Functional genomic analysis of cold acclimation in the genus Solanum
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum tuberosum
SUBMITTER: Jia Liu
PROVIDER: E-GEOD-8281 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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:Objectives: Our work focuses on the responses of Solanaceous plants to viruses that cause economically important diseases in tree fruits. Using mock inoculated leaf tissue as a reference, we plan to compare the gene expression profiles of Nicotiana Benthamiana plants infected with one of three viruses; Plum Pox Potyvirus (PPV), Tomato Ringspot Nepovirus (ToRSV), and Prunus Nectrotic Ringspot Nepovirus (PNRSV). Our goals are as follows: (1) Identify genes that are induced/repressed in response to individual viruses. (2) Identify genes that are induced/repressed in response to all 3 viruses. (3) Compare results to existing potato array data to look for similarities in responses to other pathogens. Experimental Design: Nicotiana benthamiana plants were inoculated with one of three viruses: PPV, ToRSV, or PNRSV. 3 week old plants were inoculated by rubbing virus infected plant sap onto leaves dusted with carborundum. Control plants were mock inoculated using sap from healthy plants. All plants were maintained in a growth chamber at 22C for 18 days. 8 plants were inoculated with each virus or mock inoculated. This experiment was repeated twice. 4 biological replicates derived from 2 virus infected plants from each replica experiment (4 plants) are to be used for hybridizations. RNA from all mock inoculated plants was similarly pooled to create 4 biological replicates. Each replicate control will serve as a universal reference sample that is to be hybridized pair wise with each of the three virus infected samples. RNA extraction: After 18 days, un-inoculated leaves displaying clear symptoms were harvested and immediately frozen in liquid N2. Total RNA was purified using Trizol according to TIGRs listed protocol. RNA was subsequently treated with Turbo DNA-free RNase (Ambion cat#1907). Finally, total RNA was further purified on RNeasy columns (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop spectrophotometer. Keywords: Reference design 23 hybs total
2007-09-01 | E-GEOD-8256 | 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 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: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:Potato leaves From Solanum tuberosum var. Kennebec will be wounded and oral secretions from 4th instar CPB will be isolated and added to the plants as described by Kruzmane et al (2002, Physiol. Plantarum 115:577-584). The leaf from the 6th node of the potato plant will be wounded or wounded and treated with oral secretions from CPB. Unwounded leaves from node 1-5 of the wounded and wounded plus oral secretions plants will be harvested as systemic material. The leaves will be harvested after 4 hrs and RNA will be isolated. 4 hrs was chosen because this represents a time when early and late induced genes should both be present. In addition, the leaf from the 6th node will be subjected to feeding by CPB that have been raised on potato leaves and starved for 16 hrs immediately prior to infestation. Insects will be allowed to feed for 1 hr and the leaves will be harvested after 3 additional hrs. An additional set of plants will be used to infest the leaf on the 6th node for 4 hrs. Leaves from the 6th node will be collected from uninfested plants after 4 hrs as a control. Three sets of 6-12 plants will be used for each sample. Keywords: Direct comparison 24 hybs total
2007-09-01 | E-GEOD-8255 | biostudies-arrayexpress
Project description:N. benthamiana plants were grown under 16 hour light/8 hour dark cycle in a plant growth room at 24°C for approximately six weeks before subjected to virus-induced gene silencing. Agrobacterium stain GV2260 (OD600=1.0) carrying silencing constructs were infiltrated into 2 fully expended leaves for inducing gene silencing. Samples were collected at 8, 10, 12, 14, and 16 days post Agro-inoculation (DPI) for RPN9-silenced plants and N-silenced control. For RPN8-silencing, samples were collected at 8, 10, and 12 DPI, and the empty vector treated plants were used as a control. Each sample was a pool of 6 silenced leaves collected from 3 individual plants. All the samples were in biological triplicates from 3 sets of independently silenced plants. Total RNA was extracted using Trizol and DNA was removed with DNase I treatment before cDNA synthesis. Keywords: Reference design 25 hybs total
2007-09-01 | E-GEOD-8259 | biostudies-arrayexpress
Project description:The quality of the pepper fruit is significantly influenced by the properties of its surface such as color, glossiness and texture. The fruit surface is composed of a peel containing several layers including the cuticle, epidermis and the hypodermis. The peel acts as a protective barrier against biotic and abiotic stresses and is the most critical tissue affecting water loss during post harvest storage. The peel is composed of an outer epidermis with thick waxy (lipid) cuticle and few cell layers of thick-walled hypodermal cells. Despite its agronomic importance and due to the fact that the majority of studies in fruits have been conducted using flesh and peel tissues as a whole, the biochemical and genetic bases of variation in peel properties are largely unknown. In this proposal we aim to determine peel-specific gene expression in pepper by micro array hybridizations of peel and flesh RNA extracted at different developmental stages of the fruit. The cultivar Celica (Capsicum annuum) that has a large blocky fruit will be used for studying gene expression in the peel and flesh. Plants were grown in the greenhouse during the spring of 2006. Fruits were harvested at three developmental stages: young- 10 days after anthesis, mature green- 30 days after anthesis and ripe red- 45 days after anthesis. These stages were chosen because each represents a distinct phase in fruit development. At each stage, a biological replicate consists of bulked tissue from 3 fruits from each of 3 plants (a total of 9 fruits). We have a total of 4 biological replicates. For each fruit, the peel was separated from the flesh by manual dissection using thin forceps and scalpel blade. Peel and flesh samples were immediately frozen in liquid nitrogen and stored at -800C until RNA extraction. Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep kit (Sigma). Keywords: Reference design 12 hybs total
2007-08-31 | E-GEOD-8282 | 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
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