MAF variation
The MAF for each SNP was calculated from the genotypic data and is presented in Table 2. Analysis of 7,045 markers revealed that the mean MAF was 0.23, 0.22, 0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo cattle, respectively. A significant difference was observed between the Ethiopian indigenous cattle populations and Hanwoo (p < 0.001). The average value for Hanwoo was 32% higher than the value for Ethiopian cattle populations. The overall MAF in the present finding for indigenous Ethiopian cattle breeds is higher than an earlier report for indicine breeds but lower than the average value reported for most taurine breeds [3]. The value found for Hanwoo cattle was comparable with the previous results for taurine breeds but higher than the reported average for the same breed [10, 12]. This could be attributed to the different marker density used, and a higher density marker (Illumina Bovine 50K SNP BeadChip) was used in the previous study. The higher values for taurine breeds can be explained by the fact that SNP loci used in this study were detected in taurine breeds, and their average minor allele frequency was much lower in indicine breeds.
Across the Ethiopian cattle populations, common variant MAFs (≥0.10 and ≤0.5) accounted for 74% of the total SNPs (Table 3). Hanwoo cattle displayed a higher proportion of common variant SNPs (90%). Rare variant MAFs were observed in about 9% and 4% of markers in the Ethiopian and Hanwoo breeds, respectively. The relatively higher proportion of fixed alleles in Ethiopia cattle populations could be attributed to the inbreeding as a result of uncontrolled breeding practices. A common variant MAF proportion of 83% was reported in sheep breeds [5]. The distribution of MAFs revealed that nearly 34.08% of the markers in Ethiopian cattle populations and 53% in Hanwoo cattle displayed a high degree of polymorphisms (0.3 ≤ MAF ≤ 0.5). Yet, this value was higher than an earlier report both for Hanwoo (25%) and Holstein (28%) [12]. Much higher MAFs were detected in Bos taurus breeds than in Bos indicus breeds [3]. The proportion of fixed markers varied among the sampled populations. Among the Ethiopian cattle populations, the highest (8.96%) and lowest (6.30%) were obtained in the Borana and Ambo populations, respectively. The Hanwoo breed displayed a lower level of fixed SNPs (1.10%).
On average, 83.36% of the markers displayed polymorphisms (MAF > 0.05) within Ethiopian cattle populations, and the remaining 16.64% of the SNPs considered as monomorphic. The Hanwoo breed showed the highest proportion of polymorphisms (94%) (Fig. 3). The level of polymorphic SNPs in the present study was higher than what was previously reported for taurine breeds [10]. But, it was in close agreement with the value reported for sheep breeds using genome-wide SNPs [5]. Similarly, Gautier et al. [13] reported a lower rate of polymorphisms using 696 SNPs localized in BTA03 from European and West African cattle breeds (94.6% and 81.8%), respectively. The higher observed polymorphisms in Hanwoo cattle could explained by the fact that most of the bovine sequence data available in the database are from Bos taurus breeds.