Effect of TIF on gene expression under inductive and non-inductive photoperiods
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum tuberosum
SUBMITTER: Jia Liu
PROVIDER: E-GEOD-8280 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The primary objective of this project is to determine the physiological and developmental differences between photoperiod and root induced tuberization responses in potato using genomic techniques. These experiments will establish baseline genomic and proteomic response associated with a partially characterized root-produced compound (TIF) that either substitutes for, or over-rides, the primary leaf perceived photoperiod induction signal in potato. The proposed work will answer the following questions. Are photoperiod and root induced tuberization responses the same? Do photoperiod and root induced tuberization trigger the same developmental processes in the stolon? How are photoperiod and root induced signals expressed in the genome of the leaf, stolon and roots? The data from the proposed experiments will prove invaluable in identifying key pathways in specific tissues to target in subsequent experiments in order to determine identify of, and establish the mode of action of the TIF compound. Keywords: Direct comparison
2007-09-01 | GSE8280 | GEO
Project description:The response to moderate and heavy drought of two Solanum tuberosum ssp. Andigena varieties, Sullu (NP 03.03) and SA 2563 (NP 03.01), planted in rain- and soil water protected fields in the Peruvian highlands are compared. Previous experiments indicate that Sullu has a greater capacity for yield maintenance under drought than SA 2563. Both clones have similar morphological properties, vegetative periods and rooting depths, so it can be assumed that the cause for increased drought tolerance of clone NP 03.03 is rather due to physiological or biochemical mechanisms, than to drought escape by deep rooting or earliness. Sullu and SA 2563 were planted in a random block design with 5 plants per bloc and 7 repetitions per treatment. Treatments: (1) drought stress, (2) irrigated control The plants were drip-irrigated in both treatments until tuberization (until day 84 after planting). Subsequently, the irrigation was stopped in the drought field, but continued in the control field. The soil moisture content in the control field was kept near field capacity. Planting date: October 05 2004 Start of drought treatment (during tuberization, 84 days after planting): December 28 2004 First sampling (soil water potential: -0.3 mPa 114 days after planting): January 27 2005 Second sampling (soil water potential –0.6 MPa, 134 days after planting): February 15 2005 Harvest: March 19 2005 (165 days after planting) The experimental design includes gene expression analysis in leaves, roots and stolons at two time points, when soil water potential reaches -0.3 and –0.6 MPa. Gene expression changes will be set in relation with physiological and agronomical data obtained in the same experiment. Keywords: Direct comparison 19 hybs total
2007-09-01 | E-GEOD-8243 | biostudies-arrayexpress
Project description:Blackspot bruising is the tuber discoloration resulting from mechanical damage in susceptible crops and is a major quality and environmental problem for the potato industry. The present study is aimed at identifying differences in gene expression which are correlated with the development of bruise susceptibility or resistance in tubers. This may produce markers or diagnostic tests for use in predicting enhanced bruise susceptibility in field grown potato crops. Different potato cultivars were grown in field plots at ADAS Gleadthorpe, Nottinghamshire, UK during three growing seasons – 2003, 2004 and 2005. Random samples of tubers (8) were harvested by hand and cores excised from the subdermal tissues of the stolon end of the tubers and immediately frozen and stored in liquid nitrogen for RNA isolations. The remainder of the crops were stored at 4oC for bruise susceptibility testing - samples of tubers (30) from each crop were impacted and incubated for 48h at 30oC. Bruise susceptibility was scored, according to the intensity of pigmentation and the volume of tuber tissue affected, on a scale of 0 (very resistant) – 10 (very susceptible). Crops representing 'very susceptible', 'susceptible', 'moderate' and 'resistant' to bruising, were selected for RNA isolation. Total RNA’s were isolated from frozen cores by the TIGR hot phenol extraction method, precipitated by LiCl and treated with DNase. RNA concentrations were adjusted to ~2ug/ul and analysed on 1% TBE gels after formamide treatment. Any RNA’s which were not pure enough or showed degradation were discarded. Total RNA’s were pooled and 25ul samples aliquotted according to the required hybridisations indicated in the Excel spreadsheet and the on-line information form. Keywords: Direct comparison 32 hybs total
2007-09-01 | E-GEOD-8274 | biostudies-arrayexpress
Project description:Transgenic tobacco (Nicotiana tabacum) expressing Caenorhabditis elegans cell death genes, Ced4 and Ced3, show evidence suggesting such expressions protect the plants from infestation by the plant parasitic nematode Meloidogyne incognita. Although positive results have been correlated with the gene expressions (data in preparation for publication; a draft of the publication can be provided upon request), the mechanism by which the nematode protection is manifested is not clearly understood. One possibility is that the C. elegans cell death proteins produced by the transgenic plants are being ingested and incorporated into the nematode’s own cell death pathway, leading to their demise. Alternatively, it is also possible that expression of the C. elegans cell death genes promotes the endogenous resistance genes of the plant, leading to nematode resistance. We want to test the later hypothesis by conducting a reference design microarray experiment to establish the expression profile of Ced3, and Ced4 homozygous plants and Ced3xCed4 double heterozygous plants in comparison with wild-type tobacco plants. If the hypothesis is correct, we expect to detect increased expression of pathogenicity-related genes in the transgenic plants. Furthermore, characterization of the expression profiles in these transgenic plants will provide us directionality for our future research on the elucidation of this resistance mechanism. Keywords: Reference design 27 hybs total
2007-09-01 | E-GEOD-8277 | biostudies-arrayexpress
Project description:The goal of this study was to calculate the degree of substantial equivalence between a GM potato line modified for late blight resistance and corresponding non-GM controls in the presence/absence of P. infestans inoculation. The GM phenotype was conferred through the introduction of the Rb gene which has been previously cloned from Solanum bulbocastanum (Song et al. 2003). The resulting GM phenotype was characterised by the expression of strong, partial resistance to P. infestans. By obtaining an expression profile from a GM and non-GM population before and after exposure to P. infestans, this effectively provides for the completion of two risk assessments: impact on the potato transcriptome of plus/minus genetic modification; before and after exposure to the pathogen. For each biological replicate, individuals from three separate GM lines (A, B, C) and three separate non-GM lines (D, E, F) were randomly sorted and cultivated for analysis. Each GM line contained an independent, single transgene insertion, which was verified through Southern Blot analysis. One day prior to pathogen exposure, the 4-week-old potato plants were transferred into a growth chamber with a 16-h light period, 90% relative humidity at a temperature of 15C. Plants were randomly selected and 14 individuals/line were inoculated with a field isolate of P. infestans. An additional 14 plants/line were sprayed with water. Inoculations were made with a sporangial suspension of 20,000/mL and plants were sprayed until run-off. Twenty-four hours post-inoculation, leaf tissue was collected from 9 plants per treatment, flash frozen in liquid nitrogen and pooled. Total leaf RNA was extracted using Trizol and the whole experiment was repeated three times (three biological replicates). Keywords: Direct comparison 19 hybs total
2007-09-01 | E-GEOD-8258 | biostudies-arrayexpress
Project description:Whole plants of a clone of S. cajamarquence and a clone of S. tuberosum were spray inoculated with Phytophthora infestans sporangial suspension 3000 sporangias/ml until run off. Two isolates were used: PE84006 (race 0) and POX067 (avr 8, 9). Leaves in the middle part of the plants were collected at 72 h and 96 h after inoculation. Leaves of untreated plants were collected as control treatment. Keywords: Direct comparison 24 hybs total
2007-09-01 | E-GEOD-8250 | biostudies-arrayexpress
Project description:Floral Nectaries Many plants secrete a rich floral nectar to entice visitation by insect and avian pollinators. In turn, these pollinators transfer pollen between flowers increasing plant fecundity. The nectary is the floral organ that secretes nectar into the base of the flower. The size and abundance of the ornamental tobacco nectaries (Nicotiana sp.) will permit us to isolate up to several grams of nectaries at each stage to obtain the necessary amounts of RNA for probe preparation. Our primary goals to understand the biochemistry the nectary, so that we can manipulate nectary function to increase pollinator visitation. We have previously conducted an EST study and have identified 13596 cDNAs from three different stages of nectary development (Stage 6, immature, presecretory nectaries; Stage 12, mature nectaries at floral anthesis; and nectaries, 44 hours after fertilization. In our efforts to evaluate the transcriptional program for the Nicotiana nectary we are proposing to evaluate nectary mRNAs by hybridization with the potato microarrays. We have preliminary evidence that wholesale transcriptional reprogramming (60% of the transcriptome) occurs during nectary maturation and again following fertilization. Our goal is to understand these processes at a biochemical level so that we can begin manipulating nectary function to improve nectar quality and quantity thereby increasing the attractiveness of flowers to insect pollinators. Such improvements have the potential to result in increases in insect visitation, seedset, and ultimately yield for insect pollinated crops. We are also making significant efforts to understand the restructuring of the nectary during its lifecycle. Many changes occur during nectary development and the observed transcriptional reprogramming makes sense the when these many changes are accounted for. Keywords: Loop design 30 hybs total
2007-09-01 | E-GEOD-8245 | biostudies-arrayexpress
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2007-09-01 | E-GEOD-8255 | biostudies-arrayexpress
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2007-09-01 | E-GEOD-8256 | biostudies-arrayexpress
Project description:Treatment of the seeds. The Solanum lycopersicum var. Money Maker wild type (MM) and fri1-1 mutant seeds were incubated on distilled-water saturated cotton wool in clear plastic boxes wrapped in black plastic sheets in darkness during 3 hours at 25°C. After that, the seeds were treated as follows: a) 24 hr of continuous irradiation with far-red light, FRc; b) 24 hr of FRc follow by a 10 min red light pulse (Rp), FRc+Rp; and c) complete darkness. After the light treatments, the seeds were incubated in darkness (25°C) until sampling. Red light (35umol/m2sec) was provided by 40W fluorescent lamps (Phillips 40/15) in combination with a red translucid acrylic. FRc light (100 umol/m2sec) was provided by a set of 150W incandescent internal reflector lamps (Phillips) in combination with a red acetate filter, six 2mm thick blue acrylic filters Paolini 2031 and 10cm water filter. Total RNA isolation. The seeds were grinded in liquid nitrogen and extracted with two volumes of extraction buffer (1% SDS, 6% p-aminosalycilic acid, 1% NaCl, 6% water-saturated phenol and 2% 2-mercaptoethanol) and two volumes of acid phenol:chloroform solution. The aqueous phase was sequentially extracted with one volume of acid phenol:chloroform solution and one volume of chloroform. The nucleic acids in the aqueous phase were precipitated with 0.15 volumes of 3M NaCl and 2.5 volumes of 100% ethanol at –80°C for 20 minutes. After centrifugation, the pellet was washed with 70% ethanol, resuspended in RNase-free water and precipitated with one volume of 4M LiCl over night at 4°C. The LiCl was removed after centrifugation and the pellet was rinsed with 2M LiCl and resuspended in RNase-free water. The total RNA was treated with RNase-free DNase (Promega) and cleaned up with mini spin columns (RNeasy Plant Mini Kit, Qiagen). The mRNA was amplificated with Message Amp II aRNA Amplification Kit (Ambion) and concentrated by vacumm centrifugation. Keywords: Direct comparison 21 hybs total
2007-09-01 | E-GEOD-8246 | biostudies-arrayexpress