Effect of SlNOR-like1 knockout on gene expression related to cuticle metabolism in tomato exocarp
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ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE227629 | GEO | 2023/03/22
REPOSITORIES: GEO
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Project description:Effect of SlNOR-like1 knockout on gene expression related to cuticle metabolism in tomato exocarp
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Project description:In order to find the specific promoter of tomato exocarp, we extracted RNA extraction from the red ripe exocarp, red ripe mesocarp, mature green exocarp, mature green exocarp and leaf cells, and then performed RNA seq to find the differential genes from the Transcriptome data. Our data provides gene expression data for three tissues of tomato during the red ripe and mature green stages, laying the foundation for the search for differential genes
2023-06-20 | GSE235023 | GEO
Project description:Mature green fruits of the tomato (Solanum lycopersicum L.) cultivar MicroTom were investigated (fruit developmental category II). After harvest, fruits were immediately utilized or stored in darkness at 25 C until further processing. After 0, 1, 2 or 4 days of storage stem scar tissues of tomato fruits were excised with a scalpel to a depth of approximately 2 mm, immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2151 | biostudies-arrayexpress
Project description:Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. Fruits were separated to the flesh and the peel. These two tissue types indeed showed remarkably different gene expression profiles. We also collected data from 4 different ripening stages (mature green, yellow, orange, and red) to detail the changes during ripening. By using this gene expression dataset, we calculated pair-wise Pearsonâs correlation coefficients, and performed network-based coexpression analysis. The analysis generated a number of coexpression modules, some of which showed an enrichment of genes associated with specific functional categories. This result will be useful in inferring functions of uncharacterized tomato genes, and in prioritizing genes for further experimental analysis. We used Affymetrix GeneChip Tomato genome Arrays to detail the global gene expression change using 24 different tomato tissue types (67 hybridizations). We collected gene expression data from 24 different tomato tissue types using 67 hybridizations. Root, hypocotyl, cotyledon, and leaf were sampled from 3-week-old or 5-weekâold plant of Solanum lycopersicum cultivar Micro-Tom. Fruit tissues were sampled from S. lycopersicum cultivars Micro-Tom, Anthocyanin fruit (Aft, LA1996), Line27859, and Momotaro 8 (Takii, Japan). From Micro-Tom fruit, the peel and the flesh were separately sampled from 4 different ripening stages: mature green (MG, approximately 30 day after anthesis), yellow (Y, approximately 35 days after anthesis), orange (O, approximately 38-40 days after anthesis), and red (R, approximately 45-48 days after anthesis). From fruits of Aft and Line27859, the peel and the flesh were sampled at mature green (MG, approximately 40 days after anthesis) and red (R, approximately 50-55 days after anthesis) stages. From Momotaro 8, the peel and the flesh were sampled at red (R, 50- approximately 50-55 days after anthesis) stages. For each tissue type, 2-4 biological replicates were made in RNA preparation.
2010-02-21 | E-GEOD-19326 | biostudies-arrayexpress
Project description:By using parallel analysis of RNA ends (PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development we identified a large number of target genes of miRNAs. PARE libraries were produced, one each, for tomato fruits at 5 days after pollination, mature green fruit, Breaker fruit, and 7 days after Breaker stge fruits
2013-04-05 | E-GEOD-42661 | biostudies-arrayexpress
Project description:Mature green fruits of the tomato (Solanum lycopersicum L.) cultivar MicroTom were investigated (fruit developmental category II). For removal of the epicuticular wax layer a thin film of 1 g ml-1 aqueous gum arabic (Roth, Karlsruhe, Germany) as a fixative was applied to the fruit surface. After 1 h the dried polymer including the outermost epicuticular waxes was mechanically removed. This procedure was repeated once. During this experiment the tomato fruits remained on the tomato plant. Untreated (0 days) and gum arabic stripped tomato fruits harvested 2 days after treatment were compared. Samples contained exclusively the fruit peel, which was removed with a scalpel to a depth of approximately 1 mm. After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2163 | biostudies-arrayexpress
Project description:Mature green fruits of the tomato (Solanum lycopersicum L.) cultivar John Baer and Pearson were investigated (fruit developmental category II). John Baer wild type, John Baer LA0063 and Pearson wild type, Pearson 2-303 fruits were used. Tomato mutant plants LA0063 and 2-303 were positional sterile (PS mutants). Samples contained exclusively the fruit peel, which was removed with a scalpel to a depth of approximately 1 mm. After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2164 | biostudies-arrayexpress
Project description:Fruits and leaves of the tomato (Solanum lycopersicum L.) cultivar MicroTom were investigated. MicroTom wild type and lecer6 mutant with a deficiency in a fatty acid beta-ketoacyl-CoA synthase (LeCER6) were used. The samples were composed of mature green, whole fruits with seeds being removed (fruit developmental category II). The locular tissue (gel) that surrounded the seeds and fills the locular cavity were detached. Otherwise, the samples contained fully developed leaves. After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2162 | biostudies-arrayexpress
Project description:Anthocyanins are high value plant antioxidants which are not present in the fruits of cultivated tomato. However, both the dominant gene Anthocyanin fruit (Aft) and the recessive gene atroviolacea (atv), introgressed into domesticated tomato from two different wild Solanum species, stimulate a limited anthocyanin pigmentation. Surprisingly, double mutant Aft/Aft atv/atv tomatoes are characterised by the presence of anthocyanins in the fruit peel, resulting in intensely purple pigmented fruit. We carried out a transcript profiling analysis using GeneChip® Tomato Genome Arrays, in order to identify differentially expressed genes when comparing wild type, Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits. The expression pattern of several genes involved in the anthocyanin pathway was analyzed in detail. Among the fruit peel-associated differentially expressed transcripts, genes involved in phenylpropanoid pathway, cell wall composition, biotic and abiotic stress responses, sugar and hormone metabolism were overrepresented in Aft/Aft atv/atv. Transcriptomic analysis thus revealed that the activation of anthocyanin synthesis in tomato fruit was accompanied by a complex remodulation of gene expression, likely affecting important agronomic and merceological traits. Wild type (Cv. Ailsa Craig, accession number LA2838A), Aft/Aft (accession number LA1996), atv/atv (accession number LA0797) and double mutant (Aft/Aft atv/atv) were grown during the winter season in a controlled heated greenhouse. Fruits were collected at mature green, turning red and red stages of development. The transcriptional profile in Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits when compared to the wild type was analyzed using the GeneChip® Tomato Genome Array.
2010-07-30 | E-GEOD-19792 | biostudies-arrayexpress
Project description:To understand the AtJUB1 mediated regulation of tomato fruit development. To test how the NAC transcription factor JUNGBRUNNEN1 from Arabidopsis thaliana (AtJUB1, identical to ANAC042; At2g43000) affects the development of tomato fruits, AtJUB1-GFP was expressed in transgenic tomato plants under the control of the CaMV 35S promoter. AtJUB1-GFP fusion protein was previously shown to encode a functionally active transcription factor in Arabidopsis (Wu et al., 2012). We then performed gene expression profiling of fruits from AtJUB1-GFP lines (AtJUB1-OX plants) and non-modified wild-type (WT) plants. Fruits at two developmental stages, namely mature green (MG) and Breaker+7 days (B+7), were analysed. To this end, the pericarp was separated from the rest of the fruits and quickly frozen in liquid nitrogen for subsequent RNA extraction. Gene expression analysis was performed using GeneChip Tomato Genome Arrays (Affymetrix). Probe preparation and microarray hybridizations were performed by ATLAS Biolabs (Berlin, Germany).
2017-03-31 | GSE87507 | GEO