Whole Genome Linkage Disequilibrium Pattern in US Brangus Heifers

The success of quantitative trait loci (QTL) detection and genomic prediction depend largely on the amount of linkage disequilibrium (LD) between QTL and markers and available records to estimate marker effects. The level and extent of LD in Brangus heifers was characterized between markers using the squared correlation (r²). Genotypes for 802 Brangus heifers were obtained using the BovineSNP50bead chip. Genotype call rates averaged 98.1 ± 0.001% for 54,001 SNPs. Removal of SNPs inconsistent with Hardy-Weinberg equilibrium reduced the genotypes to 53,692. Average genotypic values were assumed at loci with missing genotypes. Results of calculated LD averaged across all chromosomes within an interval of one million base pairs was 0.09 ± 0.14 and overall average was 0.03 ± 0.08. The average distance between markers on chromosomes ranged from 15.24Kb± 10.81 for chromosome 25 to 54.51Kb ± 38.55 for chromosome 1. Higher LD values were observed for SNPs located in close proximity. The r² for pairs of SNPs closer than 0.1Mb was 0.14 and 15.50% of these pairs had r² larger than 0.30, a value considered the minimum for QTL mapping and genomic selection purposes.. Knowledge of the extent of LD in Brangus is critical for designing and interpretation of QTL and genomic selection experiments. Key words: Linkage disequilibrium, Brangus, heifers, QTL, SNP