ATAC sequencing and transcriptomics reveal the impact of chromatin accessibility on gene expression in Tritipyrum under salt-stress conditions

Abstract

Plants have evolved various regulatory mechanisms that adjust gene expression levels to enhance their salt adaptability. Here, the seedling height, root length, plant fresh weight, total root surface area, and total root volume of Tritipyrum ‘Y1805’ increased significantly under salt-stress and recovery conditions. The plant water content showed limited changes under salt stress. The cytokinin, amino acid, soluble protein, and pyruvate contents, as well as the peroxidase activity, increased under salt stress and decreased quickly after recovery. The MDA content and electrical conductivity increased after 5 h of salt stress, but they returned rapidly to the control level afterwards. ‘Y1805’ had strong salt tolerance and could adapt quickly to salt-stress conditions. An assay of transposase-accessible chromatin with sequencing (ATAC-seq) indicated that most peaks were located in the distal intergenic regions under salt-stress and control conditions. We found 85 motifs in the 1776 location-specific peaks and 478 motifs in altered signal peaks under salt stress. The transcription factors binding to these motifs belonged mainly to the MYB family, followed by the AP2/EREBP, bZIP, bHLH, and WRKY families. The main Gene Ontology terms organic acid catabolic process, carboxylic acid catabolic process, cellular hormone metabolic process, cytokinin metabolic process, and cellular amino acid catabolic process were significantly enriched based on the associated differentially expressed genes between ATAC-seq and transcriptomics. Based on the transcriptional regulatory network and gene expression level, the Tritipyrum ‘Y1805’ HSF6–1 gene was selected and cloned. Leaves of the wild-type plants appeared seriously wilted under salt stress, but most leaves of the TtHSF6–1 transgenic line remained upright. The seedling height, root length, plant fresh weight, and plant dry weight of the TtHSF6–1 transgenic line increased significantly compared with those of the WT plant under salt-stress and recovery conditions. The MDA content and electrical conductivity values of the TtHSF6–1 transgenic line were significantly less than those of the WT plants under salt-stress conditions. Thus, TtHSF6–1 contributed to salt tolerance. These results provided valuable genes for wheat improvement and offer fundamental insights into the transcriptional regulatory mechanisms of salt tolerance in Tritipyrum.