Fig. S1

R2 = 0,9204

-2,0

-1,0

0,0

1,0

2,0

-3 -2 -1 0 1 2

qRT-PCR (log2)

Mic

roa

rra

y (

log

2)

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.

Carrizo citrange: 869

NaCl (772)

75 697 97

KCl (794)

Cleopatra mandarin: 208

NaCl (161)

41 120 47

KCl (167)

NaCl: 877

Carrizo(772)

716 56 105

Cleopatra(161)

KCl: 924

Carrizo(794)

757 37 130

Cleopatra(167)

Carrizo citrange: 869

NaCl (772)

75 697 97

KCl (794)

Cleopatra mandarin: 208

NaCl (161)

41 120 47

KCl (167)

NaCl: 877

Carrizo(772)

716 56 105

Cleopatra(161)

KCl: 924

Carrizo(794)

757 37 130

Cleopatra(167)

Fig. S2

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

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

NaClKClNaClKClCarrizo citrange

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

NaClKClNaClKClCleopatra mandarin

0 5 10 15 20 25 30 35 40 45

1: METABOLISM

16: PROTEIN WITH BINDINGFUNCTION / COFACTOR

UNCLASSIFIED PROTEINS

34: INTERACTION WITHTHE ENVIRONMENT

98: CLASSIFICATION NOTYET CLEAR-CUT

32: CELL RESCUE,DEFENSE AND VIRULENCE

20: TRANSPORT

14: PROTEIN FATE

MIP

S F

un

ctio

na

l Cat

eg

ori

es

% of Gene Set

Cleopatra repressed

Cleopatra induced

Carrizo repressed

Carrizo induced

0 2 4 6 8 10 12 14 16 18 20

11: TRANSCRIPTION

36: SYSTEMICINTERACTION WITH THE

ENVIRONMENT

30: COMMUNICATION &SIGNALLING

10: CELL CYCLE & DNAPROCESSING

42: BIOGENESIS OFCELLULAR COMPONENTS

2: ENERGY

12: PROTEIN SYNTHESIS

41: DEVELOPMENT

18: PROTEIN ACTIVITYREGULATION

40: CELL FATE

MIP

S F

un

ctio

nal

Ca

teg

ori

es

% of Gene Set

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.

Peroxidase (Contig3148)

-1.4

-1.2

-1

-0.8

-0.6

-0.4

-0.2

0

0.2

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

Peroxidase (Contig3235)

-1.5

-1.2

-0.9

-0.6

-0.3

0

0.3

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Peroxidase (Contig938)

-1

-0.5

0

0.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Peroxidase (Contig3345)

-1.2

-0.6

0

0.6

1.2

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

Peroxidase (Contig3062)

-1

-0.75

-0.5

-0.25

0

0.25

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Ascorbate Peroxidase (Contig3142)

-1.2

-0.6

0

0.6

1.2

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

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.

Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

CBP20 Chitinase (C018001F07)

-1

-0.75

-0.5

-0.25

0

0.25

0.5

0.75

1

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Chitinase CHI1b (Contig2192)

-1.5

-1

-0.5

0

0.5

1

1.5

2

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Acidic class II chitinase (Contig3048)

-1.25

-1

-0.75

-0.5

-0.25

0

0.25

0.5

0.75

1

1.25

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Chitinase CHI1a (Contig3192)

-1

-0.75

-0.5

-0.25

0

0.25

0.5

0.75

1

1.25

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Chitinase (Contig3146)

-0.75

-0.5

-0.25

0

0.25

0.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Chitinase CHI1c (Contig1199)

-0.5

-0.25

0

0.25

0.5

0.75

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

pathogenesis-related protein 4A1 (Contig3116)

-2

-1.75

-1.5

-1.25

-1

-0.75

-0.5

-0.25

0

0.25

0.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Pathogenesis-Related 4A2 (Contig3372)

-2.4

-1.9

-1.4

-0.9

-0.4

0.1

0.6

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Pathogenesis-Related 4A3 (Contig3349)

-2

-1.5

-1

-0.5

0

0.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Pathogenesis_related 4A4 (Contig3400)

-0.5

0

0.5

1

1.5

2

2.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

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.

Lipoxygenase (C01012C11)

-0.5

-0.25

0

0.25

0.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Cleopatra KCl

Cleopatra NaCl

Lipoxygenase (Contig3219)

0

0.5

1

1.5

2

2.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Cleopatra KCl

Cleopatra NaCl

Lipoxygenase (C01012C11)

-0.75

-0.5

-0.25

0

0.25

0.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Lipoxygenase (Contig3219)

-1

-0.5

0

0.5

1

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Lipoxygenase (C20001H03)

0

1

2

3

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Cleopatra KCl

Cleopatra NaCl

Lipoxygenase (C18016E06)

0

1

2

3

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Cleopatra KCl

Cleopatra NaCl

Lipoxygenase (C20001H03)

-0.75

-0.5

-0.25

0

0.25

0.5

0.75

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Lipoxygenase (C18016E06)

-0.75

-0.5

-0.25

0

0.25

0.5

0.75

1

1.25

1.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

(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.

Lipoxygenase (Contig2847)

-0,5

-0,25

0

0,25

0,5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Cleopatra KCl

Cleopatra NaCl

Lipoxygenase (Contig2847)

-0,25

0

0,25

0,5

0,75

1

1,25

1,5

1,75

2

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Lipoxygenase (Contig609)

-1

-0,75

-0,5

-0,25

0

0,25

0,5

0,75

1

1,25

1,5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Cleopatra KCl

Cleopatra NaCl

Lipoxygenase (Contig609)

-1

-0,75

-0,5

-0,25

0

0,25

0,5

0,75

1

1,25

1,5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Lipoxygenase (C08007A11)

0

0,25

0,5

0,75

1

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Cleopatra KCl

Cleopatra NaCl

Lipoxygenase (C08007A11)

-1

-0,75

-0,5

-0,25

0

0,25

0,5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

(E)

(F)

(G)

(H) (I)SAM:JA carboxymethyltransferase (Contig3375)

-1.8

-1.2

-0.6

0

0.6

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

SAM:JA carboxymethyltransferase (Contig3375, qRT-PCR)

-3

-2.5

-2

-1.5

-1

-0.5

0

0.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Fig. S8 (continued).

ACC Synthase (Contig2182)

-0,8

-0,4

0

0,4

0,8

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

ACC Oxidase (Contig2749)

-1

-0,8

-0,6

-0,4

-0,2

0

0,2

0,4

0,6

0,8

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

ACC Oxidase (Contig3389)

-1,2

-0,8

-0,4

0

0,4

0,8

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

ACC Oxidase (Contig905)

-0,8

-0,4

0

0,4

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

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.

Cytochrome b6/f complex subunit V (C18008A05)

-0.6

-0.3

0

0.3

0.6

0.9

1.2

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Cytochrome b6/f complex subunit VI (Contig3077)

-1.2

-0.9

-0.6

-0.3

0

0.3

0.6

0.9

1.2

1.5

1.8

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Photosystem II Protein I (Contig2277)

-1.2

-0.8

-0.4

0

0.4

0.8

1.2

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

PSI subunit VIII (Contig634)

-1.8

-1.35

-0.9

-0.45

0

0.45

0.9

1.35

1.8

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

NADH Dehydrogenase subunit I (C20008G09)

-2.5

-2

-1.5

-1

-0.5

0

0.5

1

1.5

2

2.5

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Photosynthesis regulation Protein kinase (Contig1607)

-0.75

-0.5

-0.25

0

0.25

0.5

0.75

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Geranylgeranyl reductase (Contig2922)

-1.2

-0.9

-0.6

-0.3

0

0.3

0.6

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Oxygen-evolving enhancer protein 1 (Contig532)

-0.8

-0.6

-0.4

-0.2

0

0.2

0 1 2 3 4 5 6 7Weeks

log

(2)

Ra

tio

Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

Carrizo KCl

Carrizo NaCl

Cleopatra KCl

Cleopatra NaCl

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.

NRT1-2 (Contig3169)

-4

-2

0

2

4

6

8

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

NRT1-2 (Contig3169)

-4

-2

0

2

4

6

8

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

NRT1-2 (Contig3169)

-4

-2

0

2

4

6

8

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

NRT1-2 (Contig3169)

-4

-2

0

2

4

6

8

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

RD22 (Contig2928)

-1

0

1

2

3

4

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

log

(2)R

ati

o

KCl

NaCl

Ribulose biphosphate carboxylase small chain (Contig3369)

-1

-0.5

0

0.5

1

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

log

(2)R

ati

o

KCl

NaCl

Rubisco activase (Contig3311)

-3

-2

-1

0

1

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Rubisco activase (Contig3311)

-3

-2

-1

0

1

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Rubisco activase (Contig3311)

-3

-2

-1

0

1

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Rubisco activase (Contig3311)

-3

-2

-1

0

1

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Rubisco activase. Contig2829

-4.5

-3.5

-2.5

-1.5

-0.5

0.5

1.5

0 1 2 3 4 5 6 7 8 9 10 11 12

Weekslo

g(2

)R

atio

KCl

NaCl

Rubisco activase. Contig2829

-4.5

-3.5

-2.5

-1.5

-0.5

0.5

1.5

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Rubisco activase. Contig2829

-4.5

-3.5

-2.5

-1.5

-0.5

0.5

1.5

0 1 2 3 4 5 6 7 8 9 10 11 12

Weekslo

g(2

)R

atio

KCl

NaCl

Rubisco activase. Contig2829

-4.5

-3.5

-2.5

-1.5

-0.5

0.5

1.5

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Carbonic anhydrase (Contig3185)

-6

-5

-4

-3

-2

-1

0

1

2

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Carbonic anhydrase (Contig3185)

-6

-5

-4

-3

-2

-1

0

1

2

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Carbonic anhydrase (Contig3185)

-6

-5

-4

-3

-2

-1

0

1

2

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

Carbonic anhydrase (Contig3185)

-6

-5

-4

-3

-2

-1

0

1

2

0 1 2 3 4 5 6 7 8 9 10 11 12

Weeks

lo

g(2

)R

atio

KCl

NaCl

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.

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

stomatal conductanceCarrizo

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

0 20 40 60 80 100

Days

mo

l · m

-2 ·

s-1

Control

NaCl

stomatal conductanceCleopatra

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

0 20 40 60 80 100

Days

mo

l · m

-2 ·

s-1

Control

NaCl

transpiration rateCarrizo

0

0.5

1

1.5

2

2.5

0 20 40 60 80 100

Days

mm

ol H

2O ·

m-2

· s

-1

Control

NaCl

transpiration rateCleopatra

0

0.5

1

1.5

2

2.5

3

0 20 40 60 80 100

Days

mm

ol H

2O ·

m-2

· s

-1

Control

NaCl

net photosynthetic rateCarrizo

0

1

2

3

4

5

6

7

8

9

0 20 40 60 80 100

Days

mm

ol H

2O ·

m-2

· s

-1

Control

NaCl

net photosynthetic rateCleopatra

0

1

2

3

4

5

6

7

8

9

0 20 40 60 80 100

Days

mm

ol H

2O ·

m-2

· s

-1

Control

NaCl

Maximum Fluorescence yield Carrizo

0.5

0.6

0.7

0.8

0.9

0 20 40 60 80 100

Days

Control

NaCl

Maximum Fluorescence yield Cleopatra

0.5

0.6

0.7

0.8

0.9

0 20 40 60 80 100

Days

Control

NaCl

Fluorescence quantum yield Carrizo

0.45

0.55

0.65

0.75

0.85

0 20 40 60 80 100

Days

Control

NaCl

Fluorescence quantum yield Cleopatra

0.45

0.55

0.65

0.75

0.85

0 20 40 60 80 100

Days

Control

NaCl