Tef Zinc levels
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB36941 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3957810_1.fastq.gz | Fastqsanger.gz | |||
| ERR3957810_2.fastq.gz | Fastqsanger.gz | |||
| ERR3957807_1.fastq.gz | Fastqsanger.gz | |||
| ERR3957807_2.fastq.gz | Fastqsanger.gz | |||
| ERR3957808_1.fastq.gz | Fastqsanger.gz |
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Project description:Identification of genomic variants in Eragrostis tef genes which may lead to differences in Zn content of the grain.
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Project description: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
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Project description:Calcium (Ca2+) is one of the essential mineral nutrients for plant growth and development. However, the effects of long-term Ca2+ deficiency in orphan crops such as tef (Zucc.) Trotter] which accumulate high levels of Fe in the grains remained unknown. Tef is a staple crop for nearly 70 million people in East Africa, particularly Ethiopia and Eritrea. It is rich in mineral nutrients (Ca+2, Fe, Zn and Mn), vitamins and essential amino acids. In this study, tef plants were grown in hydroponic solution containing optimum (1 mM) or low (0.01 mM) Ca2+ and plant growth parameters and whole genome transcriptome were analyzed. Ca+2-deficient plants exhibited symptoms including leaf necrosis, leaf curling, and growth stunting. Ca2+ deficiency significantly decreased root and shoot Ca+2, potassium (K) and copper content in both root and shoots while it significantly increased root iron (Fe2+) content, suggesting the role of Ca2+ in the uptake and/or translocation of these minerals. Transcriptomic analysis using RNA-seq revealed that members of Ca2+ channels including the cyclic nucleotide-gated channels (CNGC) and glutamate receptor-like channels (GLRs), Ca2+-transporters, Ca2+-binding proteins (CBP) and Ca2+-dependent protein kinases (CDPK) were differentially regulated by Ca+2 treatment. Moreover, several Fe/metal transporters including members of vacuolar Fe transporters (VIT), yellow stripe-like (YSL), natural resistance-associated macrophage protein (NRAMP) and oligo-peptide transporters (OPT) were differentially regulated between shoot and root in response to Ca2+ treatment. Taken together, our findings suggest that Ca2+ deficiency affects plant growth and mineral accumulation by regulating the transcriptomes of several transporters and signaling genes.
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