Population Structure of Ugandan Taurine and Zebuine Cattle Breeds as Revealed by Medium and High Density SNP Chips

In the course of Nextgen project, an extensive sampling of Ugandan cattle was carried out to investigate the association between genotypes and resistance to endemic diseases. A total of 915 animals, representative of  the Ankole group (crossbred between Bos indicus and Bos taurus), Zebu and Ankole-Zebu crosses, were sampled over the whole country and genotyped with the Medium (Illumina BovineSNP50 BeadChip, about 54K SNPs) and High-Density (BovineHD Genotyping BeadChip, about 800K SNPs) SNP chips. A total of 815 and 102 animals have been characterized with the 54K and the 800K chips, respectively. The 54K data were compared to SNP data from 22 breeds (representative of African and European B. taurus and B. indicus) available through the Bovine HapMap project. Population structure was assessed by running a Bayesian clustering algorithm with the software Admixture. The same approach was applied to the 800K data for Ugandan cattle alone as an independent test.The results showed that the population structure of Ugandan cattle was consistent across the two datasets resolutions. The two major genomic components, roughly corresponding to Ankole and Zebu breed groups, are also geographically structured, with indicine and taurine genomes being prevalent in N-E and S-W Uganda, respectively. The indicine component was further split into two sub-clusters, suggesting a probable contribution from distinct ancestral zebu populations introduced from Asia to Africa in different historical times. Ugandan cattle possess also a few minor genomic components, the origin of which could not be assigned to any of the HapMap reference breeds.