**3.2. Linkage disequilibrium**

Genetic drift is an important cause in generating LD, the non-independence of alleles at different loci. This non-independence allows marker alleles to predict the allelic state of nearby QTL, enabling marker genotypes to predict the phenotype. The LD intensity decays with greater distance between two markers. Decay rates which vary widely across species, populations, and genomes due to forces of mutation, recombination, population size, population mating marker density must increase with increases in Ne\*c, where Ne is the effective population size and c is the recombination rate between loci. LD patterns. Marker density can be inferred by the rate of LD decay across the genome as inferred by the relationship b/w inter marker coefficient of determination r<sup>2</sup> and genetic distance. LD estimates can be used to determine target marker densities for GS at equilibrium, drift generating LD is balanced by recombination, causing it to decay, such that nearby loci are expected to be in higher LD than faraway loci. LD has a major effect on the operability of GS, so it has to be well understood before performing GS. LD is defined as the non-random association of alleles at different loci. It has been found that for high heritability trait average adjacent marker r2 of 0.15 is sufficient but for low heritability trait increasing r2 value to 0.2 improve accuracy of GEBV predictions.
