Fig. 3

ASBs correlate with allele-specific mRNA abundance. a, b Fraction of (left panel) all expressed (> 20 reads) and orthologous maize genes or (right panel) genes with an ASB in their 3 kb promoter displaying allele-specific (AS) mRNA abundance differences (orange) between a B73 and Mo17 parental alleles [34] and b B73 and Mo17 alleles in F₁ hybrids. c Fraction of ASB genes with higher BZR1 binding to B73 (left) or Mo17 (right) and the mRNA levels of the nearby gene being biased to B73 (green) or Mo17 (blue). d, g Allele-specific, cumulative HASCh-seq signal around ASBs near VP14 (d) and DWF4 (g). Normalized HASCh-seq reads (reads per genome coverage) mapping uniquely to B73 (green) or Mo17 (blue) are shown. e, h Box plots of allelic reads at two selected ASBs (red arrows in panels d and g, respectively) from the three replicates for B73xMo17 (BxM) and Mo17xB73 (MxB) F₁ hybrids. **p<0.01 f, i Transcript levels of the BR-induced VP14 (d) and BR-repressed DWF4 (g) measured by qRT-PCR in B73 and Mo17 plants treated with mock, BL inhibitor PPZ, or PPZ plus BL for 4h. *p<0.05