Genes & Genomics

, Volume 37, Issue 9, pp 759–765 | Cite as

Genome-wide linkage disequilibrium analysis of indigenous cattle breeds of Ethiopia and Korea using different SNP genotyping BeadChips

  • Zewdu Edea
  • Hailu Dadi
  • Tadelle Dessie
  • Seung-Hwan Lee
  • Kwan-Suk Kim
Research Article


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.


Ethiopian cattle Hanwoo Linkage disequilibrium Single-nucleotide polymorphism 



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.

Conflict of interest

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.

Supplementary material

13258_2015_304_MOESM1_ESM.doc (87 kb)
Supplementary material 1 (DOC 87 kb)


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Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2015

Authors and Affiliations

  • Zewdu Edea
    • 1
    • 2
  • Hailu Dadi
    • 3
  • Tadelle Dessie
    • 2
  • Seung-Hwan Lee
    • 4
  • Kwan-Suk Kim
    • 1
  1. 1.Department of Animal ScienceChungbuk National UniversityCheongjuKorea
  2. 2.International Livestock Research Institute (ILRI)Addis AbabaEthiopia
  3. 3.Department of BiotechnologyAddis Ababa Science and Technology UniversityAddis AbabaEthiopia
  4. 4.Animal Science & BiotechnologyChungnam National UniverstiyDaejeonKorea

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