System Analysis of Differentially Expressed miRNAs in Hexaploid Wheat Display Tissue-Specific Regulatory Role During Fe-Deficiency Response

Abstract

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 pinpointing microRNA (miRNA)-mediated regulation of Fe-deficiency response and its regulatory network are largely unaddressed. In the present study, we performed a small RNA-targeted whole-genome transcriptome analysis from hexaploid wheat and identified small RNAs (sRNAs) responding to Fe deficiency. Detailed analysis identified 105 differentially expressed miRNAs corresponding to Fe-deficiency response, and nine 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 that confirmed a temporal regulation. Furthermore, an attempt was made to predict their targets to speculate their participation in Fe-deficiency response. The miRNA target prediction analysis suggested a few major target genes, such as multicopper oxidases, E3 ubiquitin ligases, GRAS family, and WRKY transcription factors; those are previously known to play key roles in Fe homeostasis. The first preliminary 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.