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

J Agric Food Chem. 2009 Feb 25;57(4):1612-23. doi: 10.1021/jf802815d.


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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agriculture / methods*
  • Breeding
  • DNA, Plant / analysis
  • Environment
  • Gene Expression
  • Gene Expression Profiling*
  • Oligonucleotide Array Sequence Analysis
  • Plant Tubers / genetics*
  • Polymerase Chain Reaction
  • Solanum tuberosum / genetics*
  • Species Specificity


  • DNA, Plant