Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription changes at sub-optimal root temperature in different grafting combinations of tomato rootstocks and scions

ABSTRACT: The commercial tomato cultivar âKommeetâ was grafted either onto the tomato cultivar âMoneymakerâ (sub-optimal temperature sensitive) or onto the line accession âLA 1777â of the wild tomato species S. habrochaites (sub-optimal temperature tolerant) in a heated glasshouse. Grafted tomato plants were grown in a nutrient film technique system with re-circulating nutrient solution resulting in different root temperature (T), which was either optimal (day and night 25Â±0.6Â°C) or sub-optimal (day and night 15Â±0.4Â°C) while the air T was optimal (day and night 25Â±0.6Â°C) throughout the experimental procedure. After 30 days of differential treatment, differences in growth, physiology, and global gene expression in roots and leaves of all grafting and T combinations were investigated.

ORGANISM(S): Solanum habrochaites

SUBMITTER: Rita Maria Zrenner

PROVIDER: E-MTAB-4986 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparative proteomic analysis for revealing the advantage mechanisms of Salt-tolerant tomato (Solanum lycopersicum)

Project description:Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to deciphered the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found that there is an over-abundant proteins relevant to Nitrate and amino acids metabolisms in the Salt-tolerant cultivars. The significant increase in expression of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. And the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including Sterol side chain reductase, gamma aminobutyrate transaminase and Starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future

2022-02-08 | PXD029130 | Pride

Transcriptional characterization of tomato roots response to iron deficiency

Project description:Iron (Fe) deficiency is a yield-limiting factor for a variety of field crops across the world and generally results from the interaction of limited soil Fe bioavailability and susceptible genotype cultivation. Tomato, a Strategy I, model plant for Fe deficiency, is an important economical crop. Tomato responses in order to improve Fe uptake are based on acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Transcriptional profile obtained by roots (27-d) of 21-d-old tomato plants starved of iron for an additional week was compared with the transcriptional profile obtained for roots (27-d) of 21-d-old tomato plants grown for an additional week at 100 M-NM-<M Fe. Tomato plants were hydroponically grown in both cases. Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants (27-d-old).

2012-03-22 | E-GEOD-31112 | biostudies-arrayexpress

Transcriptional regulation research in tomato roots

Project description:To investigate the transcriptional changes induced by the fer mutant in tomato roots, roots from 3-week-old seedlings of fer, cultivated in 1/2 Hoagland’s nutrient solution, along with their respective wild-type control groups, were harvested. RNA-seq analysis was conducted with three biological replicates using the TruSeq RNA Sample Prep Kit.

2024-06-01 | E-MTAB-14084 | biostudies-arrayexpress

Root transcriptional profile of tomato Fe-deficient plants in response to supply with natural chelating agents.

Project description:Tomato, a Strategy I model plant for Fe deficiency, is an important economical crop. The transcriptional responses induced by Fe deficiency in tomato roots were previously described (Zamboni et al., 2012). The changes in trascriptome caused by the supply of Fe to plants starved fro 1 week were described in relation to the different nature of chelating agents (Fe-WEHS, Fe-CITRATE and Fe-PS). Transcriptional profile obtained by roots (27-d) of 21-d-old tomato plants starved of iron (0 Î¼M Fe-EDTA) for 1 week and supplied for 1 h with 1 Î¼M of Fe as Fe-WEHS (supply_Fe_WEHS), Fe citrate (supply_Fe_CITRATE) and Fe-PS (supply_Fe_PS). Tomato plants were hydroponically grown in all three case of Fe supply. Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants (27-d-old).

2016-01-11 | E-GEOD-69419 | biostudies-arrayexpress

Small RNA profiling Tomato, wild tomato relative and series of introgression lines

Project description:High throughput sequencing was used to investigate the production of small RNAs from cultivated tomato cultivar M82 and its wild relative Solanum pennellii. In order to understand the pattern of inheritance of the samll RNAs, interspecific hybrids (F1 and F2) along with series of introgressed lines comprising precise short genomic regions from S. pennellii in M82 background were used. Examination of small RNA production in several tomato lines.

2012-05-29 | E-GEOD-23562 | biostudies-arrayexpress

Transcription profiling of tomato - regeneration of epicuticular fruit wax

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

Expression data from root tissues of 35S:AtHMA4 and wild-type tomato plants grown in the presence of Zn

Project description:Ectopic expression of AtHMA4 in tomato modified Zn accumulation in a Zn-supply dependent manner. It suggests that HMA4-expression under a range of Zn-supply differentially modifies the expression of endogens, which contributes to different Zn-related phenotypes. To identify genes differentially regulated in 35S:AtHMA4-expressing and wild-type tomato, the transcription profiles were compared between roots of transgenic and WT-plants grown in the presence of 5 µM Zn. An effort was undertaken to recognize tissue specific alterations underlying the difference in Zn root:shoot distribution between tested plant lines and LCM technique was used to isolate epidermis+cortex and stele from roots.Understanding the interplay between the transgene and the endogens is crucial for planning genetic modification for Zn-biofortification purpose. 10-day old tomato plant (35S:AtHMA4 expressing and WT) were subjected to 5 µM Zn (added as ZnSo4) for 15 days. Three independent experiments were performed. At the end of each experiment 2.0 cm long root fragments from six plants (excluding 1.5 cm long apical fragments) were pooled, embedded in NEG-50 Frozen Section Medium (Thermo Scientific), and frozen in liquid nitrogen. Total RNA isolated from three batches of roots was amplified and used for three independent microarray analysis.

2015-05-08 | E-GEOD-68639 | biostudies-arrayexpress

Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

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

Expression data from leaf tissues of 35S:AtHMA4 and wild-type tomato plants grown in the presence of Zn

Project description:Arabidopsis HMA4 transformation facilitates Zn root-to-shoot translocation, but in Zn-supply dependent manner. It implies that distinct effects of HMA4 expression on Zn root:shoot distribution in transgenics grown under different Zn supply regimes results from the interaction between the transgene activity and the molecular background of the host plant. Microarray analysis was performed to compare expression profiles in leaves of transgenic and WT-plants grown in the presence of 5 µM Zn to identify the molecular mechanism underlying the difference in Zn root:shoot distribution between 35S:AtHMA4-expressing and wild-type tomato. To recognize tissue specific alterations in gene transcription in tomato leaves invoked by AtHMA4 expression, spongy paerenchyma + lower epidermis and palisade paerenchyma + upper epidermis were isolated using LCM technique. Understanding the interplay between the transgene and the endogens is crucial for planning genetic modification for Zn-biofortification purpose. 10-day old tomato plant (35S:AtHMA4 expressing and WT) were subjected to 5 µM Zn (added as ZnSo4) for 15 days. Three independent experiments were performed. At the end of each experiment the 3rd and 4th leaf (counting upwards) were collected, 1-2 mm long and 2-3 mm wide fragments were cut out from between the vascular bundles in the middle part of each leaf, embedded in NEG-50 Frozen Section Medium (Thermo Scientific), and frozen in liquid nitrogen. Total RNA isolated from three batches of leaves was amplified and used for three independent microarray analysis.

2015-05-08 | E-GEOD-68640 | biostudies-arrayexpress

Transcription profiling of tomato - humidity effects on fruit wax biosynthesis

Project description:After a standard cultivation program of six weeks, tomato plants (Solanum lycopersicum L.) cultivar MicroTom were grown under different conditions of atmospheric humidity and soil irrigation. The atmospheric humidity was adjusted to 40% and 80%, respectively. To regulate soil moisture, all potted plants were substrate saturated watered once a week. Furthermore, only a group of these plants was irrigated to assure optimally growing conditions (optimal watering conditions), whereas a second group had to cope with little water supply (no watering conditions). Mature green fruits were investigated (fruit developmental category II). 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-2165 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data