Table 2 shows the significant effects of genomic distances, breed groups, and chromosomes, as well as the interaction between breeds and chromosomes on the amount of LD. To display graphically the decay of LD, distances of pair-wise LD were binned into 5 kb intervals with the first bin being 10 kb large (e.g., 0–10 kb, 10–15 kb, 15–20 kb, 20–25 kb) along the first 5 Mb of each chromosome, and average r2 was computed for each interval. Figure 2 presents LD decay over varying distances of the genome. The measured LD was high for pairs of SNPs within close proximity. AN appeared to have consistently higher LD and lower rate of LD decay than CH and C at all times.