Sisay, Tesfaye (Professor)Dejene, Genet2022-03-292023-11-182022-03-292023-11-182021-11-20http://etd.aau.edu.et/handle/12345678/30985Ethiopia ranks first in Africa with the largest number of cattle populations adapted to diverse environments. Detection of selection signatures and assessment of linkage disequilibrium enable us to asses genetic diversity and genomic region under positive selections. However, in Ethiopian indigenous cattle there is few studies regarding their origin, divergency and genetic adaptability. This study investigated detection of selection signatures, breed-specific SNPs and linkage disequilibrium in Ethiopian cattle populations and European dairy breeds. A total 135 animals representing four Ethiopian indigenous cattle populations: Arsi (n = 29), Begait (n = 40), Boran (n = 40) and Sheko (n = 26) were genotyped with 80K SNP chip. Two European dairy breeds (Holstein, n = 60 and Jersey, n = 38) were used for comparison. The mean of minor allele frequency (MAF) 0.32 ± 0.12, 0.32 ± 0.12, 0.31 ± 0.13, 0.30 ± 0.13,0.19 ± 0.17 and 0.18 ± 0.17 for Arsi, Begait, Boran, Sheko, Holstein and Jersey, respectively. The common variant MAF (≥0.10 and 0.5) distribution across Ethiopian cattle populations and European cattle breeds were 89% and 57%, respectively. Ethiopian cattle specific SNPs were located in genes(CSN2, ABCA7, PDE4B, ABCA1, JAK2, B4GALT4, FOXO3, GHR, ADCY8, ACACB) associated with milk production traits, fertility and growth traits (PGR, GHR, XKR4, ADCY5, POU2F1, IGF1, ABCC2, XKR4) thermo-tolerant, coat color (HSF1, HSPH1, HSPA4, KDR, RAD50, WNT1, KIT), feed intake (XKR4, ACCN1, ACAD11) and fat thickness (XKR4, IGFBP-3 and POU2F1).The top 1% fixation index (Fst) values representing positive selection harbored candidate genes (ABCG2, ABCA7, B4GALNT1, GHR, ITGAV) involved in milk traits such as, milk protein, milk fat and mastitis, milk production and (HSPH1, HSPA4, SOD1, MATR3, RAD50, KDR) for tropical adaptation. The estimated observed heterozygosity (Ho) and expected heterozygosity (He) for Ethiopian cattle populations were found to be, 0.40 and 0.39 respectively. These values were 0.24 and 0.25 for European dairy cattle breeds respectively. Principal component analysis (PCA)clearly separated Sheko from Ethiopian zebu populations with the value of 4.34%(PCA1) and 3.33% (PCA2). Similarly, PCA1 and PCA2 accounted for 65.97 % and 9.50 % of the variation and differentiated bos indicus from European taurine. Additionally, result of the phylogenetic tree analysis supporting PCA revealed that with the exception of Sheko, Ethiopian cattle population were closely clustered and two European dairy breeds (Holstein and Jersey) were located in a clade with Sheko. The overall mean of r2 values were 0.22, 0.23, 0.23, 0.22, 0.24, 0.16, 0.16 in Arsi, Begait, Boran, Sheko, Holstein and Jersey, respectively. In broad, this study revealed that there are genomic regions under strong divergent selection harboring genes involved in milk production traits and in adaptation to tropical environment.enAdaptationLinkage DisequilibriumSelection SignatureSnpsThesis