Comparative Transcriptomes Profiling of Photoperiod-sensitive Male Sterile Rice Nongken 58S between Short Day and Long Day Condition
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE29820 | GEO | 2012/07/30
SECONDARY ACCESSION(S): PRJNA140943
REPOSITORIES: GEO
Similar Datasets
Project description:Nongken 58S is photoperiod-sensitive genic male sterile (PGMS) rice. Its pollens are fully sterile when it is treated with LD condition from glume primordium differentiation stage to pistil/stamen primordium forming stage, and its pollens are fertile when treated with SD condition during these stages. We used microarrays to detail the global programme of leaf gene expression under LD and SD condition for investigating the transcriptomes in the male sterility transition in PGMS rice to find out the genes related to this transition We compared the transcriptomes of Nongken 58S under shortday (SD) and longday (LD) at the glume primordium differentiation stage and pistil/stamen primordium forming stage, respectively. 12 samples were analyzed, and each treatment had biological triplicates. Supplementary files: SD vs LD during the glume primordium differentiation stage and the pistil/stamen primordium forming stage.
2012-07-29 | E-GEOD-29820 | biostudies-arrayexpress
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.
2021-03-30 | GSE171078 | GEO
Project description:This study aim to understand how the long and short day flowering pathways are integrated and the mechanism of photoperiod perception in rice. Trascriptome at different time points under LD and SD conditions reveal that photoperiodism in rice is controlled by the evening complex. Mutants in LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) orthologs abolish flowering. We show that light causes a rapid and sustained degradation of ELF3-1, and this response is dependent on phyB. ChIP-seq of ELF3 and LUX reveal that EC controls both LD and SD flowering pathways by directly binding and suppressing the expression of key floral repressors, including PRR7 orthologs and Ghd7.
2022-05-24 | GSE181833 | GEO
Project description:This study aim to understand how the long and short day flowering pathways are integrated and the mechanism of photoperiod perception in rice. Trascriptome at different time points under LD and SD conditions reveal that photoperiodism in rice is controlled by the evening complex. Mutants in LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) orthologs abolish flowering. We show that light causes a rapid and sustained degradation of ELF3-1, and this response is dependent on phyB. ChIP-seq of ELF3 and LUX reveal that EC controls both LD and SD flowering pathways by directly binding and suppressing the expression of key floral repressors, including PRR7 orthologs and Ghd7.
2022-05-24 | GSE181831 | GEO
Project description:Plants of Solanum tuberosum ssp andigena, which tuberize only under SD conditions, were grown in growth chambers under non-inductive LD conditions and half of the plants were transferred to inductive SD conditions for 1 or 15 days, whilst the rest of the plants were kept as controls in LD. Transgenic potato plants with reduced phyB levels, which tuberize irrespective of photoperiod, were also grown in LD conditions. All the plants, irrespective of treatment, were harvested 14 hours after the beggining of the photoperiod (i.e. immediately before dusk for plants on LD, and 8 hours after dusk for the plants on SD). A similar experimental protocol was used with plants of N. tabacum cv Hicks that flower at the same time irrespective of photoperiod and the isogenic line N. tabacum cv Hicks carrying the Maryland Mammoth mutant allele, which flower only on SD (i.e. the plants were grown under LD for 55 or 41 days in LD and then transferred for 1 or 15 days to SD conditions, respectively, whilst control plants were grown 56 days in LD). Finally, Nicotiana silvestris plants that flower only on LD were grown in non-inductive SD and then half of the plants were transferred to inductive LD conditions for 1 or 15 days. In all cases we harvested only the leaves, the organ in which daylength perception takes place and photoperiodic responses are initiated. SD conditions in this experiments were 8 hours of light/ 16 hours of darkness, 160 uEinstein, 22 °C. LD conditions were 16 hours of light/ 8 hours of darkness, 80 uEinstein, 22 °C. RNA was extracted with TRIZOL. Keywords: Direct comparison / Balanced Block Design
2007-09-01 | GSE8142 | GEO
Project description:Bud endodormancy induction response of two genotypes (‘Seyval’ a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long (15h) and short (13h) photoperiod. Three separate replicates (5 plants/replicate) were treated to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval 3-19-07; V. riparia 3/26/07) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (3-25-07) they were randomized into LD or SD treatments with 25/20 + 3C D/N in climate controlled greenhouses with automated photoperiod system (VRE Greenhouse Systems). Three replications (5 vines/replication) were harvested between 5/07-6/07 and then again in 5/08-6/08 for a total of six replications. All treatments are repeated at the same time every year and harvested at the same time of day each year to minimize biological noise. At 1, 3, 7, 14, 21, 28 and 42 days of LD and SD treatment, buds were harvested from nodes 3 to 12 of each separate replicate, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein and metabolite extraction. These time points encompass early reversible phases as well as key time points during transition to irreversible endodormancy development. After photoperiod treatments and bud harvests, all pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. Acknowledgement:This study was funded by NSF Grant DBI0604755 and funds from the South Dakota Agriculture Experiment Station. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Anne Fennell. The equivalent experiment is VV10 at PLEXdb.] 84 Samples of two genotypes compared under long and short photoperiod, 3 replicates each. Seyval (SV, Seyve Villard 5-276) : LD, 15h : 1 days (3-replications) Seyval (SV, Seyve Villard 5-276) : LD, 15h : 3 days (3-replications) Seyval (SV, Seyve Villard 5-276) : LD, 15h : 7 days (3-replications) Seyval (SV, Seyve Villard 5-276) : LD, 15h : 14 days (3-replications) Seyval (SV, Seyve Villard 5-276) : LD, 15h : 21 days (3-replications) Seyval (SV, Seyve Villard 5-276) : LD, 15h : 28 days (3-replications) Seyval (SV, Seyve Villard 5-276) : LD, 15h : 42 days (3-replications) Seyval (SV, Seyve Villard 5-276) : SD, 13h : 1 days (3-replications) Seyval (SV, Seyve Villard 5-276) : SD, 13h : 3 days (3-replications) Seyval (SV, Seyve Villard 5-276) : SD, 13h : 7 days (3-replications) Seyval (SV, Seyve Villard 5-276) : SD, 13h : 14 days (3-replications) Seyval (SV, Seyve Villard 5-276) : SD, 13h : 21 days (3-replications) Seyval (SV, Seyve Villard 5-276) : SD, 13h : 28 days (3-replications) Seyval (SV, Seyve Villard 5-276) : SD, 13h : 42 days (3-replications) V. riparia (VR, PI588259) : LD, 15h : 1 days (3-replications) V. riparia (VR, PI588259) : LD, 15h : 3 days (3-replications) V. riparia (VR, PI588259) : LD, 15h : 7 days (3-replications) V. riparia (VR, PI588259) : LD, 15h : 14 days (3-replications) V. riparia (VR, PI588259) : LD, 15h : 21 days (3-replications) V. riparia (VR, PI588259) : LD, 15h : 28 days (3-replications) V. riparia (VR, PI588259) : LD, 15h : 42 days (3-replications) V. riparia (VR, PI588259) : SD, 13h : 1 days (3-replications) V. riparia (VR, PI588259) : SD, 13h : 3 days (3-replications) V. riparia (VR, PI588259) : SD, 13h : 7 days (3-replications) V. riparia (VR, PI588259) : SD, 13h : 14 days (3-replications) V. riparia (VR, PI588259) : SD, 13h : 21 days (3-replications) V. riparia (VR, PI588259) : SD, 13h : 28 days (3-replications) V. riparia (VR, PI588259) : SD, 13h : 42 days (3-replications)
2009-08-05 | E-GEOD-17502 | biostudies-arrayexpress
Project description:Cows exposed to short day photoperiod (SD, 8L:16D) during the 60-day non-lactating period prior to parturition produce more milk in their subsequent lactation compared to cows exposed to long day photoperiod (LD,16L:8D). Although this response is well-established in dairy cows, the underlying mechanisms are not understood. We hypothesized that differential gene expression in cows exposed to SD or LD photoperiods during the dry period could be used to identify the functional basis for the subsequent increase in milk production during lactation. Pregnant, multiparous cows were maintained on a SD or LD photoperiod for 60-days prior to parturition. Mammary biopsies were obtained on days -24 and -9 relative to parturition and Affymetrix GeneChip® Bovine Genome Arrays were used to quantify gene expression. Sixty-four genes were differentially expressed (p ≤ 0.05 and fold-change ≥ |1.5|) between SD and LD treatments. Many of these genes were associated with cell growth and proliferation, or immune function. Ingenuity Pathway Analysis predicted upstream regulators to include TNF, TGFβ1, interferon γ and several interleukins. In addition, expression of 125 genes was significantly different between day -24 and day -9; those genes were associated with milk component metabolism and immune function. The interaction of photoperiod and time affected 32 genes associated with insulin-like growth factor (IGF-I) signaling. Genes differentially expressed in response to photoperiod were associated with mammary development and immune function consistent with the enhancement of milk yield in the ensuing lactation. Our results provide insight into the mechanisms by which photoperiod affects the mammary gland and subsequently lactation. Data were analyzed for the effect of photoperiod treatment (LD minus SD), time relative to parturition (day -24 minus day -9) and the interaction of photoperiod treatment and time ((LD minus SD day -9) minus (LD minus SD day -24))
2015-09-01 | GSE65059 | GEO
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
Project description:Photoperiod, the main physical synchronizer of seasonal functions, is now acknowledged as a key player for the modulation of molecule access to cerebrospinal fluid (CSF). From previous work showing a different transfer rate from steroids or protein hormones from blood to CSF according to photoperiod and, a modulation of choroid plexus (CP) tight junction protein content with photoperiod, we hypothesized that CSF proteome under long days (LD) would differ from that of CSF sampled under short days (SD) in ovariectomized-estradiol replaced ewes. CSF protein expression variability between SD- or LD-treated ewes was therefore studied from pools of CSF collected for 48H from ewes of similar age and weight.
2015-06-09 | PXD001564 | Pride
Project description:Bud endodormancy induction response of two genotypes (‘Seyval’ a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long (15h) and short (13h) photoperiod. Three separate replicates (5 plants/replicate) were treated to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval 3-19-07; V. riparia 3/26/07) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (3-25-07) they were randomized into LD or SD treatments with 25/20 + 3C D/N in climate controlled greenhouses with automated photoperiod system (VRE Greenhouse Systems). Three replications (5 vines/replication) were harvested between 5/07-6/07 and then again in 5/08-6/08 for a total of six replications. All treatments are repeated at the same time every year and harvested at the same time of day each year to minimize biological noise. At 1, 3, 7, 14, 21, 28 and 42 days of LD and SD treatment, buds were harvested from nodes 3 to 12 of each separate replicate, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein and metabolite extraction. These time points encompass early reversible phases as well as key time points during transition to irreversible endodormancy development. After photoperiod treatments and bud harvests, all pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. Acknowledgement:This study was funded by NSF Grant DBI0604755 and funds from the South Dakota Agriculture Experiment Station. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Anne Fennell. The equivalent experiment is VV10 at PLEXdb.]
2009-08-06 | GSE17502 | GEO