 75.0% and 71.7% of the farms had plants with leaf and storage root symptoms, respectively. The average CBSD leaf incidence per farm was 31.2% with levels up to 86.7% on some farms. At harvest, 88.3% of the farmers’ cassava fields exhibited storage root necrosis. Most farmers were found to lack a source of clean planting material and the lack of new improved varieties was reported as the most important constraint of cassava production, apart from CBSD. Therefore, the results suggest that education of farmers on the efficient management of this viral disease through selection of clean planting material should be provided. Early storage root bulking and agronomic traits associated with early bulking in cassava, was studied at two sites over two seasons with 16 genotypes. High yields of up to 9.5 t ha­­ˉ­­­­­­­­¹ at 6 months after planting (MAP) and 17.8 t ha­­ˉ­­­­­­­­¹ at 9 MAP were obtained and four varieties were identified as early-bulking (Mulola, Phoso, Mbundumali and Maunjili). The study further identified harvest index and shoot mass as the major selection criteria in improving fresh storage yield and dry storage root yield. The results indicated that both source and sink capacities were important for determining early yield. Therefore, these two traits are the key determinants of early storage root bulking and should be used when selecting early bulking varieties. On the effect of harvest time, the study revealed that genotype, environment and genotype x environment interaction have a significant influence on the performance of varieties, regardless of the harvest time. Most of the cassava varieties exhibited specific adaptation to certain environments. The study identified five varieties (Mulola, Phoso, Maunjili, Beatrice and Unknown) that exhibited consistent performance, stability and adaptability across the three harvest periods (6, 9 and 12, MAP). The results, therefore, showed that multi-location studies in cassava, regardless of the time of harvest, could help discriminate genotypes with superior performance, stability and general adaptation. In terms of resistance to CBSD, high significant differences in CBSD incidence and severity values were observed (some varieties reached as high as 94.9% and severity of up to 3.8). The CBSD storage root severity increased with the prolonged stay of the crop in the field. The study established that yield loss due to CBSD was significantly associated with storage root severity at different harvest times and a maximum yield loss of 43.1% was recorded at 12 MAP on Kalawe, while at 9 and 6 MAP, maximum yield loss was 24.8% and 10.9%, respectively. The study identified five varieties to be resistant/or tolerant to CBSD (Phoso, Maunjili, Mpale, Sauti and TMS4(2)1425). The results, in general, suggest that an integrated approach should be used by farmers in order to effectively manage CBSD, which among others include using varieties that are early bulking and resistant/tolerant to CBSD, selecting planting material free from CBSD, sanitation and roguing infected plants from the field, especially shortly after sprouting. Four parental genotypes (Silira, Mulola, Phoso and Mkondezi) were identified as the best general combiners for the CBSD resistance and early storage root bulking. Thirteen progenies exhibiting CBSD resistance and early storage root bulking traits were identified and selected for advancement. The study established that resistance in cassava for CBSD, as well as for early storage root bulking is controlled by both additive and non-additive gene action. However, additive gene action is more important than non-additive type of gene action in the inheritance of CBSD resistance and early storage root bulking. The implication is that mass phenotypic recurrent selection after hybridisation of elite clones could, therefore, be effective for the development of varieties resistant to CBSD as well as addressing challenges related to late storage root bulking

Geostatistical design and analysis for estimating local variations in malaria disease burden

Geostatistical design and analysis methods are increasingly used in disease mapping, particularly in resource-limited settings where uniformly precise mapping may be unrealistically costly and the priority is often to identify critical areas where interventions can have the most health impact. In this thesis, which is based on four papers, we address the problem of geostatistical sampling design. In the first paper, we consider the problem of sampling design for efficient spatial prediction taking account of uncertain covariance structure, in the context of nonadaptive designs. We propose two classes of designs, namely: simple inhibitory and inhibitory plus close pairs. We evaluate the performance of these designs using an average prediction variance criterion and show how the findings are applied to the design of a rolling Malaria Indicator Survey (rMIS) in an ongoing large-scale, five-year malaria transmission reduction project in Malawi. In the second paper, we address the problem of efficient spatial prediction in the context of adaptive geostatistical designs (AGD). We propose two classes of designs based on singleton and batch sampling. We show how our findings inform an AGD of rMIS, in the perimeter of Majete Wildlife Reserve (MWR) in Chikwawa, southern Malawi. The third paper is a commentary on a paper by Ferreira and Gamerman (2015), which addressed the effect of preferential sampling of the locations at which to measure a spatial process. In the fourth paper, we present the first epidemiological field application of AGD sampling in a malaria prevalence survey. We give an in-depth description of the project, the study area and practical implementation of our adaptive sampling strategy. We present prevalence maps for children 6–59 months in MWR perimeter, showing high malaria transmission areas, often called “hotspots”, that could be targeted with interventions

Adaptive geostatistical design and analysis for prevalence surveys

Non-adaptive geostatistical designs (NAGDs) offer standard ways of collecting and analysing geostatistical data in which sampling locations are fixed in advance of any data collection. In contrast, adaptive geostatistical designs (AGDs) allow collection of geostatistical data over time to depend on information obtained from previous information to optimise data collection towards the analysis objective. AGDs are becoming more important in spatial mapping, particularly in poor resource settings where uniformly precise mapping may be unrealistically costly and the priority is often to identify critical areas where interventions can have the most health impact. Two constructions are: singleton and batch adaptive sampling. In singleton sampling, locations xi are chosen sequentially and at each stage, xk+1 depends on data obtained at locations x1,…,xk. In batch sampling, locations are chosen in batches of size b>1, allowing each new batch, {x(k+1),…,x(k+b)}, to depend on data obtained at locations x1,…,xkb. In most settings, batch sampling is more realistic than singleton sampling. We propose specific batch AGDs and assess their efficiency relative to their singleton adaptive and non-adaptive counterparts using simulations. We then show how we are applying these findings to inform an AGD of a rolling Malaria Indicator Survey, part of a large-scale, five-year malaria transmission reduction project in Malawi

Inhibitory geostatistical designs for spatial prediction taking account of uncertain covariance structure

The problem of choosing spatial sampling designs for investigating an unobserved spatial phenomenon S arises in many contexts, for example in identifying households to select for a prevalence survey to study disease burden and heterogeneity in a study region D. We studied randomised inhibitory spatial sampling designs to address the problem of spatial prediction whilst taking account of the need to estimate covariance structure. Two specific classes of design are inhibitory designs and inhibitory designs plus close pairs. In an inhibitory design, any pair of sample locations must be separated by at least an inhibition distance δ. In an inhibitory plus close pairs design, n − k sample locations in an inhibitory design with inhibition distance δ are augmented by k locations each positioned close to one of the randomly selected n − k locations in the inhibitory design, uniformly distributed within a disc of radius ζ. We present simulation results for the Mat´ern class of covariance structures. When the nugget variance is non-negligible, inhibitory plus close pairs designs demonstrate improved predictive efficiency over designs without close pairs. We illustrate how these findings can be applied to the design of a rolling Malaria Indicator Survey that forms part of an ongoing large-scale, five-year malaria transmission reduction project in Malawi

Distinct climate influences on the risk of typhoid compared to invasive non-typhoid Salmonella disease in Blantyre, Malawi.

Invasive Salmonella diseases, both typhoid and invasive non-typhoidal Salmonella (iNTS), are seasonal bloodstream infections causing important morbidity and mortality globally in Africa. The reservoirs and transmission of both are not fully understood. We hypothesised that differences in the time-lagged relationships of rainfall or temperature with typhoid and iNTS incidence might infer differences in epidemiology. We assessed the dynamics of invasive Salmonella incidence over a 16-year period of surveillance, quantifying incidence peaks, seasonal variations, and nonlinear effects of rainfall and temperature exposures on the relative risks of typhoid and iNTS, using monthly lags. An increased relative risk of iNTS incidence was short-lasting but immediate after the onset of the rains, whereas that of typhoid was long-lasting but with a two months delayed start, implying a possible difference in transmission. The relative-risk function of temperature for typhoid was bimodal, with higher risk at both lower (with a 1 month lag) and higher (with a ≥4 months lag) temperatures, possibly reflecting the known patterns of short and long cycle typhoid transmission. In contrast, the relative-risk of iNTS was only increased at lower temperatures, suggesting distinct transmission mechanisms. Environmental and sanitation control strategies may be different for iNTS compared to typhoid disease

Investment-Cash Flow Sensitivity Around the Crisis: Are African Firms Different?

Purpose: This paper examines the contentious relationship between investment and cash flow using the 2008—09 credit supply shock as a form of quasi-natural experiment. Methodology: Panel threshold models with unknown sample separation are estimated for a sample of publicly listed firms from nine African countries over the period 2003— 2012. Using this approach reduces subjective or ex-ante sample splitting bias that is not accounted for in the extant literature. Findings: We show that investment-cash flow sensitivity is decreasing even during the Global Financial Crisis, and for firms more likely to be financially constrained. We conclude that the usefulness of investment-cash flow sensitivity as a proxy for financial constraints is diminishing over time, even after directly addressing biases from ex-ante subjective sample splitting and various forms of endogeneity. Originality: We provide new empirical evidence from sharper tests of financial con- straints for understudied African firms, and highlight the need to re-look at the usefulness of investment-cash flow sensitivity as a proxy of financial constraints

Inhibitory geostatistical designs for spatial prediction taking account of uncertain covariance structure

The problem of choosing spatial sampling designs for investigating an unobserved spatial phenomenon S arises in many contexts, for example, in identifying households to select for a prevalence survey to study disease burden and heterogeneity in a study region D. We studied randomized inhibitory spatial sampling designs to address the problem of spatial prediction while taking account of the need to estimate covariance structure. Two specific classes of design are inhibitory designs and inhibitory designs plus close pairs. In an inhibitory design, any pair of sample locations must be separated by at least an inhibition distance δ. In an inhibitory plus close pairs design, n − k sample locations in an inhibitory design with inhibition distance δ are augmented by k locations each positioned close to one of the randomly selected n − k locations in the inhibitory design, uniformly distributed within a disk of radius ζ. We present simulation results for the Matérn class of covariance structures. When the nugget variance is non-negligible, inhibitory plus close pairs designs demonstrate improved predictive efficiency over designs without close pairs. We illustrate how these findings can be applied to the design of a rolling Malaria Indicator Survey that forms part of an ongoing large-scale, 5-year malaria transmission reduction project in Malawi

Procjena mikrostrukture alatnog čelika za hladni rad nakon pretaljivanja pulsirajućim laserom

The aim of this study is the investigation of micro-structural behaviour of a Mat. No. 1.2379 (EN-X160CrMoV121; AISI D2) cold work tool steel after remelting with a precise pulsed Nd:YAG laser. The investigated steel is one of the most hard to weld tool steels, due to large amount of alloying elements. The analysis was done on single spots remelted with specific laser pulse shape and parameters, assuring crack-less solidification. Re-solidifi ed areas were investigated with microscopy, hardness measurements, X-ray spectroscopy and diffraction method. Laser treatment causes rapid solidification leading into a formation of a fine dendritic microstructures containing high amount of retained austenite causing a significant decrease of hardness.Namjena ove studije je ispitivanje ponašanja mikro strukture alatnoga čelika za rad na hladno Mat. No.1.2379 (ENX160CrMoV121; AISI D2) po pretaljivanju s preciznim pulsiranim Nd:YAG laserom. Zbog velike količine legirnih elemenata istraživani materijal spada u grupu vrlo teško zavarljivih alatnih čelika. Analiza je provedena na pojedinim pretaljenim točkama korištenjem specifi čnog oblika i parametara laserskog impulsa koji osiguravaju skrućivanje bez pukotina. Pretaljena područja su ispitivana mikroskopom, mjerenjem mikro tvrdoće, rendgenskom spektroskopijom i defrakcijskom metodom. Tretman laserom uzrokvao je brzo skrućivanje koja dovodi do formiranja fi ne dendritičke strukture s velikim udjelom zaostalog austenita što uzrokuje bitno smanjivanje tvrdoće