Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential
Fig 5
Plots modelling the decay in pairwise linkage disequilibrium coefficients (r2) as a function of the distance between markers in megabases (Mb).
Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 1; Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 4; Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 5; Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 7; Plot of pairwise linkage disequilibrium coefficients (r2) on chromosome 9. Heatmap of linkage disequilibrium (r2) across the chromosomes 4 and 5 based on data for 421 cacao accessions genotyped using 612 filtered SNPs. Markers were ordered on the x and y axes in the Heatmap according to location along the chromosomes and each cell of the heatmap represents a single marker pair. The upper triangle, above the black diagonal on the heatmap, is colour-coded based on the r2 value between SNPs while colours depicted in the lower triangle are based on P-values for the corresponding r2 values.