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Oryza sativa Japonica Group

ABSTRACT: Small RNA and PARE sequencing in rice (photoperiod sensitive male sterility lines and wild type) panicles under long-day and short-day conditions

PROVIDER: PRJNA335548 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3955340.fastq.gz	Fastqsanger.gz
	SRR3955350.fastq.gz	Fastqsanger.gz
	SRR3955360.fastq.gz	Fastqsanger.gz
	SRR3955370.fastq.gz	Fastqsanger.gz
	SRR3955341.fastq.gz	Fastqsanger.gz

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Small RNA and PARE sequencing in rice (photoperiod sensitive male sterility lines and wild type) panicles under long-day and short-day conditions

Project description:Purpose: The goals of this study are to detect the small RNAs generated from the PMS1T gene and the cleavage sites mediated by small RNAs (microRNAs or phasiRNAs). Methods: The rice panicles were collected in liquid nitrogen and their total RNA were extracted for library construction and subsequent sequencing on an Illumina HiSeq 2000. Results: Using an optimized data analysis workflow, we mapped a series of small RNAs generated from the PMS1T region of the rice genome; most of these small RNAs were 21-nt phasiRNAs. The results from PARE sequencing validated the cleavage site on the PMS1T transcript, with the cleavage mediated by miR2118. Conclusions: Our results show that the 21-nt phasiRNA generated from the PMS1T transcript are associated with photoperiod-sensitive male sterility in rice.

2016-12-18 | GSE84885 | GEO

Transcriptome profiling reveals the regulatory role of CSA-mediated photoperiod-dependent male fertility

Project description:The discovery of photoperiod-sensitive male genic sterile (PGMS) lines started the development of two-line hybrid rice, which is critical to sustain production of high-yielding hybrid rice varieties. Previous reports about the PGMS lines are mainly focused on the gene cloning and their function description. The mechanisms by which PGMS lines perceive changes in photoperiod and transmit those signals to elicit downstream effects is rarely mentioned. In this work, we described the effects of photoperiod on gene expression in wild type (WT) and csa, a PGMS line, flag leaves and anthers to identify putative central factors that transduce photoperiod signals via CSA in both leaves and anthers. We also dissect the potential mechanisms that: cause csa-induced sterility under SD conditions; partially restore fertility in csa anthers under LD conditions; and finally, are responsible to restore full WT fertility under LD and SD conditions. These results provide an overview how the PGMS rice perceives and transmits photoperiod changes, and how the CSA and its homologs response to the environmental cues by regulating down-stream gene expression. That will be helpful to understand the photoperiod-sensitive mechanism and identify new photoperiod-sensitive genes.

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Oryza sativa Japonica Group

Project description:RNase ZS1-mediated UbL40 mRNA decay controls thermo-sensitive genic male sterility in hybrid rice

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Cold acclimation process under limited light conditions in Arabidopsis thaliana

Project description:Plants in temperate regions have evolved mechanisms to survive sudden temperature drops. Previous reports have indicated that the cold acclimation mechanism is light-dependent and does not fully operate under a low light intensity. In these studies, plants were grown under a long-day photoperiod and were more sensitive to freezing stress. However, winter annuals like Arabidopsis thaliana Col-0 germinate in the fall, overwinter as rosettes, and therefore must acclimate under short photoperiods and low irradiance. The role of light intensity was analysed in plants grown under a short-day photoperiod at the growth stage 1.14. Plants were acclimated at 4 °C for seven days under 100 and 20 μmol m-2s-1 PPFD for control and limited-light conditions, respectively. All cold acclimated plants accumulated molecular markers reportedly associated with acquired freezing tolerance, including proline, sucrose, CBFs, and COR gene protein products dehydrins and low-temperature-responsive proteins LTIs. Observed changes indicated that low PPFD did not inhibit the cold acclimation process, and the freezing stress experiment confirmed similar survival rates. The molecular analysis found distinct PPFD-specific adaptation mechanisms that were manifested in contrasting content of anthocyanins, cytokinin conjugates, abundances of proteins forming photosystems, and enzymes of protein, energy, and ROS metabolism pathways. Finally, this study led to the identification of putative proteins and metabolite markers correlating with susceptibility to freezing stress of non-acclimated plants grown under low PPFD. Our data show that Arabidopsis plants grown under short-day photoperiod can be fully cold-acclimated under limited light conditions, employing standard and PPFD-specific pathways.

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Transcription profiling of Coturnix japonica during the photoinduction process.

Project description:The molecular mechanism of photoperiodic time measurement remains unknown in animals. Japanese quail is an excellent model for studying these phenomena because of their rapid and dramatic response to photoperiod. When quail are transferred from short to long day conditions, increase in plasma gonadotrophin (luteinising hormone: LH) can be observed by the end of the first long day and this phenomenon is called âfirst day release modelâ. To dissect the system dynamics and network structure regulating photoperiodism, we examined global gene expression using high-density oligonucleotide microarray for chicken (Affymetrix Chicken Genome Array). Experiment Overall Design: The mediobasal hypothalamus (MBH) of quail was collected from 6 birds for each time point during the photoinduction process. Pooled total RNA from three MBHs was labelled and hybridized to each Affymetrix chicken genome array. Samples were analyzed in duplicate set of array (two biological replicate).

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Project description:Sequencing of sRNA and PARE libraries was performed for tissues collected from developmentally staged young panicles and anthers in rice variety Nongken 58

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Coturnix japonica

Project description:Gene expression in the quail MBH under short and long day conditions.

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Fennell Grapevine Dormancy - Understanding transduction of the photoperiod signal

Project description:To begin understanding transduction of the photoperiod signal, Vitis riparia Michx. (PI588259) grapevines that had grown for 35 days in long photoperiod (long day, LD, 15h) were subjected to either continued LD or a short photoperiod (short day, SD, 13h) treatment. Shoot tips (4-node shoot terminals) were collected from each treatment at 7 and 28 days of LD and SD for proteomic analysis via two-dimensional (2D) gel electrophoresis. The peptides were identified using MALDI-TOF_TOF mass spectrometer after trypsin digestion. A master gel was made and mapped with all p roteins from both photoperiod treatments. The proteins were identified by matching the peptide sequences against the 12X Vitis vinifera grape genome in NCBI. This study was funded in part by NSF grant DBI064755 and the South Dakota Agriculture Experiment Station.

2011-01-26 | PRD000377 | Pride

Vitis riparia shoot tip transcriptome in response to long and short photoperiod.

Project description:Winter season with reduced day length (photoperiod); led to the growth cessation, dormancy induction and cold acclimation in woody perennial plants. To develop an understanding of the photoperiod signal transduction in Vitis riparia; shoot tip transcriptome profiling was performed under differential photoperiod treatments (long (LD, 15h) and short day (SD, 13h)) for 7 or 21 days after shoots reached 10 nodes (LD7, SD7, LD21 or SD21).

2023-04-28 | GSE95707 | GEO

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