The Identification and Interpretation of Differences in the Transcriptomes of Organically and Conventionally Grown Potato Tubers

In the European integrated research project SAFEFOODS,
one of the aims was to further establish the potential of transcriptomics
for the assessment of differences between plant varieties grown under
different environmental conditions. Making use of the knowledge of
cellular processes and interactions is one of the ways to obtain a
better understanding of the differences found with transcriptomics.
For the present study the potato genotype Santé was grown under
both organic and conventional fertilizer, and each combined with either
organic or conventional crop protection, giving four different treatments.
Samples were derived from the European project QualityLowInputFood
(QLIF). Microarray data were analyzed using different statistical
tools (multivariate, principal components analysis (PCA); univariate,
analysis of variance (ANOVA)) and with pathway analysis (hypergeometric
distribution (HGD) and gene set enrichment analysis (GSEA)). Several
biological processes were implicated as a result of the different
treatments of the plants. Most obvious were the lipoxygenase pathway,
with higher expression in organic fertilizer and lower expression
in organic crop protection; the starch synthase pathway, with higher
expression in both organic crop protection and fertilizer; and the
biotic stress pathway, with higher expression in organic fertilizer.
This study confirmed that gene expression profiling in combination
with pathway analysis can identify and characterize differences between
plants grown under different environmental conditions.