Identification of Breed-Specific SNPs in Ethiopian Indigenous and European Beef Cattle Breeds and how they May Influence Adaptation and Selection Signatures

Abstract

Background: Understanding the genetic foundation of locally adapted indigenous cattle breeds is critical information for developing appropriate genetic improvement and conservation initiatives. To investigate breed-specific SNPs, and minor allele frequency of three Ethiopian cattle breeds Begait, (n = 40), Boran (n = 40), and Fogera (n = 43) were genotyped with 80K SNP array. Three European beef cattle breeds (Angus, n = 42), Hereford (n = 35), and Charolais (n = 37) were also used for comparison. Results: The average minor allele frequency was 0.19 ± 0.17, 0.20 ± 0.17, 0.21± 0.17, 0.31 ± 0.13, 0.32 ± 0.12, 0.32 ± 0.13 for Angus, Herford, Charolais, Boran, Fogera, and Begait cattle, respectively. Minor allele frequency difference was observed between Ethiopian indigenous and European beef cattle breeds. Across the Ethiopian and European cattle breeds, a common variant minor allele frequency (≥0.10 and ≤ 0.5) accounted 94% and 62%, respectively. A total of 7759 and 48 SNPs were identified as breed-specific in Ethiopian cattle breeds and European beef cattle breeds respectively. These SNPs resided with 3364 genes for Ethiopian cattle breeds and 17 genes for European beef cattle breeds. Interestingly important biological processes and pathways related to tropical adaptation in Ethiopian cattle populations were identified through gene Ontology analysis. Conclusions: The higher minor allele frequency and breed-specific SNPs detected in Ethiopian indigenous breeds show the presence of high genetic variability. This genetic variation in Ethiopian cattle breeds is used as a potential source for future breeding programs.