Global transcriptome comparison reveals stress adaptation between Russet Norkotah and its Clonal Selection, TXNS278
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum tuberosum
PROVIDER: GSE87857 | GEO | 2018/02/08
REPOSITORIES: GEO
Similar Datasets
Project description:Dormant/sprouting bud or eye tissue was collected from field grown Russet Burbank tubers using melon baler. These tubers after harvest washed with 5% Clorox, dried and stored at room temperature and allowed to sprout. Tissue samples were collected from dormant and sprouting eye at different physiological stages (based on length of the sprout) of sprouting. RNA was extracted using a hot phenol method and treated with DNAse. RNA extracted from different stages of sprouting potato tubers was used as query samples. RNA collected from non-sprouting eyes of potato tubers was used as reference samples Information on RNA samples. Plant species: S. tuberosum CV Russet Burbank. Tissue harvested: Tissue was harvested from the dormant/sprouting bud/eye using ½ inch melon baler. Time points: Dormant eyes –Stage 1 Initiating buds/sprouts – Stage 2 Sprouts (1/8 inch) – Stage 3 Sprouts (1/4 inch) – Stage 4 Sprout callus (1/4 inch) – Stage 5 Sprouts (1/2 inch) – Stage 6. Growth conditions: Field grown. Replicate information: Biological replicates; A, B and C Keywords: Direct comparison
2008-02-13 | GSE10484 | GEO
Project description:Russet Nugget and the corresponding smooth skin mutant tubers harvested from disease and healthy filed plots. Tubers were washed with 10% Clorox and dried before harvesting tissue. Cortex and peel tissue was collected from healthy and infected regions of the mutant. Healthy peel and cortex tissue was collected from Russet Nugget (wild-type) potato tuber and snap-frozen in liquid nitrogen and stored at -80 °C. RNA was extracted from frozen tissues using a hot phenol method in triplicate from the different sets of tuber tissue. Extracted RNA was purified by Qiagen kits after treatment with DNAse. In all of these experiments RNA from Russet Nugget peel and cortex tissue will be used as reference samples where as mutant tissue will be used as query samples. Keywords: Direct comparison
2008-02-13 | GSE10485 | GEO
Project description:The suppression of sprout growth is critical for the long-term storage of potato tubers. 1,4-dimethylenapthlene (DMN) is a new class of sprout control agent but the metabolic mode of action for this compound has yet to be elucidated. Changes in transcriptional profiles of meristems isolated from potato tubers treated with the DMN were investigated using an Agilent 44K 60-mer-oligo microarray. RNA was isolated from nondormant Russet Burbank meristems isolated from tubers treated with DMN for three days or activated charcoal as a control. RNA was used to develop probes that were hybridized against a microarray developed by the Potato Oligo Chip Initiative (POCI). Analysis of the array data was conducted in two stages: total array data was examined using a linear model and the software limma and pathway analysis was conducted by linking the potato sequences to the Arabidopsis thaliana. DMN elicited a change in a number of transcripts associated with cold responses, water regulation, salt stress and osmotic adjustment. Additionally, repression of auxin signaling and transport were observed in DMN-treated tubers, and connections between DMN treatment and repression of FT through mi156 regulation were indicated. DMN also resulted in a repression of cyclin or cyclin-like transcripts. DMN also resulted in a 50% decrease in thymidine incorporation suggesting a repression of the S-phase of the cell cycle. QT-PCR analysis demonstrated that DMN increased transcripts for the cell cycle inhibitors KRP1 and KRP2. We conclude the DMN results in alteration of genes associated with cold responses and water regulation and maintenance of a G1/S-phase block possibly through the induction of the cell cycle inhibitors KRP1 andKRP2. Twelve samples, four treatments, three biological replicates Non dormant meristems as control (Control-rep), meristems isolated from tubers treated with water for three days (Control3Days-rep), meristems treated with DMN for three days (DMN3Days-rep), meristems treated with DMN for three days and then vented to the air for two days (DMN3Days-2Out-rep).
2012-01-01 | E-GEOD-31825 | biostudies-arrayexpress
Project description:The suppression of sprout growth is critical for the long-term storage of potato tubers. 1,4-dimethylenapthlene (DMN) is a new class of sprout control agent but the metabolic mode of action for this compound has yet to be elucidated. Changes in transcriptional profiles of meristems isolated from potato tubers treated with the DMN were investigated using an Agilent 44K 60-mer-oligo microarray. RNA was isolated from nondormant Russet Burbank meristems isolated from tubers treated with DMN for three days or activated charcoal as a control. RNA was used to develop probes that were hybridized against a microarray developed by the Potato Oligo Chip Initiative (POCI). Analysis of the array data was conducted in two stages: total array data was examined using a linear model and the software limma and pathway analysis was conducted by linking the potato sequences to the Arabidopsis thaliana. DMN elicited a change in a number of transcripts associated with cold responses, water regulation, salt stress and osmotic adjustment. Additionally, repression of auxin signaling and transport were observed in DMN-treated tubers, and connections between DMN treatment and repression of FT through mi156 regulation were indicated. DMN also resulted in a repression of cyclin or cyclin-like transcripts. DMN also resulted in a 50% decrease in thymidine incorporation suggesting a repression of the S-phase of the cell cycle. QT-PCR analysis demonstrated that DMN increased transcripts for the cell cycle inhibitors KRP1 and KRP2. We conclude the DMN results in alteration of genes associated with cold responses and water regulation and maintenance of a G1/S-phase block possibly through the induction of the cell cycle inhibitors KRP1 andKRP2. Twelve samples, four treatments, three biological replicates
2012-01-01 | GSE31825 | GEO
Project description:This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers. Keywords: Reference design
2008-02-13 | GSE10483 | GEO
Project description:We prepared QTL map of tuber starch content in potato diploid population. Then, we examined expression level of enzyme ADP-glucose pyrophosphorylase (AGPase) taking part in starch biosynthesis (marker AGPaseS-a). Based on starch content and AGPaseS-a expression, we constructed four bulks prepared from RNA isolated from tubers of F1 individuals H1 and H2 consisted of high TSC genotypes, bulks L1 and L2 were made of low TSC genotypes. Plants in bulks H1 and L1 strongly expressed AGPaseS-a, whereas those in bulks H2 and L2 exhibited low levels. Then we used RNA-seq technology for selection of genes displaying differential expression between RNA pools. For selected candidate genes we mapped expression QTL (e-QTL) and found eQTL of eAGPaseS-a and ePGRCRURSE5, were close to the corresponding loci of (AGPaseS-a) and the 12S globulin cruciferin gene (PGCRURSE5). We concluded that the cruciferin gene PGRCRURSE5 is a novel candidate involved in the regulation of starch content in potato tubers and suggests that cruciferin may be a novel PTST protein in potato tubers.
2020-06-24 | GSE153031 | GEO
Project description:The goal of the current research is to identify factors that involved with heat induced russeting of the potato tuber skin. Potato plants of the variety Desirèe were grown in pots filled with perlite, in a greenhouse under natural winter conditions (Nov 2005- Jan 2006, average temperatures range of 10-18°C). For the exposure of tubers to heat stress (H) hot water (33-35°C) was circulated in tubes lined at the internal side of the pots. The heat was applied one week before tubers harvest. Tubers were harvested at two time points: 8 weeks post sprouting and a week post mechanical vine killing. The skin (S) of young tubers was peeled by hand, as the remaining phelloderm (PH) layers, the periderm of young tubers (P) and the periderm of mature tubers (ST) were peeled using a scalpel blade. Leaves (L) and tuber flesh (TF) samples were collected as well. For each RNA sample 4 biological replicates were prepared; each one represents pooled tissues from 4-6 plants grown at different location in the greenhouse. RNA was extracted using CTAB protocol, and was further purified by RNeasy Mini Kit (Qiagen) using the On-Column DNase Digestion protocol. Keywords: Loop design
2007-09-01 | GSE8283 | GEO
Project description:Effects of different parameters on the transcriptome in potato tuber: effect of infection with potato virus Y (PVY) on potato tubers, effects of two different storage times of potato tubers compared to no storage, effect of different storage temperature on potato tubers, effect of tuber necrosis development, effects of interactions between the above parameters. Lists of interaction factors and the differentially-expressed genes associated with each factor are provided as a series of Additional Files to this submission (see http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1071).
2020-08-09 | E-MTAB-1071 | biostudies-arrayexpress
Project description:The goal of the current research is to identify factors that involved with heat induced russeting of the potato tuber skin. Potato plants of the variety Desirèe were grown in pots filled with perlite, in a greenhouse under natural winter conditions (Nov 2005- Jan 2006, average temperatures range of 10-18°C). For the exposure of tubers to heat stress (H) hot water (33-35°C) was circulated in tubes lined at the internal side of the pots. The heat was applied one week before tubers harvest. Tubers were harvested at two time points: 8 weeks post sprouting and a week post mechanical vine killing. The skin (S) of young tubers was peeled by hand, as the remaining phelloderm (PH) layers, the periderm of young tubers (P) and the periderm of mature tubers (ST) were peeled using a scalpel blade. Leaves (L) and tuber flesh (TF) samples were collected as well. For each RNA sample 4 biological replicates were prepared; each one represents pooled tissues from 4-6 plants grown at different location in the greenhouse. RNA was extracted using CTAB protocol, and was further purified by RNeasy Mini Kit (Qiagen) using the On-Column DNase Digestion protocol. Keywords: Loop design 28 hybs total
2007-08-31 | E-GEOD-8283 | biostudies-arrayexpress
Project description:To extend our understanding of systemic necrosis in susceptible potato tubers infected with the necrotic strain of Potato virus Y (PVYNTN) gene expression was compared between healthy and infected non-necrotic and necrotic (both non-necrotic and necrotic tissue) potato tubers.
2018-05-16 | E-MTAB-5776 | biostudies-arrayexpress