Figure 7
(a) Genome-wide linkage disequilibrium (LD) decay between pairs of 28,798 SNPs across all 196 cultivars, three predicted groups (G1, G2, and G3), and three wheat classes (CNHR, CPSR, and CWRS) that have 20 or more cultivars. The horizontal line shows the average squared coefficient of correlation (r2 = 0.19). Genome-wide LD fell below the average at 10 Mb. (b) Intra-chromosomal LD in the A-, B-, and D-genome based on 28,798 SNPs used for genotyping 196 cultivars. The horizontal line shows the average squared coefficient of correlation (r2) at r2 = 0.19. LD decay between 5 and 7 Mb depending on the genome. (c) Intra-chromosomal LD decay between pairs of outlier SNPs that have undergone selection among the three predicted groups (524 SNPs in red solid line), eight market classes (1520 SNPs in green dashed line), six registration or breeding periods (2314 SNPs in blue dotted line), and all 3,980 SNPs after excluding common markers(black broken line). (d) LD decay plot on chromosome 1D between 411.7 and 427.1 Mb to show SNPs with high LD around the Glu-D1 gene at 414.6 Mb.
