Fig. 2: The heterozygosity juxtaposition effect occurs in both male and female meiosis and requires adjacent recombinationally active regions.
a, Interhomologue SNP distribution in the Ku(c1,sh1,R1) crosses along chromosome 9. 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 c1–sh1 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 c1–sh1 markers in male and female backcross generations for Hybrid Ku(c1,sh1,R1) × M(R1) and Juxtaposed Ku(c1,sh1,R1) × Ku(R1) crosses. The numbers of individuals are indicated below the box plots. Each data point represents measurements from one plant. The two-sided P values were estimated by Welch’s t-test; ***P = 3.4 × 10−4, **P = 2.07 × 10−3. The centre line of the box plot shows the median, and the upper and lower bounds show the 75th and 25th percentiles. c,d, As in a and b, but for the M(sh1,wx1) crosses. ***P = 3.6 × 10−9, ****P = 9.5 × 10−11. e, The interhomologue polymorphism to the right of the sh1–wx1 interval in the Juxtaposed M(sh1,wx1) × M cross does not affect the Rf within this interval, as it lies within a recombinationally inactive chromosomal region. The grey area shows the distribution of SNPs per Mb, while blue and red lines indicate the crossover frequency (cM Mb−1) along the short chromosome arm for Flint × Flint and Dent × Dent crosses, respectively, as reported by ref. 37. Solid, dashed and dotted lines represent populations with the highest, median and lowest genome-wide recombination rates among 23 populations within each group37. f,g, As in a and b, but for the Ku(sh1,wx1) crosses. ***P = 2.9 × 10−6, ****P = 9.2 × 10−10. h, Model of crossover stimulation in heterozygous regions (shaded) when juxtaposed with homozygous regions (light blue). In maize, this effect is observed in both male and female meiosis. i, Polymorphism-triggered crossover stimulation relies on remodelling from recombinationally active chromosomal regions. The increase in crossover frequency in heterozygous region 1 (blue-grey shaded area) is primarily driven by the presence of the upstream homozygous region (large arrow) rather than the downstream homozygous region (smaller arrow), as the former is highly recombinationally active (light-grey shaded area). It remains unknown whether crossovers can be redistributed from recombinationally active regions to inactive regions, such as heterozygous region 2.
