Recombination rates along chromosomes. The x-axis indicates the physical position (Mbp) along chromosomes 2 (left panels) and 6 (right panels). The y-axis indicates the genetic position (cM; top panels), recombination rate (cM/Mbp; middle panels), and pairwise parental similarity (frequency of identical SNP alleles in 10 Mbp sliding windows with a step size of 2 Mbp; bottom panels) for six of the 23 populations, after smoothing and imputation. Blue lines: Flint × Flint crosses. Red lines: Dent × Dent crosses. In both groups, the solid, dashed and dotted lines correspond to the population with the highest, median and lowest genome-wide recombination rate within its group, respectively. Gray parts of the lines correspond to regions where the information was missing or not reliable (IBD segments, non-colinearity with B73), and was thus imputed from the other maps. Heat maps below the curves of recombination rates indicate gene density (low for cold colors and high for hot colors). Gray horizontal line below the heat-map: sketch of the chromosome organization showing centromeres (cen), knobs, and nucleolar organizer region (NOR). Centromere, knob and NOR positions are from . Color filling of chromosome features is solid when the estimated boundaries of the region are known, and hatched when the box indicates only the extremities of the bin containing the region.