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. 2023 Nov;9(6):2844-2851.
doi: 10.1002/vms3.1272. Epub 2023 Sep 19.

A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle

Charles Masembe  1 , Kirungi Katali Benda  1   2 , Oluyinka Opoola  3   4 , Mayega Johnson Francis  1 , Ruth Pamela Ndinawe  2 , Peter Beine  2 , Robert Mukiibi  3
Affiliations

A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle

Charles Masembe et al. Vet Med Sci. 2023 Nov.

Abstract

Background: 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.

Objectives: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

Keywords: MHC genes; bovine genomics; genetic analysis; genetic diversity; single nucleotide polymorphisms.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIGURE 1
FIGURE 1
Picture of some of the contested animals investigated in this study.
FIGURE 2
FIGURE 2
(a) Principal component plot showing genetic distribution and clustering of the investigated animals. (b) A dendrogram hierarchical plot showing the genetic similarity or dissimilarity among the studied animals.
FIGURE 3
FIGURE 3
(a) Principal component plot showing genetic distribution and clustering of the investigated animals and reference animals of the Bovine HapMap project. (b) Admixture bar plots showing each individual animal's (investigated and reference) genomic composition when we assumed two (K = 2), three (K = 3) and 8 (K = 8) ancestral populations.
FIGURE 4
FIGURE 4
Bar plot showing major biological processes enriched by the genes located within the runs of homozygosity regions in Ugandan cattle. The numbers of genes within each biological process are presented at the end the bar of each process.
See this image and copyright information in PMC

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