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Table 2 Summary of SNP markers associated with milling traits in 672 soft white winter wheat genotypes

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

Trait

SNPa

Chromosome

Position (bp)b

Allelesc

MAFd

P valuee

FDRf

Effect

Break flour yield

S1B_100055026

1B

100,055,026

T/C

0.08

2.96E-07

2.40E-03

1.00

Break flour yield

S1B_653681752

1B

65,368,1752

G/T

0.14

1.32E-13

3.52E-09

-1.05

Break flour yield

S2A_678005650

2A

678,005,650

C/T

0.31

1.74E-13

3.52E-09

0.55

Break flour yield

S3B_630394456

3B

630,394,456

G/T

0.06

6.94E-07

4.69E-03

0.79

Break flour yield

S4A_584538827

4A

584,538,827

A/G

0.11

7.69E-11

1.04E-06

-0.87

Break flour yield

S4B_611852943

4B

611,852,943

G/C

0.08

6.37E-09

6.45E-05

0.70

Break flour yield

S5B_508665777

5B

508,665,777

T/C

0.07

3.67E-06

1.65E-02

-0.62

Break flour yield

S7A_34527313

7A

34,527,313

G/C

0.33

9.84E-06

3.63E-02

0.27

Break flour yield

S7A_642899331

7A

642,899,331

C/G

0.14

1.23E-06

7.13E-03

-0.44

Break flour yield

S7A_732594008

7A

732,594,008

A/G

0.23

1.60E-06

8.11E-03

-0.41

Break flour yield

S7D_56065854

7D

56,065,854

C/G

0.17

4.55E-06

1.84E-02

-0.44

Flour yield

S1A_9128313

1A

9,128,313

G/T

0.39

1.09E-06

4.43E-03

0.38

Flour yield

S1A_15686346

1A

15,686,346

A/G

0.34

2.28E-06

8.40E-03

-0.31

Flour yield

S1A_587581129

1A

587,581,129

A/G

0.06

1.20E-05

3.05E-02

-0.48

Flour yield

S1B_555294134

1B

555,294,134

C/T

0.10

3.62E-06

1.20E-02

-0.48

Flour yield

S1B_585326031

1B

585,326,031

C/G

0.44

5.55E-07

3.22E-03

0.28

Flour yield

S1B_653681752

1B

653,681,752

G/T

0.14

5.38E-17

2.18E-12

-1.05

Flour yield

S2A_57924183

2A

57,924,183

A/G

0.42

9.10E-06

2.46E-02

-0.25

Flour yield

S3A_621592864

3A

621,592,864

C/T

0.31

7.74E-06

2.24E-02

-0.31

Flour yield

S5A_382294123

5A

382,294,123

G/A

0.24

1.37E-11

1.84E-07

0.55

Flour yield

S5B_508665777

5B

508,665,777

T/C

0.07

2.14E-07

1.45E-03

-0.64

Flour yield

S6B_19335996

6B

19,335,996

G/A

0.07

2.13E-13

4.32E-09

-0.89

Flour yield

S6D_471614981

6D

471,614,981

T/C

0.35

1.88E-07

1.45E-03

-0.32

Flour yield

S7A_66283612

7A

66,283,612

A/C

0.33

8.24E-07

4.17E-03

-0.34

Flour yield

S7A_735818991

7A

735,818,991

C/G

0.22

9.60E-07

4.32E-03

0.36

Flour yield

S7B_123656516

7B

123,656,516

G/C

0.15

7.25E-10

7.34E-06

-0.60

Flour ash

S1D_20702150

1D

20,702,150

G/T

0.23

2.54E-06

1.03E-02

0.01

Flour ash

S1D_488805272

1D

488,805,272

G/A

0.17

3.53E-06

1.30E-02

0.01

Flour ash

S2A_77744254

2A

77,744,254

G/A

0.09

1.18E-05

3.99E-02

-0.01

Flour ash

S2B_794429290

2B

794,429,290

C/T

0.30

5.61E-07

3.79E-03

-0.01

Flour ash

S2D_551847796

2D

551,847,796

G/C

0.10

2.19E-06

9.85E-03

-0.01

Flour ash

S3D_540232458

3D

540,232,458

C/A

0.08

1.60E-05

4.99E-02

-0.01

Flour ash

S4A_120144412

4A

120,144,412

T/C

0.10

4.63E-08

4.85E-04

-0.02

Flour ash

S5A_3649534

5A

3,649,534

C/A

0.33

3.13E-07

2.53E-03

0.01

Flour ash

S5B_64633223

5B

64,633,223

G/A

0.05

7.56E-07

3.83E-03

-0.02

Flour ash

S5B_68052478

5B

68,052,478

A/T

0.36

1.49E-09

3.02E-05

-0.01

Flour ash

S5D_416596873

5D

416,596,873

T/G

0.10

1.33E-10

5.38E-06

0.02

Flour ash

S6D_469583807

6D

469,583,807

G/C

0.10

7.00E-07

3.83E-03

0.01

Flour ash

S7B_624947199

7B

624,947,199

C/A

0.05

4.79E-08

4.85E-04

0.02

Milling score

S1D_14707739

1D

14,707,739

G/T

0.08

4.78E-08

3.88E-04

1.49

Milling score

S2B_47200283

2B

47,200,283

C/G

0.22

5.52E-06

2.24E-02

1.00

Milling score

S2B_130028901

2B

130,028,901

G/C

0.27

6.33E-06

2.33E-02

-0.59

Milling score

S2B_759735490

2B

759,735,490

T/C

0.27

3.51E-11

1.42E-06

1.01

Milling score

S3B_82495634

3B

82,495,634

G/C

0.07

1.64E-06

9.48E-03

1.17

Milling score

S4A_724316409

4A

724,316,409

G/A

0.27

1.67E-05

5.19E-02

0.58

Milling score

S5A_20640566

5A

20,640,566

C/T

0.09

1.41E-08

2.29E-04

-1.24

Milling score

S5B_68052478

5B

68,052,478

A/T

0.36

2.19E-06

1.11E-02

0.71

Milling score

S5B_503326206

5B

503,326,206

C/T

0.19

2.49E-06

1.12E-02

-0.78

Milling score

S6B_27918221

6B

27,918,221

C/T

0.24

5.81E-08

3.93E-04

0.90

Milling score

S6D_471614981

6D

47,161,4981

T/C

0.37

1.70E-08

2.29E-04

-0.83

Milling score

S7D_319849357

7D

319,849,357

G/A

0.14

4.16E-08

3.88E-04

1.25

Milling score

SUN_31626104

UN

31,626,104

G/T

0.25

1.08E-05

3.63E-02

0.65

  1. aSignificant single-nucleotide polymorphism (SNP). Markers in bold are markers with large effects
  2. bPhysical position of SNP sequence based on Wheat Chinese Spring IWGSC RefSeq v1.0
  3. cSNP major allele/minor allele, the allele in bold is the favorable allele in soft white wheat (associated with higher phenotypic values for break flour yield, flour yield, and milling score and lower phenotypic values for flour ash)
  4. dMinor allele frequency of the SNP
  5. eP value of the significant SNP
  6. fFalse discovery rate of the significant SNP
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BMC Genomics

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