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

Abstract 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 and linkage disequilibrium Ethiopian cattle populations were genotyped with an 80K SNP array. European beef cattle breeds were also used for comparison purposes. 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. Similarly, NJ-tree grouped the study cattle according to their breed group with close clustering of Ethiopian cattle populations. The average r2 values were 0.22 ± 0.25, 0.23 ± 0.25, and 0.22 ± 0.25 in Boran, Begait, and Fogera, respectively. For Angus, Herford and Charolais it was 0.17 ± 0.28, 0.17 ± 0.28 and 0.18 ± 0.29, respectively. 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. Furthermore, some of the candidate genes are associated with tropical adaptation to heat tolerance and resistance to disease. Significant SNP variation found in this study suggests that these markers could be useful for genetic research in Ethiopian cattle breeds.