Genome-wide Signature of Positive Selection Breed-Specific SNPs and Linkage Disequilibrium in Ethiopian Indigenous and European Beef Cattle Breeds
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Date
2021-09-05
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Addis Ababa University
Abstract
The detection of selection signatures in Ethiopian indigenous breeds can contribute to the identification of regions of the genome that are, or have been, functionally important and, as a consequence, have been targeted by selection. Despite the availability of genomic methods for determining the origin and divergence of domestic cattle in East Africa, particularly Ethiopia, knowledge regarding their genetic adaptability and divergence remain limited. To investigate signatures of selection, breed-specific SNPs, and linkage disequilibrium (LD), Ethiopian indigenous cattle populations, three Ethiopian cattle populations (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 purposes. 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. Across the Ethiopian and European cattle populations, a common variant minor allele frequency (≥0.10 and ≤ 0.5) accounted for 94% and 62%, of the total SNPs, respectively. A total of 7759 and 48 SNPs were identified as breed-specific in the Ethiopian cattle populations and European beef cattle, respectively. These SNPs were associated with 3364 and 17 genes, respectively. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosity were 0.403 and 0.400, respectively. Similarly, for European cattle, the observed and expected heterozygosity were 0.25 and 0.26 respectively. Principle component analysis (PCA), and neighbor-joining (NJ)-tree revealed a separation of
Ethiopian cattle breeds from European beef breeds. Similarly, the NJ-tree grouped the study cattle according to their breed group with close clustering of the three Ethiopian cattle populations. The average r2 values were 0.22 ± 0.25, 0.23 ± 0.25, and 0.22 ± 0.25 in Boran, Begait, and Fogera, respectively. For Angus, Herford and Charolais it was 0.17 ± 0.28, 0.17 ± 0.28 and 0.18 ± 0.29, respectively. It was observed that average r2 values decreased as physical distance increased. The top 1% FST values were considered to delimit genomic regions under positive selection. Some of the candidate genes are involved in biological processes and pathways linked to meat quality attributes. The candidate genes are involved in meat tenderness (CAPZB, DCTN2, KIF5A, DCTN2, RGS20, STIM1, KLHL3, and ITGB1BP1), IMF (DGAT1, LPCAT1, PLCL2, CTNNA1, and B4GALNT1) meat color (ASAP3, ADAP1, APBB1IP, RTKN2, and STAP2). Furthermore, some of the candidate genes are associated with tropical adaptation — heat tolerance, and resistance to disease (SOD1, DCTN2, GNAS, IGF1, TLN1, RRAS, GNAS, and ASAP3). The significant degree of SNP variation found in this study suggests that these markers could be useful for genetic research in Ethiopian cattle breeds. The high genetic variability observed in Ethiopian cattle breeds can be used as a potential source for future breeding programs. The identified candidate genes have to be further confirmed through GWAS, sequencing, and omics studies.
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Adaptation, Section Pressure, Selection Signature