Fig. 4

Linkage disequilibrium (LD) plot showing LD patterns among the 15 reniform nematode resistance-associated SNPs. The LD between the SNPs is shown in the intersection of the diagonals from each SNP. The numbers are based on D’ values and multiplied by 100. Values close to 0 indicate absence of LD (white shaded boxes), while those close to 100 indicate complete LD (black shaded boxes). The white block with black vertical lines on the top indicates the 15 SNPs on the reference genome (placed according to their physical positions on the reference genome). SNP markers on different chromosomes are listed, with their corresponding mapped chromosomes indicated as C1, C2, C3, C5, C6, C7, C9, and C12 in front of their ID. The two haplotype blocks (outlined in bold black line) indicate markers that are in high LD