Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Diel changes of transcriptome in cold-treated maize

ABSTRACT: 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.

ORGANISM(S): Zea mays

SUBMITTER: Maciej Jonczyk

PROVIDER: E-MTAB-1252 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of ELIP1, ELIP2, APX2 and LHCB2.4 in the phyA, phyB, cry1 and cry2 photoreceptor mutants and hy5 and hyh transcription factor mutants. Following exposure to high intensity white light for 3 h (HL, 1000 micro mol quanta m-2 s-1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific mis-regulation of ELIP1/2 and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis 24K Gene-Chip we showed that 77 of the HL responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the mis-regulation of these genes the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of PSII, indicated by reduced Fv/Fm. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component. Experiment Overall Design: All samples were done in biological triplicates (named A, B, C): Arabidopsis Col-O: growth conditions (7 d continuous white light; 100 micro mol quanta m-2 s-1, 22 Â°C), growth conditions followed by high light (3 hours 1000 micro mol quanta m-2 s-1, 22 Â°C) and growth conditions followed by blue light (3 hours; HQI-T 400 W lamps were filtered through color filter #74, 400-540 nm, absorption maximum: 470 nm (Night Blue; Rosco International)) Experiment Overall Design: cryptochrome 1 (cry1) mutant: growth conditions and growth conditions followed by 3 hours high light Experiment Overall Design: long hypocotyl 5 (hy5) mutant: growth conditions and growth conditions followed by 3 hours high light

Project description:Background: Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is limited information about gene regulation and signaling pathways related to the cold stress response in cassava. The development of microarray technology has accelerated the study of global transcription profiling under certain conditions. Results: A 60-mer oligonucleotide 4X44K Agilent microarray representing 20,840 genes was used to perform transcriptome profiling in cassava apical shoots subjected to cold at 7M-BM-0C for 0 h, 4 h, and 9 h. A total of 508 transcripts were identified as early cold-responsive genes in which 319 sequences had descriptions when they were aligned with Arabidopsis proteins. Gene ontology (GO) annotation analysis identified many interesting categories including M-bM-^@M-^XResponse to abiotic and biotic stimulusM-bM-^@M-^Y, M-bM-^@M-^XResponse to stressM-bM-^@M-^Y, M-bM-^@M-^XTranscription factor activityM-bM-^@M-^Y, and M-bM-^@M-^XChloroplastM-bM-^@M-^Y. Various stress-associated genes comprising signal transduction components (e.g., MAP kinase 4), transcription factors (TFs; e.g., RAP2.11), and ROS scavenging enzymes (e.g., catalase 2), as well as photosynthesis-related genes (e.g., PSAL), were found. Seventeen major TF families were also identified as being involved in the early response to cold stress (e.g., AP2-EREBP). Meanwhile, KEGG pathway analysis uncovered many important pathways, including M-bM-^@M-^XPlant hormone signal transductionM-bM-^@M-^Y, M-bM-^@M-^XStarch and sucrose metabolismM-bM-^@M-^Y, and M-bM-^@M-^XPlant-pathogen interactionM-bM-^@M-^Y. Furthermore, the expression changes of 18 genes under cold and other abiotic stresses conditions were validated by real-time RT-PCR. As a response to cold stress in cassava, an increase in the ROS scavenging enzyme activities of catalase and superoxide dismutases and the accumulation of total soluble sugars were also detected. Importantly, most of the tested stress-responsive genes were primarily expressed in mature leaves, stem cambia, and fibrous roots rather than apical buds and young leaves. Conclusions: The dynamic expression changes reflect the integrative controlling and transcriptome regulation of the networks in the early cold stress response of cassava. The biological processes involved in the signal perception and physiological response might shed light on the molecular mechanisms related to cold tolerance in tropical plants and provide useful candidate genes for genetic improvement. Apical shoots subjected to cold at 7M-BM-0C for 0 h, 4 h, and 9 h were collected for RNA extractions from three independent healthy 3-month-old cassava (cultivar TMS60444) plants in the greenhouse.

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Diel changes of transcriptome in cold-treated maize

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