Gene expression profiling in three inbred lines of maize affected by chilling treatment
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Maciej Jonczyk
PROVIDER: E-MEXP-3508 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We investigated effect of severe cold on transcriptome changes in two inbred maize lines, chilling-sensitive ETH-DL3 and chilling-tolerant ETH-DH7. Kernels were germinated in wet sand in darkness at 25C. Seedlings were transferred to growth chamber (day/night temperature 24/22C, photoperiod 14/10 h, light 250 umol quanta x m-2 x s-1) and grow in pots containing Knop's nutrient solution supplemented with Hoagland's micro-nutrients. After full development of the 3rd leaf (fully developed ligular region) plants were used in experiment. The experiment was begun at the start of the dark period. Half of the plants were transferred to cold chamber (day/night temperature 8/6C, photoperiod 14/10 h, light 250 umol quanta x m-2 x s-1) other half served as control (day/night temperature 24/22C, other parameters was the same as for cold treatment). After dark period (10h) and 200 minutes of light period samples were taken. Each sample consisted of the middle part of the 3rd leaf blade, pooled from three plants and frozen in liquid nitrogen. The experiment was replicated four times with two replications dye swapped.
2014-03-15 | E-MTAB-1315 | biostudies-arrayexpress
Project description:We investigated effect of severe cold to diurnal transcriptome changes in maize 3rd leaf. We used chilling-sensitive inbred line CM109. Kernels were germinated in wet sand in darkness at 25C. Seedlings were transferred to growth chamber (photoperiod 14/10h, temperature 24, light 250 umol quanta x m-2 x s-1). After full development of the third leaf (fully developed ligular region) plants were used for experiments. The experiment was begun at the start of the dark period (time zero), at which time a large sample (eight plants) was taken to serve as a reference in hybridizations. Half of the plants were transferred to cold chamber (day/night temperature 8/6°C, photoperiod 14/10 h, light 250 umol quanta•m-2•s-1) other half served as control (day/night temperature 24/22°C, other parameters was the same as for cold treatment). Further samples were taken after 200, 400, 600 (dark period) and 810, 1020, 1230, 1440 minutes (light period) of growth (total 24 hours). Each sample consisted of the middle part of the third leaf blade, pooled from three plants and frozen in liquid nitrogen. The experiment was replicated four times with two replications dye swapped.
2017-08-21 | E-MTAB-1252 | biostudies-arrayexpress
Project description:Here we studied the leaf transcriptome in maize,<br>throughout a cycle of 10 h darkness and 14 h light to look for rhythmic patterns<br>of gene expression.
2011-08-19 | E-MEXP-3212 | biostudies-arrayexpress
Project description:We take the one year old plant for chilling stress (4M-BM-0C, 10h) and controls.Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in Populus simonii leaves. We used microarrays to detail the global programme of gene expression during chilling stress (4M-BM-0C, 10h). Populus simonii leaves were taken from chilling stress (4M-BM-0C, 10h) and controls for RNA extraction and hybridization on Affymetrix microarrays.BH11269-2_Zdqe 13 and BH11269-2_Zdqe 14 from chilling stress (4M-BM-0C, 10h) treatments, CK1 and CK2 controls.
2014-05-16 | E-GEOD-43872 | biostudies-arrayexpress
Project description:This study investigated changes in gene expression of controlled environment chilled (4C) grape overwintering buds as they accumulated from 0 to 2000 chilling hours. Keywords: time course, chilling, endodormancy release, axillary bud, grape A loop design with 3 biological replicates (RNA from buds collected at 0, 500, 1000, 1500, and 2000 hr of chilling in 2002, 2004, and 2005).
2010-05-18 | E-GEOD-9903 | biostudies-arrayexpress
Project description:Plant defence against insects is well known to be affected by previous exposure to cues warning of herbivory. Using Arabidopsis thaliana and the herbivore Pieris brassicae, we addressed the question whether the maintenance of the effects of the warning cue depends on its reliability. We determined the transcriptomes of Arabidopsis leaves that were treated by P. brassicae egg deposition (i) five days after oviposition, (ii) one day after removal of the eggs following the egg treatment, (iii) three days after removal of the eggs, (iv) after two days of herbivory that started one day after removal of the eggs; or that were treated by chilling (v) five days after transfer to 4°C, (vi) one day after transfering the plants to 20°C following the chilling treatment, (vii) three days after transfering the plants to 20°C, (viii) after two days of herbivory that started one day after transfering the plants to 20°C. Arabidopsis thaliana Col-0 wild type plants were grown under short day conditions (10 h/14 h light/dark) at 20°C for 7 weeks. Subsequently (i) the plants were transferred to 4°C for 5 days, or (ii) Pieris brassicae deposited ca. 40 eggs on leaf 17 where they remained for five days, or (iii) as controls plants grew untreated for five days. Next, the plants were transferred back to 20°C and the eggs were removed, respectively. Next, all plants rested for 1 day at 20°C. Next, P. brassicae larvae were allowed to feed for 2 days on leaf 17 adjacent to the former egg deposit site or at a respective leaf region of chilling-treated or untreated plants. Control plants were not exposed to larvae. From all treated and untreated plants material from a leaf region proximal to the egg deposition and/or feeding site was harvested for transcriptome analysis.
2016-06-23 | E-GEOD-69623 | biostudies-arrayexpress
Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to low temperature, including triplicated measurements of cold, freeze/thaw cycles and de-acclimation over 33 days. Experiment Overall Design: Plants were grown at 20ºC for seven days and subject to a symmetrical cycle of acclimation, cold, freeze-thaw, and deacclimation. Chilling began by decreasing the temperature overnight from 20ºC to 4ºC at a rate of 1.3ºCâ¢h-1 and maintaining temperatures of 4 ºC in the day and 2ºC at night for 5 days. Freeze-thaw cycling lasted 12 days with day temperatures of 4ºC and night temperatures gradually decreasing from -2ºC the first night to -4ºC for three nights and -10ºC for four nights, then recovering to -4ºC for three nights and -2ºC for one night. This treatment was designed to allow daily freeze-thaw cycling and protein synthesis. Chilling conditions (4ºC day, 2ºC night) were resumed for five days, followed by deacclimation with increasing temperature to 20ºC overnight and maintaining for three days. Sampling was done at four different times, each at the 11th hour of light to avoid circadian effects: 1) before chilling treatment, 2) five days after initiation of chilling treatment, 3) eight days into freeze-thaw treatment and 4) three days into de-acclimation.
2008-06-15 | E-GEOD-6993 | biostudies-arrayexpress
Project description:We take the one year old plant for chilling stress (4°C, 10h) and controls.Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in Populus simonii leaves. We used microarrays to detail the global programme of gene expression during chilling stress (4°C, 10h).
2014-05-16 | GSE43872 | GEO
Project description:Cotton premature leaf senescence often occurred with an increasing frequency in many cotton growing areas and caused serious reduction in yield and quality of cotton has been one of the impontant factors that restrict severely the production of cotton.Our laboratory studies showed chilling stress is the key factor that induced A. alternatia infection, caused Alternaria disease and then lead to cotton leaf senescence, but the molecular mechanism of cotton premature leaf senscence is still unclear. We used microarrays to study molecular mechanism of chilling stress causing Alternaria alternata infection and leading to cotton leaf senescence and find the key genes during this process. Plants were grown in growth chamber with a 14/10 hours photoperiod, 28â/22â. Three-to-four leaves stage cotton plants were pre-treated by chilling stress with the low temperatures of 16/12â day/night for a fixed time length of 3 days. While, the normal growth plants were sustained growing at optimal temperature of 28/20â day/night. And then, both chilling stress pre-treated and normal growth cotton plants were inoculated with Alternaria. alternata isolate A1. The mock inoculations were performed with sterilized water. Cotton leaf Samples were respectively collected at 3, 6 days after inoculation (DAI) for RNA extraction and hybridization on Affymetrix microarrays. To that end, we collected 8 samples, i.e. chilling stress pre-treated cotton leaves: 3 DAI (C) and its mock control (D), 6 DAI (E) and its mock control (F); normal growth cotton leaves: 3 DAI (H) and its mock control (I), 6 DAI (J) and its mock control (K). All samples were arranged in completely randomized designed with three replications for each treatment.
2015-10-28 | E-GEOD-74412 | biostudies-arrayexpress
Project description:Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in LTH, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in LTH and strong repression in IR29. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. In present study, comprehensive gene expression using an Affymetrix rice genome array revealed a diverse global transcription reprogramming between two rice genotypes under chilling stress and subsequent recovery conditions. The dominant change in gene expression at low temperature was up-regulation in the chilling-tolerant genotype and down-regulation in the chilling-sensitive genotype. Early responses to chilling stress common to both genotypes featured up-regulated genes related to transcription regulation and signal transduction, while functional categories of LR-chilling regulated genes were clearly diverse with a wide range of functional adaptations. At the end of the chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovery capacity at the transcriptional level. Finally, analysis of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, are involved in chilling stress tolerance. In this study, parallel transcriptomic analysis in two rice genotypes with contrasting chilling-tolerant phenotypes was performed to identify and characterize novel genes involved in chilling stress tolerance in rice.
2012-12-21 | E-GEOD-38023 | biostudies-arrayexpress