Transcriptome analysis of potato tubers - effects of different agricultural practices

Jeroen P van Dijk, Katarina Cankar, Stanley J Scheffer, Henriek G Beenen, Louise V T Shepherd, Derek Stewart, Howard V Davies, Steve J Wilcockson, Carlo Leifert, Kristina Gruden, Esther J Kok

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    33 Citations (Scopus)

    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.
    Copyright © 2009 American Chemical Society
    Original languageEnglish
    Pages (from-to)1612-1623
    Number of pages12
    JournalJournal of Agricultural and Food Chemistry
    Volume57
    Issue number4
    DOIs
    Publication statusPublished - 2009

    Keywords

    • solanum tuberosum
    • cDNA microarray
    • gene expression
    • food safety
    • organic input systems

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  • Cite this

    van Dijk, J. P., Cankar, K., Scheffer, S. J., Beenen, H. G., Shepherd, L. V. T., Stewart, D., Davies, H. V., Wilcockson, S. J., Leifert, C., Gruden, K., & Kok, E. J. (2009). Transcriptome analysis of potato tubers - effects of different agricultural practices. Journal of Agricultural and Food Chemistry, 57(4), 1612-1623. https://doi.org/10.1021/jf802815d