Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton
Somatic embryogenesis (SE), by which somatic cells of higher plants can dedifferentiate andreorganize into new plants, is a notable illustration of cell totipotency. However, the precisemolecular mechanisms regulating SE remain unclear.
To characterize the molecular events ofthis unique process, transcriptome analysis, in combination with biochemical and histologicalapproaches, were conducted in cotton, a typical plant species in SE. Genome-wide profilingof gene expression allowed the identification of novel molecular markers characteristic of thisdevelopmental process.
RNA-Seq was used to identify 5,076 differentially expressed genes during cotton SE.Expression profile and functional assignments of these genes indicated significanttranscriptional complexity during this process, associated with morphological, histologicalchanges and endogenous indole-3-acetic acid (IAA) alteration.
Bioinformatics analysisshowed that the genes were enriched for basic processes such as metabolic pathways and biosynthesis of secondary metabolites. Unigenes were abundant for the functions of proteinbinding and hydrolase activity.
Transcription factor-encoding genes were found to bedifferentially regulated during SE. The complex pathways of auxin abundance, transport andresponse with differentially regulated genes revealed that the auxin-related transcriptsbelonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugatemetabolism, auxin transport, auxin-responsive protein/indoleacetic acid-induced protein(Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAAdegradation, and other auxin-related proteins, which allow an intricate system of auxinutilization to achieve multiple purposes in SE.
Quantitative real-time PCR (qRT-PCR) wasperformed on selected genes with different expression patterns and functional assignmentswere made to demonstrate the utility of RNA-Seq for gene expression profiles during cottonSE.
We report here the first comprehensive analysis of transcriptome dynamics that may serve asa gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seqtechnology to this notable development process and to analyse the gene expression profile.Complex auxin signalling pathway and transcription regulation were highlighted.
Togetherwith biochemical and histological approaches, this study provides comprehensive geneexpression data sets for cotton SE that serve as an important platform resource for furtherfunctional studies in plant embryogenesis.
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