P0558 Whole Genome Linkage Disequilibrium Pattern in US Brangus Heifers

Sunday O. Peters , Cornell University, Ithaca, NY
Kadir Kizilkaya , Adnan Menderes University, Aydin, Turkey
Milton Thomas , Colorado State University, Fort Collins, CO
Dorian J. Garrick , Iowa State University, Ames, IA
Rohan L. Fernando , Iowa State University, Ames, IA
James Reecy , Iowa State University, Ames, IA
Abdulmojeed Yakubu , Cornell University, Ithaca, NY
Marcos De Donato , Cornell University, Ithaca, NY
Ikhide Imumorin , Cornell University, Ithaca, NY
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