National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China.
BMC Plant Biol. 2012 Jul 20;12:110. doi: 10.1186/1471-2229-12-110.
Somatic embryogenesis (SE), by which somatic cells of higher plants can dedifferentiate and reorganize into new plants, is a notable illustration of cell totipotency. However, the precise molecular mechanisms regulating SE remain unclear. To characterize the molecular events of this unique process, transcriptome analysis, in combination with biochemical and histological approaches, were conducted in cotton, a typical plant species in SE. Genome-wide profiling of gene expression allowed the identification of novel molecular markers characteristic of this developmental process.
RNA-Seq was used to identify 5,076 differentially expressed genes during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process, associated with morphological, histological changes and endogenous indole-3-acetic acid (IAA) alteration. Bioinformatics analysis showed that the genes were enriched for basic processes such as metabolic pathways and biosynthesis of secondary metabolites. Unigenes were abundant for the functions of protein binding and hydrolase activity. Transcription factor-encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein/indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE.
We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis.
体细胞胚胎发生（SE）是高等植物体细胞去分化和重新组织成新植物的过程，是细胞全能性的一个显著例证。然而，调节 SE 的精确分子机制尚不清楚。为了阐明这一独特过程的分子事件，我们对棉花（SE 中的典型植物物种）进行了转录组分析，结合生化和组织学方法。对基因表达的全基因组分析允许鉴定出这一发育过程特有的新的分子标记。
我们使用 RNA-Seq 鉴定了棉花 SE 过程中 5076 个差异表达基因。这些基因的表达谱和功能分配表明，在这个过程中存在显著的转录复杂性，与形态、组织学变化和内源性吲哚-3-乙酸（IAA）变化有关。生物信息学分析表明，这些基因富集了代谢途径和次生代谢物生物合成等基本过程。基因丰富了蛋白质结合和水解酶活性的功能。发现 SE 过程中转录因子编码基因的表达受到差异调控。与差异调节基因相关的生长素丰度、运输和响应的复杂途径表明，生长素相关转录物属于 IAA 生物合成、吲哚丁酸（IBA）代谢、IAA 结合物代谢、生长素运输、生长素响应蛋白/吲哚乙酸诱导蛋白（Aux/IAA）、生长素响应因子（ARF）、小生长素 RNA（SAUR）、Aux/IAA 降解和其他生长素相关蛋白，这允许生长素利用的复杂系统在 SE 中实现多种目的。我们对具有不同表达模式的选定基因进行了定量实时 PCR（qRT-PCR），并对功能分配进行了说明，以证明 RNA-Seq 在棉花 SE 过程中用于基因表达谱的适用性。
我们在这里报告了对转录组动态的首次全面分析，这可能成为棉花 SE 中的基因表达谱蓝图。我们的主要目标是将 RNA-Seq 技术应用于这个显著的发育过程，并分析基因表达谱。突出了复杂的生长素信号通路和转录调控。与生化和组织学方法相结合，本研究为棉花 SE 提供了全面的基因表达数据集，为植物胚胎发生的进一步功能研究提供了重要的平台资源。
