Transcriptional changes in dormant and non_dormant potato meristems
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum tuberosum
PROVIDER: GSE61690 | GEO | 2014/09/24
SECONDARY ACCESSION(S): PRJNA261838
REPOSITORIES: GEO
Similar Datasets
Project description:RNA was sequenced from meristems excised from dormant and non-dormant potato tubers harvested from four different harvest years. Expression based on mapped RNA-sequences was accomplished from excised meristems from fall harvested (dormant tubers) and the same harvested tubers were stored under standard commercial conditions until sprouting was present (non-dormant). The experiment was replicated for four different harvest years.
2014-09-24 | E-GEOD-61690 | biostudies-arrayexpress
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: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:Samples from dormant and sprouting bud tissue from potato tubers were taken to enable global transcriptome analysis of active meristematic tissue. Data was used in a co-expression analysis using microarray data of different experimental backgrounds.
2016-12-12 | E-MTAB-4806 | biostudies-arrayexpress
Project description:Commercial storage of potatoes often relies on the use of sprout inhibitors to prolong storage and reduce spoilage. The compound 1,4-dimethylnaphthalene (DMN) has seen increase application as a sprout inhibitor in the potato industry as older chemistries are being phased out. The mode of action of DMN is poorly understood as is the sensitivity of potato tissues to this new class of inhibitor. During storage potato tubers transition from a state of endo-dormant to eco-dormant and it is not known if the DMN response is consistent across this developmental transition. RNA-seq gene expression profiling was used to establish if stored potato tubers (Solanum tuberosum cv La Chipper) have differential sensitivity to DMN as tubers age. DMN was applied at three different times during storage; just after harvest when tubers are in endo-dormancy, midwinter at early eco-dormancy, and in spring during late eco-dormancy when sprouting was prevented via exposure to cold storage temperatures. Changes in gene expression were lowest during endo-dormancy while midwinter and spring treatments exhibited a greater and more diverse expression response. Functional analysis of differential gene expression demonstrated gene sets associated with DNA replication, cell division, and DNA methylation are suppressed after DMN treatment. However, gene sets associated with salicylic acid, jasmonic acid, abiotic and biotic stress responses are elevated by DMN only after endodormancy terminates. Gene clusters associated with pathogenesis related proteins PR-4 and PR-5 are also upregulated in response to DMN. These results indicate that DMN sensitivity changes as potato tubers age and transition from endo-dormant to eco-dormant in storage and the overall response is a shift in gene classes that regulate growth and response to stress.
2020-06-12 | GSE145578 | GEO
Project description:Commercial storage of potatoes often relies on the use of sprout inhibitors to prolong storage and reduce spoilage. The compound 1,4-dimethylnaphthalene (DMN) has seen increase application as a sprout inhibitor in the potato industry as older chemistries are being phased out. The mode of action of DMN is poorly understood as is the sensitivity of potato tissues to this new class of inhibitor. During storage potato tubers transition from a state of endo-dormant to eco-dormant and it is not known if the DMN response is consistent across this developmental transition. RNA-seq gene expression profiling was used to establish if stored potato tubers (Solanum tuberosum cv La Chipper) have differential sensitivity to DMN as tubers age. DMN was applied at three different times during storage; just after harvest when tubers are in endo-dormancy, midwinter at early eco-dormancy, and in spring during late eco-dormancy when sprouting was prevented via exposure to cold storage temperatures. Changes in gene expression were lowest during endo-dormancy while midwinter and spring treatments exhibited a greater and more diverse expression response. Functional analysis of differential gene expression demonstrated gene sets associated with DNA replication, cell division, and DNA methylation are suppressed after DMN treatment. However, gene sets associated with salicylic acid, jasmonic acid, abiotic and biotic stress responses are elevated by DMN only after endodormancy terminates. Gene clusters associated with pathogenesis related proteins PR-4 and PR-5 are also upregulated in response to DMN. These results indicate that DMN sensitivity changes as potato tubers age and transition from endo-dormant to eco-dormant in storage and the overall response is a shift in gene classes that regulate growth and response to stress.
2020-06-12 | GSE148635 | GEO
Project description:Wildtype potato plants (Solara) and transgenic plants overexpressing a codon-optimizied version of SP6A (SP6Acop) were grown for 2 months in a greenhouse (16h light, 21°C day/ 19°C night temperature). Tubers were harvested and stored at room temperature. After 19 days dormant buds were taken from tubers of WT and 3 different transgenic lines (#3, 7, 9) and analysed by microarray.
2019-04-08 | E-MTAB-7387 | 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
2007-09-01 | GSE8283 | GEO
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
2007-09-01 | GSE8274 | GEO