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Transcriptome sequencing of the callus in subculture 21d of YIL25 versus Teqing, the complementary transgenic line (pCPL) versusTeqing , the overexpressiong transgenic line (pOE) versusTeqing .

ABSTRACT: To analyze the molecular function of BROWNING of CALLUS1 (BOC1), we performed RNA-seq experiments using callus that had been subcultured for 21 days from Teqing and YIL25, Teqing and the complementation line pCPL-BOC1-Teqing (pCPL), and also Teqing and the overexpression line pOE-BOC1-Teqing (pOE).We identified a total of 700 differentially expressed genes (DEGs), containing 410 DEGs upregulated in the callus of YIL25 versus Teqing, pCPL versus Teqing and downregulated in pOE versus Teqing. Besides, 290 DEGs downregulated in the callus of YIL25 versus Teqing and pCPL versus Teqing and upregulated in pOE versus Teqing. A large number of DEGs associated with stress response and cell death were presented.

ORGANISM(S): Oryza sativa

PROVIDER: GSE142094 | GEO | 2019/12/20

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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Transcriptome sequencing of the callus in subculture 21d of YIL25 versus Teqing, the complementary transgenic line (pCPL) versusTeqing , the overexpressiong transgenic line (pOE) versusTeqing .

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