Identification of Breed-Specific SNPs in Ethiopian Indigenous and European Beef Cattle Breeds and how they May Influence Adaptation and Selection Signatures
Dejenie Mengistie *
National Agricultural Biotechnology Research Center, P.O. Box: 31, Holeta, Ethiopia.
Zewdu Edea
Ethiopian Bio and Emerging Technology Institute, P.O. Box 2490, Addis Ababa, Ethiopia.
Tesfaye Sisay Tesema
Addis Ababa University Institute of Biotechnology, P.O.BOX 1176, Addis Ababa, Ethiopia.
Genet Zewdie
Ethiopian Bio and Emerging Technology Institute, P.O. Box 2490, Addis Ababa, Ethiopia.
Genet Dejene
Ethiopian Bio and Emerging Technology Institute, P.O. Box 2490, Addis Ababa, Ethiopia.
Tadelle Dessie
International Livestock Research Institute, Addis Ababa, Ethiopia.
Kwan Suk Kim
Chungbuk National University, South Korea.
Hailu Dadi
Ethiopian Bio and Emerging Technology Institute, P.O. Box 2490, Addis Ababa, Ethiopia.
*Author to whom correspondence should be addressed.
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.
Keywords: Breed-specific SNPs, minor allele frequency