Plants responses to environmental stresses are regulated by signalling hormones, such as jasmonic acid, salicylic acid, ethylene and abscisic acid. Plant scientists commonly use marker genes to study which signalling pathways are activated, however, these markers were designed and tested for shoot responses in Arabidopsis thaliana. It is unclear whether the paradigms based on experiments on above-ground organs of A. thaliana are entirely transferable to shoots and roots of other species.
A recent study by Papadopoulou et al. published in AoB PLANTS investigated the regulation dynamics of hormonal-related marker genes in both roots and shoots of the non-model plant Brassica rapa. The study showed some of the commonly used molecular markers developed in A. thaliana did not show specific responsiveness to single hormone applications in B. rapa. Moreover, the same marker gene may respond differently to hormone application in roots and shoots. These findings suggest that marker gene responses can be organ and species specific and should be interpreted with caution.It is therefore advisable to combine analyses of multiple marker genes with those of phytohormone levels to ascertain more certainly which hormonally regulated defence pathways are activated.