ABSTRACT

A total of 272 individuals from 12 indigenous Nigerian cattle breeds - Sokoto Gudali (21), Red Bororo (22), Adamawa Gudali (25), Kuri (2), Wadara (3), Bunaji (23), Friesian �“ Bunaji (24), N'Dama (23), Azawak (2), Keteku (13), Yakanaji (12) and Muturu (12) with five indigenous Ugandan cattle breeds - Karamonjong (16), Sereres (13), Sahiwal Zebu crosses (13), Nganda (23) and Ankole (25) were genotyped for 777,962 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, admixture levels, and relationships. Among the Nigerian cattle populations, the observed heterozygosity varied from 0.582 in Friesian �“ Bunaji to 0.773 in Muturu with a mean of 0.676 and varied from 0.648 in Karamonjong to 0.622 in Nganda with a mean of 0.637 across all Ugandan cattle populations. The expected heterozygosity in the Nigerian cattle breeds ranged from 0.642 in Muturu to 0.638 in Red Bororo with a mean of 0.641 and ranged from 0.635 in Karamonjong to 0.632 in Serele/Teso Zebu with a mean of 0.633 across all Ugandan cattle populations. The gene flow (N(nm)) value combining all 12 Nigerian breeds, amounted to 0.979 and that of Ugandan cattle breeds amounted to 0.953. In turn, when gene flow was examined within breed and country, gene migration in the Nigerian cattle population ranged from 0.981 in Muturu to 0.975 in Red Bororo with the greatest gene migration of 0.955 observed in Karamonjong and the lowest was observed in the Serere (0.950) in the Uganda cattle population. The inbreeding coefficient estimate (FIS) in Nigerian cattle revealed that within population variation accounted for approximately 10.5% of the total genetic variation and 1.6% of the total genetic variation in Ugandan cattle. In the Nigerian cattle populations, only 3056 (0.46%) of 4235 SNPs markers significantly deviated from HWE (p < 0.05, p < 0.01), as where in Ugandan cattle x populations, 98 (0.02%) of the markers appeared to be in disequilibrium. The first and second principal components explained approximately 15.54 % and 3.66% of the total variation in Nigerian and Ugandan cattle populations respectively and supported the clustering of the populations according to their historical origins and geographical locations. A considerable source of variation among cattle was exhibited at low cross-validation (K = 2, 3, and 4) clustering the populations into African Taurine, European Taurine, African Zebu and detecting the Zebu introgression in African Taurine breeds. Genetic distance, principal component analysis, and population structure analyses, admixture analyses and phylogenic tree, clearly differentiated the cattle population according to their historical origins, and confirmed that Nigerian cattle populations were genetically distinct from the Ugandan cattle populations. This study indicated the necessity for a balance between improving livestock productivity and the conservation of cattle breeds at risk of extinction in Nigeria and the Nganda in Uganda. Hitherto, these populations have represented a unique genetic resource and unexploited opportunity that warrants initiatives for their sustainable conservation and utilization.