- Martien A.M. Groenen (1)
- Robert B. Onzima (1)
- Mirte Bosse (1)
- R.P.M.A. Crooijmans (1)
- Luiz F. Brito (1)
- M.A.M. Groenen (1)
- E. Kanis (1)
- Egbert Kanis (1)
- R. Mukiibi (1)
- R.B. Onzima (1)
- Harmen P. Doekes (1)
- Richard P.M.A. Crooijmans (1)
- Maulik R. Upadhyay (1)
- M.R. Upadhyay (1)
Genome-wide characterization of selection signatures and runs of homozygosity in Ugandan goat breeds
Onzima, Robert B. ; Upadhyay, Maulik R. ; Doekes, Harmen P. ; Brito, Luiz F. ; Bosse, Mirte ; Kanis, Egbert ; Groenen, Martien A.M. ; Crooijmans, Richard P.M.A. - \ 2018
Frontiers in Genetics 9 (2018). - ISSN 1664-8021
Adaptation - Candidate genes - Capra hircus - Genetic diversity - Genomic inbreeding - Homozygosity - Selective sweeps
Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
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. - \ 2018
Animal Genetics 49 (2018)1. - ISSN 0268-9146 - p. 59 - 70.
breed composition - breed diversity - Capra hircus - heterozygosity - indigenous goats - population genetics
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.