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Table 1 Summary of SNP markers associated with grain characteristics in 672 soft white winter wheat genotypes

From: Genetic architecture of end-use quality traits in soft white winter wheat

Traita

SNPb

Chromosome

Position (bp)c

Allelesd

MAFe

P valuef

FDRg

Effect

SKCS hardness

S1A_583894689

1A

583,894,689

T/C

0.28

1.75E-05

4.44E-02

1.04

SKCS hardness

S1B_635869100

1B

635,869,100

A/G

0.24

3.84E-08

5.19E-04

-1.46

SKCS hardness

S3A_690786387

3A

690,786,387

A/G

0.23

4.73E-06

1.60E-02

1.72

SKCS hardness

S3B_718850970

3B

718,850,970

C/G

0.46

7.04E-09

1.43E-04

-1.34

SKCS hardness

S4D_509798252

4D

509,798,252

A/G

0.38

1.32E-05

3.55E-02

-0.97

SKCS hardness

S5A_480515221

5A

480,515,221

C/T

0.14

2.91E-19

1.18E-14

-3.34

SKCS hardness

S5B_549556474

5B

549,556,474

G/T

0.06

1.45E-07

1.18E-03

-2.49

SKCS hardness

S6B_11537871

6B

11,537,871

C/T

0.05

5.51E-07

3.19E-03

-3.51

SKCS hardness

S6B_130163859

6B

130,163,859

A/G

0.18

4.98E-07

3.19E-03

-1.47

SKCS hardness

S6B_233122036

6B

233,122,036

T/C

0.07

7.69E-07

3.90E-03

2.10

SKCS hardness

S6B_705613777

6B

705,613,777

G/A

0.08

1.36E-06

6.15E-03

2.14

SKCS hardness

S7A_12011069

7A

12,011,069

T/A

0.05

9.44E-06

2.73E-02

2.85

SKCS hardness

S7A_514892901

7A

514,892,901

A/T

0.12

1.56E-06

6.32E-03

-1.78

SKCS hardness

S7B_643501407

7B

643,501,407

A/G

0.46

5.79E-08

5.86E-04

1.37

SKCS hardness

S7D_56065854

7D

56,065,854

C/G

0.17

9.33E-06

2.73E-02

1.32

SKCS hardness

S7D_617377539

7D

617,377,539

C/T

0.06

3.91E-06

1.44E-02

2.27

SKCS size

S1B_569507932

1B

569,507,932

T/C

0.47

1.19E-06

5.36E-03

0.02

SKCS size

S2B_154846350

2B

154,846,350

T/G

0.40

1.72E-06

6.96E-03

0.02

SKCS size

S2D_563799166

2D

563,799,166

G/T

0.07

8.65E-06

2.50E-02

-0.04

SKCS size

S2D_586961640

2D

58,6961,640

A/G

0.20

3.38E-06

1.05E-02

0.03

SKCS size

S3A_60689591

3A

60,689,591

T/C

0.32

3.84E-07

2.25E-03

-0.02

SKCS size

S3A_721092685

3A

721,092,685

C/G

0.17

2.26E-07

1.96E-03

0.03

SKCS size

S4B_578521140

4B

578,521,140

T/C

0.23

2.91E-08

3.93E-04

0.03

SKCS size

S5A_578074731

5A

578,074,731

A/G

0.21

4.99E-07

2.53E-03

-0.03

SKCS size

S5A_583031341

5A

583,031,341

C/T

0.42

2.28E-06

7.80E-03

-0.02

SKCS size

S5A_636959783

5A

636,959,783

T/C

0.17

2.31E-06

7.80E-03

-0.02

SKCS size

S5B_615969532

5B

615,969,532

G/A

0.08

3.89E-07

2.25E-03

0.04

SKCS size

S6B_126632693

6B

126,632,693

T/G

0.05

1.31E-08

2.65E-04

0.04

SKCS size

S6B_336606108

6B

336,606,108

T/G

0.17

2.42E-07

1.96E-03

-0.02

SKCS size

S6B_583281710

6B

583,281,710

G/A

0.11

2.86E-10

1.16E-05

0.04

SKCS weight

S1B_427530823

1B

427,530,823

T/C

0.15

5.42E-07

4.39E-03

-0.87

SKCS weight

S2A_165870782

2A

165,870,782

A/T

0.38

8.34E-07

5.63E-03

0.64

SKCS weight

S2B_18326207

2B

18,326,207

C/T

0.23

4.55E-07

4.39E-03

0.63

SKCS weight

S2B_533178165

2B

533,178,165

C/G

0.09

4.42E-07

4.39E-03

-1.11

SKCS weight

S2D_563799166

2D

563,799,166

G/T

0.07

1.16E-05

5.22E-02

-1.04

SKCS weight

S2D_613442636

2D

613,442,636

G/T

0.05

1.77E-06

8.96E-03

1.36

SKCS weight

S6B_583281710

6B

583,281,710

G/A

0.11

1.77E-07

4.39E-03

0.75

SKCS weight

S7B_686004231

7B

686,004,231

G/A

0.09

3.31E-07

4.39E-03

-1.15

SKCS weight

S7D_7495567

7D

7,495,567

G/T

0.05

1.14E-06

6.57E-03

1.42

Test weight

S2A_762292662

2A

762,292,662

T/G

0.23

8.08E-06

2.89E-02

-0.31

Test weight

S4B_413497949

4B

413,497,949

C/T

0.09

4.02E-08

5.43E-04

-0.39

Test weight

S5A_611568887

5A

611,568,887

A/G

0.25

1.79E-08

3.62E-04

0.24

Test weight

S5B_506953332

5B

506,953,332

T/A

0.21

1.76E-06

1.42E-02

-0.21

Test weight

S5B_550910513

5B

550,910,513

T/C

0.43

3.72E-06

2.15E-02

0.19

Test weight

S5B_605171604

5B

605,171,604

T/C

0.09

4.76E-06

2.15E-02

0.27

Test weight

S6A_46675024

6A

46,675,024

C/G

0.06

5.32E-06

2.15E-02

-0.36

Test weight

S6A_559428977

6A

559,428,977

G/A

0.26

2.45E-09

9.93E-05

0.27

Test weight

S6B_510608440

6B

510,608,440

G/A

0.08

4.91E-06

2.15E-02

0.40

Test weight

S7A_669715941

7A

669,715,941

T/C

0.14

3.66E-06

2.15E-02

-0.29

Test weight

S7B_40194878

7B

40,194,878

G/C

0.18

2.26E-07

2.29E-03

0.25

Test weight

S7B_636744313

7B

636,744,313

T/A

0.17

8.54E-06

2.89E-02

0.28

Grain protein

S1A_585175145

1A

58,517,5145

G/C

0.10

1.33E-05

4.48E-02

0.28

Grain protein

S1B_46883868

1B

46,883,868

C/A

0.09

1.04E-10

4.22E-06

0.38

Grain protein

S1B_633974958

1B

633,974,958

A/G

0.45

9.35E-08

7.58E-04

-0.18

Grain protein

S2A_612836091

2A

612,836,091

C/T

0.05

5.91E-06

2.18E-02

-0.31

Grain protein

S3B_405161312

3B

405,161,312

T/C

0.27

2.74E-06

1.20E-02

-0.19

Grain protein

S3B_690878020

3B

690,878,020

T/C

0.44

1.72E-06

9.94E-03

-0.14

Grain protein

S4A_352495200

4A

352,495,200

G/A

0.10

1.61E-06

9.94E-03

-0.23

Grain protein

S4B_63121316

4B

63,121,316

C/T

0.10

3.36E-08

3.41E-04

0.31

Grain protein

S5D_543253602

5D

543,253,602

G/A

0.08

1.85E-09

2.50E-05

-0.38

Grain protein

S6D_471179733

6D

471,179,733

A/C

0.05

2.95E-06

1.20E-02

0.52

Grain protein

S7A_731026067

7A

731,026,067

A/T

0.26

1.43E-09

2.50E-05

0.27

Grain protein

SUN_86449317

UN

86,449,317

T/G

0.19

1.45E-05

4.53E-02

0.22

Grain protein

SUN_351152321

UN

351,152,321

A/G

0.31

2.75E-06

1.20E-02

-0.19

  1. aSKCS, Single Kernel Characterization System
  2. bSignificant single-nucleotide polymorphism (SNP). Markers in bold are markers with large effects
  3. cPhysical position of SNP sequence based on Wheat Chinese Spring IWGSC RefSeq v1.0
  4. dSNP major allele/minor allele, the allele in bold is the favorable allele in soft white wheat (associated with higher phenotypic values for SKCS size, SKCS weight, and test weight and lower phenotypic values for SKCS hardness and grain protein content)
  5. eMinor allele frequency of the SNP
  6. fP value of the significant SNP
  7. gFalse discovery rate of the significant SNP