Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
| Autor: | R. Mukiibi, R. B. Onzima, Martien A. M. Groenen, Richard P. M. A. Crooijmans, E. Kanis, Maulik Upadhyay |
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| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Veterinary medicine Genetics and Breeding Population Genetic admixture Zoology Single-nucleotide polymorphism Biology Animal Breeding and Genomics breed composition Polymorphism Single Nucleotide Crossbreed breed diversity Gene flow 03 medical and health sciences Animal and Dairy Science Genetics Animals heterozygosity Uganda Capra hircus indigenous goats Fokkerij en Genomica Genetic variability education education.field_of_study Genetic diversity Goats 0402 animal and dairy science population genetics Original Articles 04 agricultural and veterinary sciences General Medicine 040201 dairy & animal science Breed Genetics Population 030104 developmental biology WIAS Original Article Animal Science and Zoology Genome-Wide Association Study |
| Zdroj: | Animal Genetics, 49(1), 59-70 Onzima, R B, Upadhyay, M R, Mukiibi, R, Kanis, E, Groenen, M A M & Crooijmans, R P M A 2018, ' Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds ', Animal Genetics, vol. 49, no. 1, pp. 59-70 . https://doi.org/10.1111/age.12631 Animal Genetics 49 (2018) 1 Animal Genetics |
| ISSN: | 0268-9146 |
| DOI: | 10.1111/age.12631 |
| Popis: | 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 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) 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 f4 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. |
| Databáze: | OpenAIRE |
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