Fig. 3: Crossover stimulation in the measurement interval due to the juxtaposition effect is strongest when it closely coincides with the heterozygous region.

a, Interhomologue SNP distribution in the M(lg1,gl2) crosses along chromosome 2. Grey vertical bars represent SNP density per 10 kb, and the burgundy trend line shows SNP density per 1 Mb. Grey horizontal bars beneath the graph indicate estimated heterozygous regions based on SNPs. Coloured lines mark the positions of the lg1–gl2 interval used to measure Rf. The navy blue square on the x axis shows the centromere location. The inset offers a close-up of the interval, with the SNP density plots below partially trimmed. b, Rf (%) measured by segregation of lg1–gl2 markers in male and female backcross generations for Hybrid M(lg1,gl2) × Ku and Juxtaposed M(lg1,gl2) × M crosses. The two-sided P values were estimated by Welch’s t-test; *P = 0.0196, **P = 0.0029. c,d, As in a and b, but for the Ku(lg1,gl2) crosses. ***P = 1.2 × 10⁻⁵, ****P = 9.2 × 10⁻¹¹. e, Genetic structure of the combinations used in crosses for the intervals ws3–lg1–gl2 (chromosome 2) and c1–sh1–wx1 (chromosome 9). For chromosome 2, Juxtaposed A corresponds to the cross M × M(ws3,lg1), Juxtaposed B to M × M(ws3,lg1,gl2), and Juxtaposed A* to M × M(lg1, gl2). For the Hybrid category, combinations A, B and A* are the same as for the Juxtaposed category but crossed with Ku. For chromosome 9, Juxtaposed A, B and A* correspond to M × M(c1,sh1,R1), M × M(c1,sh1,wx1,R1) and M × M(sh1,wx1), respectively, while the Hybrid combinations are analogous but involve crosses with Ku. The diagram indicates only the approximate positions of heterozygous regions. Detailed polymorphism patterns for the Juxtaposed A and A* configurations are shown in a, and in Figs. 1l and 2c. For the Juxtaposed B combinations, precise sequence data are not available; however, the homozygous regions are expected to span large portions of the chromosomes outside the measurement intervals, as the lines were generated through six to eight rounds of backcrossing. f, Rf in the ws3–lg1 and lg1–gl2 intervals for the combinations shown in e. Statistical significance was determined using two-sided Welch’s ANOVA, followed by the Games–Howell post hoc test (see Supplementary Table 17 for details). g, Similar to f, but depicting the c1–sh1 and sh1–wx1 intervals for the genotype combinations presented in e. For b, d, f and g, the number of individuals is indicated below the box plots. Each data point represents measurements from a single plant. Different colours within the same group indicate data collected in different years. The centre line of each box plot represents the median, and the upper and lower bounds correspond to the 75th and 25th percentiles, respectively.