Transcriptome analysis of dormant and sprouting bud tissue from potato (Solanum tuberosum L.)
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ABSTRACT: 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.
Project description:Differential analysis of the potato-Rhizoctonia solani AG3 interaction. Samples were extracted from R. solani inoculated potato sprouts at two time points. R. solani is one of the most prominent fungal pests of potato and therefore of great economic relevance.
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).
Project description:Transcriptome Analysis of the potato (genotype RH89-039-16). To aid annotation and address a series of biological questions, we generated RNA-Seq data from 16 RH libraries representing all major tissue types, developmental stages and responses to abiotic and biotic stresses.
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
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.
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. Data set 2
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.
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.
Project description:This SuperSeries is composed of the following subset Series: GSE24440: Sprouting transcriptome in cortical neurons: young GSE24441: Sprouting transcriptome in cortical neurons: aged Refer to individual Series
Project description:Selective isolation of total RNA and then whole genome expression analysis of sprouting neurons in peri-infarct cortex of the adult rat after stroke, compared to adjacent neurons that have not sprouted a new connection, in young adult (2 months) and aged (2 years) animals. Two different fluorescent conjugates of the tracer cholera toxin B (CTb), CTb-Alexa 488 and CTb-Alexa 647 (Molecular Probes), were sequentially injected into peri-infarct cortex at the sites of post-stroke axonal sprouting using a picospritzer pressure injection system. After survival periods of 7 days and 21 days (separate cohorts of animals), CTb-647 was injected exactly within CTb-488 injection site. Seven days after the second tracer injection, laser capture microdissection (LCM) was used to capture ~300 neurons for each cell type. Total RNA was isolated from captured cells and subjected to two rounds of T7 amplification.