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

Onzima, R. B. and Upadhyay, Maulik and Mukiibi, R. and Kanis, E. and Groenen, M. A. M. and Crooijmans, R. P. M. A. (2018). Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds. Animal genetics. 49, 59-70
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Official URL: https://dx.doi.org/ 10.1111/age.12631

Abstract

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.

Authors/Creators:Onzima, R. B. and Upadhyay, Maulik and Mukiibi, R. and Kanis, E. and Groenen, M. A. M. and Crooijmans, R. P. M. A.
Title:Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
Series/Journal:Animal genetics (1365-2052)
Year of publishing :2018
Volume:49
Page range:59-70
Number of Pages:12
Publisher:John Wiley & Sons Ltd, Stichting International Foundation for Animal Genetics
ISSN:1365-2052
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 402 Animal and Dairy Science > Animal and Dairy Science.
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Agrovoc terms:goats, genetics, Uganda
Keywords:breed composition, breed diversity, Capra hircus, heterozygosity, indigenous goats, population genetics
URN:NBN:urn:nbn:se:slu:epsilon-e-4791
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-4791
ID Code:15346
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:06 Mar 2018 08:02
Metadata Last Modified:06 Mar 2018 08:02

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