Genome-wide analysis of goat genetic diversity and production systems in Uganda

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The indigenous Ugandan goat breeds are poorly characterised, and they are at risk of extinction, due to the introduction of exotic breeds. To prevent undesired loss of genetic diversity, there is need to characterize the production environment as well as the breeds to properly assess the value of breeds and to guide decision making in livestock development and breeding programs. The development of genetic markers and fast genotyping methods in the last decade, have created important tools for genetic characterization of breeds. However, the molecular information on its own does not capture the economic value and adaptive capacity of breeds in local conditions. An important adaptation trait is the resistance to nematode parasites. But the degree of resistance to these parasites of goat breeds is difficult to quantify. To conserve an indigenous breed, breed improvement programs are required which are tailored towards the needs of the farmers and fit with the local conditions. In this thesis, we first assessed the production systems and undertook a farmer participatory definition of breeding goal traits (Chapter 2). Next, we evaluated between breed variation in resistance to the gastrointestinal parasite Haemonchus contortus in three indigenous breeds in Uganda (Chapter 3). Secondly, using genome-wide SNP data, we assessed the genetic diversity, population structure and admixture levels in Ugandan goat breeds (Chapter 4), and analysed signatures of selection and genomic inbreeding in the goat breeds (Chapter 5). Descriptive statistics showed that the indigenous goat production systems did not differ significantly in the nature of the farms and producers’ trait preferences for goats. Adaptive traits were generally considered more important than or equally important as production traits. Therefore, sustainable breeding programs should emphasize breeding goal traits that maintain adaptation to local environmental conditions, biodiversity, and economic benefits (Chapter 2). Evaluation of between breed differences showed the indicator traits for resistance and resilience i.e. faecal egg count (FEC) and packed cell volume (PCV) to be weakly significant at later stages of infection with a higher parasite burden, suggesting potential variation in resistance to Haemonchus contortus (Chapter 3). These differences can be exploited in designing breeding programs with disease resistance in indigenous goat breeds. Genome-wide analysis using the Goat SNP50 BeadChip showed weak population sub-structuring among Ugandan goat breeds (Chapter 4). This suggests a common ancestry but also some level of geographical differentiation. Admixture analysis and f4-statistics revealed gene-flow from the South African breed Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. In Chapter 5, we assessed signatures of selection and genomic inbreeding. The study identified several putative genomic regions and genes in Ugandan goat populations, which may be underlying adaptation to local environmental conditions such as heat tolerance, disease and parasite resistance, and production traits. The genomic regions were enriched with genes involved in signalling 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 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. In the absence of pedigree data, the genomic information based on the runs of homozygosity (ROH) reveals the level of genomic inbreeding. Generally, the Ugandan indigenous goat breeds showed very low levels of genomic inbreeding as compared to the higher levels observed in Boer goats. Short ROH were more frequent than long ROH, except in the indigenous breed Karamojong, suggesting long-term relatedness during the developmental history of the goat breeds. Finally, the salient issues in this thesis were discussed in Chapter 6. It is worth noting that sustainable breed improvement programs require knowledge of the production environment and of the breeds. Production system characterization and participatory definition of breeding goal traits ensure sustainability of the breeding programs. Advances in genomic technologies yet provide an accurate method to decipher the variation between and within breeds. I therefore conclude that combining knowledge of production systems and breeds, both at the phenotypic and genotypic level, will significantly improve breeding programs in Uganda. Moreover, the community-based breeding programs advocated for the rest of sub-Saharan Africa, could be improved by utilizing genomic selection as genotyping costs become affordable.