Browsing by Author "Mukiibi, Robert"

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    A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle
    (Veterinary Medicine and Science, 2023-09-19) Masembe, Charles; Benda, Kirungi Katali; Opoola, Oluyinka; Ndinawe, Ruth Pamela; Beine, Peter; Mukiibi, Robert
    The cattle industry contributes to Uganda's agricultural output. It faces challenges that include theft and parentage ascertainment. These challenges can benefit from recent molecular genomics and bioinformatics technologies. We employed genomic analyses to establish potential ownership of a group of nine cattle that were being claimed by two farmers in Uganda. We investigated the genetic relationship of Ugandan cattle with regional indigenous breeds as well as exotic breeds that are currently present in Uganda. In addition, we investigated regions that are likely to be under selection in the Ugandan cattle. Hair samples were collected from seven and two animals from farmers A and B, respectively. They were genotyped for 53,218 Single Nucleotide Polymorphism markers. To establish genetic relationships between the sampled animals, we performed genomic analyses including, principal component analysis (PCA), hierarchical clustering analysis and identity by state/descent. We also performed admixture and runs of homozygosity analyses to assess the ancestry composition and identify regions potentially under selection in Ugandan cattle, respectively. The seven animals from Farmer A were genetically close to each other but showed minimal relationship with the disputed animals. The two animals from Farmer B were genetically distant from each other but showed greater similarity to four of the disputed animals. Four of the disputed animals showed great dissimilarity from the animals of both farmers. Comparison of these with the reference breeds revealed minimal European exotic genetic introgression into these animals, but rather high similarity to the Sheko. Results also revealed high homozygosity in the major histocompatibility complex regions. Our results demonstrate the use of currently available genomic tools to empirically establish the ownership of cattle; these could be scaled up as a resourceful and viable tool that could be employed to support conflict resolution where reliable livestock identification is unavailable.
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    Efficacy of Commercially Available Anthelmintics in Controlling Gastrointestinal Nematodes in Goats Managed Under Natural Conditions in the South Western Highlands of Uganda
    (American Journal of Clinical and Experimental Medicine, 2015-12) Benda, Katali Kirungi; Ampaire, Andrew; Komungyeyo, Jenninah; Mukiibi, Robert; Masembe, Charles; Onzima, Robert
    Goat production is of great importance especially to the rural farmers in Uganda, serving a number of socioeconomic functions. Among the limitations of goat production in Uganda are Gastro Intestinal Nematodes (GINs). These are usually controlled using commercial Anthelmintic compounds. Due to continual improper usage of these drugs by the farmers, evolution of resistant strains has resulted thus affecting their effectiveness in controlling the GINs. The aim of this study was to determine the efficacy of four commercially available anthelmintics used for controlling Gastro Intestinal Nematodes (GINs) in goats on natural pastures in the south western highlands of Uganda. A mini survey was conducted prior to the current study to get information about the most commonly used anthelmintics in the study area. Initially, 240 goats were enrolled into the study and, 210 were used in the final analysis. The goats were randomly allocated to 5 different treatment groups at district level namely; untreated controls (CTRL), Albendazole 10% (ABZ), Ivermectin (IVE), Levamisole (LEV) and Closantel (CL). Faecal and blood samples were collected from each animal at 0, 14, 28 and 42 days post-treatment respectively and analysed for faecal egg counts (FEC) using the modified McMaster method. The percentage reduction, FECR % was calculated from the arithmetic mean and difference in FEC between breeds, district and age were assessed by univariate analysis of variance in SPSS. Results at day zero indicated that age and district had significant effect on FEC (P-value= 0.001 and 0.035respectively) while breed had no significant effect (P-value=0.465). At 14 days post-treatment, district, breed and treatment had significant effects on FEC (P-value=0.00, 0.02 and 0.05 respectively) while age was not (P=0.931). Albendazole and Levamizol were the most used drugs in the study area while Closantel and Ivermectin were the least used. Drug efficacy varied between districts, with the highest mean Fecal Egg Count Reduction (FECR) achieved with Closantel (FECR%=100%), while the lowest mean FECR observed with Albendazole (FECR%=49%) in Rukungiri and Kisoro districts respectively. Ivermectin was effective in all the four districts (FECRT% > 95%). Our study confirmed presence of Anthelmintic resistance (AR) by GIN in goats in the south western highlands of Uganda. Closantel is highly effective against GINs, but albendazole is not due to its wide spread usage. Further research is necessary to find and validate alternative strategies for the control of GINs in goats.
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    Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs
    (Genomics, 2024-01-07) Robledo , Diego; Ogwang, Joel; Byakora, Ezra; Katali, Kirungi Benda; Beine, Peter; Mukiibi, Robert
    Nile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in Africa, yet the relationship between wild and farmed populations is unknown in most of the continent. Genetic characterization of the species in Africa has the potential to support the conservation of the species as well as supporting selective breeding to improve the indigenous strains for sustainable and profitable aquaculture production. In the current study, a total of 382 fish were used to investigate the genetic structure, diversity, and ancestry within and between Ugandan Nile tilapia populations from three major lakes including Lake Albert (L. Albert), Lake Kyoga (L. Kyoga) and Lake Victoria (L. Victoria), and 10 hatchery farms located in the catchment regions of these lakes. Our results showed clear genetic structure of the fish sourced from the lakes, with L. Kyoga and L. Albert populations showing higher genetic similarity. We also observed noticeable genetic structure among farmed populations, with most of them being genetically similar to L. Albert and L. Kyoga fish. Admixture results showed a higher (2.55–52.75%) contribution of L. Albert / L. Kyoga stocks to Uganda's farmed fish than the stock from L. Victoria (2.12–28.02%). We observed relatively high genetic diversity across both wild and farmed populations, but some farms had sizable numbers of highly inbred fish, raising concerns about management practices. In addition, we identified a genomic region on chromosome 5, harbouring the key innate immune gene BPI and the key growth gene GHRH, putatively under selection in the Ugandan Nile tilapia population. This region overlaps with the genomic region previously identified to be associated with growth rate in farmed Nile tilapia.