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The effect of heat stress on the expression profile of potato tuber periderm genes

ABSTRACT: 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

ORGANISM(S): Solanum tuberosum

PROVIDER: GSE8283 | GEO | 2007/09/01

SECONDARY ACCESSION(S): PRJNA101243

REPOSITORIES: GEO

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The effect of heat stress on the expression profile of potato tuber periderm genes

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

Genetics of internal heat necrosis (IHN) in potato (Solanum tuberosum) via microarray analysis of gene expression

Project description:Potato plants of the cultivar 'Atlantic', which is IHN-susceptible, were grown in the greenhouse under a 16-hour photoperiod and 22 C day/18 C night temperatures for 46 days, after which they were transferred to growth chambers with a 14-hour photoperiod and normal (20 C day/18 C night) temperatures. At 71 DAP (days after planting), half of the plants were subjected to high (28 C day/20 C night) temperatures for the remainder of the study. Tubers from both normal and high temperature regimes were harvested at two-week intervals, beginning at 76 DAP and ending at 118 DAP. For each RNA sample, equal amounts of peeled tuber tissue (sampled from the center of the tuber using a cork borer) was pooled from three randomly chosen plants. RNA was extracted using a hot-phenol and high salt (2.4 M) CTAB-based extraction buffer. Keywords: Loop design

2008-02-03 | GSE10338 | GEO

Transcriptional profiling of S. tuberosum cv. Agria leaf and tuber samples after mild heat stress

Project description:The consequences on tuber transcriptome of a short heat period during tuber development was investigated in this study with special regard to the development of secondary tuber growth. Plants were grown for 47 days in the greenhouse under ambient conditions (21Â°C/ 19Â°C, 16h light, 8h dark) before application of mild heat stress temperatures (29Â°C/27Â°C) to one group of plants for 7 days and a stress release period on control temperature for 2 more weeks until harvest. Leaves were sampled before the heat period, at the end of the heat period and at harvest, two weeks after stress release. Tuber samples were taken at harvest. Tubers grown at normal temperatures and exhibiting a normal growth phenotype were used as control. Tubers subjected to the heat treatment and exhibiting a second-growth phenotype (chain tubers) were grouped into primary (attached to stolon from plant) and secondary tubers (attached to stolon from primary tuber).

2016-12-12 | E-MTAB-4805 | biostudies-arrayexpress

Studies of mechanisms in development of tuber necrosis due to PVY infection

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

The transcriptome of StRIK-silenced periderms suggests a role of this potato gene in RNA processing and stress

Project description:The periderm is a protective barrier crucial for land plants survival, but genetic factors involved in its regulation are fairly unknown. In a previous transcriptomic approach in the cork oak periderm (Quercus suber) we identified a RS2-INTERACTING KH PROTEIN (RIK) homolog, of unknown function and with a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. To gain insight into the function of RIK in periderm, the potato (Solanum tuberosum) tuber periderm was used as a model. The StRIK transcript profile showed ubiquitous accumulation in all vegetative tissues analyzed, including periderm and other suberized tissues such as root and wound-healing tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show evident effects in tuber periderm anatomy but unexpectedly unlike Wild type, the transgenic plants flowered. Nevertheless, the periderm of StRIK-RNAi lines did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis ortholog. Altogether those findings suggest that the potato StRIK might play roles in RNA maturation and stress response throughout diverse plant developmental processes such as flowering and periderm formation.

2021-06-21 | GSE153641 | GEO

Potato tuber gene expression during spraing formation in response to Tobacco rattle virus infection

Project description:Field-grown tubers of potato were examined for infection by Tobacco rattle virus and consequent production of corky ringspot or spraing symptoms. A microarray study identified tuber genes that are differentially expressed in response to TRV infection and to spraing production, showing that hypersensitive response (HR) pathways are activated in spraing-symptomatic tubers. This was confirmed by quantitative RT-PCR (Q-RT-PCR) of a selected group of HR-related genes and by histochemical staining of excised tuber tissue with spraing symptoms. Q-RT-PCR of TRV in different areas of the same tuber slice showed that non-symptomatic areas contained higher levels of virus than did spraing-symptomatic areas. This suggests that spraing formation is associated with an active plant defence that reduces the level of virus in the infected tuber. Expression of two plant defence genes was similarly upregulated in spraing-symptomatic tubers that were infected with another virus, Potato mop-top-virus, suggesting that spraing is a generalised response to virus infection of tubers.

2016-11-15 | E-MTAB-4670 | biostudies-arrayexpress

Potato tuber development

Project description:An in vivo and in vitro potato tuber development gene expression study. For in vitro tuber development expression analysis, RNA was isolated from in vitro microtubers at 2, 5, 10, 20 and 30 days following observed tuber induction. Two microtuber populations were used as biological replicates for the developmental stages. The RNA from all developmental stages was pooled to generate the reference samples. Ten microarray hybridizations were performed. For in vivo tuber development expression analysis, RNA was isolated from tubers growing in growth chamber conditions. Tissues were divided into six group, according to developmental size: stolon (no tuber formation), 1-5 mm tubers, 6-10 mm tubers, 11-15 mm tubers, 16-25 mm tubers, and 26-35 mm tubers. Two biological replicates of ten plants each were grown sequentially in the same growth chamber. The RNA from all developmental stages was pooled to generate the reference samples. Twelve microarray hybridizations were performed. For all experiments, the RNA was labeled using the indirect labeling method with random hexamer primers. Amplified cRNA was used as labeling template for stolons. Total RNA was used as labeling template in all other labeling reactions.

2010-07-01 | E-GEOD-5360 | biostudies-arrayexpress

Identification of TIMING OF CAB EXPRESSION 1 as an environmentally sensitive negative regulator of tuberisation in potato

Project description:For many potato cultivars, tuber yield is optimal at average day time temperatures in the range of 14-22 ⁰C. Further rises in ambient temperature can reduce or completely inhibit potato tuber production, with damaging consequences for both producer and consumer. In our previous work we observed that the steady-state expression level of the core circadian clock gene, TIMING OF CAB EXPRESSION 1 (TOC1), in potato tubers increased at moderately elevated temperature, whereas expression of the tuberisation signal gene StSP6A decreased along with tuber yield. In this study we investigated the potential roles of StTOC1 in linking environmental signalling and potato tuberisation. We show that transgenic lines with decreased expression of StTOC1 exhibit enhanced StSP6A transcript levels in tuberising stolons, and show changes in gene expression consistent with elevated tuber sink strength.

2019-09-02 | E-MTAB-7443 | biostudies-arrayexpress

Transcription profiling by array of the potato (Solanum tuberosum L.) plant response to moderately elevated temperature

Project description:Although significant work has been undertaken regarding the response of model and crop plants to heat shock during the acclimatory phase, few studies have examined the steady state response to the mild heat stress encountered in temperate agriculture. In the present work we therefore exposed tuberising potato plants to mildly elevated temperatures (30/20C), day/night) for up to five weeks and compared tuber yield, physiological and biochemical responses, and leaf and tuber metabolomes and transcriptomes with plants grown under optimal conditions (22/16C). Growth at elevated temperature reduced tuber yield despite an increase in net foliar photosynthesis. This was associated with major shifts in leaf and tuber metabolite profiles, a significant decrease in leaf glutathione redox state and decreased starch synthesis in tubers. Furthermore, growth at elevated temperature had a profound impact on leaf and tuber transcript expression with large numbers of transcripts displaying a rhythmic oscillation at the higher growth temperature. RT-PCR revealed perturbation in the expression of circadian clock transcripts including StSP6A, previously identified as a tuberisation signal. Our data indicate that potato plants grown at moderately elevated temperatures do not exhibit classic symptoms of abiotic stress but that tuber development responds via a diversity of biochemical and molecular signals. In this submission we are looking at gene expression changes with respect to both temperature and time, every 4h over a 24h period whereby diurnal changes may be apparent.

2013-08-01 | E-MTAB-1655 | biostudies-arrayexpress

Quantitative proteomic analysis of differentially expressed proteins in tubers of potato plants differing in resistance to Dickeya solani

Project description:To identify differently expressed proteins in tuber tissue of potato cultivars and diploid interspecific hybrids of Solanum, differing in resistance to Dickeya solani, comparative analysis was performed. Two highly resistant (Bea and Humalda) and three susceptible (Irys, Katahdin, Ulster Supreme) potato cultivars, as well as the highly resistant (DG 00-270) and the susceptible (DG 08-305) diploid clones, were studied. DG 00-270 exhibited higher resistance to D. solani than the cultivars Bea and Humalda. Proteins were extracted from wounded potato tubers inoculated with bacteria at an early symptomatic phase and from controls, i.e., intact tubers and wounded mock-inoculated tubers. Protein profiles were analyzed using nano-liquid chromatography coupled with tandem mass spectrometry (LC-MS-MS/MS).

2019-05-21 | PXD013009 | Pride

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