Fig. 3: Effects of InDels and structural variation on CO frequency within the ChP interval.

a Generation of Col-pseudo-ChP (Col-ΨChP). Cas9 sgRNAs were used to simultaneously generate mutations in the dsRed and eGFP cassettes, leading to the loss of fluorescence. Nonfluorescent seeds were sequenced and crossed with Col-ChP to measure CO frequency. b CO frequency for Col × Col-ChP and Col × Col-ΨChP. Measurements for Col-ChP × Ler are shown for comparison. The center line of a boxplot indicates the mean; the upper and lower bounds indicate the 75th and 25th percentiles, respectively. Each dot represents a measurement from one individual. The number of individuals are also indicated above the boxplots. The two-sided P value was estimated by Welch’s t-test. c Alignments of the ChP region between different Arabidopsis accessions. The blue horizontal bar shows the query sequence (Col), red horizontal bars indicate homologous sequences in other accessions, colored vertical tick marks indicate short regions of lower similarity, and gray lines indicate nonhomologous regions. Insertion of an 8.7-kb fragment next to the ChP interval in Ler is also indicated. d CO frequency (in cM) for different crosses between Col-ChP and the accessions shown in (c). The center line of a boxplot indicates the mean; the upper and lower bounds indicate the 75th and 25th percentiles, respectively. Each dot represents a measurement from one or two pooled individuals. The numbers of individuals are indicated on the right from the boxplots. Two-sided P values indicate the statistical difference in ChP CO rate in hybrids versus inbreds (Welch’s t-test). Green triangles indicate the polymorphism level (SNPs+InDels) for each cross within the ChP interval. Source data are provided as a Source Data file.