Genome-Wide Genetic Diversity, Population Structure and Admixture Analysis in African and Asian Cattle Breeds

Knowledge of genetic diversity and population structure are useful for designing effective strategies for improving production, management and conservation of farm animal genetic resources. We present here comprehensive analysis of genetic diversity, population structure and admixture based on 308 individuals sampled from 10 cattle populations inhabiting three different countries of Asia and African continents and genotyped for 69,903 autosomal SNPs mainly derived from the indicine breed. The overall mean minor allele frequency (MAF) was 0.32, 0.29 and 0.27 for Ethiopian, Bangladeshi and Korean (Hanwoo) cattle breeds, respectively. Average expected heterozygosity varied from 0.26 in Hanwoo to 0.42 in Ethiopian cattle populations. The lowest F_ST (0.003) was detected between the Arado and Gurgahe populations of Ethiopian cattle, while the largest F_ST (0.339) was found between Hanwoo (taurine) and Bangladeshi zebu. Ethiopian cattle populations displayed considerable levels of introgression from Asian zebu (76%), while Bangladeshi populations predominantly represented zebu (98.7%). Sheko, the only remnant of East African short horned taurine cattle showed considerable levels of zebu admixture (58%). Our PCA, STRUCTURE and phylogeny analyses clearly revealed that the largest genetic difference was identified between taurine and indicine, while as expected the Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. The relationship among Ethiopian cattle populations reflects their history of origin and admixture rather than their phenotypic based discriminations. It was demonstrated that populations drawn from Ethiopia displayed high levels of diversity that could be explained by their hybrid nature and strong gene flow.