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Table 4 Identified significant SNPs-traits associations in genome wide study on the MAGIC population

From: Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition

Traits

SNP

Chr

Position

QTL span (kb)

2015WS

2016DS

Source: http://qtaro.abr.affrc.go.jp

p-value

R2 (%)

FDR

p-value

R2 (%)

FDR

Gene

QTLs

NR3

S4_31728342

4

31728342

 

2.06 × 10− 7

9

0.0050

2.28 × 10− 7

16

0.00552

nal1(nal5) [48]

rfw4a [49], Root thickness [50, 51], Rooting depth [50]

RHL

S5_15470847

5

15470847

0.033a

1.99 × 10− 7

11

0.0048

5.20 × 10−8

12

0.00126

OsIPT3 [52]; OsEXPA3 [53]

 

S5_15470880

5

15470880

4.31 × 10−6

9

0.0523

6.79 × 10− 7

10

0.00823

RHD

S5_15470880

5

15470880

 

4.34 × 10−6

12

0.0603

2.04 × 10− 7

11

0.00495

OsIPT3 [52]; OsEXPA3 [531]

 

FLA

S5_15133031

5

15133031

 

2.88 × 10− 8

19

0.0007

1.50 × 10− 7

18

0.00357

  

S4_21832119

4

21832119

 

4.75 × 10− 6

16

0.0575

2.95 × 10− 7

18

0.00357

tdd1 [54]

 

FLAngle

S9_19178976

9

19178976

 

1.82 × 10− 7

12

0.0044

2.99 × 10− 7

13

0.00725

TAC1 [55]

Ta1 [56], Ta [57]

DTFirst

S6_16444037

6

16444037

0.045a

2.04 × 10− 7

18

0.0032

3.40 × 10− 7

19

0.00824

 

qGP-6 [58]

S6_16444038

6

16444038

2.62 × 10− 7

18

0.0032

1.00 × 10− 6

19

0.01212

S6_16444082

6

16444082

      

DTFull

S11_24806601

11

24806601

0.036a

1.67 × 10− 7

15

0.0040

    

qGP-11, qGI-11 [58], yld11.1, gpl11.1, gw11.1 [59]

S11_24806565

11

24806565

   

2.47 × 10−7

20

0.00600

S11_24806596

11

24806596

3.41 × 10−7

15

0.0041

2.84 × 10−6

18

0.03302

Spad

S2_16191048

2

16191048

177

2.43 × 10−7

14

0.0059

5.18 × 10−9

18

0.00013

OsWRKY42 [60]

Ghd7 [61]

S2_16013833

2

16013833

   

1.26 × 10− 6

14

0.01523

BS

S3_21737519

3

21737519

 

9.39 × 10−8

12

0.0023

2.76 × 10−7

19

0.00669

  

SD

S2_31078747

2

31078747

 

3.69 × 10−7

12

0.0089

2.47 × 10− 7

17

0.00599

bc3 [62]

 

CD

S2_30984762

2

30984762

93.99

9.97 × 10− 7

13

0.0024

2.83 × 10− 7

27

0.00686

bc3 [62]

 

S2_30987475

2

30987475

1.03 × 10−6

12

0.0125

     

S2_31078747

2

31078747

1.26 × 10−7

10

0.1020

     

PHT

S11_17805610

11

17805610

 

1.88 × 10−7

26

0.0035

1.77 × 10− 7

29

0.00260

  

S1_38481437

1

38481437

 

2.87 × 10−7

26

0.0035

2.15 × 10− 7

29

0.00260

Sd1 [63], qDTY1.1 [64]

 

GY

S11_17412133

11

17412133

0.005a

2.12 × 10− 7

26

0.0051

3.02 × 10− 7

26

0.00073

 

yld11.1, gpl11.1, gw11.1 [59]

S11_17412134

11

17412134

4.11 × 10−6

24

0.0498

1.08 × 10−6

24

0.00869

 

S11_17412139

11

17412139

6.80 × 10−6

24

0.0549

2.91 × 10−7

24

0.00352

 

SY

S11_15708717

11

15708717

 

3.15 × 10−7

17

0.0076

2.20 × 10−7

15

0.00534

  

DTF

S11_17316419

11

17316419

 

7.71 × 10−8

24

0.0019

1.87 × 10−8

30

0.00045

 

VVG

S1_37653811

1

37653811

14a

1.52 × 10− 8

17

0.0004

2.23 × 10− 8

15

0.00054

Lax [65], moc [66]

 

S1_37639734

1

37639734

1.70 × 10−7

15

0.0021

     

S11_25462225

11

25462225

    

2.68 × 10−7

13

0.00325

  

Fe uptake

S2_29221003

2

29221003

0.012 a

3.49 × 10−7

86

0.0083

   

OsYSL15 [67], OsCKI1 [68], OsGPX3 [69], MAIF1 [70]

 

S2_29221015

2

29221015

 

6.84 × 10− 7

81

0.0083

    

N uptake

S5_14987295

5

14987295

 

3.43 × 10−7

90

0.0083

   

OsIPT3 [52]

 

S6_30887442

6

30887442

 

9.82 × 10−6

72

0.1190

   

OsPTR9 [71]

 

P uptake

S5_14987295

5

14987295

 

3.36 × 10−7

92

0.0081

   

OsIPT3 [52]

 

S6_27868961

6

27868961

3018

7.64 × 10−5

71

0.2644

   

OsPTR9 [71]

 

S6_30887442

6

30887442

6.45 × 10−6

80

0.0781

    

Zn uptake

S7_26042045

7

26042045

 

3.29 × 10−7

90

0.0080

   

OsNAS3 [72], aldolase [73]

7–3 [74]

  1. NR3 number of nodal roots at 29 DAS, RHL root hair length, RHD root hair density, FLA flag leaf area, FLAngle Flag leaf angle, DTFirst days to first emergence, DTFull days to full emergence, SPAD cholorophyll content, BS bending strength, SD stem diameter, CD culm diameter, PHT plant height, GY grain yield, SY straw yield, DTF days to 50% flowering, VVG vegetative vigor, Fe uptake iron uptake, N uptake nitrogen uptake, P uptake phosphorus uptake, Zn uptake zinc uptake, DS dry season, WS wet season, R2 percent phenotypic variance (PV) explained by SNPs, FDR false discovery rate
  2. aThe associated SNPs with very small interval (≤14 kb) can be considered as the same locus
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BMC Genomics

ISSN: 1471-2164

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