We identify genes in plants that are responsible for agricultural or agronomic properties. To this end, we analyse their genome-wide expression at the level of transcription. For this purpose, in particular comparative questions are suitable: e.g. high- vs. low producers, or resistant / tolerant vs. sensitive varieties. From all detectable genes of a plant, those are identified which show a reproducible difference in their mRNA level between two or more contrasting phenotypes. The advances in sequencing technology with ever-increasing amounts of data coupled with decreasing costs enable comprehensive analyses of gene expression with unprecedented sensitivity and accuracy.