RNA isolation and microarray scanning  
Root tissue from 15-day-old plants cultivated under hydroponic conditions was recollected at 48 hours after initiating the treatments. At least 12 plants per line and treatment were pooled to perform 3 biological replicates. Leaves were immersed in liquid nitrogen, homogenized to a fine powder, and stored at -80º C. The total RNA of about 100 mg of leaf powder for each biological replicate was extracted using the Maxwell® plant RNA kit (Promega Corporation, WI, USA) following the manufacturer’s instructions. To ensure a high quality and quantity RNA material, Experion RNA Analysis Kit (Biorad) was performed. After quality control, total RNA was tag, hybridized and cleaning using  GeneChip® 3’ IVT Express Kit. Microarray expression analysis were performed by Affymetrix GeneChip™ Arabidopsis Genome ATH1 Array Agilent 2100 Bioanalyzer.
Differential expression analysis:  The function gcrma(package gcrma) was used to adjust background intensities in Affymetrix array data, which include optical noise and non-specific binding. The R package ‘limma’ was used to test the expression data and search for differentially expressed genes (DEGs) when pairs of experimental groups were compared. A model matrix was defined by specifying the groups that belonged to each sample. Then, limma’s functions lmFit andcontrasts.fit , together with the model matrix, were used to adjust the expression data to a linear model in order to extract fold changes and confidence statistics associated to the comparisons of interest. Function eBayes was then used to rank genes in order of evidence for differential expression.  The R libraryath1121501.db was used to include names and descriptions of the genes associated to the microarray’s features probed. The resulting p-values were adjusted using the Benjamini and Hochberg’s approach [31] for controlling the false discovery rate (FDR). To perform a list of DEGs, genes were filtered by adj p-value (adjusted p-value) <0.05 and LFC >1 and LFC <-1.
Gene ontology, KEGG pathway and functional protein association networks analysis: Gene Ontology (GO) enrichment analysis of DEGs was implemented by AgriGO V2 [32] and FLAME [33]. Significant GO terms (p-values less than 0.05) were classified into 3 categories: biological function, molecular process, and cellular component. KEGG pathway and STRING version 11.0 were used to understand high-level function and gene interaction network from differential expressed genes [34].