Fig. 3: The characteristics of intraspecifically constrained ACRs and domestication-associated ACRs.

a Distribution of ACRs in B73 according to their constraint in other non-B73 maize genomes. b The distribution of genomic features of five ACR groups including highly constrained, moderately constrained, weakly constrained, domestication-associated ACRs and randomly selected ACRs as control. c Barplot exhibiting the composition of different TE superfamilies in different ACR categories as shown in (b). d The ranking of enriched motifs in domestication-associated ACRs. Different TF families are depicted by colored dots. The P-value of each motif was estimated using one-sided Fisher’s exact test. e The proportions of DEGs among genes targeted by domestication-associated ACRs and randomly selected control ACRs (n = 856). The P-values were calculated by two-sided Wilcoxon test. The error bars represent the average value ± SD. f The chromatin accessibility of bHLH68 (Zm00001d025752) and its ~90 kb flanking region. The red region indicates domestication-associated ACR; the blue region indicates the target gene; the red and blue lines represent chromatin interactions between domestication-associated ACR and bHLH68 identified by ChIA-PETs and HiChIP, respectively. The structure of genes is shown in the bottom track. Source data are provided as a Source Data file.