Analysis of B. taurus and B. indicus Admixture in Uganda as Revealed by the Illumina BovineSNP50 Genotyping BeadChip.

The NextGen project investigates disease resistance in indigenous Ugandan cattle. A total of 915 animals from 10 populations belonging to Ankole (crossbred between B. indicus and B. taurus), Zebu and Ankole-Zebu crosses have been sampled in 52 grid cells throughout the country. We recorded animal health status, sampling site GPS coordinates, vector distribution and disease prevalence to identify selection signatures from whole genome sequencing and SNP data. Since population structure and stratification may produce biased results, we have investigated the genomic structure of sampled animals genotyped with the BovineSNP50 Genotyping Beadchip. The software Admixture identified four ancestral genomic components. Three of them likely correspond to indicine, African taurine and probably European taurine components. The fourth has a still unidentified origin. None of the components has strong geographic structure. Most individuals investigated have a remarkable level of admixture. Overall, about 20% of the Zebu genome is of African taurine origin, confirming previous data on the foundation of African Zebu. The likely European taurine is a minor component, rare in Zebu and evenly distributed in Ankole, other Sanga and Ankole-Zebu crosses. In total only 133 animals have more than 90% of the genome from a single component: 123 African taurine, 1 zebuine and 9 from the unidentified component.