Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats.

Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.

Phenotypic ranking experiments in identifying breeding objective traits of smallholder farmers in northwestern Ethiopia.

We executed two live animal ranking experiments, own-flock and group-animal ranking, to identify the breeding objectives of Arab and Oromo goat keepers in northwestern Ethiopia as a preliminary step towards designing sustainable breeding programs for two goat populations. In the own-flock ranking experiment, a total of 147 households, out of which 46 were Arab and 101 were Oromo goat keepers that live in semi-arid and sub-humid agroecologies respectively, were visited at their homesteads and were asked to choose their first best, second best, third best and the most inferior does from their own flock. The reasons of ranking and life history of the does (age, previous production and reproduction information) were inquired and recorded; live body weight and some linear body measurements were taken. In the group-animal ranking experiment, 12 breeding does and 12 breeding bucks from Arab goats and the same number of animals from Oromo goats were randomly selected. Life history of selected does and bucks (age, birth type, libido and temperament) were inquired from the owners. The selected animals were randomly grouped into four in Arab goats (three animals per group) and the same was applied in Oromo goats. Twelve farmers for Arab goats and the same number of farmers for Oromo goats who have not known the experimental animals were invited to do the ranking. Each person ranked the three animals in each group as 1st, 2nd and 3rd, giving reasons of ranking. After a first round of ranking, s/he was then provided with the history of each individual animal and asked whether s/he would consider re-ranking them. This procedure was continued eight times until a person covered all groups of does and bucks. It was found out that in own-flock ranking experiment, keepers focus on productive, reproductive and behavioral traits (such as body size, mothering ability, twinning rate, kidding interval and temperament) while in group-animal ranking experiment, there was a general tendency to focus on observable physical traits like coat color, body size and body conformation. Simultaneous use of both own-flock and group-animal ranking experiments is advisable to identify breeding objective traits in production systems where record keeping is absent.

Production systems and breeding practices of Arab and Oromo goat keepers in northwestern Ethiopia: implications for community-based breeding programs.

We conducted a household survey in the semi-arid and sub-humid parts of Benishangul Gumuz region in northwestern Ethiopia to better understand and describe production systems and breeding practices of Arab and Oromo goat keepers. Multistage random sampling was employed to select peasant associations, while probability proportional to size sampling was used to select households. Data were collected from 249 households, out of which 86 were Arab and 163 were Oromo goat keepers that live in semi-arid and sub-humid agroecologies, respectively. Personal observations, focus group discussions, and structured questionnaires were used to collect data. Data were analyzed using SPSS and results were presented using descriptive statistics and indices. Ninety-two percent of Arab and 86% of Oromo goat keepers indicated crop and livestock production as their main occupation. Goats were kept for a variety of purposes. Income generation, meat, and savings were the highest priorities. The average flock size owned by Arab goat keepers (12.5 ± 4.0) was significantly (p < 0.01) higher than that of Oromo goat keepers (9.9 ± 3.8). Breeding does constituted the largest average flock size followed by kids, young does, and young bucks. Body size, twining ability, coat color, and kid growth were considered important in selecting breeding does, while body size, growth rate, coat color, and libido were the most preferred traits for buck selection. Mating was predominantly uncontrolled mainly due to communal grazing lands. Castration of bucks was significantly (p < 0.01) more frequent in Arab goat keepers than in Oromo goat keepers. Arab goats have better reproductive performance than Oromo goats. On average, female goats in the study areas gave first births at the age of 1.2 years, kidded every 7.5 months, stayed on reproduction for about 7.6 years, and produced 10.7 kids per lifetime. Compared with Arab goats, Oromo goats had significantly (p < 0.01) higher average age at first mating, age at first kidding, kidding interval, and reproductive lifetime but produced lower average number of kids per lifetime. Nucleus breeding schemes are recommended to optimize the limited available resources in the study areas. A single nucleus could serve both Arab and Oromo goat keepers. In conclusion, breeding programs implemented in the study areas should consider the production systems and breeding practices of Arab and Oromo goat keepers appropriately.