概要: We conducted a genome-wide transcriptomic analysis in soybean leaves and roots treated with zinc (Zn) deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for Zn-sufficient leaves (ZSL), Zn-deficient leaves (ZDL), Zn-sufficient roots (ZSR), and Zn-deficient roots (ZDR). Therefore a total of eight libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified Zn-deficiency responsive genes. At least 20 genes that are potentially involved Zn homeostasis were significantly changed by Zn deficiency, including 7 ZIP (ZRT, IRT-related protein) transporter genes, 3 nicotianamine synthase genes, and 7 metallothionein genes. At least 48 genes encoding likely Zn-binding proteins were found to be responsive to Zn deficiency in leaves or roots. Eighty-five transcription factor genes were significantly changed by Zn deficiency in leaves or roots, including 5 bZIP members and 10 Golden 2-like members. In addition, some other groups of genes which are possibly related to reactive oxygen species scavenging, calcium and hormone signaling, and protein phosphorylation and dephosphorylation also differentially expressed under Zn deficiency.
项目整体设计: The first trifoliate true leaves and roots of soybean were harvested after 12 days treatment with or without zinc element in the nutrient solution, and RNA was extracted and sequenced by paired-end sequencing. RNA sequencing reads were aligned against the soybean reference genome and differentially expressed genes between treatments were detected.
Soybean (Glycine max var. Williams 82) seeds were soaked in sterilized water for 4 hours, and then incubated at room temperature in the dark between two layers of moistened filter paper. Four days later, seedlings were grown hydroponically in a 10 L tank filled with half-strength modified Hoagland nutrient solution containing 2.5 mM Ca(NO3)2, 2.5 mM KNO3, 0.5 mM KH2PO4, 1.25 mM MgSO4, 10.0 μM Fe-EDTA, 3.4 μM MnSO4, 0.16 μM CuSO4, 0.38 μM ZnSO4, 23.0 μM H3BO3, 0.25 μM Na2MoO4, with pH adjusted to 5.6. Nutrient solution was changed every two days. Plants were grown in a growth chamber with a photoperiod set at 16-h-light/8-h-dark at 26/22 ◦C and light intensity set at 150 μmol m-2 s-1.
处理方案:
After 8 days of cultivation, soybean seedlings with the first trifoliate true leaves fully expanded were transferred into Zn-sufficient (0.38 μM ZnSO4) or Zn-deficient (0 μM ZnSO4) nutrient solutions.
提取方案:
-
建库方案:
RNA libraries were prepared for sequencing using standard Illumina protocols
测序信息
分子类型:
poly(A)+ RNA
库的片段类型:
PAIRED
库的链类型:
Reverse
测序平台:
ILLUMINA
测序仪型号:
Illumina HiSeq 2000
链特异性:
Specific
样本
基本信息:
样本描述:
生物条件:
实验变量:
方案:
测序信息:
质量评估:
数据来源
GEN样本编号
GEN数据集编号
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样本名称
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物种
种族
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年龄
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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
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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
文章
Transcriptome profiles of soybean leaves and roots in response to zinc deficiency.
Physiologia plantarum . 2019-02-09 [PMID:
30536844]
