概要: Genetic/genome diversity underlying variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.
项目整体设计: Transcriptome comparison of nine different soybean varieties
All soybean (Glycine max (L.) Merrill) lines were grown in growth chambers with temperature set at 25°C day/ 23°C night, the humidity at 50% and 16 hour days at up to 1,000 µmol of supplemental lighting. The plants were watered, fertilized and managed for pests and disease as needed. Seeds at the S6 stage of seed maturation were carefully selected based on seed weight and color, and were harvested for RNA preparation.
处理方案:
The oil composition of soybean seeds was determined with the Agilent 7890A GC with S/Sl injection and FID detection at the USDA-ARS Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia. Three single seeds per soybean line were measured with two replications each. The oil content of soybean seeds was determined with the MQC Benchtop NMR Analyser, Oxford Instruments. Six g of seeds per line were measured with two biological and three technical replicates.
提取方案:
Samples were ground in liquid nitrogen. Then rna was separated out with phenol chloroform and then purified and precipitated out using a Qiagen RNeasy Kit
建库方案:
RNA-seq libraries were constructed and sequenced at Expression Analysis, Inc., Durham NC (www.ExpressionAnalysis.com). RNA-seq libraries were prepared with the TruSeqTM RNA Sample Preparation Kit v2 from Illumina, Inc., San Diego, CA, and 100 bp paired-end reads were generated on the Illumina HiSeq 2000 platform.
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 2000
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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物种
种族
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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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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
Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content.