Improvement of resistance to fusarium root rot through gene pyramiding and validation of SSR PVBR87 marker in common bean

Fusarium root rot caused by Fusarium solani f. sp. phaseoli is among the most serious diseases of the common bean in Uganda causing total crop loss in susceptible cultivars. Studies have indicated that 2-9 genes located at different loci govern resistance to Fusarium root rot among different resistance sources. Accumulation of several of these genes from the different sources into a single genetic background has been proposed to result in an increased level of resistance to Fusarium root rot, and more effective transfer of this resistance into consumer-preferred cultivars. Use of molecular markers together with phenotypic selection could speed up breeding progress for Fusarium root rot resistance. A simple sequence repeat (SSR) PVBR87 marker linked to Fusarium root rot resistance quantitative trait loci (QTL) was identified in a previous study but its use in identifying resistant genotypes outside the original two mapping populations has not been determined. This study estimated the number of pyramided Fusarium root rot resistance genes from four sources of resistance, their interaction and effectiveness in improving Fusarium root rot resistance levels. The study also validated the association of the SSR PVBR87 marker with resistance to Fusarium root rot in an additional population. The study was conducted at the International Centre for Tropical Agriculture (CIAT) based at the National Agricultural Research Laboratories – Kawanda, Uganda. Four Fusarium root rot resistant (R) inbred lines: MLB-48-89A (48), MLB-49-89A (49), G2333 (G2) and G685 (G6), and two susceptible (S) lines: K20 and Kanyebwa (Kan) were used in the study. A double cross (DC) was developed from the four resistant parents. The DC F1 and each resistant parent were crossed to the two susceptible cultivars to form five-parent crosses and single crosses, respectively. Parental, F1 and F2 populations were subjected to Fusarium solani f. sp. phasoeli isolate-3. Twenty one days xi after planting, symptom severity was assessed on a scale of 1-9 (varied at 1,2,3,4,5,6,7,8,9). Plants of each cross were grouped into resistant (score 1-4) and susceptible (score 5-9). F2 plants of K20 x G2 and 49 x Kan were screened with SSR PVBR87 marker. The estimated number of genes and gene interactions were determined using X2 goodness-of-fit test (P = 0.05) and means were compared by “Students t-test” (P = 0.05). The association of SSR PVBR87 marker to Fusarium root rot resistance was determined using X2 test of independence and single marker regression analysis (P = 0.05). Two to three genes segregated in the R x R single crosses and at least four genes segregated in the double cross population indicating three of the four resistant parents differed from each other by at least one gene and two of the four parents have at least one gene in common. Genetic effects among the crosses included additive and dominance effects and epistatic interactions. Five-parent crosses performed better than the single crosses, demonstrating the potential of using combined resistance in improving resistance to Fusarium root rot in susceptible bean cultivars. The SSR PVBR87 marker showed significant association to Fusarium root rot resistance in both K20 x G2 and Kan x 49 indicating its stability in different genetic background but still requires further validation in different environments and in additional genetic backgrounds to determine its use for marker-assisted breeding for improving resistance to Fusarium root rot. The genes responsible for the higher levels of Fusarium root rot resistance in the pyramids are not specifically known. It is necessary that these resistance genes be tagged with molecular markers. Tagging of the genes with molecular markers would provide knowledge of their genomic locations, the nature of their interactions and also facilitate the transfer of these genes or alleles, through molecular marker-assisted gene introgression, into other agronomically superior, but Fusarium root rot susceptible cultivars. Since no selection for Fusarium root rot resistance or any other desirable agronomic traits was practiced in this study, there is need to select between and within families from among the five-parent cross populations and the single crosses for resistance to Fusarium root rot. However, the predominance of non-additive gene effects for Fusarium root rot resistance, especially in the five-parent crosses suggests that selection for resistance would be more effective at advanced generations of selfing. The bean parents used in constructing the five-parent cross populations are of diverse seed character, growth habit, maturity period, and have varied response to several abiotic and biotic constraints. There is also need to select for these traits in the populations developed in this study as these traits eventually affect acceptability of any potential new variety. The amounts of phenotypic variation explained by the SSR PVBR87 in two populations were low; hence, there is still need to further validate the marker in additional populations and in several environments to determine its efficacy for marker-assisted breeding for Fusarium root rot resistance

Study of inheritance and identification of molecular markers for seed protein content in pigeonpea (Cajanus cajan (L.) Millsp.).

Doctor of Philosophy in Plant Breeding. University of KwaZulu-Natal, Pietermaritzburg 2017.Abstract available in PDF file

The relationship between urban land conflicts and inequity: the case of Nairobi.

This thesis sets out to deepen our understanding of the linkages between urban dynamics that influence access, use and ownership of land in developing countries. This is because land scarcity, increased competition for land and inequitable allocation of land in African cities and the mediation of power, politics, ethnicity and corruption, coupled with inequitable access to land, often contribute to conflicts over land. The thesis explores this reality through the case of Nairobi. Two arguments premise this thesis; one argument posits that urban land conflicts persisting in Africa are largely resulting from land commodification which is not in conformity with existing African land relations. The second argument is that the persistence of urban inequity well beyond colonialism into the present time has produced reinforced inequity in access to and ownership, thereby producing patronage, ethnic and corrupt approaches to land management and allocation processes. These have invariably led land conflicts. As such the study sought to answer one major question that could help establish the links between land scarcity, ethnicity, corruption and conflicts. The question is: what is the relationship between land conflicts and inequity? The thesis aimed to explain the linkage between land commodification processes and inequity, exploring the nature, causes, extent, dimensions and dynamics of land conflicts. It further sought to explore the linkage of the existing institutional arrangements to urban land conflicts. It anticipated the drawing of conclusions on the linkages between land conflicts, land management, commodification, ethnicity, corruption and political patronage and how these linkages contribute to inequity and, subsequently, land conflicts. The study applied a qualitative case study approach, exploring the relationships between land conflicts and inequity. Four in depth case studies, Tassia, Embakasi Jua Klai, Pipeline and Mathare North, were conducted in Nairobi. The study drew on a combination of theories, including ethnic manipulation, structure and agency, institutional analysis, uneven development, grounded theories and group interest. These helped in the analysis and informed the data collection approaches. In addition, they assisted in the development of appropriate explanations of the dynamics between factors such as ethnicity, corruption, and the market, among others. In drawing conclusions, they were useful in unraveling the relationships between land conflicts and the various mediating factors. The results from this study include the establishment of the fact that urban land conflicts result from social, political and economic factors. The factors are mediated by several factors that are institutional, ethnic and patronage-based. The thesis reveals the linkage between ethnicity and corruption, and the simultaneous relationships between power, corruption, institutions and ethnicity. For the Nairobi case, the study brings to the fore the central role of ethnicity in resource conflicts. It also reveals the dynamic nature of land conflicts, thereby suggesting that land issues are social, economic and political. Addressing land conflicts conclusively requires a careful political process that must also be embedded in the legal systems of the particular country. The study concludes by proposing areas for further study, including ethnicity and land ownership in Kenya’s urban areas; corruption, politics and landlordism in Nairobi; land markets and conflicts in urban areas; the development of appropriate models for urban land management, and the links between land tenure and conflicts over land in urban area

The role of Escherichia coli in the etiology of piglet diarrhea in selected pig producing districts of central Uganda

Background: Pig production in Uganda is highly constrained by rampant piglet mortalities with diarrhea being a key feature. The present study was conducted to determine possible involvement of Escherichia coli (E. coli) as agents of diarrhea in piglets and elucidate the factors for their spread and virulence, towards development of mitigation strategies in the smallholder pig value chains in Uganda. Methodology: This was a cross-sectional study carried out from January to August 2020 on pre- and post-weaned piglets from households in Kayunga and Mityana districts of Central Uganda, selected by snowballing method to redundancy. Data about herd management and risk factors for colibacillosis were collected from selected farmers in the two districts. A total of 179 faecal samples were collected from randomly selected neonatal and pre-weaning piglets for bacteriological isolation of Escherichia coli. Virulence (enterotoxin and fimbrial) genes from the isolates were detected by multiplex polymerase chain reaction (PCR) assay. Results: From the 179 faecal samples, a total of 158 (88.3%) E. coli isolates were obtained. Virulence gene markers were detected in 18.4% (29/158) of the isolates. Among the investigated genes encoding for enterotoxin production, STb was the most prevalent (16/158, 10.13%), followed by STa (12/158, 7.59%), while gene for LT was not detected. The gene coding for F4 adhesin was the only one detected while F18 adhesin was not detected from the isolates. On multiple logistic regression analysis, only tertiary educational level (OR=0.141; 95% CI=0.30-0.666; p=0.013) and infrequent use of antibiotics (OR=0.231, 95% CI=0.062-0.859; p=0.029) among the farmers, were the two factors significantly protective of the piglets from diarrhoea. Conclusion: This study reports a high prevalence of enterotoxin gene markers among E. coli isolates in piglets and revealed the potential role of these bacteria in the aetiology of piglet diarrhoea and mortalities in Uganda. Additionally, this study identified risk factors that can be useful in formulating treatment and control strategies of infection caused by these bacteria. Further studies are needed to identify more adhesins these E. coli isolates employ for intestinal colonization, a step that will help inform vaccine development.   French title: Le rôle d'Escherichia coli dans l'étiologie de la diarrhée des porcelets dans certains districts producteurs de porcs du centre de l'Ouganda   Contexte: La production porcine en Ouganda est fortement limitée par la mortalité généralisée des porcelets, la diarrhée étant une caractéristique clé. La présente étude a été menée pour déterminer l'implication possible Escherichia coli piglet diarrhea in Uganda  d'Escherichia coli (E. coli) en tant qu'agents de diarrhée chez les porcelets et élucider les facteurs de leur propagation et de leur virulence, vers le développement de stratégies d'atténuation dans les chaînes de valeur des petits producteurs de porcs en Ouganda. Méthodologie: Il s'agit d'une étude transversale réalisée de janvier à août 2020 sur des porcelets pré- et post-sevrés issus de ménages des districts de Kayunga et Mityana du centre de l'Ouganda, sélectionnés par la méthode boule de neige jusqu'à la redondance. Les données sur la gestion du troupeau et les facteurs de risque de colibacillose ont été recueillies auprès d'éleveurs sélectionnés dans les deux districts. Au total, 179 échantillons de matières fécales ont été prélevés sur des porcelets néonatals et en pré-sevrage sélectionnés au hasard pour l'isolement bactériologique d'Escherichia coli. Les gènes de virulence (entérotoxine et fimbrial) des isolats ont été détectés par une amplification en chaîne par polymérase (PCR) multiplex. Résultats: À partir des 179 échantillons de matières fécales, un total de 158 (88,3%) isolats d'E. coli ont été obtenus. Des marqueurs du gène de virulence ont été détectés dans 18,4% (29/158) des isolats. Parmi les gènes étudiés codant pour la production d'entérotoxines, STb était le plus répandu (16/158, 10,13%), suivi de STa (12/158, 7,59%), tandis que le gène de la LT n'a pas été détecté. Le gène codant pour l'adhésine F4 était le seul détecté alors que l'adhésine F18 n'a pas été détectée dans les isolats. Sur l'analyse de régression logistique multiple, seul le niveau d'enseignement supérieur (OR=0,141; IC à 95%=0,30-0,666; p=0,013) et l'utilisation peu fréquente d'antibiotiques (OR=0,231, IC à 95 %=0,062-0,859; p=0,029) parmi les éleveurs, étaient les deux facteurs de protection significative des porcelets contre la diarrhée. Conclusion: Cette étude rapporte une prévalence élevée de marqueurs génétiques d'entérotoxines parmi les isolats d'E. coli chez les porcelets et a révélé le rôle potentiel de ces bactéries dans l'étiologie de la diarrhée et de la mortalité des porcelets en Ouganda. De plus, cette étude a identifié des facteurs de risque qui peuvent être utiles dans la formulation de stratégies de traitement et de contrôle de l'infection causée par ces bactéries. D'autres études sont nécessaires pour identifier plus d'adhésines que ces isolats d'E. coli utilisent pour la colonisation intestinale, une étape qui aidera à éclairer le développement de vaccins

Pengaruh Dimensi-Dimensi Pembentuk Merek Perusahaan Pemberi-Kerja terhadap Niat Melamar Pekerjaan dengan Reputasi Perusahaan sebagai Peubah Pemediasi

Tujuan penelitian ini adalah untuk mengetahui pengaruh dimensi-dimensi pembentuk merek perusahaan pemberi-kerja (employer brand)terhadap niat melamar pekerjaan, dengan reputasi perusahaan sebagai peubahpemediasi. Untuk pengujian hipotesis penelitian ini menggunakan Partial Least Square (PLS). Teknik pengambilan sampel menggunakan sampel probabilitas dengan metode acak sederhana dengan jumlah sampel sebanyak 105 responden. Hasil penelitian menunjukkan dimensi nilai ekonomi dan nilai aplikasi berpengaruh signifikan terhadap reputasi perusahaan, sedangkan nilai inovasi, nilai pengembangan dan nilai sosial tidak berpengaruh signifikan terhadap reputasi perusahaan. Penelitian ini juga menunjukkan reputasi perusahaan memengaruhi niat melamar pekerjaan secara signifikan.Kata kunci: employer branding, reputasi perusahaan, niat melamar pekerjaan

Pengaruh Dimensi-Dimensi Pembentuk Merek Perusahaan Pemberi-Kerja terhadap Niat Melamar Pekerjaan dengan Reputasi Perusahaan sebagai Peubah Pemediasi

Tujuan penelitian ini adalah untuk mengetahui pengaruh dimensi-dimensi pembentuk merek perusahaan pemberi-kerja (employer brand)terhadap niat melamar pekerjaan, dengan reputasi perusahaan sebagai peubahpemediasi. Untuk pengujian hipotesis penelitian ini menggunakan Partial Least Square (PLS). Teknik pengambilan sampel menggunakan sampel probabilitas dengan metode acak sederhana dengan jumlah sampel sebanyak 105 responden. Hasil penelitian menunjukkan dimensi nilai ekonomi dan nilai aplikasi berpengaruh signifikan terhadap reputasi perusahaan, sedangkan nilai inovasi, nilai pengembangan dan nilai sosial tidak berpengaruh signifikan terhadap reputasi perusahaan. Penelitian ini juga menunjukkan reputasi perusahaan memengaruhi niat melamar pekerjaan secara signifikan.Kata kunci: employer branding, reputasi perusahaan, niat melamar pekerjaan

Malaria “hotspots” within a larger hotspot; what’s the role of behavioural factors in fine scale heterogeneity in western Kenya?

Background: Malaria remains a major public health problem in Kenya accounting for the highest morbidity and mortality especially among children. Previous reports indicate that infectious agents display heterogeneity in both space and time and malaria is no exception. Heterogeneity has been shown to reduce the effectiveness of interventions. Previous studies have implicated genetic (both human and parasite) and environmental factors as mainly responsible for variation in malaria risk. Human behaviour and its potential risk for contributing to variation in malaria risk has not been extensively explored.Objective: To determine if there were behavioural differences between the people living in hotspots (high malaria burden) and coldspots (low malaria burden) within a geographically homogeneous and high malaria transmission region.Design: A prospective closed cohort study.Setting: The study was conducted in the Health and Demographic Surveillance Site in Bungoma East sub-County.Subjects: A total of 400 people in randomly selected households in both the fever hotspots and cold spots were tested for malaria at quarterly intervals using malaria rapid diagnostic tests (RDTs).Results: Significant heterogeneity in malaria incidence and prevalence was observed between villages. Incidence of malaria was significantly higher in the hotspots (high malaria burden areas) compared to the coldspots (low malaria burden) (49 episodes per 1000 person months compared to 26/1000, ttest p < 0.001). The incidence also varied significantly among the individual villages by season (P: 0.0071). Knowledge on malaria therapy was significantly associated with whether one was in the cold spot or hotspot (P: 0.033). Behavioural practices relating to ITN use were significantly associated with region during particular seasons (P: 0.0001 and P: 0.0001 respectively).Conclusion: There is marked and significant variation in the incidence of malaria among the villages creating actual hotspots of malaria within the larger hotspot. There is a significant difference in malaria infections between the hotspots and cold spots. Knowledge on malaria therapy and behavioural factors such as ITN use may contribute to the observed differences during some seasons

QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea

To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement

Prevalence, heterogeneity of asymptomatic malaria infections and associated factors in a high transmission region

Background: Although current reports have shown a reduction in malaria cases, the disease still remains a major public health problem in Kenya. In most endemic regions, the majority of infections are asymptomatic which means those infected may not even know and yet they remain infectious to the mosquitoes. Asymptomatic infections are a major threat to malaria control programs since they act as silent reservoirs for the malaria parasites.Objective: The study sought to determine the prevalence of asymptomatic malaria infections, whether they show heterogeneity spatially, across age groups and across time as well as their determinants in a high transmission region.Study Design: This was part of a larger prospective cohort study on malaria indices in the HDSS.Study Setting: The study was conducted in the Webuye Health and Demographic Surveillance Site in Bungoma East Sub-County.Study Subjects: Quarterly parasitological surveys were conducted for a cohort of 400 participants from randomly selected households located in known fever “hotspots” and “coldspots”. Follow-up of all the participants continued for a period of one year. Generalized estimating equations were used to model risk factors associated with asymptomatic parasitemia.Results: Of the total 321 malaria infections detected during the five cross-sectional surveys conducted over the period of one year, almost half (46.3%) of these were asymptomatic. Overall, most of the asymptomatic cases (67%) were in households within known fever “hotspots”. The proportion of infections that were asymptomatic in the coldspots were 73.1%, 31.8%, 13.3%, 55.6% and 48.2% during the first, second, third, fourth and fifth visits respectively. In the known fever “hotspots”, the proportion of infections without symptoms was 47.7%, 48.5%, 35%, 41.3% and 47.5% during the first, second, third, fourth and fifth visits respectively. Factors associated with asymptomatic malaria include; the village one lives: people living in village M were twice likely to be asymptomatic (A.O.R: 2.141, C.I: 0.03 - 1.488), age: children aged between 6 to 15 years were more than twice likely to be asymptomatic (A.O.R: 2.67, C.I. 0.434 - 1.533) and the season: infections during the dry season (January) were less likely to be asymptomatic (A.O.R: 0.26, C.I: -2.289 - 0.400).Conclusion: The prevalence of asymptomatic infections in this region is still very high. The highest proportion of asymptomatic infections was registered in a fever coldpspot village which may explain why the village is a fever coldspot in the first place. There is a need for active surveillance to detect the asymptomatic cases as well as treat them in-order to reduce the reservoir. Targeting interventions to the asymptomatic individuals will further reduce the transmission within this region

Expanding Access to Malaria Diagnosis through Retail Shops in Western Kenya: What Do Shop Workers Think?

Background. The common symptoms of malaria reduce the specificity of clinical diagnosis. Presumptive treatment is conventional but can lead to overdiagnosis of malaria, delay of appropriate treatment, overprescription of antimalarials, and drug resistance. Routine use of diagnostic tests can address many of these concerns. Though treatment is often procured from retailers, there is low availability of rapid diagnostic tests for malaria (MRDTs), a simple, inexpensive, and accurate diagnostic solution. We know little about the challenges to expanding access to diagnostics through these outlets. Methods. To understand the perceptions of the benefits and challenges to selling rapid diagnostic tests for malaria, we conducted focus group discussions with antimalarial retailers who serve the residents of the Webuye Health and Demographic Surveillance Site in western Kenya. Results. Medicine retailers perceived MRDTs to be beneficial to their customers and businesses but also included cost, fear of the tests, risks of self-treatment, and regulatory concerns among the challenges to using and selling MRDTs. Conclusion. MRDTs represent a viable approach to increase access to malaria diagnostic testing. Medicine retailers are eager for MRDTs to be made available to them. However, certain challenges remain to implementation in retail outlets and should be addressed in advance