Genome-wide linkage disequilibrium in a Thai multibreed dairy cattle population

Abstract

The level of linkage disequilibrium (LD) plays an important role in increasing the power to detect associations for mapping quantitative trait loci in the genome and in increasing the accuracy of prediction of genomic estimated breeding values (GEBV). Thus, the objectives of this study were to evaluate the extent of LD in Thai multibreed dairy cattle and to determine factors that influence the estimation of LD. A total of 1413 multibreed dairy cows were genotyped for 8220 SNPs, covering 2507.24Mb of the genome. The mean of minor allele frequencies (MAF) across autosomes was 0.37. All possible SNP pairs on the same chromosome were used to estimate LD across the 29 autosomes. High levels of LD were found in autosomes, particularly between SNP pairs at distances shorter than 50kb. The mean of D′ (linkage disequilibrium relative to its maximum) and r2 (coefficient of correlation squared) for SNPs at 40–50kb apart were 0.694 and 0.202, respectively. Overestimation of D′ occurred when the MAF threshold was low (0.05). The r2 was high when the MAF threshold was higher than 0.20, especially when the distance between markers was shorter than 50kb. The minimum sample sizes required to obtain accurate measures of LD were 177 for D′ and 89 for r2. Results from this research will be useful for genome-wide association studies and genomic selection of dairy cattle in tropical regions.