Browsing by Author "Beine, Peter"

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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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    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.