chenyambuga, Sebastian Wilson2023-07-042023-07-042002http://www.suaire.sua.ac.tz/handle/123456789/5341Phd ThesisTwo studies were carried out to genetically characterize the sub-Saharan African goats using 19 microsatellite markers. The aims were to understand the genetic uniqueness and relationships among breeds and to quantify the level of genetic diversity within each breed. The first study investigated the genetic relationships among the major goat types in sub-Saharan Africa. Ten African breeds were sampled from eastern Africa (Maasai. Kigezi, Mubende, North West Highland, Arsi-Bale), southern Africa (Ndebele, Pafuri) and West Africa (West African Dwarf, Maure, Djallonke). Two European breeds (Grisons Striped, Toggenburg). two Asian breeds (Mongolian Cashmere, Bandipur) and one Middle East breed (Arab) were included as reference breeds. Twenty to forty eight animals per breed breed genetic diversity was determined as the mean number of alleles per locus and average gene diversity. Two measures of population differentiation, Gst and 0 were computed to measure the genetic differentiation among the breeds. Breed assignment test was performed to identify the source populations of individual animals. Three measures of genetic distances, Ds, DA, and (bp.)2 were used to estimate the genetic distances between pairs of breeds. These distances were used to construct neighbour joining (NJ) trees to assess the relationships among breeds. The genetic relationships among breeds were further assessed using principal component analysis (PCA) and multidimensional scaling (MS). were genotyped at the 19 microsatellite loci. Within iii In total, 263 alleles were detected across all the breeds. Among the sub-Saharan African breeds, the mean number of alleles per locus ranged from 5.26 ± 0.464 (Djallonke) to 7.05 ±0.516 (Mubende). The lowest and highest average gene diversities were observed in Pafuri (0.542 ± 0.036) and Ndebele (0.672 ± 0.031), respectively. For all the breeds, the within breed genetic diversities of European breeds were slightly less than those of African and Asian breeds. Between 14.6% (0) and 15.7% (Gst) of the total genetic variation was due to differences between breeds. In the assignment test, 92.1% of all animals were correctly assigned to their original population. The three measures of genetic distances indicated that the largest genetic distances were observed between West African and southern African breeds and the lowest genetic distances were found between the pairs of breeds within the same country. The (5p)2 distances were found less effective in revealing the true genetic relationships among the breeds compared to differences, however, both grouped the breeds according to their geographic origins. The PCA and MS supported the grouping of the breeds according to their geographic origins. Unlike the NJ trees, the PCA and MS clearly separated the European breeds from the Asian breeds. Furthermore, the MS separated the Arab breed from the other breeds more clearly. Ds, and Da distances. The NJ trees constructed from Ds, and Da showed some iv The second study examined the genetic diversity and structure of Small short-eared eastern African goats as a case study. The same 19 microsatellite markers were used to genotype 13 populations. The populations sampled were Afar, North East Highland, Boran, Galla, Kenyan Small East African, Maasai, Ugogo, Sukuma, Ujiji, Tanzanian Coastal, Newala, Mbeya and Landim. The reference breeds were Tswana, Venda, West African Dwarf, Red Sokoto and Toggenburg. The Galla had the lowest (5.53 ± 0.599) mean number of alleles per locus while Afar had the highest (6.53 ± 0.646). The level of gene diversity ranged from 0.667 ± 0.035 (Afar) to 0.553 ± 0.036 (Newala). Between 11% (0) and 12% (Gst) of the total genetic variability could be attributed to differences among the populations. In the assignment test, 79.1% of the individuals were correctly assigned to their source populations. NJ tree using individual animals as the taxonomic units was constructed to study the structure of eastern African goats. Among the Tanzanian populations, only the Newala appeared to be tightly clustered together, the rest of the populations were mixed together. Among the Kenyan and Ethiopian populations, only the Afar and Kenyan Small East African featured in their distinct clusters, the rest of the populations showed unclear pattern of clustering. The NJ trees based on Ds, and Da distances, though differed in their topology, clearly marked the separation of the Tanzanian populations from the Ethiopian and Kenyan populations. The Landim was grouped together with the Tswana and Venda goats from southern Africa. The MS supported the separation of the Tanzanian populations from the Ethiopian-Kenyan populations. However, the PCA indicated that the eastern African goat populations are genetically close to each otherenGenetic characterisationindigenous goatmicrosatellitednaThesis