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Analysis of MiRNAs responsive to long-term Ca deficiency in tef (Eragrostis tef (Zucc.) Trotter)

ABSTRACT: 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

ORGANISM(S): Eragrostis tef

PROVIDER: GSE193130 | GEO | 2022/05/27

REPOSITORIES: GEO

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Project description:Background: The unprecedented rise in atmospheric CO2 concentration and injudicious fertilization or heterogeneous distribution of Mg in the soil warrant further research to understand the synergistic and holistic mechanisms involved in the plant growth regulation. The objective of this work is to understand responses in plants along with interactive effect of elevated CO2 and Mg levels by comparing data on single stress with that of combined stresses. Results: This study investigated the influence of elevated CO2 (800 μL L−1) on physiological and transcriptomic profiles in Arabidopsis cultured in hydroponic media treated with 1 μM (low), 1000 μM (normal) and 10000 μM (high) Mg2+. Following 7-d treatment, elevated CO2 increased the shoot growth and chlorophyll content under both low and normal Mg supply, whereas root growth was improved exclusively under normal Mg nutrition. Notably, the effect of elevated CO2 on mineral homeostasis in both shoots and roots was less than that of Mg supply. Irrespective of CO2 treatment, high Mg increased leaf number but decreased root growth and absorption of P, K, Ca, Fe and Mn whereas low Mg increased the concentration of P, K, Ca and Fe in leaves. Elevated CO2 decreased the expression of genes related to cadmium response, cell redox homeostasis and lipid localization, but enhanced photosynthesis, signal transduction, protein phosphorylation, NBS-LRR disease resistance proteins and subsequently programmed cell death in low-Mg shoots. By comparison, elevated CO2 enhanced the response of lipid localization (mainly LTP transfer protein/protease inhibitor), endomembrane system, heme binding and cell wall modification in high-Mg roots. Some of these transcriptomic results are substantially in accordance with our physiological and/or biochemical analysis. Conclusions: Contrasting changes were found between roots and shoots with the shoot transcriptome being more severely affected by low Mg while the root transcriptome more affected by high Mg. Elevated CO2 had a greater effect on transcript response in low Mg-fed shoots as well as in high Mg-fed roots. The present findings broaden our current understanding on the interactive effect of elevated CO2 and Mg levels in the Arabidopsis, which may help to design the novel metabolic engineering strategies to cope with Mg deficiency/excess in crops under elevated CO2.

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Analysis of MiRNAs responsive to long-term Ca deficiency in tef (Eragrostis tef (Zucc.) Trotter)

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