Genes & Genomics

, Volume 37, Issue 9, pp 759–765

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

DOI: 10.1007/s13258-015-0304-3

Cite this article as:
Edea, Z., Dadi, H., Dessie, T. et al. Genes Genom (2015) 37: 759. doi:10.1007/s13258-015-0304-3

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 r2 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 (r2 = 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 r2, 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.

Keywords

Ethiopian cattle Hanwoo Linkage disequilibrium Single-nucleotide polymorphism 

Supplementary material

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

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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