Experimental design for salt stress treatment. (A) Genotypic pairs with differences in salt tolerance and similar genetic backgrounds were selected for the transcriptome analysis using the Affymetrix GeneChip format. Comparable developmental stage and tissue were used for assay. (B) Stress treatment for rice and barley were implemented based on previous yield loss data. Green bar represents growth under unstressed/nutrient solution. Red bar indicates a gradual increase in salt levels. Blue bar represents growth under stress after reaching the final salt levels. Both control and stressed plants were harvested at the same time (circle). (C) Differential expression analysis comparisons for rice and barley. Current work focuses on comparisons 1 and 2 for rice and comparisons 5 and 6 for barley. Genes commonly regulated in both genotypes were considered the species specific responses. Genotypic comparisons 3, 4, 7 and 8 were not considered for present work.