1. Fig. S1 Fig. S1 Correlation between microarray and qRT-PCR expression analyses. The linear regression compares expression ratios of salinity to control treatment measured by qRT-PCR and the citrus cDNA microarray.

2. Fig. S2 Fig. S2 Venn diagrams showing the distribution of the significant differentially expressed unigenes in salt- stressed Carrizo citrange and Cleopatra mandarin rootstocks.

3. Fig. S3 Cluster analysis of gene expression profiles in Carrizo citrange Carrizo citrange

4. Fig. S4 Cluster analysis of gene expression profiles in Cleopatra mandarin Cleopatra mandarin

5. Fig. S5 Analysis of Munich Information Center for Protein Sequences (MIPS) functional categories of all genes significantly induced or repressed in salt-stressed Carrizo citrange and Cleopatra mandarin rootstocks. The percentage is based upon the number of unigenes in each set.

6. Fig. S6 Expression profiles of unigenes encoding peroxidases in response to salt treatments obtained from microarray hybridizations. Intensities are expressed relative to the corresponding control value.

7. Carrizo KCl Carrizo NaCl Cleopatra KCl Cleopatra NaCl Fig. S7 Expression profiles of unigenes encoding chitinases in response to salt treatments obtained from microarray hybridizations. Intensities are expressed relative to the corresponding control value.

8. (A) (B) (C) (D) Fig. S8 Expression profiles of unigenes involved in Jasmonic Acid biosynthesis in response to salt treatments obtained from microarray hybridizations and qRT-PCR. Intensities are expressed relative to the corresponding control value. The figure continues in the following page.

9. (E) (F) (G) (H)(I) Fig. S8 (continued).

10. Fig. S9 Expression profiles of unigenes involved in ethylene biosynthesis in response to salt treatments obtained from microarray hybridizations. Intensities are expressed relative to the corresponding control value.

11. Fig. S10 Expression profiles of unigenes involved in photosynthesis-light reactions in response to salt treatments obtained from microarray hybridizations. Intensities are expressed relative to the corresponding control value.

12. Fig. S11 Real time RT-PCR expression of representative genes in Carrizo seedlings exposed to NaCl and KCl stress during 2, 5, 7 and 12 weeks treatments. Intensities are expressed in relation to the corresponding control value. Values are means (n=4) ±SD.

13. Fig. S12 Photosynthetic inhibition in NaCl-treated Carrizo and Cleopatra rootstocks. Different gas exchange and chlorophyll fluorescence parameters are presented in control and NaCl-treated seedlings. Photosynthetic efficiency data are mean values of eight independent measurements ± standard errors. Fluorescence quantum yield in light- adapted leaves (FPSII) are mean values of 36 independent measurements ± standard errors