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Transcriptomic response of apple (Malus x domestica Bork. cv. Húsvéti rozmaring) shoot explants to in vitro cultivation on media containing thidiazuron or 6-benzylaminopurine riboside

ABSTRACT: Transcriptomic response of apple (Malus x domestica Bork. cv. Húsvéti rozmaring) shoot explants to in vitro cultivation on media containing thidiazuron or 6-benzylaminopurine riboside

PROVIDER: PRJNA1213791 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32064614_1.fastq.gz	Fastqsanger.gz
	SRR32064614_2.fastq.gz	Fastqsanger.gz
	SRR32064615_1.fastq.gz	Fastqsanger.gz
	SRR32064615_2.fastq.gz	Fastqsanger.gz
	SRR32064616_1.fastq.gz	Fastqsanger.gz

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Transcriptomic response of apple (Malus x domestica Bork. cv. Húsvéti rozmaring) shoot explants to in vitro cultivation on media containing thidiazuron or 6-benzylaminopurine riboside

Project description:The effects of two cytokinins (thidiazuron and 6-benzylaminopurine riboside), each applied at 4.5 μM, were studied on mRNA transcription of in vitro apple shoots. Transcriptomic response was investigated at two time points; at 48 h and 4 weeks (end of the subculture) after the cytokinin application

2025-04-18 | GSE287596 | GEO

Gene expression profile of Arabidopsis thaliana wild type and siz1-2 mutant during in vitro shoot regeneration on callus inducing media (CIM) and shoot inducing media (SIM)

Project description:Plants form callus and regenerate new organs when incubated on phytohormone-containing media. While accumulating evidence suggests that these regenerative processes are governed by transcriptional networks orchestrating stress responses and developmental transitions, it remains unknown if post-translational regulatory mechanisms are involved in this process. Here, we find that SIZ1, which encodes an E3 ligase catalyzing attachment of the SMALL UBIQUITIN-LIKE MODIFIER (SUMO) to proteins, regulates wound-induced signal transduction and organ regeneration. We show that loss-of-function mutants for SIZ1 exhibit over-production of shoot meristems under in vitro tissue culture conditions, while this defect is rescued in a complementation line expressing pSIZ1::SIZ1. RNA-sequencing analysis revealed that siz1-2 mutant exhibits enhanced transcriptional responses to wound stress, resulting in the hyper-induction of over 500 genes immediately after wounding. Among them, we show that elevated level of WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) and WIND2 contribute to enhanced shoot regeneration observed in siz1 mutants, as the dominant-negative WIND1-SRDX partly rescues this phenotype in siz1-3. Although compromised SIZ1 function does not modify transcription of genes implicated in auxin-induced callus formation and/or pluripotency acquisition, it does lead to enhanced induction of cytokinin-induced shoot meristem regulators like WUSCHEL (WUS), promoting the formation of WUS-expressing foci in explants. This study thus suggests that SIZ1 negatively regulates shoot regeneration in part by repressing wound-induced cellular reprogramming.

2020-05-31 | GSE141188 | GEO

Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

Project description:Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we show that warm temperature promotes both callus formation and shoot regeneration efficiency in Arabidopsis thaliana. Our RNA sequencing analysis unveil that this accompanied by the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1), encoding a transcription factor involved in shoot meristem formation, and ISOPENTENYLTRANSFERASE (IPT1) and YUCCA1/4 (YUC1/4), encoding key enzymes for cytokinin and auxin biosynthesis, respectively. Consistently, mutations in CUC1 and IPT1 or chemical inhibition of YUCs reduce the enhancement of shoot regeneration at warm temperature. When combined with ChIP sequencing analyses, our RNA sequencing data further reveal that histone variant H2A.Z is enriched on these differentially expressed loci at 17°C and that its occupancy level decreases when the ambient temperature increases to 27°C. This study thus unveil a new epigenetic mechanism that influences hormone-induced regeneration and brings further insights on how incubation temperature is a crucial parameter in optimizing protocols for in vitro tissue culture.

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Potential link between biotic defense activation and recalcitrance to induction of somatic embryogenesis in shoot primordia from adult trees of white spruce (Picea glauca)

Project description:The goal is to examine the molecular aspects underpinning somatic embryogenesis (SE) within shoot tissues of adult white spruce trees by conducting transcriptome-wide expression profiling of shoot explants taken from responsive and nonresponsive genotypes.

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Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

Project description:Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

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CPL4 is a suppressor of de novo shoot organogenesis from roots of Arabidopsis thaliana

Project description:De novo shoot organogenesis (DNSO) is a commonly used pathway for plant biotechnology, and is a hormonally regulated process, where auxin and cytokinin coordinates suites of genes encoding transcription factors, general transcription factors, and RNA metabolism machinery genes. Here we report that silencing Arabidopsis thaliana CTD phosphatase-like 4 (CPL4RNAi), which increases phosphorylation level of RNA polymerase II (pol II) CTD, altered lateral root development and DNSO efficiency of the host plants, suggesting an importance of precise control of pol II activities during DNSO. Under standard condition, roots of CPL4RNAi lines produced no or few lateral roots. When induced by high concentration of auxin, CPL4RNAi lines failed to produce focused auxin maxima at the meristem of lateral root primordia, and produced fasciated lateral roots. By contrast, root explants of CPL4RNAi lines were highly competent for DNSO. Efficient DNSO of CPL4RNAi lines were observed even under 10 times less cytokinin required for wild type explants. Transcriptome analysis showed CPL4RNAi but not wild type explants expressed high levels of shoot meristem related genes during priming by high auxin/cytokinin ratio, and subsequent shoot induction with cytokinin. These results indicate that CPL4 functions as a repressor of the early stage of DNSO, during acquisition of competency by high auxin/cytokinin ratio, perhaps via regulation of pol II activities.

2020-09-19 | GSE104083 | GEO

Nicotamide riboside attenuates age-associated transcriptional changes in hemoatpoietics stem cells

Project description:Nicotamide riboside attenuates age-associated transcriptional changes in hemoatpoietics stem cells

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Temporal and Spatial Expression Analysis of Shoot-Regeneration Regulatory Genes during the Adventitious Shoot Formation in Hypocotyl and Cotyledon Explants of Tomato (CV. Micro-Tom).

Project description:Enhancing the competence for plant regeneration in tissue culture studies is an important issue not only for efficient genetic transformation of commercial crops but also for the reproducibility of scientific reports. In this study, we investigated optimization of several tissue culture conditions including plant growth regulators, types and ages of explants, culture densities, and plant position in order to improve the competence of adventitious shoot formation of the tomato (Solanum lycopersicum cv. Micro-Tom). In addition, we examined the differential expression of D-type cyclin (CYCD3-1) and several shoot regeneration regulatory genes from hypocotyl and cotyledon explants of tomato during shoot organogenesis. A treatment of 1 mg L-1 Zeatin and 0.1 mg L-1 Indole-3-acetic acid (IAA) in Murashige and Skoog (MS) medium containing 3% sucrose was optimal for adventitious shoot formation from hypocotyl and cotyledon explants. The younger explants exhibited more shoot formation regardless of explant types. Additionally, those closest to the shoot apical meristem produced more shoots compared to the other regions in the hypocotyl and the cotyledon explants. Gene expression of CYCD3-1, SHOOT MERISTEMLESS (STM), and cytokinin dependent WUSCHEL (WUS) was significantly higher in younger explants than in older ones. Furthermore, an increase in CYCD3-1, STM, and WUS expression was evident at the distal part of hypocotyls and the proximal part of cotyledons compared to other regions. These differential gene expression profiles exhibited good agreement with the results of shoot formation obtained from diverse explants of tomato. These results suggest that temporal and spatial gene expression of shoot regeneration regulatory genes plays an important role in enhancing the competence and the reproducibility of adventitious shoot formation from tomato explants.

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Transcriptional Profiling of Apple (Malus x domestica Borkh) Floral Induction in Shoot Apical Meristems

Project description:Effect of the presence of fruits on the expression of genes possibly involved in floral induction in the terminal meristem of spur bourse shoot. Investigation on mecanisms involved in Biennial Bearing in mature apple trees cultivar Royal Gala.

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ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana

Project description:Injured plant somatic tissues regenerate themselves by establishing the shoot or root meristems. In Arabidopsis (Arabidopsis thaliana) a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, it remains elusive whether and how the environmental factors influence this process. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyl as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of the HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristem through the regulatory network governed by HY5, thus, highlighting the influence of light signals on plant developmental plasticity.

2024-09-16 | GSE236147 | GEO

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