Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

Abstract

BackgroundSomatic 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.ResultsRNA-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.ConclusionWe 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.

The content of endogenous hormones and sugars in the process of early somatic embryogenesis in the tree fern Cyathea delgadii Sternb.

“…Therefore, in excised stipes of C. delgadii about threefold reduction in the concentration of IAA, ABA and CKs was observed. The similar decline in IAA content was also noticed in excised cotton hypocotyl explants (Yang et al 2012). Furthermore, it is worth mentioning that although a dramatic decline in the hormone concentration occurred, the balance between IAA/CKs, ABA/CKs and ABA/IAA ratios remained almost unchanged, and significantly greater concentration of CKs than IAA was still maintained in C. delgadii explants.…”

“…For example, exogenously applied plant growth regulators (PGRs) can interact with phytohormones and change their concentrations (AyilGutiérrez et al 2013). Another factor causing hormonal balance disorders is explant excision (Thornburg and Li 1991;Yang et al 2012). It was showed that wounding is the first event that provides signals for triggering the entire regenerative process (Iwase et al 2011;Chen et al 2016).…”

“…Only a few reports on the progressive hormonal changes that occur during SE are available, but they differ in the type of explant, method (plant growth regulators or other stress factors) and manner of somatic embryo induction (i.e. direct or indirect), and culture conditions (photoperiodic or darkness) employed (Grieb et al 1997;Charrière et al 1999;Jiménez and Bangerth 2001b;Yang et al 2012;Ayil-Gutiérrez et al 2013). In these studies, the dynamic changes in the content of indole-3-acetic acid (IAA) (Ayil-Gutiérrez et al 2013), or IAA and ABA and cytokinins (Grieb et al 1997;Charrière et al 1999), and also in gibberellin concentrations (Jiménez and Bangerth 2001a) during the induction of SE were described for Coffea canephora Pierre ex Froehner, Daucus carota L., Helianthus annuus L., and Zea mays L., respectively.…”

Callus induction and plant regeneration in lemon verbena ( Lippia Citrodora L. ), an important medicinal plant

“…In an investigation aimed to find out the effect of plant growth regulators to generate a method of propagation of lemon verbena, callus induction was observed in treatments which were supplemented with auxin [5]; this result was in accordance with present work, as there were no callus formation in free auxin media but only callus induction was occurred from meristem explants, these results suggest that auxin is necessary for callus induction; since the mentioned hormone is cause to an increase in protein synthesis through enhancing transcription of RNA [12], so it would be related to proliferation in cells and forming a callus.…”

LEAFY COTYLEDON1-CASEIN KINASE I-TCP15-PHYTOCHROME INTERACTING FACTOR4 Network Regulates Somatic Embryogenesis by Regulating Auxin Homeostasis

“…Cotton (Gossypium hirsutum), as a key fiber crop, requires a highly successful regeneration procedure from somatic cells to perform genetic manipulation. Although we have conducted research on SE in cotton by expression profile analysis and showed that transcriptional regulation in SE is a complex process with the interaction of multiple molecules (Zeng et al, 2006;Yang et al, 2012), the detailed functions of key transcriptional regulators and the mechanisms underlying the different developmental processes are less well understood, and only a few genes that regulate SE in cotton have been identified (Hu et al, 2011). SE comprises two styles: direct SE and indirect SE, in which embryos are formed from explant tissues without or with a callus phase, respectively.…”