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

Plants have evolved various regulatory mechanisms that adjust gene expression levels to enhance their salt adaptability. Here, many leaves of Tritipyrum Y1805 appeared wilted at 1 d after salt stress. However, most of the leaves resumed upright positions after 2 d, indicating adaptation to salt stress. The seedling height, plant fresh weight, root length, total root surface area, and total root volume increased significantly under salt-stress and recovery conditions. The plant water content showed limited changes. The cytokinin, amino acid, soluble protein, and pyruvate contents, as well as the peroxidase activity, increased under salt stress and decreased quickly after recovery. An assay of transposase-accessible chromatin with sequencing indicated that the number, width, and fold enrichment of total peaks under salt-stress conditions were less than those under normal culture conditions. The enriched peaks were strongest around the center of transcriptional start sites under normal and salt-stress conditions. Under salt-stress and control conditions, most peaks were located in the distal intergenic regions. In total, 1,776 specific peaks were identified under salt stress. We found 85 motifs in the 1,776 location-specific peaks and 478 motifs in altered signal peaks. The transcription factors binding to these motifs belonged mainly to the MYB family, followed by the AP2EREBP, 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 TtHSF6-1 gene was selected and successfully cloned. Leaves of the wild-type plants appeared seriously wilted under salt stress, but most leaves of the TtHSF6-1 transgenic line remained upright. Thus, TtHSF6-1 contributed to salt tolerance. These results provided valuable candidate genes for wheat improvement and offer fundamental insights into the transcriptional regulatory mechanisms of salt tolerance in Tritipyrum.