Genome-Wide Linkage Disequilibrium Patterns in 10 Beef Cattle Breeds

Quantitative Trait Loci (QTL) detection and Genomic Selection (GS) depends largely on the amount of Linkage Disequilibrium (LD) between QTL and markers and also on the number of records available to estimate marker effects.  Genomic selection using genome-wide approaches exploits ancestral LD in domesticated animals; therefore, knowledge of the extent of LD is critical for designing and interpretation of QTL and genomic selection experiments. In this study, the level and extent of LD in 10 beef cattle breeds were estimated using the squared correlation of alleles at 2 loci (r²) based on genotypes from the Illumina BovineSNP50 high density chip. Genotypes call rate averaged 98.1±0.001% for the 54,001 SNPs. Quality control included removal of SNPs inconsistent with Hardy-Weinberg equilibrium. Average values of the population were inserted at loci where missing genotypes existed. Results of calculated LD averaged across all chromosomes within intervals of 1 million base pairs as squared correlation between alleles was 0.07 for Angus influenced composite, Charolais, Maine-Anjou and South Devon. It was 0.08 for Angus, Limousin and Shorthorn while it was 0.09, 0.12 and 0.20 for Brangus, Hereford and Brahman respectively.  Average r² between adjacent SNP across all chromosomes ranged from 0.01±0.04 for Angus influenced composite breed to 0.13±0.16 for Brahman. The average distance between markers on chromosomes ranged from 14.79±10.50 for chromosome 25 to 57.02±40.46 for chromosome 1. Higher LD values were observed for SNPs located in close proximity. The r² for pairs of SNPs closer than 0.1Mb ranged from 0.14±0.21 in Brangus to 0.28 ± 0.31 in Brahman and 15.50% to 32.99% of these pairs had r² larger than 0.30, which has been considered the minimally useful for QTL mapping and genomic selection purposes. Disequilibrium decreased with increasing distance between SNPs in these cattle breeds.

 Key words: Linkage disequilibrium, Cattle breeds, QTL, SNP