概要: Pod dehiscence is an important agronomic trait. Pod dehiscence would cause huge yield losses before soybean maturity. Although some of soybean pod dehiscence associated genes have been identified, the underlying mechanism of pod dehiscence is still not comprehensively explained. In this study, we have identified differentially expressed genes (DEGs) between shattering-resistant and shattering-susceptible soybean accessions based on transcriptome analyses of 10 soybean accessions. Long non-coding RNAs (lncRNAs) that may be involved in soybean pod dehiscence were also identified, and we constructed co-expression networks between mRNAs and lncRNAs. RNA sequencing results were further verified by real-time PCR. Furthermore, DEGs were screened through analyzing positions of soybean pod dehiscence quantitative trait locus (QTLs) and phenotypes of soybean pod dehiscence for achieving pod-dehiscence candidate genes.
项目整体设计: High-depth paired-end RNA-seq from pods of soybeans
For growing soybean plants, seeds were grown on fields.
处理方案:
The pod dehiscence percentage was analyzed according to the previous study (Romkaew and Umezaki 2015). In brief, 50 brown pods (fully mature) were collected and kept in an oven at 60 °C for 7 h, then the number of shattering pods was counted. Pod shatteringmechanicalforce wasmeasuredusing a digital mechanical force gauge (HANDPI, China) according to the previous study (Dong et al. 2014), and at least five pods were selected and measured for each soybean accession.
提取方案:
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
建库方案:
Libraries were constructed through applying TruSeq RNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.
测序信息
分子类型:
poly(A)+ 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 2500
链特异性:
Unspecific
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
系列编号
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样本编号
样本名称
生物样本编号
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最后更新时间
物种
种族
族裔
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
测序平台
测序仪型号
细胞数
测序片段数
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
Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression.
