Abstract Background Iron (Fe) is an essential mineral element, and its deficiency in soil largely affects crop productivity. In plants, the molecular mechanisms underlying the genetic regulation of Fe deficiency responses have yet to be well understood. Specifically, microRNA (miRNA) mediated regulation of Fe deficiency response and its regulatory network is largely elusive. In the current work, we utilized a whole genome transcriptomic approach to identify the Fe deficiency-responsive miRNAs to understand the molecular mechanisms of Fe deficiency response in wheat seedlings. The study also identifies nine novel miRNAs putatively involved in Fe deficiency response. Further, the identified miRNAs showed tissue preferences relating them to differential mechanisms against Fe deficiency. Results In the present study, we performed small RNA-targeted whole genome transcriptome analysis to identify the involvement of sRNAs in Fe deficiency response. The analysis identified 105 differentially expressed miRNAs corresponding to Fe deficiency response, among them, 9 miRNAs were found to be novel in this study. Interestingly, tissue-specific regulation of Fe deficiency response also participates through miRNA-mediated regulation. We identified 17 shoot specific miRNAs and 18 root-specific miRNAs with altered expression. We validated the tissue specificity of these miRNAs by stem-loop quantitative RT-PCR. Further, an attempt was made to predict their targets to speculate their participation in Fe deficiency response. This miRNA target prediction analysis suggested a few major targets of the identified miRNAs, such as multicopper oxidases, E3 ubiquitin ligases, GRAS family, and WRKY transcription factors previously known to play key roles in Fe homeostasis. Our analysis of selected miRNAs also confirmed a temporal regulation of the response. Conclusion The first information generated here will classify the repository of wheat miRNAs (with few novel miRNAs) for their role in Fe deficiency response. Our work provides insights into miRNA-mediated regulatory pathways during Fe deficiency.

System analysis of differentially expressed miRNAs in hexaploid wheat display tissue-specific regulatory role during Fe deficiency response