Phenotypic and Genetic Characterization and Design of Community-Based Breeding Programs for Two Indigenous Goat Populations of Ethiopia

The aim of the dissertation was to undertake phenotypic and genetic characterization and design community-based breeding programs for two indigenous goat populations in Ethiopia, namely Arab and Oromo. The dissertation was based on five manuscripts. Papers I, II, IV and V were based on data generated from production system, morphological characterization and ranking experiments. Paper III was based on whole genome data generated from three indigenous goat populations (Arab, Fellata and Oromo). Genomic data of ten additional goat breeds including four Ethiopian (Abergelle, Gumuz, Keffa, Woiyto-Guji), four African (Kenyan Boran, Morrocan Unknown, Malawian Thyolo, Malian Guera), one Asian (Chinese Tibetan) and one European (French Saanen), obtained from the database, were included for comparison purposes. Reconnaissance survey, focus group discussion and interview with structured questionnaires were used to collect data from 249 households (Paper I). Ten qualitative and nine quantitative traits were recorded/measured from 747 randomly selected goats (Paper II). Genetic diversity metrics within each of three goat populations were assessed and population structure was investigated using principal component analysis (PCA), ADMIXTURE and TREEMIX. Candidate genes underlying strong selection signatures were identified by combining two approaches: pooled hetrozygosity (Hp) and population differentiation (Fst) (Paper III). Two live animal ranking experiments (own flock and group) were conducted to identify breeding objective traits of Arab and Oromo goat keepers. In the own-flock ranking experiment, a total of 147 households ranked their first, second and third best and the most inferior does in their own flock. In the group-animal ranking experiment, 24 breeding does and bucks were randomly selected and placed into eight groups. Twelve farmers from Arab and Oromo goat keepers, respectively with no knowledge of the experimental animals, ranked the three goats in each group as 1st, 2nd and 3rd, giving reasons for their ...