Ultrasound, as a hypomethylating agent, remodels DNA methylation and alters mRNA transcription in winter wheat (Triticum aestivum L.) seedlings

Any treatment that affects seed germination and seedling development is of paramount importance from an agricultural point of view since they are critical prerequisites for successful crop production. In present study, we have examined the after‐effect of ultrasonication (at 30 kHz, 70 W for 5 min) of winter wheat (Triticum aestivum L. cv. SE15) seeds on the early seedling growth and development, and accompanying changes in the DNA methylation and transcriptomic pattern in 7‐day‐old seedlings. We used mRNA‐sequencing and whole genome bisulfite sequencing (WGBS) to identify significantly differentially expressed genes (DEGs), significantly differently methylated regions (DMRs) and genes (DMGs). Ultrasonication of seeds did not alter the germination rate but increased both the length and weight of roots and shoots of 7‐day‐old seedlings significantly by 23%–68% and 16%–28%, respectively. Analyzing the expression intensity of 107,891 genes, significantly differentially expressed sequences related mainly to starch biosynthesis, IAA biosynthesis, photosynthesis and TCA cycle pathways. The same pathways were also affected by DNA‐methylation changes. DNA hypomethylation occurred in the global methylation profile after ultrasound treatment altering the accessibility of some genes for transcription. Transcriptomic changes suggested alterations in the crosstalk between IAA and sucrose signaling, enhancement of growth processes, and increased activity of nuclear transcription factor stimulating the transcription of genes having CCAAT motif in the promoter. In the present first whole genome level study, we have identified seed ultrasonication as a priming technique that can act as a hypomethylating agent and thereby is able to modify the mRNA transcription allowing enhanced seedling growth.