Fig. 2: Construction of a maize leaf pan-cistrome.
a, Mapping strategies comparison showing the density of AMPs (allele-specific occupied sites) over the percentage of binding to B73. B73 × HP301 F1 MOA data were analyzed using either only B73 as reference genome (single ref.), a pseudo-genome with B73/HP301 SNPs replaced by Ns (SNP-replaced) or our dual-parent mapping strategy using a concatenated B73 × HP301 genome (dual ref.). Without mapping bias, a symmetric distribution is expected (as observed for dual ref.), while a higher density at higher B73 allelic bias indicates biased mapping to the reference genome B73 (single ref. and SNP-replaced). For the A619 F1 (no assembled genome available), our ‘reference-guided’ strategy (see Methods for details) showed similar AMP-balanced haplotypes without reference bias (A619 dual ref.). b, Additive percent of B73 MOA peak covered by MPs (brown) and AMPs (red) relative to the number of F1s analyzed. c, Density of mean MOA binding frequencies over all F1s carrying a SNP at positions where at least one, two, three or four F1s had AMPs, compared to a control with randomized binding frequencies. d, Overview of bQTL (red arrows), MOA coverage (blue) and Hi-C interaction sites (black lines, Hi-C from a previous publication32) near the classical flowering repressor RAP2.7. bQTL overlap with both known enhancers, vgt1 and vgt1-DMR (green), associated with RAP2.7 expression. An additional bQTL, termed vgt1-MOA (magenta), also interacts with vgt1 and the RAP2-7 promoter.
