Temporal Regulation of Gene Expression During Auxin-Triggered Crown Root Formation in Barley: An Integrated Approach

In this study, we investigated the molecular events occurring during the early stages of crown root (CR) initiation in barley (Hordeum vulgare L.), a crucial process for plant development. For this purpose, we utilized the auxin-based crown root inducible system (CRIS). CRIS employs N-(1-naphthyl)phthalamic acid (NPA) to inhibit polar auxin transport and 1-naphthaleneacetic acid (1-NAA) to induce CR formation. We collected stem base samples at 3, 6, 9 and 24 hours post-treatment to capture dynamic molecular changes associated with CR initiation. We performed RNA-seq to profile transcriptomic changes and ATAC-seq to assess chromatin accessibility alterations associated with early CR initiation. Additionally, we focused on two transcription factors, HvNAC013 and CBF12C, which likely play roles in both CR initiation and abiotic stress responses. By performing DAP-seq analysis, we determined their genome-wide binding sites and identified their potential downstream targets. By integrating transcriptomic, epigenomic, and transcription factor binding data, we have provided a foundation for understanding the interplay between CR development and abiotic stress responses in cereals, supporting the discovery of novel regulators for this crucial developmental process.