Transcriptome analysis of potato tubers--effects of different agricultural practices.
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.
van Dijk
Jeroen P
JP
RIKILT Institute of Food Safety, Bornsesteeg 45, P.O. Box 230, 6700 AE Wageningen, The Netherlands. jeroen.vandijk@wur.nl
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
D000383:Agriculture / Q000379:methods*; D001947:Breeding; D018744:DNA, Plant / Q000032:analysis; D004777:Environment; D015870:Gene Expression; D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis; D035281:Plant Tubers / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011198:Solanum tuberosum / Q000235:genetics*; D013045:Species Specificity
D018744:DNA, Plant