Abstract
Knowledge of the extent of linkage disequilibrium (LD) between markers is crucial for determining the number of markers required for quantitative trait loci mapping, genome-wide association studies, and application of marker-assisted selection. In this study, we surveyed genome-wide LD using three genotyping BeadChips (9, 50, and 80 K) in 11 indigenous Ethiopian cattle populations and the Korean (Hanwoo) cattle breed. The overall mean r 2 values were 0.05 ± 0.12, 0.12 ± 0.20, and 0.20 ± 0.24 in the Ethiopian cattle populations for the 9, 50, and 80 K genotyping BeadChips, respectively. In Hanwoo cattle, these values were respectively 0.06 ± 0.13, 0.15 ± 0.23, and 0.15 ± 0.26. The level of LD was significantly affected by breed, genotyping BeadChip, and chromosome (P < 0.0001). For Ethiopian cattle populations, a moderate level of LD (r 2 = 0.22) extended at marker distances of 20–40 kb for the indicine-derived 80 K BeadChip, whereas it was only 0.14 for the 50 K BeadChip. As a consequence of the moderate r 2, genome-wide association studies in Ethiopian cattle populations require 75,000–150,000 indicine-derived SNPs (with a MAF ≥ 0.05). We suggest that indicine-derived SNPs maybe more suitable for genome-wide association studies and genomic selection in indigenous Ethiopian (or African) cattle populations.
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Acknowledgments
This work was supported by the research grant of Chungbuk National University in 2013. The authors extend their gratitude to International Livestock Research (ILRI), Addis Ababa (Ethiopia), for providing logistical support. The indisputable cooperation of livestock officials, farmers and pastoralists during sampling is deeply acknowledged.
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The authors declare that there is no conflict of interest
Ethics of animal experimentation
The research was conducted in the absence of any ethical issue on animal research.
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Edea, Z., Dadi, H., Dessie, T. et al. Genome-wide linkage disequilibrium analysis of indigenous cattle breeds of Ethiopia and Korea using different SNP genotyping BeadChips. Genes Genom 37, 759–765 (2015). https://doi.org/10.1007/s13258-015-0304-3
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DOI: https://doi.org/10.1007/s13258-015-0304-3