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Series GSE12936 Query DataSets for GSE12936
Status Public on Jun 30, 2009
Title Transcriptomic analysis of the effect of silicon on wheat plants infected or uninfected with powdery mildew
Organism Triticum aestivum
Experiment type Expression profiling by array
Summary The supply of soluble silicon (Si) to plants has been associated with many benefits that remain poorly explained and often contested. In this work, the effect of Si was studied on wheat plants under both control and pathogen stress (Blumeria graminis f.sp. tritici (Bgt)) conditions by conducting an exhaustive transcriptomic analysis (55,000 genes) aimed at comparing the differential response of plants under four treatments. The response to the supply of Si on control (uninfected) plants was limited to 47 genes providing little evidence of regulation of a specific metabolic process. Plants reacted to inoculation with Bgt by an up-regulation of many genes linked to stress and metabolic processes and a down-regulation of genes linked to photosynthesis. Supplying Si to inoculated plants largely prevented disease development, a phenotypic response that translated into a nearly perfect reversal of genes regulated by the effect of Bgt alone. These results suggest that Si plays a limited role on a plant’s metabolism in absence of stress, even in the case of a high-Si accumulating monocot such as wheat. On the other hand, the benefits of Si, in the form of biotic stress alleviation, were remarkably aligned with a counter-response to transcriptomic changes induced by the pathogen Bgt.

Keywords: stress type and molecule effect
Overall design Wheat culture in hydroponic system :
Hydroponic systems were used to precisely control Si feeding of plants and to reduce external Si contamination. Seeds of wheat cultivar AC Drummond, chosen for its known high susceptibility to Bgt, were sown in 9-cm pots in a nylon bed consisting of nylon stockings cut into small ribbons. Hydroponic systems were set up to immerse roots for 15 minutes every 30 minutes. The plants were grown in a greenhouse (16 h light at 22°C and 8h dark at 18°C, 80% humidity). Plants were immersed in distilled water only during the first week following sowing.

Si amendment and Bgt inoculation:
Wheat plants were grown in the presence (Si+) or absence (Si-) of Si and inoculated (B+) or not (B-) with Bgt for a total of four treatments: Si-B-, Si+B-, Si-B+, and Si+B+. These treatments were applied in the following manner. One week after sowing, distilled water was replaced by a Hoagland solution amended or not with potassium silicate (Kasil 6, PQ Corp etc) at a concentration of 1.7 mM (Si+ Hoagland). Twice a week, Si was added to the Si+ nutrient solution in order to maintain Si concentration at 1.7 mM. Every other week, both Si- and Si+ Hoagland solutions were renewed and the pH adjusted to 5.8 in all systems at each Si addition or nutrient solution renewal.
Four weeks after sowing (i.e. three weeks after Si amendment started), half the plants were inoculated with Bgt as described previously. Briefly, one day prior to inoculation, reservoir wheat plants heavily infected with Bgt were gently shaken to remove old spores and to stimulate the production of fresh ones. The inoculation was performed by shaking these infected wheat plants over the experimental plants .

RNA preparation:
Total RNA was extracted from leaves of three plants per treatment (three biological replicates) with the RNeasy plant kit (Qiagen, Hilden, Germany). Concentration and quality of RNA were assessed on a Nanodrop spectrophotometer (Nanodrop, Wilmington, De, USA) and 2100 Bioanalyzer (Agilent, Palo Alto, Ca, USA). Biotin-labeled cRNAs were synthesized using MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, Tx, USA) following the manufacturer’s instructions using 1 µg total RNA. Labelled cRNA was then fragmented using 5X Array Fragmentation Buffer supplied with the MessageAmp II-Biotin Enhanced Kit.

Microarray hybridization:
The labeled samples were added to an Affymetrix GeneChip® Wheat Genome Array (Affymetrix, Santa Clara, CA, USA), according to the manufacturer’s instructions. The wheat chip contains probe sets representing 55,052 transcripts for all 42 chromosomes in the wheat genome. The chips were hybridized for 16 h at 45 °C in a rotisserie oven at 60 rpm. Following hybridization, the arrays were washed and stained in an Affymetrix Fluidics Station 450, according to the standard protocol from Affymetrix, and scanned using an Affymetrix Scanner 3000. Twelve chips were prepared and corresponded to three biological replications of each of the four treatments (Si-B-, Si+B-, Si-B+, and Si+B+).
Contributor(s) Chain F, Côté-Beaulieu C, Belzile F, Menzies JG, Bélanger RR
Citation(s) 19810802
Submission date Sep 25, 2008
Last update date Dec 04, 2018
Contact name Florian Chain
Organization name INRA
Department Institut Micalis
Lab Probihote
Street address Domaine de Vilvert
City Jouy en Josas
ZIP/Postal code 78352
Country France
Platforms (1)
GPL3802 [wheat] Affymetrix Wheat Genome Array
Samples (12)
GSM324484 Si- B- rep1
GSM324485 Si- B- rep2
GSM324486 Si- B- rep3
BioProject PRJNA110861

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Supplementary file Size Download File type/resource
GSE12936_RAW.tar 57.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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