(A) Diagram illustrating chromosome 3 genotypes (black = Col, red = Ct) in RG/++ F1 individuals and their F2 progeny. A single chromosome is shown for simplicity. Gametes or progeny are analysed for patterns of fluorescence following meiosis to measure genetic distance. (B) The program Rqtl was used to test for association between Col/Ct genotypes and 420 cM in a 420/++ F2 population. The logarithm of odds (LOD) score is plotted along the 5 chromosomes with the positions of markers shown along the x-axis by ticks. The red horizontal line shows the 5% genome-wide significance threshold calculated with Hayley-Knott regression and by running 10,000 permutations. (C) As for (B) but analyzing Col/Ct markers on chromosomes 2 and 3 for an I2f/++ F2 population. (D) 420 cM measurements from Col/Ct 420/++ F2 (black), Col/Col homozygotes (red) and Col/Ct F1 (blue) individuals. Mean values are indicated by horizontal dotted lines. See Figure 4—source data 1. (E) Chromosome 3 genotypes shown for 420/++ F2 individuals ranked by crossover frequency. Each horizontal row represents a single F2 individual. X-axis ticks show marker positions, and which are coloured red when they showed significantly higher homozygosity in the hottest vs coldest quartiles (FDR-corrected chi square test). Fluorescent T-DNAs are indicated by triangles, in addition to the centromere (Cen). (F) Heterozygosity along chromosome 3 in the hottest (red), coldest (blue) 420 F2 quartiles and the mean (green). The locations of reporter T-DNAs and the centromeres are indicated by vertical dashed lines. (G–I) As for (D–F) but for interval I2f. See Figure 4—source data 2.