Chromosome-Wide Distribution of SFPs, Recombination Rate, and Segregation Ratio

<div><p>Figures for the remaining four chromosomes are included in Supporting Information.</p><p>(A) Feature and SFP-distribution on Chromosome 1. The chromosome was divided into 50-kb windows. Red triangles represent number of features per window. The number of SFPs per feature in each window was compared to the number of SFPs per feature in all windows using Fisher's exact test. A <i>p</i>-value was calculated and a Bonferroni multiple testing correction was applied to test for significance. Blue diamonds indicate windows with significantly higher SFP density (<i>p</i>-value ≤ 0.05).</p><p>(B) Variation of recombination rate along Chromosome 1. Recombination rate was calculated as the genetic distance (in cM/50 kb) between pairs of neighboring informative SFP markers and plotted versus the average physical distance between the same markers. Pink stars indicate hot spots of recombination that exceed the expected recombination rate significantly (<i>p</i>-value ≤ 0.001, Chi-square test, after Bonferroni-correction). <i>P</i>-values are depicted next to the peaks. All values were normalized to 50 kb. Average genome-wide recombination rate is marked as a dotted horizontal line. The location of the centromere is marked with a black bar.</p><p>(C) Segregation distortion of SFP markers on Chromosome 1. Segregation ratios of genotypes for each informative SFP marker were calculated across 98 RILs and plotted along the chromosome. The vertical scale shows allele ratios. The expected equal distribution of Col and L<i>er</i> alles accross 98 lines should result in a ratio of 1 and is depicted as a dotted horizontal line. SFP markers with allele ratios above the line indicate segregation distortion towards the Col allele, SFP markers with allele ratios below the line indicate segregation distortion towards the L<i>er</i> allele. Empty diamonds represent SFP markers with no significant segregation distortion from the expected ratio of 1 between Col and L<i>er</i> genotypes. Filled triangles represent markers that show a significant (<i>p</i> ≤ 0.05, Fisher's exact test) segregation distortion towards the Col genotype.</p>