Genetic regulation of gene expression of barley in response to stem rust (Pgt isolate TTKS)
Ontology highlight
ABSTRACT:
ORGANISM(S): Hordeum vulgare
SUBMITTER: Roger Wise
PROVIDER: E-GEOD-20416 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The QxSM doubled-haploid mapping population was generated from a single Q21861 x SM89010 F1 plant (Borovkova et al. 1995; Steffenson et al. 1995). Four flats (each flat contained 75 DH lines + 4 replicates of each parent = 81 cones/flat) were grown in a completely randomized design at the ARS Cereal Disease Lab, University of Minnesota, St. Paul. The four flats were divided into two replicates of two flats each. Nine days after sowing, one flat of each replicate was inoculated (INOC) with TTKS urediniospores were suspended in Soltrol oil with an inoculum weight of 0.25 mg per flat and the other was mock-inoculated (MOCK). Each (MOCK and INOC) replicate was incubated in its own dew chamber overnight. After inoculation, replicates were placed in separate mist chambers for 16 hours in the dark, followed by lights for 5 hours, and then moved to the greenhouse for 2 hours. The growth stage of barley was first leaf unfolded (PO:0007094) and five seedlings were harvested and placed in liquid nitrogen for each line in the population within a 1.5 hour period at 24 hours after inoculation (hai). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P. Wise. The equivalent experiment is BB64 at PLEXdb.]
2010-11-15 | GSE20416 | GEO
Project description:Time-course expression profiles of Bgh challenged barley cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1, were compared using the 22K Barley1 GeneChip. Planting, stage of seedlings, harvesting, and experimental design were part of a larger experiment described by Caldo et al. (2004). PLEXdb BB4. Experiment Design: C.I. 16151 (wildtype) and bcd1 (mutant) were planted in separate 20 x 30-cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest time points (0, 8, 16, 20, 24, and 32 hai). Seedlings grown to the 1st leaf stage with 2nd leaf unfolded were inoculated with a high density of fresh conidiospores (84 +/- 19 spores/mm2). Groups of flats were placed at 18C (8-hour darkness, 16-hour light) in separate controlled growth chambers corresponding to the Bgh isolates. Rows of plants were harvested at each assigned time points and snap frozen in liquid nitrogen. The entire experiment was repeated three times in a standard split-split-plot design with 72 experimental units (2 genotypes x 2 pathogen isolates x 6 time points x 3 replications). Treatment Description: The samples constituted pairwise combinations of the the cultivar C.I. 16151(containing the Mla6 resistance allele), and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1 with the two Bgh (Blumeria graminis f. sp. hordei) isolates, 5874 (AvrMla6, AvrMla1) and K1 (AvrMla13, AvrMla1). For each replication, individual genotypes were planted in separate 20 x 30 cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest times (0, 8, 16, 20, 24, and 32 hai). Seedlings were grown to the 2nd-leaf stage with 1st leaf unfolded, and inoculation was performed at 4 PM Central Standard Time by tipping the flats at 45oC and dusting the plants with a high density of fresh conidiospores [84 +/- 19 spores/mm2]. This procedure was repeated from the opposite angle to ensure that a high proportion of the cells are in contact with the fungus. This conidial density per unit leaf area routinely results in greater than 50% of epidermal cells that are successfully infected. Groups of flats were placed at 18oC (8 hours darkness, 16 hours light, 8 hours darkness) in separate controlled growth chambers corresponding to the Bgh isolate. Rows of plants were harvested at their assigned harvest times and flash-frozen in liquid nitrogen. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P Wise. The equivalent experiment is BB46 at PLEXdb.] genotype: Mla6 - pathogen isolates: 5874 - time: 0(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 8(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 16(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 20(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 24(3-replications); genotype: Mla6 - pathogen isolates: 5874 - time: 32(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 0(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 8(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 16(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 20(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 24(3-replications); genotype: Mla6 - pathogen isolates: K1 - time: 32(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 0(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 8(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 16(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 20(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 24(3-replications); genotype: 11542 - pathogen isolates: 5874 - time: 32(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 0(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 8(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 16(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 20(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 24(3-replications); genotype: 11542 - pathogen isolates: K1 - time: 32(3-replications)
2009-02-25 | E-GEOD-14930 | biostudies-arrayexpress
Project description:RESEARCH SUMMARY Bacterial blight and bacterial leaf streak, two of the most serious diseases of rice, are caused by Xanthomonas oryzae pathovar (pv.) oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) respectively. Xoo is a vascular pathogen that invades the xylem, whereas Xoc is non-vascular and colonizes the mesophyll apoplast. These distinctive types of infection represent the two most common ways plant pathogenic bacteria produce disease. As closely related pathogens of a model plant host, Xoo and Xoc constitute a powerful comparative system. We hypothesize that tissue-specific susceptibility to pathogenic bacteria can be explained partially by differential host responses during infection. To establish the global structure of susceptible responses to infection by Xoo and Xoc, we used the Affymetrix Rice Genome Array to analyze the abundance of transcripts in rice plants over four days after inoculation with virulent strains. MATERIAL AND METHODS - Plant Material: Oryza sativa ssp. japonica cv. Nipponbare plants were grown in pots containing LC-1 soil mixture, and arranged in flats of 20 pots, in growth chambers under a 12-h, 28ºC light and a 12-h, 25ºC dark cycle. To allow inversion of the flats for inoculation (modified dip-inoculation method, Niño-Liu et al, 2005, Journal of Phytopathology) seeds were sown through 1-cm perforations in a fibreglass tray resting on top of the pots. Peters Professional Fertilizer and iron chelate micronutrient were applied with watering every two days at rates of 0.25 and 4.5 g/L, respectively, until the day before inoculation. - Bacterial Strains and preparation of inoculum: Xoo strain PXO99A and Xoc strain BLS256 were used. For each, a single colony from a glucose yeast extract (GYE) agar plate was transferred to 5 ml of GYE liquid medium and incubated for 24 h at 28ºC with constant shaking at 250 rpm. Subsequently, 2 ml of this culture was transferred to 300 ml of fresh GYE liquid medium and incubated as above for an additional 18 h. Cells were pelleted by centrifugation at 4000 rpm. for 10 min, washed twice and resuspended in sterile 10 mm MgCl2 to an OD600 of 0.05, yielding 7 liters of inoculum. Tween-20 was added to a final concentration of 0.5%. - Modified dip-inoculation method: Fourteen days after sowing, and 2 h after the beginning of the light period, seedlings were inverted into inoculum, one flat each for Xoo, Xoc and Mock inoculum consisting of sterile 10 mM MgCl2 with 0.5% Tween-20, and vaccuum infiltrated at 500mm Hg for two minutes, two consecutive times, in a custom-made chamber. Following inoculation, plants were returned to the growth chamber. During growth, plants were cycled weekly in the same order through three growth chambers. In this way all plants could be incubated in the same final chamber following inoculation. For each replicate, position of the flats in the growth chamber (from left to right, used also for the order of inoculation and harvest) was determined by a split-plot design. - Timepoints, tissue collection: Within flats, assignment of pots for the harvest of inoculated tissue at 2, 4, 8, 24 and 96 h was made using a separate randomized complete block design. Tissue was harvested from plants in four pots (approximately 2g fresh weight) for each timepoint per inoculum per replication. Harvested tissue was immediately frozen in liquid nitrogen and stored at -80ºC until processing. - RNA isolation, purification, labeling, hybridizations, scanning: Total RNA was initially isolated from frozen whole plant tissue using the hot TRIzol reagent protocol for barley as described by Caldo et al (Plant Cell, 2004). The RNA was purified using Qiagen RNeasy spin columns, and adjusted to a final concentration of 1 ug/uL. Probe synthesis, labeling, and hybridization were performed at the Iowa State University GeneChip Core facility. ACKNOWLEDGEMENTS This work was supported by a grant (0227357) from the Plant Genome Research Program of the National Science Foundation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David O Niño-Liu. The equivalent experiment is OS3 at PLEXdb.] XOC - time: 2 hai (4-replications) XOC - time: 4 hai (4-replications) XOC - time: 8 hai (4-replications) XOC - time: 24 hai (4-replications) XOC - time: 96 hai (4-replications) XOO - time: 2 hai (4-replications) XOO - time: 4 hai (4-replications) XOO - time: 8 hai (4-replications) XOO - time: 24 hai (4-replications) XOO - time: 96 hai (4-replications) MOCK - time: 2 hai (4-replications) MOCK - time: 4 hai (4-replications) MOCK - time: 8 hai (4-replications) MOCK - time: 24 hai (4-replications) MOCK - time: 96 hai (4-replications)
2009-06-24 | E-GEOD-16793 | biostudies-arrayexpress
Project description:Time-course expression profiles of Bgh challenged barley cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1, were compared using the 22K Barley1 GeneChip. Planting, stage of seedlings, harvesting, and experimental design were part of a larger experiment described by Caldo et al. (2004). PLEXdb BB4. Experiment Design: C.I. 16151 (wildtype) and bcd1 (mutant) were planted in separate 20 x 30-cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest time points (0, 8, 16, 20, 24, and 32 hai). Seedlings grown to the 1st leaf stage with 2nd leaf unfolded were inoculated with a high density of fresh conidiospores (84 +/- 19 spores/mm2). Groups of flats were placed at 18C (8-hour darkness, 16-hour light) in separate controlled growth chambers corresponding to the Bgh isolates. Rows of plants were harvested at each assigned time points and snap frozen in liquid nitrogen. The entire experiment was repeated three times in a standard split-split-plot design with 72 experimental units (2 genotypes x 2 pathogen isolates x 6 time points x 3 replications). Treatment Description: The samples constituted pairwise combinations of the the cultivar C.I. 16151(containing the Mla6 resistance allele), and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1 with the two Bgh (Blumeria graminis f. sp. hordei) isolates, 5874 (AvrMla6, AvrMla1) and K1 (AvrMla13, AvrMla1). For each replication, individual genotypes were planted in separate 20 x 30 cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest times (0, 8, 16, 20, 24, and 32 hai). Seedlings were grown to the 2nd-leaf stage with 1st leaf unfolded, and inoculation was performed at 4 PM Central Standard Time by tipping the flats at 45oC and dusting the plants with a high density of fresh conidiospores [84 +/- 19 spores/mm2]. This procedure was repeated from the opposite angle to ensure that a high proportion of the cells are in contact with the fungus. This conidial density per unit leaf area routinely results in greater than 50% of epidermal cells that are successfully infected. Groups of flats were placed at 18oC (8 hours darkness, 16 hours light, 8 hours darkness) in separate controlled growth chambers corresponding to the Bgh isolate. Rows of plants were harvested at their assigned harvest times and flash-frozen in liquid nitrogen. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P Wise. The equivalent experiment is BB46 at PLEXdb.]
2009-02-25 | GSE14930 | GEO
Project description:Global gene expression analysis of grapevine cv. Pinot Noir berries during development and ripening. Time-course comparison of samples collected at three developmental stages (stages 33, 34 and 36 according to the modified E-L system, ref: Coombe BG, Aust J Grape Wine Res 1995, 1: 104-110) during three seasons (2003, 2005 and 2006). Data for each of the three seasons were normalized independently within each season, using gcRMA. PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Stefania Pilati. The equivalent experiment is VV11 at PLEXdb. year: 2003 - developmental stage: UD:0000034 33E-L (3-replications); year: 2003 - developmental stage: UD:0000035 34E-L (3-replications); year: 2003 - developmental stage: UD:0000037 36E-L (3-replications); year: 2005 - developmental stage: UD:0000034 33E-L (3-replications); year: 2005 - developmental stage: UD:0000035 34E-L (3-replications); year: 2005 - developmental stage: UD:0000037 36E-L (3-replications); year: 2006 - developmental stage: UD:0000034 33E-L (3-replications); year: 2006 - developmental stage: UD:0000035 34E-L (3-replications); year: 2006 - developmental stage: UD:0000037 36E-L (3-replications)
2011-08-26 | E-GEOD-31674 | biostudies-arrayexpress
Project description:Barley florets (cv. Morex) were treated with 2.0 microgram deoxynivalenol per floret via a 10 microliter solution or mock inoculated with water. Samples were collected at 1, 12, 24, and 48 hours after inoculation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Stephanie A. Gardiner. The equivalent experiment is BB62 at PLEXdb.] time: 1 hai - treated or untreated: Deoxynivalenol(3-replications); time: 1 hai - treated or untreated: Water(3-replications); time: 12 hai - treated or untreated: Deoxynivalenol(3-replications); time: 12 hai - treated or untreated: Water(3-replications); time: 24 hai - treated or untreated: Deoxynivalenol(3-replications); time: 24 hai - treated or untreated: Water(3-replications); time: 48 hai - treated or untreated: Deoxynivalenol(3-replications); time: 48 hai - treated or untreated: Water(3-replications)
2011-11-22 | E-GEOD-33405 | biostudies-arrayexpress
Project description:Barley cv. Morex inoculated with Fusarium graminearum (isolate Butte 86) or water (mock). Sampled at 24, 48, 72, 96 and 144 hours after treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Jayanand Boddu. The equivalent experiment is BB9 at PLEXdb.] time: 24 - Treated or untreated: WATER(5-replications); time: 24 - Treated or untreated: Fusarium(5-replications); time: 48 - Treated or untreated: WATER(4-replications); time: 48 - Treated or untreated: Fusarium(4-replications); time: 72 - Treated or untreated: WATER(5-replications); time: 72 - Treated or untreated: Fusarium(5-replications); time: 96 - Treated or untreated: WATER(4-replications); time: 96 - Treated or untreated: Fusarium(4-replications); time: 144 - Treated or untreated: WATER(4-replications); time: 144 - Treated or untreated: Fusarium(4-replications)
2011-11-22 | E-GEOD-33407 | biostudies-arrayexpress
Project description:Comparison of 2 P. s. tritici-inoculated and mock-inoculated isolines that differ for the putative Yr5 resistance gene over a time course (6, 12, 24, 48h) ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tristan Coram. The equivalent experiment is TA9 at PLEXdb.] Yr5 and yr5 isolines 6, 12, 24, and 24h after inoculation with P. s. tritici
2011-08-30 | E-GEOD-31753 | biostudies-arrayexpress
Project description:Comparison of 2 P. s. tritici-inoculated and mock-inoculated genotypes that differ for the Yr39 high-temperature adult-plant resistance phenotype over a time course (12, 24, 48h) ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tristan Coram. The equivalent experiment is TA11 at PLEXdb.] Yr39 and yr39 isolines 12, 24, and 48h after inoculation with P. s. tritici
2011-08-30 | E-GEOD-31756 | biostudies-arrayexpress
Project description:Experimental design: 1 genotype: PI- (resistant USDA Plant Introduction (PI462312) line containing SBR Rpp3 resistance gene) 3 treatments: Virulent soybean rust (Phakopsora pachyrhizi Tw80-2) challenge, avirulent soybean rust challenge (Hw94-1) & mock infection 3 replications 6 time points: 12, 24, 72, 144, 216 and 288 hours after inoculation TOTAL: 54 Affymetrix GeneChip(R) Soybean Genome Arrays Mock treatment: 0.01% Tween 20 Hawaii 94 treatment: 500,000 spores per ml in 0.01% Tween 20 Taiwan 80-2 treatment: 500,000 spores per ml in 0.01% Tween 20 ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Martijn van de Mortel (for Steve Whitham). The equivalent experiment is GM36 at PLEXdb.] pathogen isolates: Mock - time: 12 hai(3-replications); pathogen isolates: Mock - time: 24 hai(3-replications); pathogen isolates: Mock - time: 72 hai(3-replications); pathogen isolates: Mock - time: 144 hai(3-replications); pathogen isolates: Mock - time: 216 hai(3-replications); pathogen isolates: Mock - time: 288 hai(3-replications); pathogen isolates: Taiwan 80-2 (vir) - time: 12 hai(3-replications); pathogen isolates: Taiwan 80-2 (vir) - time: 24 hai(3-replications); pathogen isolates: Taiwan 80-2 (vir) - time: 72 hai(3-replications); pathogen isolates: Taiwan 80-2 (vir) - time: 144 hai(3-replications); pathogen isolates: Taiwan 80-2 (vir) - time: 216 hai(3-replications); pathogen isolates: Taiwan 80-2 (vir) - time: 288 hai(3-replications); pathogen isolates: Hawaii 94-1 (avir) - time: 12 hai(3-replications); pathogen isolates: Hawaii 94-1 (avir) - time: 24 hai(3-replications); pathogen isolates: Hawaii 94-1 (avir) - time: 72 hai(3-replications); pathogen isolates: Hawaii 94-1 (avir) - time: 144 hai(3-replications); pathogen isolates: Hawaii 94-1 (avir) - time: 216 hai(3-replications); pathogen isolates: Hawaii 94-1 (avir) - time: 288 hai(3-replications)
2011-11-28 | E-GEOD-29740 | biostudies-arrayexpress