Figure 3.

Validation of microarray results by quantitative PCR analysis. The y axis refers to the relative expression ratio between treated samples versus the control (untreated sample). (A) and (B) Real-time PCR results for ABA and MeJA treatments, respectively. The ratios were calculated in relation to the sample from untreated plants (0h). Transcript levels of the selected genes were profiled throughout the treatment time course. Also shown are the results for plant-endophytic bacteria association (C), drought (D), phosphate starvation (E) and herbivory (F). For these treatments, the real-time PCR reactions were carried out exclusively for the experimental point(s) in which the gene was considered differentially expressed. Only validated results are shown here. The RNA samples used in the real-time PCR experiments are from a third biological sample. All reactions were carried out in parallel and each reaction was performed in triplicates. Error bars were calculated as described previously [135]. Herb. = sample from plants inoculated with Herbaspirillum seropedicae and Herbaspirillum rubrisubalbicans; Gluc. = sample from plants inoculated with Gluconacetobacter diazotrophicus. The transcript levels for the reference genes were verified to not vary in response to the treatments. The reference genes used encode a polyubiquitin gene (SCCCST2001G02.g [CA179923]) for the ABA and drought dataset, a GAPDH for the MeJA and herbivory dataset (retrieved from [38]), a 25S rRNA for the endophytic inoculation (retrieved from [38]) and a 14-3-3 gene (SCCCLR1048F12.g [CA119519]) for phosphate starvation