Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Naturally Occurring Alleles Diversity of StNADC Promote Foliage Senescence and Tuberization in the Tetraploid Potato (Solanum tuberosum L.)

PROVIDER: PRJNA917150 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22944109_1.fastq.gz	Fastqsanger.gz
	SRR22944109_2.fastq.gz	Fastqsanger.gz
	SRR22944110_1.fastq.gz	Fastqsanger.gz
	SRR22944110_2.fastq.gz	Fastqsanger.gz
	SRR22944111_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

RNA-Seq of allotetraploid wild potato Solanum acaule and autotetraploid potato Solanum tuberosum cv. Atlantic

Project description:Potato wild relatives (Solanum section Petota) are a source of genetic diversity for improving traits in modern cultivars (S. tuberosum) to meet climate challenges. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. The allotetraploid S. acaule Bitter has been used to introgress cold tolerance into potato breeding germplasm. The cold challenged transcriptome of S. acaule was compared with that of autotetraploid S. tuberosum cv. Atlantic, and was found to have fewer differentially expressed genes than the latter. Specifically, subgenome 1 has less downregulated alleles compared to subgenome 2 and S. tuberosum.

2025-05-31 | GSE268611 | GEO

The function of the GIGANTEA gene StGI.04 in potato: Uncovering a new function affecting the anthocyanin content of tuber skin

Project description:GIGANTEA (GI) is a plant-specific, circadian clock-regulated, nuclear protein with pleiotropic functions studied in many plant species. It is involved in flowering, circadian clock control, chloroplast biogenesis, carbohydrate metabolism, stress responses and synthesis of volatiles. In potato (Solanum tuberosum L.), however, only its role in tuber initiation is reported. Based on the findings in other plant species we hypothesized that the function of GI is not restricted to tuberization in potato. To test this hypothesis we repressed the expression of a GI gene, StGI.04 in the commercial potato cultivar ‘Désirée’ and investigated the effect of repression at morphological and transcriptome level. We found that, like GI in other plant species, StGI.04 influences the expression of the key genes of circadian clock, flowering, starch synthesis and stress responses. Furthermore, we detected a novel function of a GI gene in influencing the anthocyanin synthesis and skin colour of potato tubers.

2022-03-30 | GSE189956 | GEO

JHI St WM daylength

Project description:Recent advances have defined some of the components of photoperiodic signalling that lead to tuberisation in potato including orthologues of FLOWERING LOCUS T (StSP6A) and CYCLING DOF FACTOR (StCDF1). The aim of the current study is to investigate the molecular basis of permissive tuber initiation under long days in Solanum tuberosum Neo-Tuberosum by comparative analysis with an obligate short day Solanum tuberosum ssp. Andigena accession. We show that the Neo-Tuberosum accession, but not the Andigena, contains alleles that encode StCDF1 proteins modified in the C-terminal region, likely to evade long day inhibition of StSP6A expression. We also identify an allele of StSP6A from the Neo-Tuberosum accession, absent in the Andigena, which is expressed under long days. Other leaf transcripts and metabolites that show different abundances in tuberising and non-tuberising samples were identified adding detail to tuberisation-associated processes. Overall, the data presented in this study highlight the subtle interplay between components of the clock-CONSTANS-StSP6A axis which collectively may interact to fine-tune the timing of tuberisation.

2013-11-01 | E-MTAB-1799 | biostudies-arrayexpress

Effect of potato tuber bruising on gene expression 2h after mechanical shock in tetraploid potato genotypes

Project description:Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economical importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still a lot to learn about this complex phenotype. Here, we used genotype by sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis for tuber bruising. In addition, we collected transcriptomics data to enrich the GWAS results, by performing a differential expression analysis between samples with high- and low-bruising susceptibility.

2022-11-29 | GSE208439 | GEO

Potato_tuber_sprout

Project description:Chemotyping dataset of n-butanol peptide extract of Solanum tuberosum ('Red potato') tuber sprout

2018-06-29 | MSV000082529 | MassIVE

Solanaceae comparative gene expression profiling

Project description:Six different Solanaceae species, Potato (Solanum tuberosum), Tomato (Lycopersicum esculentum), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were grown at 25C, 16h light and 8h darkness. Mature leaves were harvested after 4-6 weeks. RNA was isolated using Qiagen RNeasy. Tomato, pepper, petunia tobacco and N. benthamiana samples were hybridized against potato samples. Keywords: Direct comaprison

2007-09-01 | GSE8234 | GEO

Transcriptomics of shade avoidance and drought in Solanum tuberosum.

Project description:The intent was to study, from transcriptome analysis, shade and drought responses in Solanum tuberosum (potato). We performed Illumina 50 bp single-end RNA-seq in tissues of control and treated var. Spunta wild-type plants. Drought experiments also included two independent AtBBX21-overexpressing (BBX21-OE) potato lines.

2023-07-12 | E-MTAB-12771 | biostudies-arrayexpress

Transcriptional profiles associated with altered StCEN expression in non-swelling stolons from RNAi and overexpressing potato (subspecies Andigena) transgenic lines demonstrating altered tuberization phenotypes

Project description:Two independent Solanum tuberosum ssp. Andigena ADG StCEN RNAi and two ADG StCEN 35S overexpressing OE transgenic lines and a wild type WT control were grown under standard glasshouse conditions for 6 weeks prior to being moved to controlled growth cabinet conditions. Plants were grown under 4 different daylengths (8,10,12 and 16 hr) at 20 °C day and 14 °C night temperatures. ADG StCEN RNAi lines showed signs of early tuberization phenotype compared with the WT control after 23 days in the cabinets. Non-swelling stolons were harvested at this timepoint. ADG StCEN 35S OE lines demonstrated a delayed tuberization phenotype compared with the WT control. Non-swelling stolons were harvested after 38 days in the controlled cabinet conditions.

2020-07-01 | E-MTAB-8346 | biostudies-arrayexpress

Heat stress in 7 Solanaceae species, replicate 1 and 2

Project description:Seven different Solanaceae species, Potato (Solanum tuberosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melongena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabacum), Petunia and Nicotiana benthamiana were subjected to heat stress. Plants were grown for 4-6 weeks at 25 C after which heat stress was initiated by exposing the plants to 35 C for 6, 12, 24, 48 and 96 hours. Control samples were isolated from plants just before initiating the heat stress. RNA was isolated using Qiagen RNeasy. Keywords: Direct comparison

2007-09-01 | GSE8202 | GEO

Argonaute 15 controls MITE-generated sRNAs in potato: implications on plant defense

Project description:Canonical ribonucleases like Argonautes (AGOs) participate in RNA-based gene regulatory processes. They are important for the small RNA association and formation of the RNA-induced RNA silencing complexes (RISCs). Potato (Solanum tuberosum, St) has 14 AGO-encoding genes, among those is the Solanum-specific StAGO15, which is activated upon infection by filamentous pathogens. Here, we analyzed sRNAs associated to StAGO15 during leaf infection with the aim to clarify its role in plant immunity

2025-04-08 | GSE244421 | 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