Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat

Dissecting the genetic basis of seed traits in wheat is impeded by limited genetic polymorphisms and significant variations caused by environmental conditions and seed position in a spikelet. Seed performance is largely determined by endosperm development controlled by spatiotemporal variation in gene activities, which is greatly affected by chromatin status. Here, we map genome-wide dynamic distributions of H3K27me3, H3K4me3 and H3K9ac modifications and profile gene transcription across wheat endosperm development. The combinatorial effects of active and repressive marks ensure spatiotemporal dynamic gene expression, especially for starch biosynthesis. By scanning the transcription factor binding motifs in the ATAC-seq peaks, hub regulators are identified from the regulatory network. In addition, we observe significant correlations between sequence polymorphisms of hub regulators and variations in seed traits in a germplasm population. Thus, the analysis of genomic regulatory activities together with genetic variation provides a robust approach to dissect seed traits in bread wheat.