Detection and Evaluation of Breed-specific SNPs and Minor allele frequency in Ethiopian Indigenous and European Beef Cattle Breeds

Abstract Introduction Understanding the genetic foundation of locally adapted indigenous cattle breeds is critical information for developing appropriate genetic improvement and conservation methods and initiatives. Methods To investigate breed-specific SNPs, and minor allele frequency in three Ethiopian cattle breeds Begait, (n = 40), Boran (n = 40), and Fogera (n = 43) were genotyped with a high-density 80K SNP array. Three European beef cattle breeds (Angus, n = 42), Hereford (n = 35), and Charolais (n = 37) were also used for comparison. The SNP markers were screened for a call rate of ≥ 90%, a minor allele frequency (MAF) of > 0.01, and a sample call rate of > 90%. 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 significance 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 for an overall estimated 94% and 62%, of the SNPs respectively. A total of 7759 and 48 SNPs were identified as breed-specific in the Ethiopian cattle breeds and European beef cattle respectively. These specific SNPs resided with 3364 genes for Ethiopian cattle breeds and 17 genes for European beef cattle breeds. According to Gene Ontology analysis, interestingly important biological processes and pathways related to tropical adaptation were detected in Ethiopian cattle breeds. 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.