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 () and Wenhao Yan ()
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Chao He: Huazhong Agricultural University
Siteng Bi: Huazhong Agricultural University
Yuqi Li: Huazhong Agricultural University
Chengxiang Song: Huazhong Agricultural University
Heping Zhang: Huazhong Agricultural University
Xintong Xu: Huazhong Agricultural University
Qiang Li: Huazhong Agricultural University
Sulaiman Saeed: Huazhong Agricultural University
Wei Chen: Huazhong Agricultural University
Chunjie Zhao: Huazhong Agricultural University
Caixia Lan: Huazhong Agricultural University
Handong Su: Huazhong Agricultural University
Hailiang Mao: Huazhong Agricultural University
Wenhao Yan: Huazhong Agricultural University

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-53300-7

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