Identification of candidate genes for nonhost resistance to powdery mildew in wheat
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Agilent G2505B scanner
ORGANISM(S): Triticum aestivum
SUBMITTER: Rajaraman Jeyaraman
PROVIDER: E-MTAB-3803 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To identify the non-host responsive genes, a time-series based global expression profiling was performed in barley using Agilent chip. Seven-day-old barley plants of cv. Vada were inoculated with spore density of 50-80 conidia mm-2 of Bgh or Bgt, and the abaxial epidermis of inoculated primary leaves or from non-inoculated control leaves was peeled 6, 12, 24 and 74 h after inoculation. Total RNA was extracted by using the RNeasy plant mini kit with on-Column DNase digestion (Qiagen, Hilden, Germany), and hybridized to a 44K Agilent oligonucleotide custom array of barley.
2014-10-24 | E-MTAB-2916 | biostudies-arrayexpress
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 22°C and 8h dark at 18°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 µg 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 GeneChip® 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 °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+).
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2017-12-02 | E-MTAB-5635 | biostudies-arrayexpress
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2020-08-18 | PXD015089 | Pride
Project description:In this experiment the transcriptome reprogramming in wheat during host and nonhost interaction with Puccinia sp. was analyzed in a time-series approach. Ten days old wheat plants of cv. Renan were mock-inoculated or inoculated with P. triticina (Pt), BRW96258 isolate, or P. hordei (Ph), 1.2.1 isolate. After 12, 24, 36 and 48 hours first leaves were sampled. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), the Ambion TURBO DNA-free DNase Kit was used for DNA elimination, and RNA was hybridized to Agilent 44k oligonucleotide arrays.
2017-12-02 | E-MTAB-5656 | biostudies-arrayexpress
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2009-01-14 | E-GEOD-13660 | biostudies-arrayexpress
Project description:We undertook a time course analysis of gene expression between mock (non)-inoculated and pathogen (Puccinia triticinia)-infected wheat samples using RNA sequencing (RNA-Seq).
2022-06-26 | E-MTAB-9791 | biostudies-arrayexpress
Project description:Wheat leaf rust caused by the pathogenic fungus Puccinia triticina, is a serious threat to bread wheat and durum production in many areas of the world. This plant-pathogen interaction has been studied extensively at the molecular genetics level, however proteomics data are still relatively scarce. The present study investigated temporal changes in the abundance of the apoplastic fluid proteome of wheat leaves infected with either virulent or avirulent races of P. triticina, using a label-free LC-MS-based approach. In general, there was very little difference between inoculated and control apoplastic proteomes as a result of either race of pathogen, until haustoria had become well established in the incompatible interaction, although the resistant host responds to pathogen challenge sooner than the susceptible. In the earlier samplings (up to 72 h after inoculation), there were 46 host proteins with significantly changing abundance, however pathogen proteins were detected only rarely and not reproducibly. This is consistent with the hemi-biotrophic life-style of P. triticina; the pathogen infection is characterized by an early phase of a symbiosis-like relationship, followed by a later stage of pathogenesis, with tissue damage and parasitism. The majority of the host proteins with altered abundance up to 72 h post-inoculation were pathogen-response-related, including peroxidases, chitinases, β-1-3-endo-glucanases and PR-proteins. Five days after inoculation with the incompatible race it was possible to detect 150 PT proteins and 117 host proteins which had significantly increased in abundance as well as 33 host proteins which had significantly decreased in abundance and which represent potential targets of pathogen effectors. The pathogen-expressed proteins – seen most abundantly in the incompatible interaction – were mostly uncharacterized proteins, however many of their functions could be inferred through homology-matching with pBLAST. Pathogen proteins also included several candidate effector proteins, some novel and some which have been reported previously from the purified haustoria proteome.
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Project description:The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted by comparing mock- and P. triticina-inoculated leaves harvested at 3 and 7 days post inoculation (dpi). SUBMITTER_CITATION: Bolton, M.D., Kolmer, J.A., Xu, W.W., and Garvin, D.F. 2008. Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways. Molecular Plant-Microbe Interactions 21:1515-1527. Experiment Overall Design: The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted on leaves harvested at 3 and 7 days post inoculation (dpi). The study utilized a randomized complete block design with three replicates for each genotype, and employed univariate analysis (t-tests) between mock- and P. triticina-inoculated plants within each genotype at each timepoint, for a total of six comparisons across the entire experiment, utilizing a total 36 Affymetrix Wheat Genome Array GeneChips.
2008-11-13 | E-GEOD-9915 | biostudies-arrayexpress