Genome-Wide Signature of Positive Selection in Ethiopian Indigenous and European Beef Cattle Breeds

Abstract

Abstract Background: Despite the availability of genomic methods for determining the origin and divergence of domestic cattle in East Africa, particularly Ethiopia, knowledge regarding their genetic adaptability and divergence remain limited. To investigate signatures of selection Ethiopian cattle populations were genotyped with an 80K SNP array and European beef cattle breeds were also used for comparison purposes. Results: Across Ethiopian cattle populations, the mean observed and expected heterozygosity were 0.403 and 0.400, respectively. Similarly, for European cattle, observed and expected heterozygosity were 0.25 and 0.26 respectively. PCA and NJ-tree revealed a separation of Ethiopian cattle breeds from European beef breeds. NJ-tree grouped the study cattle according to their breed group with close clustering of Ethiopian cattle populations. The top 1% FST values were considered to delimit genomic regions under positive selection. Some of the candidate genes are involved in biological processes and pathways linked to meat quality attributes determined. Furthermore, some of the candidate genes are associated with tropical adaptation to heat tolerance and resistance to disease. Conclusion: The levels of genetic variation for SNPs on the Bovines GGP-80K assays obtained in this study indicate that these assays have utility for genetic studies in Ethiopian indigenous cattle breeds. The genetic distance of the indigenous Ethiopian breeds from European beef breeds coincides with existing knowledge, that European beef breeds considered under this study are artificially selected and are taurine, while Ethiopian indigenous breeds are naturally selected.