GSE193130
Analysis of MiRNAs responsive to long-term Ca deficiency in tef (Eragrostis tef (Zucc.) Trotter)
miRNAs play an important role in growth, development, stress resilience and epigenetic modifications of plants. However, the effect of calcium nutrition on miRNA expression in orphan crops such as tef ((Eragrostis tef) remained unknown. In this study, we analyzed genome-wise miRNAs of roots and shoots in response to long-term calcium deficiency in tef. MiRNA-seq followed by bioinformatic analysis identified a large number of small RNAs with size ranging from 17bp to 35bp. A total 1380 miRNAs were identified in plants experiencing long-term Ca deficiency, while 1495 miRNAs were identified in the control plants. Among the miRNAs identified in this study, 161 miRNAs were known, and 348 miRNAs were novel while the remaining miRNAs were uncharacterized. Putative target genes and their functions were predicted for all the known and novel miRNAs. Based on gene ontology (GO) analysis, the target genes were found to have various biological and molecular functions including calcium uptake and transport. Pairwise comparison of differentially expressed miRNAs revealed that some of the miRNAs were specifically enriched in roots or shoots of low calcium treated plants as compared to control plants. Further characterization of the miRNAs and their targets detected in this study will help in identifying Ca deficiency responses not only in tef but also in related orphan crops Overall design: two different calcium treatments, 1. low calcium treatment. 2. optimum calcium