Fig. 7

Average LD decay within PAV and between PAVs and their flanking regions. a Average LD between PAVs and their flanking genomic regions. Flanking regions is genotyped using SNPs, PAV is genotyped either as 0/1 (red) or using the within-PAV SNP closest to the breakpoint (kaki). For comparison, LD in random maize regions (green), maize random regions from gene space (blue), and maize random regions from inter-genic space (purple) are also plotted. b Comparison of average LD within PAVs to LD within flanking regions (upstream, red and downstream, kaki). PAVs are separated in 3 classes of size, 1–4 kb (green), 5–10 kb (blue), 10–40 kb (purple). LD is estimated by the squared correlations of allele frequency (r²) and plotted against distance between polymorphic sites (0 to 10 kb)