Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of potato tubers: Effects of different agricultural practices

ABSTRACT: The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments. Keywords: experiment with factorial design

ORGANISM(S): Solanum phureja Solanum tuberosum

PROVIDER: GSE11875 | GEO | 2009/02/02

SECONDARY ACCESSION(S): PRJNA105687

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of potato tubers: Effects of different agricultural practices

Project description:The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments. Keywords: experiment with factorial design factorial design; 2 potato cultivars (Sante, Lady Balfour); 2 fertilizers (dairy manure compost, chicken manure pellets); 3 plant protection treatments (copper oxychloride, comcat, water), 3 biological replicates, 48 samples

2009-02-01 | E-GEOD-11875 | biostudies-arrayexpress

Differences in the transcriptomes of organically and conventionally grown potatoes.

2011-12-31 | E-MTAB-605 | biostudies-arrayexpress

Differences in the transcriptomes of organically and conventionally grown potatoes.

2012-01-31 | GSE27662 | GEO

Differences in the transcriptomes of organically and conventionally grown potatoes.

Project description:Microarray analysis was performed on a well-defined set of potato tuber samples grown under different, well-recorded environmental conditions. The data were analysed to assess the potential of transcriptomics to detect differences in gene expression as a result of these environmental conditions. Differences were found for both factors, both in PCA and in ANOVA analysis. Factorial design; 1 potato cultivar (Sante); 2 fertilizers (organic, conventional); 2 crop protection treatments (organic, conventional), 4 biological replicates, 16 samples. Raw data files: columns 1 - 11 is Cy3, 12 - 21 is Cy5

2012-01-31 | E-GEOD-27662 | biostudies-arrayexpress

Transcription profiling of pigmented and non-pigmented tubers of Solanum tuberosum

Project description:Transcriptional analysis of pigmented and non-pigmented potato tuber flesh using POCI 44k microarrays

2010-01-01 | E-TABM-787 | biostudies-arrayexpress

Transcription profiling of pigmented and non-pigmented tubers of Solanum tuberosum

Project description:Transcriptional analysis of pigmented and non-pigmented potato tuber flesh using POCI 44k microarrays

2010-01-01 | E-TABM-788 | biostudies-arrayexpress

Transcription profiling by array of potato tubers with altered PME activity

Project description:Although processed potato tuber texture is an important trait that influences consumer preference, a detailed understanding of tuber textural properties at the molecular level is lacking. Previous work has identified tuber pectin methyl esterase activity (PME) as a potential factor impacting on textural properties and the expression of a gene encoding an isoform of PME (PEST1) was associated with cooked tuber textural properties. In this study a transgenic approach was undertaken to investigate further the impact of the PEST1 gene. Antisense and over-expressing potato lines were generated. In over-expressing lines tuber PME activity was enhanced by up to 2.3 fold whereas in antisense lines PME activity was decreased by up to 38%. PME isoform analysis indicated that the PEST1 gene encoded one isoform of PME. Analysis of cell walls from tubers from the over-expressing lines indicated that the changes in PME activity resulted in a decrease in pectin methylation. Analysis of processed tuber texture demonstrated that the reduced level of pectin methylation in the over-expressing transgenic lines was associated with a firmer processed texture. Thus there is a clear link between PME activity, pectin methylation and processed tuber textural properties.

2010-12-01 | E-TABM-1062 | biostudies-arrayexpress

Transcription profiling by array of Andigena SP5G RNAi leaves, tubers and tuber sprouts

Project description:To analyze the gene regulatory network controlled by SP5G in potato, we hybridized an Agilent 60-mer microarray with probes corresponding to the RNA extracted out of leaf, tuber and tuber sprout tissues from WT and StSP5Gi lines.

2018-10-17 | E-MTAB-6438 | biostudies-arrayexpress

Transcription profiling of potato tubers for the investigation of methionine content

Project description:BSA pooling experiment for methionine content in a segrating diploid potato population (CxE). RNA of constrasting individuals for methionine content are pooled together based on their tuber methionine content and marker association with either or both of the identified QTLs for methionine content

2009-11-20 | E-MEXP-2441 | biostudies-arrayexpress

Identification of TIMING OF CAB EXPRESSION 1 as an environmentally sensitive negative regulator of tuberisation in potato

Project description:For many potato cultivars, tuber yield is optimal at average day time temperatures in the range of 14-22 ⁰C. Further rises in ambient temperature can reduce or completely inhibit potato tuber production, with damaging consequences for both producer and consumer. In our previous work we observed that the steady-state expression level of the core circadian clock gene, TIMING OF CAB EXPRESSION 1 (TOC1), in potato tubers increased at moderately elevated temperature, whereas expression of the tuberisation signal gene StSP6A decreased along with tuber yield. In this study we investigated the potential roles of StTOC1 in linking environmental signalling and potato tuberisation. We show that transgenic lines with decreased expression of StTOC1 exhibit enhanced StSP6A transcript levels in tuberising stolons, and show changes in gene expression consistent with elevated tuber sink strength.

2019-09-02 | E-MTAB-7443 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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