Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing of tomato germplasm for cold tolerance and yield studies

ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is genome wide association mapping for cold tolerance and yield studies in tomato (Solanum spp.) by phenotyping the genotypes under six diffrent temporal arrangments. Also for conducting quantitative reverse transcription polymerase chain reaction (qRT–PCR) assay of cold tolerant genes.

ORGANISM(S): Solanum habrochaites Solanum lycopersicum Solanum chilense Solanum lycopersicum var. cerasiforme Solanum peruvianum Solanum pimpinellifolium

PROVIDER: GSE200034 | GEO | 2023/04/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Combined analysis of ATAC-Seq and RNA-Seq reveal a potential role of WRKY34 in tomato response to cold stress [ATAC]

Project description:To further clarify the differences in the potential regulatory mechanisms of cold tolerance between wild and cultivated tomatoes, we subjected cold-sensitive cultivated tomato (Solanum lycopersicum) Ailsa Craig (AC) and cold-tolerant wild tomato (S. habrochaites) LA1777 to cold stress for 6 h, and performed ATAC-Seq and RNA-Seq, respectively.

2024-02-23 | GSE254893 | GEO

Next Generation Sequencing of tomato germplasm for cold tolerance and yield studies

Project description:Next Generation Sequencing of tomato germplasm for cold tolerance and yield studies

| PRJNA822769 | ENA

Cold stress in 7 Solanaceae species, replicate 1 and 2

Project description:Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Lycopersicum esculentum), Eggplant (Solanum melangena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were subjected to cold stress. Plants were grown at 25 C for 4-6 weeks after wich cold stress was initiated by exposing the plants to 4 C for 4, 8, 12, 24 and 48 hours. Control samples were isolated from plants just before the cold stress was initated. RNA was isolated using Qiagen RNeasy. Keywords: Direct comparison

2007-09-01 | GSE8203 | GEO

TOR balances plant growth and cold tolerance by orchestrating amino acid-derived metabolism in tomato

Project description:The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth and development. It is increasingly evident that TOR also has a significant impact on plant stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that the inhibition of SlTOR transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. Furthermore, a widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition. This disruption led to the accumulation of two important defense metabolites: salicylic acid (SA) and putrescine (Put). Subsequent gain- and loss-of-function analyses validated the crucial roles of salicylic acid and putrescine in enhancing tomato cold tolerance. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.

2024-12-19 | GSE266850 | GEO

DIA-based deep proteome and phosphoproteome profiling of early cold response in tomato fruits

Project description:Low temperature storage, a widely used technique for extending shelf life of tomato (Solanum lycopersicum) fruits, also induces chilling injury and results in fruit quality loss and consumer dissatisfaction. Numerous studies have been performed to dissect the molecular mechanisms of the cold tolerance of tomato fruits, mainly with long-time cold treatments. However, the early signal events of cold response in fruits are largely unknown. In this study, we construct mass spectral libraries of proteome (corresponding to over 11,000 proteins) and phosphoproteome (corresponding to over 24,000 high-conﬁdence phosphosites) of tomato fruits, and then perform data-independent acquisition (DIA) based comprehensive proteome and phosphoproteome profiling of tomato fruits at red-ripe stage upon cold treatment of 30 minutes.

2024-06-18 | PXD053222 |

Gene expression study after 3 days of cold or salt exposure in a Solanum tuberosum cultivar called Desirée

Project description:This SuperSeries is composed of the following subset Series: GSE34110: Gene expression study after 3 days of cold exposure in a Solanum tuberosum cultivar called Desirée GSE34116: Gene expression study after 3 days of salt exposure in a Solanum tuberosum cultivar called Desirée Refer to individual Series

2011-12-03 | E-GEOD-34118 | biostudies-arrayexpress

cold-responsive genes in tomato

Project description:cold-responsive genes in tomato Raw sequence reads

| PRJNA1201737 | ENA

Genome-Wide Identification of microRNAs and Their Targets in Cold-Stored Potato Tubers by Deep Sequencing and Degradome Analysis

Project description:Two small RNA libraries and 2 degradome libraries were constructed from potato tubers stored at room temperature or exposed to cold stress for deep sequencing. Through small RNA sequencing, 53 known miRNAs and 59 novel miRNAs were identified. Seventy genes were identified as miRNA targets by degradome sequencing. Small RNA sequencing and degradome sequencing of control and cold treated Solanum tuberosum tubers

2015-12-24 | E-GEOD-43237 | biostudies-arrayexpress

Transcriptome Sequencing in wild and domesticated tomato species

Project description:RNA-seq of seedlings of four tomato species Solanum habrochaites, Solanum lycopersicum, Solanum pimpinelliolium, and Solanum pennellii. An additional panel of samples include many tissues from Solanum lycopersicum and Solanum pennellii in two light conditions

2013-04-05 | GSE45774 | GEO

SlWRKY33 confers cold tolerance through activation of various downstream signaling pathways in cultivated tomato

Project description:To determine which genes were directly regulated by SlWRKY33 under cold stress, we performed ChIP-seq of SlWRKY33-OE plants with and without cold treatment.

2023-02-07 | GSE202902 | GEO

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