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Table 2 The 24 significant SNPs and their rice genomic information

From: Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage

Trait

marker

population-identyfied

allele

Chr

Pos

p-value

candidate genes

functional annotations

RN

seq3_1727891

full, Pop2

C/T

3

1727891

6.54E-06

CDPK13 (Ho et al., 2013)

gibberellin biosynthesis

        

drought stress

MRL,RGA,RL

seq4_5315034

full, Pop2

A/G

4

5315034

9.69E-07

OsCyc1 (Otomo et al., 2004);

allelopathy

       

OsDTS2 (Wilderman et al., 2004)

allelopathy

MRL,RGA,RL

seq4_15403602

full, Pop2

T/C

4

15403602

8.52E-10

  

MRL

seq4_18740406

Pop1

C/G

4

18740406

1.84E-08

SLL1/OsSAD5 (Shelley et al., 2013)

lateral root length

        

,fatty acid denatures

RGA

seq5_6882162

Pop2

T/C

5

6882162

2.88E-05

OsPYL (Kim et al., 2014);

abscisic acid receptor

       

OsGA2ox10 (Lo et al., 2008)

gibberellin 2-oxidases

RGA

seq5_6884530

Pop2

C/A

5

6884530

2.88E-05

  

RGA

seq5_6890004

Pop2

G/A

5

6890004

2.88E-05

  

RGA

seq5_6908893

Pop2

T/C

5

6908893

2.88E-05

  

RGA

seq5_6935074

Pop2

T/G

5

6935074

2.88E-05

  

RGA

seq5_6945,054

full, Pop2

T/C

5

6945054

5.54E-06

  

RGA

seq5_6959356

Pop2

G/A

5

6959356

2.88E-05

  

RGA

seq5_6981293

Pop2

T/C

5

6981293

2.88E-05

  

MRL,RL

seq6_12537542

full, Pop2

T/C

6

12537542

3.73E-06

OsPT9 (Wang et al., 2014)

phosphate uptake

MRL,RGA

seq6_29405495

full, Pop1

C/T

6

29405495

3.30E-08

OsMPK4 (Agrawal et al., 2003)

salicylic acid and jasmonic

        

acid-signaling pathway

MRL,RL,RGA

seq7_5182658

full, Pop2

A/G

7

5182658

1.25E-08

SQS (Manavalan et al., 2012)

root length

        

drought tolerance

MRL,RL

seq8_433198

full, Pop1

G/T

8

433198

1.25E-05

  

RN

seq8_15949787

Pop2

G/C

8

15949787

6.51E-07

qtl (Lilley et al., 1996)

dehydration tolerance

MRL,RN

seq8_18343904

Pop1,Pop2

T/G

8

18343904

1.05E-08

  

MRL,RN

seq8_18364190

full, Pop1,Pop2

C/T

8

18364190

1.77E-08

  

MRL

seq8_18365309

Pop1

C/T

8

18365309

1.00E-07

  

MRL,RL,RGA

seq9_11941704

Pop1

T/C

9

11941704

6.28E-09

  

MRL,RL

seq9_15520580

Pop1

A/C

9

15520580

2.45E-07

OsGL1–1 (Islam et al., 2009)

drought tolerance

MRL,RL

seq11_368662

full, Pop2

A/G

11

368662

5.23E-06

  

MRL

seq12_16592156

Pop1

T/C

12

16592156

2.00E-08

DEC (Itoh et al. 2012)

cytokinin signaling pathway

root length