Allele pair linkage disequilibrium matrices for each linkage group across the entire common bean genome for the full group of genotypes and for the Andean and Mesoamerican group genotypes. Linkage groups are indicated as B1 through B11 based on map order from Blair et al. (2003). Darker squares indicate higher linkage disequilibrium in terms of correlation coefficient (r2) as indicated in the legend. B04, the linkage group with the APA locus is highlighted. Genepools are abbreviated as Mesoamerican (Meso), Andean (Andean) and both together (All).