Pathway enrichment analysis showed several pathways were enriched by salinity and ecotype effects.

1NF: Normalized frequency = sample frequency of each category in this experiment/background frequency of each category in the Arabidopsis genome.Genes with P-value 2.0 were loaded and annotated in the Classification SuperViewer Tool (http://bar.utoronto.ca/ntools/cgi-bin/ntools_classification_superviewer.cgi). MapMan was used as the classification source to assign functional categories for each gene. Group 1: pathways enriched by both salt and ecotype effects; Group 2: pathways enriched by salt effect and ecotype effect in the presence of salt; Group 3: pathways mainly enriched by salt effect; –: no significant enrichment. The color scales indicated different normalized frequencies which were described in Materials and Methods.