Temporal regulation of gene expression during auxin-triggered crown root formation in barley: an integrated approach

Cereal plants possess a fibrous root system in which crown roots form the major component. Crown roots develop post-embryonically from the lower, mostly underground nodes of the stem base. A strict spatiotemporal regulation of gene expression governs this process. Much of the knowledge about signaling pathways controlling crown root initiation (CRI) and development comes from rice. However, distinct regulatory mechanisms may have evolved in other cereals to adapt to different habitats. In this study, using a Crown Root Inducible System (CRIS), we aimed to investigate the early molecular regulation of barley CRI. We revealed dynamic transcriptomic changes within the first 24 hours following auxin stimulation. Among the differentially expressed genes, we identified orthologs of important CRI regulators from other cereals, demonstrating that CRIS is suitable for uncovering genes involved in CRI. Further, ATAC-seq revealed that CRI relies on changes in chromatin accessibility near root development-related genes and within distal intergenic regions. Finally, we focused on two transcription factors, HvNAC013 and CBF12C, which likely play roles in both CRI and abiotic stresses. By performing DAP-seq, we determined their genome-wide binding sites and identified their potential downstream targets. Data suggest that CBF12C is a putative target of HvNAC013, along with other auxin-responsive genes implicated in CRI. We propose that HvNAC013 and CBF12C function as part of a transcription factor network involved in CRI and potentially modulate root architecture in response to environmental conditions. This study enhances our understanding of the CRI mechanism in barley.