Genome-Wide Diversity, Selection Signatures and Linkage Disequilbrium in Ethiopian Cattle Populations

In this study, we applied single nucleotide polymorphisms (SNPs) BeadChips of different density and origins to genotype samples of cattle breeds with geographically diverse origins (African and Asian) with the objective to investigate genome-wide genetic diversity, trace patterns of admixture, detect outlier loci under directional selection and estimate the extent of linkage disequilibrium. DNA samples were collected from a total  of 12 populations representing the four major groups of African cattle populations inhabiting diverse agro-ecologies, 2 Asian (Bangladeshi) zebus and one taurine reference breed (Hanwoo). In Ethiopia cattle populations, the mean minor allele frequencies (MAFs) values were 0.22, 0.15, and 0.31 for 9K, 50K and 80K BeadChips, respectively. The mean observed heterozygosity for 9K, 50K and 80K BeadChips in Ethiopian cattle was 0.38, 0.27 and 0.41, respectively. In Hanwoo cattle, the respective values were 0.40, 0.34 and 0.28. Some of outlier loci detected were located within genes that are involved in metabolism, hypoxia response and heat stress. The overall mean r ² values were 0.05, 0.12 and 0.20 for Ethiopian cattle populations using the 9K, 50K and 80K BeadChips, respectively. A moderate level of LD (r² = 0.22) extended at marker distances of 20 to 40 kb for the indicine-derived 80KBeadChip, whereas it was only 0.14 for the 50K BeadChip. From comparison of different chips, we can conclude that the indicine-derived SNPs are more informatics and  more suitable for genome-wide association studies and genomic selection in indigenous Ethiopian (or African) cattle populations.