Seasonal variation in leafy spurge crown bud gene expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Manihot esculenta Euphorbia esula
PROVIDER: GSE3913 | GEO | 2005/12/29
SECONDARY ACCESSION(S): PRJNA94167
REPOSITORIES: GEO
Similar Datasets
Project description:This submission contains the RNAseq data from one (just the study on paradormancy release) of several studies used to assemble the leafy spurge tranacriptome. These assembled transcrptome was built from 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (this study). 2) A study of leafy spurge crown buds through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy (Series GSE71321). 3) A study identical to #2 above but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 4) A previously submitted study (Series GSE56509) of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome.
2015-08-05 | GSE71317 | GEO
Project description:This submission contains the RNAseq data from one (just the study on paradormancy release) of several studies used to assemble the leafy spurge tranacriptome. These assembled transcrptome was built from 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (this study). 2) A study of leafy spurge crown buds through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy (Series GSE71321). 3) A study identical to #2 above but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 4) A previously submitted study (Series GSE56509) of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome. The paradormancy study (#1) contained 4 time points (0hr, 6h, 1d, 3d) with 3 biological replicates at 0hr and 4 biological replicates at each of the other time points.
2015-08-05 | E-GEOD-71317 | biostudies-arrayexpress
Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 3) A previously submitted study of leafy spurge shoots following treatment with glyphosate was also used to assemble the transcriptome (Series GSE56509).
2015-08-05 | GSE71321 | GEO
Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 3) A previously submitted study of leafy spurge shoots following treatment with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).
2015-08-05 | E-GEOD-71321 | biostudies-arrayexpress
Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course following glyphosate treatments where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were not treated with glyphosate (Series GSE71321). 3) A previously submitted study of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome (Series GSE56509).
2015-08-05 | GSE71406 | GEO
Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course following glyphosate treatments where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were not treated with glyphosate (Series GSE71321). 3) A previously submitted study of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course following a glyphosate treatment study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).
2015-08-05 | E-GEOD-71406 | biostudies-arrayexpress
Project description:This study is a time course of growth induction (0, 12, 24, 48, and 72 hrs) following the breaking of paradormancy in underground buds of the perennial weed leafy spurge (Euphorbia esula). Keywords: Time course, growth induction, apical dominance, paradormancy, root buds, leafy spurge
2005-06-15 | GSE2786 | GEO
Project description:Persistence of the invasive perennial weed leafy spurge is mainly attributed to seasonal production of underground adventitious buds (UABs), which undergo well-defined phases of dormancy (para-, endo- and eco-dormancy). These well-defined phases of dormancy also allow UABs of leafy spurge to survive extreme seasonal variations, including dehydration-stress. Consequently, objectives of this study include understanding the effects of dehydration-stress on vegetative reproduction, flowering competence, and transcript profiles at different phases of bud dormancy. The vegetative growth potential of UABs was monitored by removing the aerial portion of dehydration-stressed plants and re-watering the root system. Further, microarray analysis was used to follow transcriptome profiles to identify critical defense- and signaling-pathways at different phases of dormancy in UABs. Surprisingly, only 3 days of dehydration-stress is required to break the endodormant phase in UABs. In leafy spurge, vernalization of endodormant UABs has previously been shown to induce flower competence, while breaking of endodormancy via dehydration-stress did not induce floral induction. Thus, these two environmental treatments open a unique approach to independently dissect molecular mechanisms involved in endodormancy maintenance and floral competence. Bioinformatics analysis of transcriptome data helped to identify models and overlapping pathways. During endodormancy break, LEC1, PHOTOSYSTEM I RC, and brassinosteroids were identified as ooverlapping hubs of up-regulated genes, and DREB1A, CBF2, GPA1, MYC2, BHLH, BZIP, and flavonoids were identified as overlapping hubs of down-regulated genes. Additionally, key genes involved in metabolic activity, chromatin modification, and cross-talk between growth regulators were identified as playing a role during endodormancy maintenance.
2011-04-05 | GSE28047 | GEO
Project description:This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December. Keywords: Dormancy leafy spurge adventitious-buds
2007-08-24 | GSE8849 | GEO
Project description:Leafy spurge (Euphorbia esula) is an herbaceous perennial weed that produces vegetatively from an abundance of underground adventitious buds. The objectives of this study were to determine how mimicking natural seasonal conditions (photoperiod and temperature) under controlled environmental conditions affect dormancy and flowering competence; to determine molecular mechanisms associated with well-defined phases of seasonal dormancy transitions based on transcript profiles obtained by microarray analysis; and to link mechanisms regulating induction and release of endodormancy and flowering competence. Reduction in temperature (27 to 10°C) and photoperiod (16 to 8 h) over a three-month period induced a para- to endo-dormant transition in crown buds. An additional eleven weeks of prolonged cold (5-7°C) and short-photoperiod treatment resulted in accelerated shoot growth from crown buds, and 99% floral competence when plants were returned to growth promoting conditions. Exposure of paradormant plants to short-photoperiod and prolonged cold treatment alone had minimal affect growth potential or on flowering (~1%); whereas endodormant crown buds without prolonged cold treatment, had delayed shoot growth and approximately 2% flowering when returned to growth promoting conditions. Transcriptome analyses revealed that 373 and 260 genes were differentially expressed (p<0.005) during para- to endo-dormant and endo- to eco-dormant transitions, respectively. Transcripts from flower competent vs. non-flower competent crown buds identified 607 differentially expressed genes, and genes involved in cell cycle and DNA processing, oxidative stress, flower regulation, and proteolysis were over-represented. Further, sub-network analysis identified expression targets and binding partners associated with circadian clock, dehydration/cold signaling, phosphorylation cascades, and response to abscisic acid, ethylene, gibberellic acid, and jasmonic acid, suggesting these central regulators affect well-defined phases of dormancy. Potential genetic pathways associated with these dormancy transitions and flowering were used to develop a proposed conceptual model. Leafy spurge is an herbaceous perennial weed that undergoes vegetative reproduction from an abundance of underground adventitious buds which exhibit phases of para-, endo-, and eco-dormancy (defined by Lang et al. 1987) during summer, fall, and winter, respectively (Anderson et al. 2005). In this study a population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001. Paradormant crown buds from three-month old greenhouse plants were collected after one week of acclimation under growth chamber conditions. Induction of endodormancy in crown buds was accomplished by subjecting greenhouse grown and growth chamber acclimated plants to a ramp down (RD) treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C â 10°C) and a decreasing photoperiod of 40 min week-1 (16h â 8h light) for 12 weeks as previously established by Foley et al. (2009). These conditions mimic the average seasonal environmental conditions experienced in Fargo, ND (46°54â² N, 96°48â² W) during the transition from para- to endo-dormancy (Anderson et al. 2005). To induce a transition of crown buds from endo- to eco-dormancy, plants subjected to the RD treatment were given prolonged cold treatment for 11 weeks at 5-7°C, under constant 8 h:16 h day:night cycle; light fluencies were approximately 250 μmol m-2 s-1. To compare the effects of the prolonged cold with or without RD treatment on dormancy status and flowering competence in crown buds, greenhouse-grown and growth chamber acclimated plants were subjected directly to an extended cold treatment for 11 weeks at 5-7°C, as previously described, without a RD treatment. For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols. Labeled cDNAs were hybridized to a custom made 23K element microarray that contained 19,808 unigenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 unigenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In our microarray analyses experiment, each of the four biological replicates included four technical replicates using two different dyes, resulting in a total of 16 technical replicates for each treatment. Microarray hybridization was visualized using a GenePix 4000B scanner and probe intensities and background were quantified using GenePix 6.0 software (Molecular Devices, Sunnyvale, California, USA). A quality control value of â1â was assigned to all probes that had intensity values greater than 2 times the standard deviation over average of the negative control and empty probe intensities (after deletion of 1% of the most intense negative/empty probe values). Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other.
2010-05-19 | E-GEOD-19217 | biostudies-arrayexpress