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

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 C 0.05). We suggest that indicine-derived SNPs maybe more suitable for genomewide association studies and genomic selection in indigenous Ethiopian (or African) cattle populations.

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds

“…The value of adjacent LDs for Brown Hanwoo in the present study was lower compared to the value reported by Edea et al . (). The difference could be because of the distinctive types of Hanwoo populations that were analyzed, i.e.…”

“…Furthermore, SNP densities also have influence on the N e because they depend on LD, which is biased for low marker density (Edea et al . ). We used about 43K cleaned SNPs from 667 proven bulls (sires), a higher density than did Li & Kim (), who used about 36K cleaned SNPs from 61 sires and 486 steers, and Lee et al .…”

“…This result agrees with similar studies in Hanwoo (Edea et al . ) and other cattle breeds (Gautier et al . ; de Roos et al .…”

Genotype imputation as a cost-saving genomic strategy for South African Sanga cattle: A review

“…The GGP indicus chip was also optimized for high imputation accuracy in indicine breeds, with imputation to the Illumina HD bead chip being up to 97% accurate in these breeds (Ferraz et al, 2018). Previous research has shown improved MAF and LD estimates for indigenous Ethiopian cattle (Edea et al, 2015) and improved imputation accuracy for indicine Gyr cattle (Boison et al, 2015) when indicus-derived SNP panels were used. Since Sanga cattle are taurine-indicine hybrids, it would be recommended to test the utility of this panel for Sanga breeds, in contrast to taurine-derived SNP panels.…”

“…The decay of LD with increasing inter-marker distance has been reported widely, and specifically for non-exotic and admixed populations (e.g. Lashmar et al, 2018;Edea et al, 2015;Mokry et al, 2014). Owing to the costs of acquiring high-density SNP genotypes and whole-genome sequencing data, especially for researchers in developing countries, improving SNP densities through genotyping and sequencing more SNPs is not economically feasible.…”