Linkage Disequilibrium in Animal Genetics – Definition, Measures and Applications

The non-random connection of alleles at various loci is known as linkage disequilibrium (LD). Combinations of alleles inside haplotypes occur at frequencies that differ from those expected on independence when two alleles at two distinct loci are in LD. When genetic variation at a locus is linked to a trait, it means that either the genetic variation at that locus directly impacts the phenotype of interest or the locus is in LD with the causal mutation. The level of LD, which dictates how many markers should be typed in a genome scan to discover a quantitative trait locus (QTL) using LD, is critical to the practicality of association studies. This review explores the origin of LD in genetics and how it applies to animal breeding and genetics.