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Transcriptomic analysis of the effect of silicon on wheat plants infected or uninfected with powdery mildew

ABSTRACT: 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

ORGANISM(S): Triticum aestivum

PROVIDER: GSE12936 | GEO | 2009/06/30

SECONDARY ACCESSION(S): PRJNA110861

REPOSITORIES: GEO

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Project description: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 plantâs 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. Experiment Overall Design: Wheat culture in hydroponic system : Experiment Overall Design: 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 22Â°C and 8h dark at 18Â°C, 80% humidity). Plants were immersed in distilled water only during the first week following sowing. Experiment Overall Design: Si amendment and Bgt inoculation: Experiment Overall Design: 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. Experiment Overall Design: 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 . Experiment Overall Design: RNA preparation: Experiment Overall Design: 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 manufacturerâs instructions using 1 Âµg total RNA. Labelled cRNA was then fragmented using 5X Array Fragmentation Buffer supplied with the MessageAmp II-Biotin Enhanced Kit. Experiment Overall Design: Microarray hybridization: Experiment Overall Design: The labeled samples were added to an Affymetrix GeneChipÂ® Wheat Genome Array (Affymetrix, Santa Clara, CA, USA), according to the manufacturerâs 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 Â°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+).

Project description:The role and essentiality of silicon (Si) in plant biology has been debated for over 150 years in spite of numerous reports describing its beneficial properties. To obtain unique insights regarding the effect of Si on plants, we performed a complete transcriptome analysis of both control and powdery mildew-stressed Arabidopsis plants, with or without Si application, using a 44K microarray. Surprisingly, the expression of all but two genes was unaffected by Si in control plants, a result contradicting reports of possible direct effect of Si as a fertilizer. In contrast, inoculation of plants, treated or not with Si, altered the expression of a set of nearly 4,000 genes. Following functional categorization, many of the up-regulated genes were defense-related whereas a large proportion of down-regulated genes were involved in primary metabolism. Regulated defense genes included R genes, stress-related transcription factors, genes involved in signal transduction, the biosynthesis of stress hormones (SA, JA, ethylene), and the metabolism of reactive oxygen species. In inoculated plants treated with Si, the magnitude of down-regulation was attenuated by over 25%, an indication of stress alleviation. Our results demonstrate that Si treatment had no effect on the metabolism of unstressed plants suggesting a non essential role for the element, but that it has beneficial properties attributable to modulation of a more efficient response to pathogen stress. Experiment Overall Design: A loop design with complete dye-swap was used as experimental design for comparing plants submitted to four treatments and three biological replicates for a total of 24 Agilent Arabidopsis 3 microarrays. Two factors experimental factors : response to a compound (Silicon, treated or not treated) and disease state (Erysiphe cichoracearum, normal vs. diseased). Each factor had two levels. For each of the four combinations of factors, three plants were randomly selected. Thus a total of 12 plants were used for the experiment. RNA was extracted from rosette leaves.

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Transcriptomic analysis of the effect of silicon on wheat plants infected or uninfected with powdery mildew

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