'Bois noir' phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine
ABSTRACT: Transcriptional profiling of Vitis vinifera cv. Chardonnay healthy vs. Phytoplasma-infected plants (Bois noir phytoplasma). Study was conducted on grapevine plants grown in the same vineyard (leaf midribs were sampled). Keywords: disease state analysis Overall design: Two-condition experiment: healthy vs. infected plants/shoots. Biological replicates: 4 healthy, 4 infected. No replicates. Each sample was prepared as a pool of several samples (each sample was collected from a different shoots/plants) of the same disease status. Each sample was co-hybridized to a common reference cRNA (pool of all samples).
INSTRUMENT(S): INRA Vitis vinifera 14k oligo array version 2.0
Project description:Transcriptional profiling of Vitis vinifera cv. Chardonnay healthy vs. Phytoplasma-infected plants (Bois noir phytoplasma). Study was conducted on grapevine plants grown in the same vineyard (leaf midribs were sampled). Keywords: disease state analysis Two-condition experiment: healthy vs. infected plants/shoots. Biological replicates: 4 healthy, 4 infected. No replicates. Each sample was prepared as a pool of several samples (each sample was collected from a different shoots/plants) of the same disease status. Each sample was co-hybridized to a common reference cRNA (pool of all samples).
Project description:Transcriptional changes in field-grown plants of Vitis Vinifera cultivars 'Chardonnay' and 'Incrocio Manzoni' naturally infected with Bois Noir phytoplasma, compared to healthy samples. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Nicola Pecchioni. The equivalent experiment is VV14 at PLEXdb.] Overall design: genotype: Chardonnay - disease type: Bois Noir infected(3-replications); genotype: Chardonnay - disease type: Healthy(3-replications); genotype: Incrocio Manzoni - disease type: Bois Noir infected(2-replications); genotype: Incrocio Manzoni - disease type: Healthy(2-replications)
Project description:Transcriptional changes in field-grown plants of Vitis Vinifera cultivars 'Chardonnay' and 'Incrocio Manzoni' naturally infected with Bois Noir phytoplasma, compared to healthy samples. SUBMITTER_CITATION: Albertazzi G., Caffagni A., Milc J.A., Francia E., Roncaglia E., Ferrari F., Tagliafico E., Stefani E., Pecchioni N. (2009) Gene expression in grapevine cultivars in response to Bois Noir phytoplasma infection. Plant Science 176: 792-804. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Nicola Pecchioni. The equivalent experiment is VV14 at PLEXdb.] Experiment Overall Design: genotype: Chardonnay - disease type: Bois Noir infected(3-replications); genotype: Chardonnay - disease type: Healthy(3-replications); genotype: Incrocio Manzoni - disease type: Bois Noir infected(2-replications); genotype: Incrocio Manzoni - disease type: Healthy(2-replications)
Project description:Background: Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems. Results: Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity from the same experimental vineyard and ˚Brix-to-titratable acidity ratio. Identical sample aliquots were analyzed for transcripts by grapevine whole-genome oligonucleotide microarray and RNA-seq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies showed similar results across cultivars in all Omic datasets. Comparison of the processed data of genes mapped in RNA-seq and microarray data revealed a strong Pearson's correlation (0.80). The exclusion of probesets associated with genes with potential for cross-hybridization on the microarray improved the correlation to 0.93. The overall concordance of protein with transcript data was low with a Pearson's correlation of 0.27 and 0.24 for the RNA-seq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, which distinguished red from white grapes, yet provided detail of individual cultivar differences. Conclusions: The five Omic technologies were consistent in distinguishing cultivar variation. There was high concordance between transcriptomic technologies, but generally protein abundance did not correlate well with transcript abundance. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species. Vitis vinifera L. cv. Cabernet Sauvignon, Chardonnay, Merlot, Pinot Noir, Semillon berries were harvested from Nevada Agricultural Experiment Station Valley Road Vineyard, Reno, NV, USA. Whole-genome microarray analysis was used to assess the transcriptomic response of berry skins at harvest, approximately 24 °Brix (2011 vintage). Vines were grown under water deficit and well-watered conditions. At least two clusters harvested from non-adjacent vines were used for each of five experimental replicates.
Project description:Soil qualities and rootstocks are among the main factors that have been acknowledged to influence grape development as well as fruit and wine composition. Despite the role of the soil and rootstock in establishing a successful vineyard in terms of grape quality, almost no molecular evidence linking soil and rootstock properties to the gene expression have been reported. The transcriptome variation in response to different soils and rootstocks was investigated through microarray technology. The cv. Pinot Noir was grown on different soils: sand, turf and vineyard soil. The plants were grafted on the contrasting 101-14 and 1103 Paulsen rootstocks. The modulation of genes expression in response to different soils and rootstocks was evaluated considering their potential impact on primary (carbohydrate) and secondary (phenylpropanoid) metabolisms. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is VV41 at PLEXdb.] Overall design: treatment1: Turf - treatment2: 101-14 rootstock(3-replications); treatment1: Turf - treatment2: 1103-P rootstock(3-replications); treatment1: Sand - treatment2: 101-14 rootstock(3-replications); treatment1: Sand - treatment2: 1103-P rootstock(3-replications); treatment1: Asti soil - treatment2: 101-14 rootstock(3-replications); treatment1: Asti soil - treatment2: 1103-P rootstock(3-replications)
Project description:Several systemic diseases affect Vitis vinifera worldwide with important consequent management costs. Phytoplasma and viruses represent the most detrimental pathogens inducing symptoms and metabolic alterations that modify quantitatively the crop production. In the aim to investigate the plant/pathogen interactions, different grapevine samples, naturally affected (in mixed or single infections) by Stolbur phytoplasma (agent of Bois Noir disease) and viruses, in comparison to healthy and recovered controls, to identify the plant response to systemic pathogen infection. The preliminary results showed that expression levels of thousands of genes were altered in infected plants, involving various metabolic pathways. Total RNA was extracted from central leaf midribs and petioles from different V. vinifera cultivars in different conditions (healthy, infected and recovered). Microarray analyses were conducted using different biological replicates for treatment. The submitter of this dataset can no longer locate the raw data
Project description:Eutypa dieback is a vascular disease that may severely affect vineyards throughout the world. In the present work, microarrays analysis were made in order (i) to improve our knowledge of grapevine (Vitis vinifera cv. Cabernet-Sauvignon) responses to Eutypa lata, the causal agent of Eutypa dieback and (ii) to identify genes that may prevent symptom development. Qiagen/Operon grapevine microarrays bearing 14,500 probes were used to compare between three experimental conditions (in vitro, greenhouse, vineyard), foliar material of infected symptomatic plants (S+R+), infected asymptomatic plants (S-R+), and healthy plants (S-R-). These plants were characterized by symptoms notation after natural (vineyard) or experimental (in vitro, greenhouse) infection, re-isolation of the fungus located in the lignified parts, and the formal identification of E. lata mycelium by PCR. Semi-quantitative RT-PCR experiments were run to confirm the expression of some genes of interest in response to E. lata. Their expression profiles were also studied in response to other grapevine pathogens (E. necator, P. viticola, B. cinerea). (i) Five functional categories including metabolism, defense reactions, interaction with environment, transport and transcription were up-regulated in S+R+ plants compared to S-R- plants. These genes, which cannot prevent infection and symptom development, are not specific since they were also upregulated after infection by powdery mildew, downy mildew and black rot. (ii) Most of the genes that may prevent symptom development are associated with the light phase of photosynthesis. This finding is discussed in the context of previous data on the mode of action of eutypin and Eutypa secreted polypeptide fraction.
Project description:Berry skin total protein from Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay and Semillon. Treatments were control (well-watered) versus restricted irrigation (water-deficit). Samples were taken from harvest-ripe whole berry clusters following a seasonal water deficit in treatment vines. A comparative analysis between the cultivars and treatments was performed. Associated dataset identifiers: GSE72421, PRJNA268857.
Project description:12plex_vitis_2012_04 - cold stress - In temperate species, low temperatures adversely affect plant growth and development, constraining spatial expansion and productivity. Cold can trigger adaptive process or lead to alterations in physiological traits when stress intensity exceeds a certain threshold. Grapevine flower development and fruit set are influenced by cold nights in the vineyard. The correct formation of sexual organs and the success of reproduction are dependent upon sugar supply which can be affected by low temperatures. Many pathways of carbon metabolism may be affected by low temperatures however limited information is available about fluctuations in carbon metabolism in inflorescences. - Experiments were performed on inflorescence of Vitis vinifera L. cv. Pinot noir fruiting cuttings. First, inflorescences at female meiosis were collected the day of the experiment, then cuttings with the inflorescence were placed at 0°C for a 8 h night. Control plants were maintained in a growth chamber for 8 h at 19°C. Inflorescences were collected after 1 h and 8 h of cold. Additional time point was performed 2 h after the end of the cold night by placing the inflorescence at 25°C after the end of the cold night. Control plants were also collected. Overall design: 12 dye-swap - treated vs untreated comparison
Project description:Plant cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes involved in Cys biosynthesis and located in different subcellular compartments. These enzymes are made up of a complex variety of isoforms resulting in different subcellular Cys pools. To unravel the contribution of cytosolic Cys to plant metabolism, we characterized the knockout oas-a1.1 and osa-a1.2 mutants, deficient in the most abundant cytosolic OASTL isoform in Arabidposis thaliana. Total intracellular Cys and glutathione concentrations were reduced, and the glutathione redox state was shifted in favour of its oxidized form. Interestingly, the capability of the mutants to chelate heavy metals did not differ from that of the wild type, but the mutants have an enhanced sensitivity to Cd. With the aim of establishing the metabolic network most influenced by the cytosolic Cys pool, we used the ATH1 GeneChip for evaluation of differentially expressed genes in the oas-a1.1 mutant grown under non-stress conditions. The transcriptomic footprints of mutant plants had predicted functions associated with various physiological responses that are dependent on reactive oxygen species and suggested that the mutant was oxidatively stressed. To further elucidate the specific function(s) of the OAS-A1 isoform in the adaptation response to cadmium we extended the trasncriptome experiment to the wild type and oas-a1.1 mutant plants exposed to Cd. The comparison of transcriptomic profiles showed a higher proportion of genes with altered expression in the mutant than in the wild type, highlighting up-regulated genes identified as of the general oxidative stress response rather than metal-responsive genes. Overall design: Wild type and oas-a1.1 mutant plants were grown hydroponically and, after a two-week acclimation period, the roots and shoots were harvested separately. Total RNA was then prepared and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array. Three biological replicates were performed for each sample. We made two different comparisons to classify the differently expressed genes in the mutant plant: oas-a1.1 roots versus wild-type roots and oas-a1.1 shoots versus wild-type shoots. Hydroponically-grown wild type and oas-a1.1 mutant plants were further treated with 50µM CdCl2 and 18h-treated-roots and 24h-treated-shoots were harvested. Total RNA was then prepared and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array. Three biological replicates were performed for each sample. Different comparisons were performed as follows: 18h Cd-treated wild type roots versus untreated wild type roots; 24h Cd-treated wild type shoots versus untreated wild type shoots; 18h Cd-treated oas-a1.1 roots versus untreated oas-a1.1 roots; 24h Cd-treated oas-a1.1 shoots versus untreated oas-a1.1 shoots; 18h Cd-treated oas-a1.1 roots versus 18h Cd-treated wild type roots; 24h Cd-treated oas-a1.1 shoots versus 24h Cd-treated wild type shoots