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Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis

ABSTRACT: The aim of this study was to uncover the differential transcription regulation pathways between immature embryo (IME)- and mature embryo (ME)-derived callus formation through transcriptome sequencing. We showed that incubation of embryos on auxin-rich medium caused dramatic changes in gene expression profiles within 48 h. A total of 9330 and 11318 differentially expressed genes (DEGs) were found in the IME and ME systems, respectively. 3880 DEGs were found specific to IME_0h/IME_48h, and protein phosphorylation, regulation of transcription, and oxidative-reduction process were the most common gene ontology categories of this group. Twenty-three IAA, 14 ARF, 8 SAUR, 3 YUC, and 4 PIN genes were found to be differentially expressed during callus formation. The effect of callus-inducing medium (CIM) on IAA genes was broader in the IME system than in the ME system, indicating that auxin response in regulating cell reprogramming during callus formation. BBM, LEC1 and PLT2 exhibited a significant increase in expression level during IME system but were not activated in the ME system, WUS showed a more substantial growth trend in the IME system than in the ME system, suggesting that these embryonic, shoot, and root meristems genes play crucial roles in determining the acquisition of competency. In addition, epigenetic regulators—including SUVH3A, SUVH2A, HDA19B/703—exhibited differential expression patterns between the two induction systems, indicating that epigenetic reprogramming might contribute to gene expression activation/suppression in this process.

ORGANISM(S): Hordeum vulgare

PROVIDER: GSE165487 | GEO | 2022/01/22

REPOSITORIES: GEO

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Project description:Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle. In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis. Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates. To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed. Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation. Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity. Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile. The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity. Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation. Comparison of young and mature Arabidopsis hypocotyls either with or without auxin treatment for 1 day

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Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis

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