PRJNA828134: Genome Wide Transcriptome Analysis of tef (Eragrostis tef) Under Long-Term Low Calcium Stress
概要: 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.
项目整体设计: N = 4 SAMPLES PER TREATMENT GROUP
| 测序方法: |
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| 细胞类型: |
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| 生长方案: |
Plants were grown in hydroponic solution with low calcium and optimum calcium |
| 处理方案: |
In this study, tef plants were grown in hydroponic solution containing optimum (1 mM) or low (0.01 mM) Ca2+. 4 replicates for each treatment |
| 提取方案: |
RNA was extracted and sequenced |
| 建库方案: |
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. |
| 分子类型: |
polyA(+)RNA |
| 库的片段类型: |
PAIRED |
| 库的链类型: |
- |
| 测序平台: |
ILLUMINA |
| 测序仪型号: |
Illumina HiSeq 4000 |
| 链特异性: |
Unspecific |
| 数据来源 |
GEN样本编号 |
GEN数据集编号 |
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样本编号 |
样本名称 |
生物样本编号 |
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物种 |
种族 |
族裔 |
年龄 |
年龄单位 |
性别 |
来源名称 |
组织 |
细胞类型 |
细胞亚型 |
细胞系 |
疾病 |
疾病状态 |
发育阶段 |
突变/变异 |
表型 |
Condition Detail |
生长方案 |
处理方案 |
提取方案 |
建库方案 |
分子类型 |
库的片段类型 |
链特异性 |
库的链类型 |
加标（Spike-In） |
测序方法 |
测序平台 |
测序仪型号 |
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碱基数 |
平均测序片段长度_1 |
平均测序片段长度_2 |
唯一比对率 |
多重比对率 |
覆盖度 |
