Fig. 5: Inter-allelic interactions detected in F1 hybrids.
From: Conservation and variability of long-range interactions in structurally diverse maize genomes
a The inter-allelic interaction (blue lines) could be detected when an interaction was detected in a hybrid and either anchor of the valid read pairs overlapped with a different allele-specific SNP. Yellow stars indicate the SNPs between B73 and Mo17. b, c The number of valid read pairs in BM and MB was shown for all the candidate inter-allelic interactions. The dots in dark green indicates the interactions with at least one valid read pairs, while the dots in black, red, and yellow indicate the number of detected valid-pair reads be greater than 5, 3 or 4, and 2, that supported inter-allelic interactions between two alleles was determined by both reciprocal hybrids (BM and MB) for H3K4me3 (b) and H3K27ac (c). d The proportion of the anchor-sequences that overlap with syntenic or non-syntenic genes as well other types was determined for inter-allelic interactions. e Expression of genes targeted by H3K4me3 inter-allelic interactions overlapping with syntenic genes in inbred or hybrid lines. The boxplots depict the median (central line), interquartile range (box boundaries), and 1.5×IQR whisker ranges, with outliers shown as individual points (Wilcoxon test (two-sided). The p-values and sample size are: < 2.2e−16 (B73 compare to MB, n = 255), 3.714e−15 (B73 compare to BM, n = 255), < 2.2e−16 (Mo17 compare to BM, n = 239), 0.056 (Mo17 compare to MB, n = 239). f The browser view of the inter-allelic interaction on chromosome 7. The left anchor (Chr7: 20,505,000 – 20,510,000) overlapped Zm00001d019180 (from B73), and the right anchor (chr7: 21,065,000 – 21,070,000) overlapped Zm00014a006917 (from Mo17). The numbers below the black straight line represent inter-allelic valid read pairs number from HiChIP data, and the numbers below the blue curved line are presented validated reads number from 4C-seq. g, h The expression level of Zm00001d019180 (g) and Zm00014a006917 (h) in inbred or hybrid lines. The boxplots depict the median (central line), interquartile range (box boundaries), and 1.5 × IQR whisker ranges, with outliers shown as individual points. Source data are provided as a Source Data file.
