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Research article - Peer-reviewed, 2018

Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

Onzima, R. B.; Upadhyay, M. R.; Mukiibi, R.; Kanis, E.; Groenen, M. A. M.; Crooijmans, R. P. M. A.


Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H-O) and expected (H-E) heterozygosity across breeds was 0.355 +/- 0.147 and 0.384 +/- 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f(4) statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes.


breed composition; breed diversity; Capra hircus; heterozygosity; indigenous goats; population genetics

Published in

Animal Genetics
2018, volume: 49, number: 1, pages: 59-70

Authors' information

Onzima, R. B.
Wageningen University & Research Centre (Wageningen UR)
Upadhyay, Maulik
Wageningen University & Research Centre (Wageningen UR)
Upadhyay, Maulik
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Mukiibi, R.
University of Alberta
Kanis, E.
Wageningen University & Research Centre (Wageningen UR)
Groenen, M. A. M.
Wageningen University & Research Centre (Wageningen UR)
Crooijmans, R. P. M. A.
Wageningen University & Research Centre (Wageningen UR)

Sustainable Development Goals

SDG2 Zero hunger

UKÄ Subject classification

Animal and Dairy Science

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