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Table 2 QTLs associated with rice blast resistance identified by GWAS

From: Pangenome-Wide Association Study and Transcriptome Analysis Reveal a Novel QTL and Candidate Genes Controlling both Panicle and Leaf Blast Resistance in Rice

QTL

Marker

Position on NIP genome

Marker type

MAF

P-value

FDR

Phenotype contribution

Co-location gene

 

PBR

        

qPBR1

Chr1_9116925

8,118,681

SNP

0.22

1.15E-07

5.97E-02

5.10

  

qPBR2

Chr2_37198859

33,002,918

SNP

0.12

7.16E-08

5.97E-02

5.27

  

qPBR3

Chr3_37987685

32,981,449

SNP

0.32

1.24E-07

5.97E-02

5.07

  

qPBR12

Chr12_12599463

10,798,977

SNP

0.14

2.08E-07

5.97E-02

4.88

Ptr

 

Chr12_12637980

10,833,939

PAV

0.22

4.45E-07

1.59E-01

4.56

 

LBR

        

qLBR1

Chr1_9115897

8,117,653

SNP

0.22

1.06E-09

1.72E-04

6.87

  

qLBR2a

Chr2_24921088

21,953,715

SNP

0.19

3.34E-08

2.80E-04

5.58

Pid1

 

qLBR2b

Chr2_37198859

33,002,918

SNP

0.12

5.43E-09

1.72E-04

6.26

  

qLBR3a

Chr3_20356924

18,120,630

SNP

0.22

1.05E-08

1.78E-04

6.01

  

qLBR3b

Chr3_37987664

32,981,428

SNP

0.22

1.24E-10

1.72E-04

7.69

  

qLBR4a

Chr4_5270980

4,054,328

PAV

0.34

1.24E-07

1.12E-03

5.25

  

qLBR4b

Chr4_8785383

6,618,386

SNP

0.20

1.17E-07

7.14E-04

5.12

  

qLBR4c

Chr4_16027200

12,470,034

PAV

0.23

8.67E-07

6.23E-03

4.52

  

qLBR6a

Chr6_27624040

23,022,166

PAV

0.12

2.32E-07

1.94E-03

5.02

  

qLBR6b

Chr6_30626962

25,619,840

SNP

0.39

3.53E-07

1.84E-03

4.72

  

qLBR7a

Chr7_12449656

11,050,922

SNP

0.20

4.38E-08

3.34E-04

5.49

  

qLBR7b

Chr7_16306460

14,422,872

PAV

0.50

3.76E-08

4.04E-04

5.70

  

qLBR9

Chr9_4512315

3,546,374

SNP

0.22

1.09E-09

1.72E-04

6.86

  

qLBR10

Chr10_10257687

8,056,337

SNP

0.24

1.06E-09

1.72E-04

6.87

  

qLBR11a

Chr11_1397560

1,286,775

PAV

0.21

8.74E-10

8.26E-05

7.14

  

qLBR11b

Chr11_23163296

19,007,058

SNP

0.20

1.16E-08

1.78E-04

5.97

  

qLBR12a

Chr12_12645340

10,841,299

PAV

0.23

5.75E-11

8.26E-05

8.21

Ptr

 

Chr12_12653788

10,849,747

SNP

0.22

1.23E-09

1.72E-04

6.82

 

qLBR12b

Chr12_16714680

13,838,432

PAV

0.28

1.35E-08

1.89E-04

6.09

  
  1. PBR: panicle blast resistance QTL (GWAS with phenotypes in the field)
  2. LBR: leaf blast resistance QTL (GWAS with phenotypes in the field)