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Table 1 Trait-associated SNP identified within each sub-population of 3K-RGP

From: Explore the genetics of weedy traits using rice 3K database

Trait

Pop

SNP

P-value

No. gene ± 100 kb

Candidate genes

Annotation

AWCO_REV

ind

S1_2222938

2.34E−08

19

  
 

temp

S1_26642467

1.64E−09

18

  
 

temp

S1_34999638

6.77E−07

25

Os01g0820700

OsWRKY116

 

ind

S1_38893251

1.26E−07

32

Os01g0894500

Sep15/SelM redox domain containing protein

 

aus

S2_5126277

1.35E−08

36

  
 

aus

S2_18016425

3.79E−08

15

  
 

ind

S2_20021623

3.27E−07

19

  
 

aus

S2_35221348

1.99E−07

42

  
 

aus

S3_14604626

7.34E−08

26

  
 

trop

S3_22066093

1.37E−08

22

  
 

temp

S4_3569126

8.05E−10

13

  
 

ind

S4_32368836

9.04E−09

40

Os04g0636500

BTB domain containing protein

 

trop

S5_23650885

3.36E−07

30

  
 

aus

S6_7624195

3.23E−10

25

  
 

trop

S6_21261276

1.08E − 11

19

  
 

ind

S6_22232682

2.78E−07

25

  
 

aus

S7_671056

2.97E−08

27

  
 

ind

S7_8538306

1.93E−08

8

Os07g0253100

Conserved hypothetical protein

 

ind

S7_27892037

1.19E−09

36

  
 

temp

S8_23747966

2.51E−07

22

  
 

trop

S8_24022229

7.43E−12

37

Os08g0485800

Barwin-related endoglucanase domain containing protein

     

Os08g0485500 (− 23.4 kb)

RAE2; Regulation of awn development and elongation

 

ind

S10_10954998

1.67E−08

16

  
 

trop

S12_14872482

1.84E−11

11

  

PSH

temp

S2_18492267

1.99E−07

19

  
 

temp

S3_3398933

1.35E−08

34

  
 

aus

S4_4462336

7.23E08

21

  
 

aus

S4_4462447

2.33E07

21

  
 

temp

S4_4464494

1.28E07

21

  
 

aus

S4_4488660

9.51E08

21

Os04g0166000

Conserved hypothetical protein

 

temp

S4_5387818

4.08E−07

10

  
 

temp

S12_1917244

5.88E−08

35

Os12g0139400

OsRR10

PTH

trop

S2_24505237

1.22E−07

23

  
 

trop

S7_13096799

5.14E−12

12

  
 

trop

S8_20373414

1.06E−10

20

  

SCCO_REV

ind

S1_8264505

2.21E−07

30

  
 

ind

S1_14709154

2.38E−14

18

  
 

ind

S1_19343008

2.26E−07

18

  
 

trop

S2_20541410

5.66E−08

10

  
 

ind

S2_35121783

1.35E−07

34

Os02g0818700

Similar to tumor-related protein

 

temp

S3_4766628

8.81E−07

36

  
 

temp

S3_12419022

3.69E−09

32

  
 

trop

S3_16978020

4.30E−07

18

  
 

aus

S3_29290186

4.03E−08

20

  
 

trop

S7_6062746

3.98E54

15

Os07g0211500 (-0.1 kb)

Rc

 

ind

S7_6067855

1.15E114

15

Os07g0211500

Rc

 

aus

S7_6068017

1.81E40

15

Os07g0211500

Rc

 

temp

S7_23073822

7.43E−15

29

Os07g0571500

Similar to transmembrane protein 49

 

ind

S8_8581885

1.39E−08

15

  
 

aus

S8_9105408

4.44E−11

22

Os08g0249100

OsRLCK249

 

ind

S9_1298020

2.85E−08

14

  
 

temp

S10_10394027

1.15E−08

13

Os10g0346300

OsLAC17

 

trop

S11_17682735

8.45E−09

10

  
 

trop

S11_19853800

6.99E−08

12

  

SDHT_CODE

aus

S1_15921134

1.38E−07

11

  
 

aus

S1_30508051

1.69E−08

37

  
 

temp

S1_31283533

4.33E−07

27

  
 

ind

S2_19154582

8.69E−08

19

  
 

aus

S2_19678534

3.74E−08

24

  
 

aus

S4_21716120

1.96E−07

35

  
 

ind

S8_8643208

4.52E−13

11

  
 

ind

S8_25508381

2.02E−09

25

Os08g0242400 (-2.4 kb)

OsWOX10

 

ind

S11_20514671

4.20E−11

20

Os11g0551900 (+7.3 kb)

OsGRF8

 

ind

S11_24872440

2.62E−11

12

  
 

aus

S12_154948

4.55E−08

26

  
 

ind

S12_365399

6.12E−08

34

  
 

ind

S12_25154542

2.89E−11

26

  
  1. The meaning for each trait abbreviation is as follows: AWCO_REV: awn color; PSH: panicle shattering degree; PTH: panicle threshability, SCCO_REV: seed coat color; SDHT_CODE: seedling height. Pop: sub-populations, including aus, indica (ind), temperate japonica (temp), and tropical japonica (trop). Markers were named based on their genomic position on the reference sequence (cv Nipponbarre, IRGSP v1) for S[chromosome]_[bp position on the chromosome]. When the trait-associated SNP fell into an annotated gene, the gene name was indicated in the column of “Candidate gene”. If a gene, whose function was related to the trait of interest, fell within ± 100 kb of the trait-associated SNP, the distance between the SNP and the start of the gene is indicated in the parentheses: minus sign means before the SNP, plus sign means after the SNP. Annotation was from RAP-DB. Closely positioned SNPs for which the same genes were identified within the ± 100 kb region were underlined in bold