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Solanum lycopersicum

ABSTRACT: Solanum pennellii Introgression Lines RNA-seq data

PROVIDER: PRJNA526494 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8711390.fastq.gz	Fastqsanger.gz
	SRR8711400.fastq.gz	Fastqsanger.gz
	SRR8711410.fastq.gz	Fastqsanger.gz
	SRR8711420.fastq.gz	Fastqsanger.gz
	SRR8711430.fastq.gz	Fastqsanger.gz

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Solanum lycopersicum

Project description:Solanum lycopersicoides introgression lines of cultivated tomato RNA-seq data

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

Project description: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. A possible regulatory role for suberin in root growth angle control was also identified.

2018-01-01 | GSE87162 | GEO

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

Project description: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. lycopersicum X S. pennellii), were employed to identify genes and metabolic pathways associated with resistance against broomrape. Comparative transcriptomic analysis revealed a multitude of differentially expressed genes (DEGs) in roots, especially in the resistant genotype IL6-3, several of which were validated by quantitative PCR. DEG and pathway enrichment analysis (PEA), revealed diverse molecular mechanisms that can potentially be implicated in the host’s defense response and the establishment of resistance. Further research into these genes and associated metabolic pathways will contribute to our understanding of host-parasite interactions and resistance to broomrapes. Findings will be valuable in molecular breeding for generating resistant genotypes, ultimately providing alternative solutions for weed management in tomato and other valuable crops.

2024-09-02 | GSE245472 | GEO

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

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

Project description: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. These associations occurred in functionally coherent hotspots that represent coordinated perturbation of metabolic pathways and ripening-related processes. We demonstrated the efficacy of our approach by discovering yet undisclosed components of the renowned Solanum alkaloids pathway and moreover, showing that fruit fungal resistance is associated with changes in the ripening regulatory network.

2020-07-28 | GSE151451 | GEO

Multiscale gene expression profiling of 1 cm root tips of control and submerged Oryza sativa, Medicago truncatula, Solanum lycopersicum and Solanum pennellii seedlings

Project description:Climate change has increased the frequency and intensity of floods that impact global agricultural productivity. To better understand the response mechanisms and evolutionary history of gene family member regulation across angiosperm phyla, we studied the rapid submergence response of rice, the legume Medicago truncatula, and two Solanum species, domesticated tomato (S. lycopersicum cv. M82) and its dryland-adapted wild relative S. pennellii. Response to hypoxic conditions was measured by analyzing transcriptional and post-translational regulation in root tips of each species. This was achieved by the use of Nuclei Tagged in specific Cell Types (INTACT) and Translating Ribosome Affinity Purification to obtain chromatin and sub-populations of gene transcripts. (1) Chromatin accessibility was evaluated by coupling INTACT with ATAC-seq (assay for Transposon-Accessible Chromatin). (2) INTACT was used to capture nuclear RNA (nRNA). (3) Polyadenylated mRNA (polyA RNA) was obtained by standard oligo(dT) selection. (4) Ribosome-associated polyA mRNA (polyA RNA) was obtained by use of Translating Ribosome Affinity Purification (TRAP). Ribosome footprinting (Ribo-seq) was accomplished by using TRAP to capture ribosome protected fragments after RNAseI digestion. Samples evaluated include the apical root tip (four species) and shoot region (Solanum species only) under control conditions and after 2 h of submergence

2019-09-19 | GSE128680 | GEO

Tomato Solanum lycopersicum and Solanum pennellii

Project description:Transcriptome of Solanum lycopersicum and Solanum pennellii under abiotic stresses

| PRJNA641520 | ENA

Solanum lycopersicum

Project description:Solanum lycopersicum RNA-seq

| PRJNA392868 | ENA

Solanum lycopersicum Transcriptome or Gene expression

Project description:Lines nearly isogenic for fw3.2 in the cultivated background Solanum lycopersicum c.v. Yellow Stuffer were grown in the greenhouse in a completely randomized design. fw3.2 (ys) and fw3.2 (wt) are NILs carrying cultivated and wild alleles for fw3.2 locus. Young flower buds were harvested. For each sample, three replicates were used. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.

2013-07-27 | E-MTAB-4793 | biostudies-arrayexpress

Solanum lycopersicum Transcriptome or Gene expression

Project description:Lines nearly isogenic for fw3.2 in the cultivated background Solanum lycopersicum c.v. Yellow Stuffer were grown in the greenhouse in a completely randomized design. fw3.2(ys) and fw3.2(wt) are NILs carrying cultivated and wild alleles for fw3.2 locus. Flowers were tagged a day before anthesis and self-pollinated at anthesis. Fruits at stage five, seven, and ten days post anthesis (dpa) were harvested. Pericarp and seed tissues were separately isolated. Four replicates were collected for each sample. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.

2013-03-11 | E-MTAB-4792 | biostudies-arrayexpress

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