Distribution of genetic diversity, allele frequency, and recombination across the wheat genome. (a) Distribution of genetic diversity in the A (green), B (red), and D (blue) genomes: (π, top left), Tajima’s measure of site frequency spectrum (D, top right), historic recombination (ρ, bottom left), and LD (bottom right). (b) Distribution of nucleotide diversity π (shaded polygon), FST between cultivars and landraces (solid black line), and site frequency spectrum (D) along chromosomes 5A (top panel), 5B (middle panel) and 5D (bottom panel). Gray shaded boxes represent the approximate location of the centromere. Rug plots represent lower (red) and upper (blue) 2.5% tails of test statistic distribution. Black X above the plot represents upper 2.5% tail of ρ statistic. The location of domestication (Q) gene is shown by arrow. (c). Distribution of alleles of the AL8/78 genotype of Ae. tauschii along the chromosomes of the D genome in the 26 wheat landraces. The average frequency of AL8/78 alleles was calculated in a 3 Mb sliding window. The color scale shows the proportion of the AL8/78 alleles in each window (red - highest, blue - lowest).