High-throughput sequencing reveals that microRNA-based regulation, cell wall remodeling and phytohormone signaling orchestrate wheat seminal root development

Abstract

Using a combined RNA and small RNA sequencing approach, this study decodes the precise molecular mechanisms and microRNA-gene networks that govern early seminal root development in wheat. The findings pinpoint specific genetic and hormonal targets that can be leveraged through precision breeding to engineer climate-resilient crops with optimized root architectures. Climate change exerts immense pressure on wheat, threatening both its development and productivity. The transition from dormancy to seedling establishment is a critical yield checkpoint, where seminal roots act as the hidden architects of success. Within days of germination, roots must rapidly construct complex systems and adapt to environmental shifts. This early developmental phase determines seedling fate, yet the molecular mechanisms governing it are yet to be fully explored. Thus, in this study, we employed an integrative RNA and small RNA sequencing approach to dissect the regulatory networks governing Triticum aestivum seminal root development during the first weeks after seeding. Our work reveals that this stage requires the coordinated action of 385 genes and 12 microRNAs (miRs). Identified as differentially expressed, these molecules orchestrate cell division, metabolic reprogramming, and developmental patterning. Functional enrichment analysis showed that cell wall biosynthesis and remodeling, SNARE-mediated vesicular trafficking, terpenoid metabolism, and phytohormone signaling pathways are dynamically regulated during early root growth. Among all, miR166, miR168, and miR171 emerged as pivotal post-transcriptional regulators. These miRs exhibited expression patterns inversely correlated with their predicted targets, encoding HD-ZIP III transcription factors, spliceosomal kinases, and GRAS like family proteins, which are essential factors for vascular patterning, microRNA biogenesis, and lignin deposition, respectively. Notably, these genetic programs are synchronized with dramatic hormonal recalibration, marking the transition from dormancy to active growth. Beyond advancing our fundamental understanding of root biology, the present findings identify specific molecular targets (i.e., stage-related expressed genes and miRs) that could be manipulated through precision breeding or genome editing to develop wheat varieties with enhanced root systems resilient to environmental changes.