Assessment of variability in on-farm trials : a Uganda case.

Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2002.On-farm trials techniques have become an integral part of research aimed at improving agricultural production especially in subsistence farming. The poor performance of certain technologies on the farmers' fields known to have performed well on stations have been of concern. Traditionally, on-farm trials are meant to address such discrepancies. The main problems associated with on-farm trials in most developing countries are high variability and inappropriate application of statistical knowledge known to work on station to on-farm situation. Characterisation of various on-farm variability and orientation of existing statistical methods may lead to improved agricultural research. Characterization of the various forms of variability in on-farm trials was conducted. Based on these forms of variability, estimation procedures and their strength have been assessed. Special analytical tools for handling non-replicated experiments known to be common to on-farm trials are presented. The above stated procedures have been illustrated through a review of Uganda case. To understand on-farm variability require grouping of sources of variability into agronomic, animal and socioeconomic components. This led to a deeper understanding of levels of variability and appropriate estimation procedures. The mixed model, modified stability analysis and additive main effects and multiplicative interaction methods have been found to play a role in on-farm trials. Proper approach to on-farm trials and application of appropriate statistical tools will lead to efficient results that will subsequently enhance agricultural production especially under subsistence farming.Rockefeller Foundation and Makerere University

Genotype by environment effects on promiscuous nodulation in soybean (Glycine max L. Merrill)

Open Access Journal; Published:17 March 2017Background Understanding factors influencing the expression of a trait is key in designing a breeding program. Genotype by environment interaction has great influence on most quantitative traits. Promiscuous nodulation is a trait of importance for soybean production in Africa, because of the soil bacteria Bradyrhizobium japonicum not being indigenous in most African soils. Most soybean cultivars require B. japonicum for nodulation leading to the need for seed inoculation before sowing soybean in Africa. Few cultivars have capability to nodulate with Bradyrhizobia spp. that are different from B. japonicum and native in African soils. Such cultivars are termed “promiscuous cultivars.” Field experiments were conducted in six locations in Uganda for two seasons, to investigate the extent of environmental influences on the nodulation ability of promiscuous soybean genotypes. Results Additive main effect and multiplicative interaction effects showed highly significant environment and genotype by environment (G × E) interaction effects on all nodulation traits. G × E interaction contributed more to the total variation than genotypes. The genotypes Kabanyolo I and WonderSoya were the most stable for nodules’ dry weight (NDW), which is the nodulation trait the most correlated with grain yield. Genotype UG5 was the most stable for nodules’ number (NN), and Nam II for nodules’ effectiveness (NE). The genotype NamSoy 4M had the highest performance for NN, NFW, and NDW, but was less stable. WonderSoya had the highest NE. Genotype and genotype by environment analysis grouped environments into mega-environments (MEs), and four MEs were observed for NDW, with NamSoy 4M the winning genotype in the largest ME, and Kasese B the ideal environment for that nodulation trait. Conclusion This study provides information that can guide breeding strategies. The low genetic effect that led to high environmental and G × E interaction effects raised the need for multi-environments testing before cultivar selection and recommendation. The study revealed genotypes that are stable and others that are high performing for nodulation traits, and which can be used as parental lines in breeding programs

Strategic planning process in a general rural hospital: an experience at Dr. Ambrosoli memorial hospital, Uganda

Dr. Ambrosoli Memorial Hospital is a general rural hospital located in Kalongo (Northern Uganda). The hospital isfacing new difficulties that call for urgent actions, which imposed a plan for its development. The strategic planning process was guided by engagement of stakeholders through a step-by-step participatory process.The plan acknowledges four Strategic Goalsthat integrate different dimensions (economic, social and environmental) around the themes of service delivery, infrastructure, partnership and education. The purpose is to communicate the hospital’s strategic vision, creating a framework that enables to prepare work plans and budgets, as well as monitor progresses over time

Phenotypic and genotypic screening for rust resistance in common bean germplasm in Uganda

Peer Revie

Genetic diversity and population structure of Peronosclerospora sorghi isolates of Sorghum in Uganda

Sorghum is the third most important staple cereal crop in Uganda after maize and millet. Downy mildew disease is one of the most devastating fungal diseases which limits the production and productivity of the crop. The disease is caused by an obligate fungus, Peronosclerospora sorghi (Weston & Uppal) with varying symptoms. Information on the genetic diversity and population structure of P.sorghi in sorghum is imperative for the screening and selection for resistant genotypes and further monitoring possible mutant(s) of the pathogen. Isolates of P. sorghi infecting sorghum are difficult to discriminate when morphological descriptors are used. The use of molecular markers is efficient, and reliably precised for characterizing P. sorghi isolates. This study was undertaken to assess the level of genetic diversity and population structure that exist in P. sorghi isolates in Uganda. A total of 195 P. sorghi isolates, sampled from 13 different geographic populations from 10 different regions (agro-ecological zones) was used. Eleven (11) molecular markers, comprising of four Random amplified microsatellite (RAM) and seven (7) Inter-Simple Sequence Repeat (ISSR) markers were used in this study. The analysis of molecular variation (AMOVA) based on 11 microsatellite markers showed significant (P < 0.001) intra-population (88.9 %, PhiPT = 0.111) and inter-population (8.4 %, PhiPR = 0.083) genetic variation, while the genetic variation among regions (2.7 %, PhiRT = 0.022) was not significant. The highest genetic similarity value (0.987 = 98.7 %) was recorded between Pader and Lira populations and the lowest genetic similarity (0.913 = 91.3 %) was observed between Namutumba and Arua populations. The mean Nei's genetic diversity index (H) and Shannon Information Index (I) were 0.308 and 0.471 respectively. Seven distinct cluster groups were formed from the 195 P. sorghi isolates based on their genetic similarity. Mantel test revealed no association between genetic differentiation and geographical distance (R2 = 0.0026, p = 0.02) within the 13 geographic populations

Genetic basis of maize resistance to multiple insect pests: integrated genome-wide comparative mapping and candidate gene prioritization

Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to fall armyworm (FAW), whilst bulked grains were subjected to a maize weevil (MW) bioassay and genotyped with Diversity Array Technology’s single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance levels of 0.05 and 0.01, respectively, and located within or close to multiple insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple traits, of which, six were associated with resistance to both FAWandMW, suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10–30 kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of the five of the six combined resistance QTNs, thus reinforcing the pleiotropy hypothesis. In addition, through in silico co-functional network inferences, an additional 107 network-based CGs (NbCGs), biologically connected to the 64 GbCGs, and di erentially expressed under biotic or abiotic stress, were revealed within MIRGRs. The provided multiple insect resistance physical map should contribute to the development of combined insect resistance in maize

Factors influencing genomic prediction accuracies of tropical maize resistance to fall armyworm and weevils

Genomic selection (GS) can accelerate variety improvement when training set (TS) size and its relationship with the breeding set (BS) are optimized for prediction accuracies (PAs) of genomic prediction (GP) models. Sixteen GP algorithms were run on phenotypic best linear unbiased predictors (BLUPs) and estimators (BLUEs) of resistance to both fall armyworm (FAW) and maize weevil (MW) in a tropical maize panel. For MW resistance, 37% of the panel was the TS, and the BS was the remainder, whilst for FAW, random-based training sets (RBTS) and pedigree-based training sets (PBTSs) were designed. PAs achieved with BLUPs varied from 0.66 to 0.82 for MW-resistance traits, and for FAW resistance, 0.694 to 0.714 for RBTS of 37%, and 0.843 to 0.844 for RBTS of 85%, and these were at least two-fold those from BLUEs. For PBTS, FAW resistance PAs were generally higher than those for RBTS, except for one dataset. GP models generally showed similar PAs across individual traits whilst the TS designation was determinant, since a positive correlation (R = 0.92***) between TS size and PAs was observed for RBTS, and for the PBTS, it was negative (R = 0.44**). This study pioneered the use of GS for maize resistance to insect pests in sub-Saharan Africa

Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina

YesPlant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1707492115/-/DCSupplemental

Incidence and predictors of hospital readmission in children presenting with severe anaemia in Uganda and Malawi: a secondary analysis of TRACT trial data

Background: Severe anaemia (haemoglobin < 6 g/dL) is a leading cause of recurrent hospitalisation in African children. We investigated predictors of readmission in children hospitalised with severe anaemia in the TRACT trial (ISRCTN84086586) in order to identify potential future interventions. Methods: Secondary analyses of the trial examined 3894 children from Uganda and Malawi surviving a hospital episode of severe anaemia. Predictors of all-cause readmission within 180 days of discharge were identified using multivariable regression with death as a competing risk. Groups of children with similar characteristics were identified using hierarchical clustering. Results: Of the 3894 survivors 682 (18%) were readmitted; 403 (10%) had ≥2 re-admissions over 180 days. Three main causes of readmission were identified: severe anaemia (n = 456), malaria (n = 252) and haemoglobinuria/dark urine syndrome (n = 165). Overall, factors increasing risk of readmission included HIV-infection (hazard ratio 2.48 (95% CI 1.63–3.78), p < 0.001); ≥2 hospital admissions in the preceding 12 months (1.44(1.19–1.74), p < 0.001); history of transfusion (1.48(1.13–1.93), p = 0.005); and missing ≥1 trial medication dose (proxy for care quality) (1.43 (1.21–1.69), p < 0.001). Children with uncomplicated severe anaemia (Hb 4-6 g/dL and no severity features), who never received a transfusion (per trial protocol) during the initial admission had a substantially lower risk of readmission (0.67(0.47–0.96), p = 0.04). Malaria (among children with no prior history of transfusion) (0.60(0.47–0.76), p < 0.001); younger-age (1.07 (1.03–1.10) per 1 year younger, p < 0.001) and known sickle cell disease (0.62(0.46–0.82), p = 0.001) also decreased risk of readmission. For anaemia re-admissions, gross splenomegaly and enlarged spleen increased risk by 1.73(1.23–2.44) and 1.46(1.18–1.82) respectively compared to no splenomegaly. Clustering identified four groups of children with readmission rates from 14 to 20%. The cluster with the highest readmission rate was characterised by very low haemoglobin (mean 3.6 g/dL). Sickle Cell Disease (SCD) predominated in two clusters associated with chronic repeated admissions or severe, acute presentations in largely undiagnosed SCD. The final cluster had high rates of malaria (78%), severity signs and very low platelet count, consistent with acute severe malaria. Conclusions: Younger age, HIV infection and history of previous hospital admissions predicted increased risk of readmission. However, no obvious clinical factors for intervention were identified. As missing medication doses was highly predictive, attention to care related factors may be important. Trial registration: ISRCTN ISRCTN84086586. Keywords: Severe anaemia, Readmissio

Effect of Distance from Wetland Borders on Hymenopteran Wasps and Spider Abundance in Maize-soybean Cropping System

The non-crop habitats within agroecosystems are important resources for ecological and biological insect pest management. Diversified cropping systems are known to influence pests populations, however, how neighboring habitats to the agricultural fields affect insect pest natural enemies population dynamics is not clear. This study focused on understanding the influence of wetland borders on Hymenoptera wasps and predatory spider prevalence in a maize-soybean intercrop system. The Hymenoptera wasps and spiders population estimates were carried out in twelve farmers’ fields stratified within 0-300 and 500-1100 meters from the wetland borders. Data were collected once a week starting one week from the emergence of maize and soybean plants until post-flower growth of the two crops. Results showed crop fields within 0-300 meters from the wetland borders had significantly higher numbers of wasps and spiders, while crop fields set up at 500-1100 meters from the wetland borders, the population of Hymenoptera wasps and spiders was significantly reduced. The findings of this study indicate that stable habitats such as wetland borders harbour higher numbers of natural enemies of crop pests and crop fields at close proximity benefit from quick migration of natural enemies from the pool in stable habitats. These findings can be used to design field architectures such as field margins or borders that can support insect pest natural enemies survival and migration into crop fields