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

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 +/- A 0.12, 0.12 +/- A 0.20, and 0.20 +/- A 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 +/- A 0.13, 0.15 +/- A 0.23, and 0.15 +/- A 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 a parts per thousand yen 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.

publication date

  • 2015
  • 2015