Transcriptional profiling of heat responses and genotype effects in potato crossbreeding lines and their parental strains
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum tuberosum
SUBMITTER: Sophia Sonnewald
PROVIDER: E-MTAB-11723 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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 (21°C/ 19°C, 16h light, 8h dark) before application of mild heat stress temperatures (29°C/27°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
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:Jerusalem artichoke (JA) tubers are an important bio-economy developing crop because of its invaluable bioproducts in both food and biofuel aspects. However, the molecular mechanism of its tuberization, and the differences among different cultivars have been little studied to date. Here, we conducted a comparative proteome profiling of the JA tubers of three different cultivars including PJA, DJA, and HJA, showing phenotypic characteristics. Tuber epidermal pigmentation and underground tuberization habit were different phenological characters in the three cultivars and inulin content was also a physiological character exceptionally DJA regardless of the similar level of total carbohydrate amount. We identified a total of 420 proteins in the tubers and out of 114 showed significantly modulated among the cultivars. GO classification of the DEPs revealed biosynthesis amino acid and carbohydrate metabolic enzymes were differentially expressed in the three cultivar tubers. Integrated physiological inulin content and the biosynthetic protein expression levels among the cultivars suggest that Sucrose:sucrose 1-fructosyltransferase (1-SST) prioritizes inulin biosynthesis rather than rate-limiting enzyme fructan:fructan 1-fructosyltransferases (1-FFT). Furthermore, we confirmed the relationship between transcript-protein expression levels was in discord within inulin biosynthesis enzymes 1-SST and 1-FFT with the terms in previous RT-qPCR results using the same tubers. Our data represent the first report that comparative proteome profiling in JA tubers among the different cultivars and provides the metabolic and molecular basis for understanding carbohydrate metabolism in storage tuber tissue.
2019-05-29 | PXD010835 | Pride
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:72 plants have been grown in 2 phytochambers for 30 days under control temperature (21°C/19°C) and short day conditions (8 hours light/16 hours darkness). After 30 days the plants were switched to long day conditions (16 hours light/8 hours darkness) and the temperature of one phytochamber was increased to 29°C/27° (heat chamber). Moreover,a heatplate was located in the control chamber and a coldplate was located in the heat chamber. 18 plants have been grown on the heatplate with a constant temperature of 29°C. 18 plants have been grown on the coldplate with a constant temperature of 22°C. After 9 days of the heat period leaf samples (end of night) were taken for micorarray analysis. After 10 days of heat, tuber samples were taken for microarray analysis.
2016-12-12 | E-MTAB-4808 | biostudies-arrayexpress
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: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
Project description:In plants, drought stress is a major growth limiting factor causing cell water loss through open stomata. In this study, guard cell-specific transcripts from drought-stressed Arabidopsis plants were analyzed and a down-regulation of β-amylase 1 (BAM1) was found. In previous studies, BAM1 was shown to be involved in stomatal starch degradation under ambient conditions. Impaired starch breakdown of bam1 mutant plants was accompanied by decreased stomatal opening. Here, we show that drought tolerance of bam1 mutant plants is improved as compared to wild type controls. Microarray-analysis of stomata-specific transcripts from bam1 mutant plants revealed a significant down-regulation of genes encoding aquaporins, auxin- and ethylene-responsive factors and cell-wall modifying enzymes. This expression pattern suggests that reduced water-uptake and limited cell wall extension are associated with the closed state of stomata of bam1 mutant plants. Together these data suggest that regulation of stomata-specific starch turnover is important for adapting stomata opening to environmental needs and its breeding manipulation may result in drought tolerant crop plants. Stress induced gene expression in Arabidopsis stomata was measured after exposure to single heat stress. Heat stress conditions were analyzed for both Col-0 plants and a T-DNA insertion line for β-amylase 1. Three days before harvesting heat stress was applied (32°C/28°C). Samples were taken by pooling the stomata of six to eight leaves per sample.
2015-06-30 | E-GEOD-66105 | biostudies-arrayexpress
Project description:There are numerous examples in plants, where certain organs or developmental stages are desiccation tolerant and can withstand extended periods of severe water loss. One prime example are seeds and pollen of many spermatophytes. However, in some plants, also vegetative organs can be desiccation tolerant as for example the tubers of yellow nutsedge (Cyperus esculentus) that also store larger amounts of lipids similar to seeds. Interestingly, the closest relative purple nutsedge (Cyperus rotundus) generates tubers that do not accumulate oil and are not desiccation tolerant. We generated nanoLC-MS/MS-based proteomes of yellow nutsedge in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to the tuber proteome of the closest relative purple nutsedge (Cyperus rotundus) and a previously published proteome of Arabidopsis seeds and seedlings indicates that indeed a seed-like proteome was found in yellow but not purple nutsedge. This was further supported by an analysis of the proteome of a lipid-droplet enriched fraction of yellow nutsedge, which also displayed seed-like characteristics. One reason for the differences between the two nutsedge species might be the expression of certain transcription factors homolog to ABSCISIC ACID INSENSITIVE3, WRINKLED1 and LEAFY COTYLEDON1 that drive gene expression in Arabidopsis seed embryos.
2022-10-31 | PXD031123 | Pride
Project description:Senescent sweetening results in the accumulation of reducing sugars in potato tubers following extended periods of storage at moderate temperatures, used to avoid the separate condition of cold-induced sweetening. Transcriptional profiling was performed using microarrays on potato genotypes with contrasting response; cultivars Arsenal and VR808, were considered to be senescent sweetening susceptible and resistant, respectively. Tubers were stored at 13 °C for two weeks prior to the application of chlorpropham (CIPC) to inhibit sprouting, and then transferred for long-term storage in the dark at 9 °C for different periods. Data indicated changes in carbohydrate metabolism were associated with the onset of senescent sweetening.
2021-07-01 | E-MTAB-10145 | biostudies-arrayexpress