Transcriptomics

Dataset Information

5

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 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

ORGANISM(S): Solanum tuberosum  

SUBMITTER: Jeroen van Dijk   Kok J Esther  Jeroen P van Dijk  Katarina Cankar 

PROVIDER: E-GEOD-11875 | ArrayExpress | 2009-02-01

SECONDARY ACCESSION(S): GSE11875PRJNA105687

REPOSITORIES: GEO, ArrayExpress

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Transcriptome analysis of potato tubers--effects of different agricultural practices.

van Dijk Jeroen P JP   Cankar Katarina K   Scheffer Stanley J SJ   Beenen Henriek G HG   Shepherd Louise V T LV   Stewart Derek D   Davies Howard V HV   Wilkockson Steve J SJ   Leifert Carlo C   Gruden Kristina K   Kok Esther J EJ  

Journal of agricultural and food chemistry 20090201 4


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 transcriptomic  ...[more]

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