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Plastic glutamine synthetase (GS2) is responsible for ammonium assimilation. The reason that  TaGS2  homoeologs in hexaploid wheat experience different selection pressures in the breeding process remains unclear.  TaGS2  were minimally expressed in roots but predominantly expressed in leaves, and  TaGS2-B  had higher expression than  TaGS2-A  and  TaGS2-D . ChIP assays revealed that the activation of  TaGS2-B  expression in leaves was correlated with increased H3K4 trimethylation. The transcriptional silencing of  TaGS2  in roots was correlated with greater cytosine methylation and less H3K4 trimethylation. Micrococcal nuclease and DNase I accessibility experiments indicated that the promoter region was more resistant to digestion in roots than leaves, which indicated that the closed nucleosome conformation of the promoter region was important to the transcription initiation for the spatial-temporal expression of  TaGS2 . In contrast, the transcribed regions possess different nuclease accessibilities of three  TaGS2  homoeologs in the same tissue, suggesting that nucleosome conformation of the transcribed region was part of the fine adjustment of  TaGS2  homoeologs. This study provides evidence that histone modification, DNA methylation and nuclease accessibility coordinated the control of the transcription of  TaGS2  homoeologs. Our results provided important evidence that  TaGS2-B  experienced the strongest selection pressures during the breeding process.

Chromatin modification contributes to the expression divergence of three TaGS2 homoeologs in hexaploid wheat