Application of Association Mapping to Understanding the Genetic Diversity of Plant Germplasm Resources

Figure 2

The TASSEL generated triangle plot for pairwise LD between marker sites in a hypothetical genome fragment, where pairwise LD values of polymorphic sites are plotted on both the X- and Y-axis; above the diagonal displays 𝑟² values and below the diagonal displays the corresponding p-values from rapid 1000 shuffle permutation test. Each cell represents the comparison of two pairs of marker sites with the color codes for the presence of significant LD. Colored bar code for the significance threshold levels in both diagonals is shown. The genetic distance scale for a hypothetical genome fragment was manually drawn. Note: this is for demonstration purposes only and does not have any real impact or correspond to any genomic fragment of an organism.