Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat
Chao He, Siteng Bi, Yuqi Li, Chengxiang Song, Heping Zhang, Xintong Xu, Qiang Li, Sulaiman Saeed, Wei Chen, Chunjie Zhao, Caixia Lan, Handong Su, Hailiang Mao, Wenhao Yan
Abstract
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. Dynamic changes of histone modification and how it affects gene transcription during wheat endosperm development remain largely unknow. Here, the author fulfill this knowledge gap and reveal the role of ethylene response factor ERF5 in the regulatory network during grain filling, and starch and protein accumulation.