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Table 3 Differentially expressed genes encoding proteins shown to have a role in biotic/abiotic stress resistance, when knocked-out (KO)/over-expressed (Ox)

From: Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress

Probe Set ID

Bacteria

Parasite

Fungus

Virus

Abiotic

MSU gene identifier

Name

Phenotype

Reference

1

2

3

4

5

6

7

8

9

10

11

12

13

Os.11773.1.s1_at

2.1

  

2.8

2.3

9.2

7.1

2.0

 

2.4

2.4

2.3

−2.0

LOC_Os05g27730.1

OsWRKY53

Ox - enhanced resistance

[38]

Os.12032.1.s1_at

2.0

 

2.9

8.3

8.5

80.7

25.5

2.2

 

3.4

2.8

4.8

 

LOC_Os02g08440.1

OsWRKY71

Ox - enhanced resistance

[23]

Os.37565.2.s1_at

2.8

  

11.3

2.9

6.5

4.7

2.2

 

1.3

 

8.3

−1.9

LOC_Os05g25770.1

OsWRKY45-1

Ox - increased susceptibility

[10]

Os.48082.1.s1_at

1.6

6.1

 

15.3

 

25.8

 

12.0

 

2.2

9.2

2.2

 

LOC_Os09g25070.1

OsWRKY62

Ox - increased susceptibility

[44]

Os.50015.1.s1_at

1.5

2.1

7.0

46.7

21.0

219.4

22.3

4.6

 

8.9

44.5

7.7

1.7

LOC_Os06g44010.1

OsWRKY28

Ox - enhanced resistance

[21]

Os.2160.2.s1_x_at

1.4

 

1.6

 

2.1

1.6

−1.5

  

1.8

1.8

 

−2.5

LOC_Os01g54600.1

OsWRKY13

Ox - enhanced resistance

[11]

Os.15708.1.s1_a_at

1.2

     

−3.4

   

2.2

1.7

−9.2

LOC_Os04g38720.1

OsNAC2

Ox- increased shoot branching

[39]

Os.4385.1.s1_at

1.5

 

1.9

 

1.4

1.9

−1.7

  

11.1

8.7

2.2

1.7

LOC_Os11g08210.1

OsNAC5

Ox-increase stress tolerance

[22]

Os.12199.1.s1_at

1.4

  

1.7

1.6

8.9

   

6.9

5.7

3.4

1.4

LOC_Os01g66120.1

OsNAC6

Ox-increase stress tolerance

[22]

Os.26695.1.s1_at

1.6

 

2.0

2.7

3.4

55.6

4.0

3.0

 

7.0

5.3

4.9

5.9

LOC_Os03g60080.1

NAC9/SNAC1

Ox-increase stress tolerance

[40]

Os.35020.1.s1_at

4.1

11.1

2.2

3.9

4.1

112.1

   

53.1

35.1

3.3

 

LOC_Os11g03300.1

NAC10

Ox-increase stress tolerance

[20]

Os.25621.2.s1_at

10.0

3.9

3.4

10.7

8.1

65.1

15.5

  

9.5

6.0

 

4.6

LOC_Os12g16720.1

SL1

KO/KD - enhanced resistance

[33]

Os.12372.2.s1_x_at

−1.4

 

−2.4

−1.5

−2.1

−3.4

−1.8

  

−5.9

−3.4

−3.1

 

LOC_Os08g06280.3

OsLSD1

Ox - increased susceptibility

[45]

Os.42024.1.s1_at

 

−1.7

  

1.6

−4.0

2.2

  

−2.0

−2.3

1.8

−15.2

LOC_Os01g56420.1

COPT1

Ox - increased susceptibility

[46]

Os.40018.1.s1_at

2.0

  

6.1

2.1

36.5

54.5

2.6

  

4.0

1.9

 

LOC_Os05g45410.1

SPL7

KO/KD -increased susceptibility

[34]

Os.12767.1.s1_a_at

−1.5

  

−1.7

 

22.0

−2.3

−2.5

 

1.5

1.5

 

−2.3

LOC_Os07g34570.1

OsDR8

KO/KD -increased susceptibility

[47]

Os.12501.1.s1_at

8.0

   

1.6

66.7

−2.1

   

6.0

−2.0

−4.5

LOC_Os01g55940.1

GH3-2

Activation - enhanced resistance

[48]

Os.11798.1.s1_at

1.7

 

10.8

   

8.5

  

11.7

2.8

1.7

1.7

LOC_Os07g40290.1

OsGH3-8

Ox - enhanced resistance

[49]

Os.2448.1.s1_at

−2.7

  

−2.1

−2.2

2.5

−1.4

  

−1.6

−1.8

 

4.4

LOC_Os02g02840.1

OsRacB

Ox - increased susceptibility

[30]

Os.4684.1.s1_at

1.6

   

−1.8

4.5

   

−2.0

−2.3

 

1.4

LOC_Os01g49290.1

Rack1

Ox - enhanced resistance

[50]

Os.10401.1.s1_s_at

 

14.5

   

46.2

     

−1.8

 

LOC_Os08g42350.1

xa13/8N3

KO/KD - enhanced resistance

[51]

Os.5491.1.a1_s_at

2.4

2.4

−2.3

  

4.5

−1.5

  

1.2

1.6

  

LOC_Os12g29220.1

MtN3/saliva

Expression - enhanced resistance

[36]

Os.27244.1.a1_s_at

−7.3

 

−4.9

  

−3.3

   

−1.4

1.2

  

LOC_Os04g32850.1

Pi21

KO/KD - enhanced resistance

[52]

Os.1311.1.s1_at

2.9

    

4.0

   

−2.3

−1.6

−1.5

 

LOC_Os02g02410.1

BiP3

Ox - increased susceptibility

[53]

Os.19321.1.s1_at

1.4

   

1.9

6.4

5.1

3.5

  

1.4

1.7

−1.8

LOC_Os03g60650.1

XB15

KO/KD - enhanced resistance

[54]

Os.8901.1.s1_at

1.6

  

1.8

2.3

3.1

2.9

    

2.6

 

LOC_Os02g22130.1

OsGAP1

Ox - enhanced resistance

[55]

Os.9338.1.s1_at

1.4

    

1.9

   

1.2

1.2

  

LOC_Os01g43540.1

OsSGT1

Ox - enhanced resistance

[56]

Os.8353.1.s1_at

 

2.8

    

−1.9

−3.0

 

4.3

3.9

1.9

2.2

LOC_Os01g68770.1

OsSBP

Ox - enhanced resistance

[57]

Os.27112.1.s1_at

1.7

  

1.9

1.8

12.7

   

2.5

3.2

 

−5.1

LOC_Os01g09800.1

NH1

Ox - enhanced resistance

[58]

Os.19086.2.s1_x_at

−1.8

   

−1.4

1.5

   

1.3

  

1.7

LOC_Os01g68860.1

C3H12

KO/KD -increase susceptibility

[37]

Osaffx.19417.2.s1_x_at

 

−1.1

           

LOC_Os11g47210.1

xa26

Ox - enhanced resistance

[59]

Os.406.1.s1_a_at

1.7

 

2.2

1.8

 

19.7

9.0

2.7

2.6

2.9

 

3.2

−3.4

LOC_Os03g17700.1

BIMK1/OsMPK5

KO/KD - enhanced resistance

[60]

Os.6126.1.s1_at

 

−1.6

   

3.8

3.6

3.2

 

1.4

3.2

1.9

2.1

LOC_Os04g41160.1

OsOxi1 (90%)

Ox - enhanced resistance

[61]

  1. The Affymetrix probeset ID, fold-change responses to: Bacterial infection; 1. Resistant (Xoo.), 2. Susceptible (Xoo.), 3. Susceptible (Xoc.) [16], Parasite infection [14]; 4. Resistant (S.hermonthica), 5. Susceptible (S.hermonthica), Fungus; 6. Susceptible (M. grisea) [13], 7. Susceptible (M.oryzae) [19], Virus; 8. Resistant (Rice stripe virus), 9. Susceptible (Rice stripe virus) – GSE11025, Abiotic stress [17]; 10. Drought, 11. Salt, 12. Cold, 13. Heat [18]. In addition, the locus identifier (MSU), gene name, phenotype and reference are also shown for each gene.
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