Triticum aestivum Raw sequence reads. Triticum aestivum

Here we generated open chromatin interaction maps for hexaploid wheat and its tetraploid and diploid relatives using OCEAN-C. The anchors of chromatin loops showed high chromatin accessibility and were concomitant with several active histone modifications, about 67% of which interacted with multiple loci. Binding motifs of various transcription factors were significantly enriched in the hubs of open chromatin interactions (HOCIs). The genes linked by HOCIs represented higher expression level and lower coefficient of expression variance than the genes linked by other loops, which suggest HOCIs may coordinate co-expression of linked genes. Thousands of interchromosomal loops were identified but limited interchromosomal loops (0.4%) occurred between homoeologous genes in hexaploid wheat. Moreover, we found that structure variations contributed to chromatin interaction divergence of homoeologs and chromatin topology changes between different wheat species. The genes with discrepant chromatin interactions showed expression alteration in hexaploid wheat compared with its tetraploid and diploid relatives.