txid872925[Organism:noexp] - GEO DataSets

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Select item 2002454721.

Transcriptomic exploration of Solanum spp. resistance upon early-stage broomrape parasitism

(Submitter supplied) Tomato (Solanum lycopersicum) is a major crop of high economic value. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, a wild tomato species, has been used as breeding material for S. lycopersicum. In the present study a commercial tomato hybrid and two Introgression Lines (ILs), (S. more...

Organism:: Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL27957 GPL33844
18 Samples

Download data: RESULTS

Series

Accession:: GSE245472

ID:: 200245472

PubMed

Select item 2001514512.

A Multimodal Study of Wild Tomato Species Introgressions Unravels the Genetic Basis of Transcriptome and Metabolome Variation in Important Fruit Traits

(Submitter supplied) Here, we report RNAseq data from a Solanum lycopersicum-pennellii introgression population (IL) and a backcross introgression population (BIL), to establish the genetic basis of gene expression and chemical variation accompanying transfer of wild species-associated fruit traits. Transcriptome analysis of these lines resulted in the identification of genomic loci significantly linked with levels of hundreds of transcripts and metabolites. more...

Organism:: Solanum lycopersicum x Solanum pennellii

Type:: Expression profiling by high throughput sequencing

Platform:: GPL22468
523 Samples

Download data: TSV

Series

Accession:: GSE151451

ID:: 200151451

SRA Run Selector

Select item 2001284093.

Deciphering the biological processes underlying tomato biomass production and composition.

(Submitter supplied) After tomato fruits harvesting huge amounts of biomass residues, including plant and immature fruit, remaining in the field can be utilized to produce bioenergy. Little is known about the molecular aspects underlying tomato plant biomass production and hydrolysis. To identify genes involved in the regulation of plant biomass accumulation and composition, two Solanum pennellii introgression lines (ILs) with contrasting phenotypes for plant architecture and biomass characteristics, were analyzed. more...

Organism:: Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL26313 GPL26312
7 Samples

Download data: TXT

Series

Accession:: GSE128409

ID:: 200128409

SRA Run Selector

Select item 2000871624.

RNA-seq of Solanum lycopersicum cv. M82 and S. pennellii introgression line 3-5 day old root tip tissue

(Submitter supplied) The goal of this study was to perform RNA-seq expression analysis on Solanum lycopersicum cv. M82 X S. pennellii introgression lines, deriving expression Quantitative Trait Loci which were analyzed together with pre-existing genomic and phenotypic data to define genes and regulatory pathways controlling tomato root development and observed natural variation. We completed the RNAseq expression profiling analysis and developed a tool to display this information graphically in collaboration with Nicholas Provart at the University of Toronto: http://bar.utoronto.ca/efp_tomato/cgi-bin/efpWeb.cgi?dataSource=ILs_Root_Tip_Brady_Lab To identify candidate genes and pathways we focussed on one root growth trait, root growth angle, and identified two statistically significant genomic regions within tomato root growth angle QTL containing two candidate genes that likely control the gravitropic setpoint angle (CDC73 and PAP27), both of which are conserved between Arabidopsis and tomato, and which we tested using transgenic lines of the Arabidopsis orthologs. more...

Organism:: Solanum pennellii; Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL16345 GPL22467 GPL22468
305 Samples

Download data: TSV, TXT

Series

Accession:: GSE87162

ID:: 200087162

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000972475.

Paramutation of natural epialleles in tomato

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Solanum lycopersicum; Solanum pimpinellifolium; Solanum lycopersicum x Solanum pennellii; Solanum pennellii

Type:: Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

8 related Platforms
39 Samples

Download data: TXT

Series

Accession:: GSE97247

ID:: 200097247

PubMed Full text in PMC Similar studies

Select item 2000972066.

Paramutation of natural epialleles in tomato [sRNA]

(Submitter supplied) By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. more...

Organism:: Solanum pennellii; Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii; Solanum pimpinellifolium

Type:: Non-coding RNA profiling by high throughput sequencing

6 related Platforms
31 Samples

Download data: TXT

Series

Accession:: GSE97206

ID:: 200097206

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000971927.

Paramutation of natural epialleles in tomato [BiSulfite-seq]

Organism:: Solanum lycopersicum x Solanum pennellii; Solanum lycopersicum

Type:: Methylation profiling by high throughput sequencing

4 related Platforms
8 Samples

Download data: TXT

Series

Accession:: GSE97192

ID:: 200097192

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000772358.

Post-pollination carpels of S. pennellii introgression lines

(Submitter supplied) Expression in carpels of three pennellii NILs were contrasted to the recurrent parent (S. lycopersicum)

Organism:: Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:: Expression profiling by array

Platform:: GPL4741
17 Samples

Download data: CEL

Series

Accession:: GSE77235

ID:: 200077235

Select item 2000772329.

Pre-anthesis anthers of S. pennellii introgression lines

(Submitter supplied) Expression in pollen of four pennellii NILs were contrasted to the recurrent parent (S. lycopersicum)

Organism:: Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:: Expression profiling by array

Platform:: GPL4741
21 Samples

Download data: CEL

Series

Accession:: GSE77232

ID:: 200077232

Select item 20002356210.

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

(Submitter supplied) 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.