Solar UV-B regulation of high altitude maize
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE1807 | GEO | 2005/01/20
SECONDARY ACCESSION(S): PRJNA90287
REPOSITORIES: GEO
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Project description:Additional to GSE1807 A comparative analysis, by expression profiling of maize, was performed to identify novel components in the mechanisms of maize responses to UV-B. Five high-altitude landraces grown from 2,000 to 3,400 m naturally receive higher UV-B fluence than plants at lower altitudes and similar latitudes. These high-altitude landraces were compared directly with a low-altitude line and with literature reports for other temperate maize lines. A microarray analysis demonstrated that among the UV-B responsive transcripts, several types of gene implicated in chromatin remodeling are differentially expressed before and after UV-B treatment in high-altitude lines. RNAi transgenic plants with lower expression of four such chromatin-associated genes exhibited hypersensitivity to UV-B by measurements of leaf arching, increased leaf chlorosis and necrosis, and altered UV-B regulation of selected genes. These results collectively suggest that genes involved in chromatin remodeling are crucial for UV-B acclimation and that some high-altitude lines exhibit adaptations to this challenge.
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2012-03-29 | E-GEOD-34951 | biostudies-arrayexpress
Project description:Measurement of changes in the mRNA transcript abundance of 1709 cDNAs in Xerophyta humilis leaves at 6 relative water contents (RWC) (100%, 80%, 60%, 40%, 20% and 5%RWC respectively). 3105 cDNA clones (corresponding to 1709 unique cDNAs) were randomly selected from X. humilis cDNA libraries (Leaf Dehydration (LD), Leaf Rehydration (LR), Root Dehydration (RD) and Root Rehydration (RR)), amplified by PCR, and printed on each glass slide multiple times (ranging from 4 to 12X), such that each printed block contained a random unbiased mixture of cDNAs from the 4 different cDNA libraries. Total RNA extracted from each X. humilis leaf sample was linearly amplified, labelled with Cy3, and simultaneously hybridized with Cy5 labelled common reference RNA, to the printed cDNA arrays. The reference RNA comprised equal amounts of total RNA pooled from 6 different RWC experimental samples. Data was recorded for five biological replicates for each of the 6 RWC stages being investigated.
2012-03-29 | E-GEOD-34952 | biostudies-arrayexpress
Project description:Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B
2013-10-31 | GSE19768 | GEO
Project description:Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B 4-week maize plants were grown in the greenhouse in the absence of UV-B. Then, they were divided in two groups. One group was treated with UV-B lights provided once for 8 h, starting 3 h after the beginning of the light period, using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) at a UV-B intensity of 2 W m-2, UV-A: 0.65 W m-2. The bulbs were covered with cellulose acetate to exclude wavelengths <280 nm. For the second control group, plants were exposed for 8 h under the same lamps covered with polyester film (no UV-B treatment, UV-B: 0.04 W m-2, UV-A: 0.4 W m-2). Lamp output was recorded using a UV-B/UV-A radiometer (UV203 A+B radiometer, Macam Photometrics, Ltd, Livingston, UK) to insure that both the bulbs and filters provided the designated UV dosage in all treatments. Leaf samples were collected immediately after irradiation. RNA was extracted immediately after the treatments, and used for the microRNA microarray experiments.
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Project description:In order to understand the function of the Tra1p transcription factor we identified potentially Tra1p-regulated genes by comparison of transcript abundance in aerial mycelium of the tra1- mutant and the parental strain 70-15. Two-condition experiment, wild-type vs. TRA1-deleted mutant. 4 biological replicates with dye-swaps. Each microarry slide had 2 arrays with 44k spots (22k spots printed twice). Thus, rep1 and rep2 are technical replicates of the same biological sample (derived from one raw data file).
2012-03-03 | E-GEOD-36224 | biostudies-arrayexpress
Project description:UV radiation (UV) alters secondary metabolism in the skin of Vitis vinifera L. berries, which may affect on the final composition of both, grapes and wines. We compared berry skin transcriptome and phenolic composition between Tempranillo berries grown in the presence or absence of solar UV in a mid-altitude Tempranillo vineyard. By analysing two different ripening degrees, expression of 121 genes was significantly altered. Functional enrichment identified that, principally, secondary metabolism-related transcripts were induced by UV, including VvFLS1, VvGT5 and VvGT6 flavonol biosynthetic genes induction. Concurrently, flavonol accumulation was the most evident impact of UV on the berry skin phenolic composition. Monoterpenoid biosynthetic transcripts were also up-regulated by UV, whereas induction of stilbenoid biosynthetic transcripts and stilbenes accumulation was probably induced by the joint action of UV and other condition under the UV-blocking filter, likely higher temperature. Among regulatory genes, VvMYBF1, VvMYB24 and three bHLH transcription factors were up-regulated by UV. Homologs to Arabidopsis UVR8-dependent UV-B-induced genes were also induced, including VvHY5-1, VvHY5-2 and VvRUP UV-B signalling genes. This suggests that the UV-B-specific signalling pathway is activated in the skin of grapes grown at low-medium altitudes. The biosynthesis and accumulation of UV-absorbing compounds that are appreciated for winemaking were almost specifically triggered, which indicates that viticultural practices increasing solar UV incidence may improve grape features important to wine production.
2014-09-09 | GSE54636 | GEO
Project description:Mutant maize lines expressing RNAi gene silencing constructs directed to two distinct classes of chromatin associated proteins show heightened sensitivity to UV-B including sunburned necrosis and down regulation of chromatin genes (Casati and Walbot, 2006). We have available transgenic maize expressing an RNAi for these chromatin factors: a subunit of a chromatin remodeling complex R, which is a SWI2/SNF2-like protein containing a SNF2 N and a helicase C domain (CHC101, AI746001); and a methyl-CpG-binding protein (MDB101, AI737448). To better understand the processes that involve chromatin remodeling proteins in UV-B responses, we conducted transcriptome analysis of chromatin remodeling knockdown plants in under two radiation regimes: plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with CA filters to exclude wavelengths lower than 280 nm (UV-B). As a control, the bulbs were covered with PE filters to exclude wavelengths lower than 320 nm (minus UV-B). We analyzed genes that are changed upon UV-B irradiation in the transgenic plants and compared to the responses in non transgenic plants. To differentiate between differences due to background specific genes expression, we used non-transgenic sibling as controls. For these experiments, we used Long oligonucleotides arrays from Agilent Technologies. These studies will help to dilucidate how alteration in chromatin remodeling protein proteins affect gene expression, and the transcriptome analysis will help to understand why transgenic plants are hypersensity to UV-B. Keywords: genetic modification-stress response
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Project description:The entomopathogen Metarhizium anisopliae contains strains with wide host ranges and specialist strains adapted to particular hosts. Patterns of gene duplication, divergence and deletion in three generalist and three specialist strains were investigated by heterologous hybridization of genomic DNA to genes from the generalist strain ARSEF 2575. Many sequences from 2575 that are highly conserved in fungi showed rapid evolution and loss in specialist Metarhizium genomes. Some poorly hybridizing genes in specialists were functionally coordinated, including several involved in toxin biosyntheses and sugar metabolism in root exudates, indicative of reductive evolution. This suggests that specialists are loosing genes required to live in alternative hosts or as saprophytes. Several components of mobile genetic elements were also highly divergent or lost in specialists. Exceptionally, the genome of the specialist strain ARSEF 443 contained extra insertion elements that might play a role in generating evolutionary novelty. Three microarray slides were used in comparison (cDNAs are replicated in triplicate on each slide). 324 strainâ??s DNA was co-hybridized with strain ARSEF 2575 DNA in dye swapping replicate experiments and the relative hybridization efficiency (fluorescence ratio) of their DNA for strain ARSEF 2575 genes was compared. This array harbors PCR amplified fragments from the unique cDNA clones from M. anisopliae var. anisopliae ARSEF 2575 and a few genes from M. anisopliae var. acridum ARSEF 324 absent from the libraries of ARSEF 2575. In total, 1730 amplified clones were printed in triplicates on the slides. Additional background control was provided by 30 randomly distributed spots of 3Ã?SSC buffer. Printing, hybridization, and scanning of slides was as described before (Freimoser et al., 2005).
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