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Table 3 Summary of SNP markers associated with flour functionality 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

Flour protein

S1B_46883868

1B

46,883,868

C/A

0.09

1.67E-09

3.37E-05

0.29

Flour protein

S2A_159882069

2A

159,882,069

C/T

0.09

4.24E-07

2.46E-03

0.24

Flour protein

S2D_28763299

2D

28,763,299

G/A

0.34

1.17E-08

1.19E-04

-0.18

Flour protein

S3B_690878020

3B

690,878,020

T/C

0.44

8.56E-09

1.16E-04

-0.19

Flour protein

S4A_514430898

4A

514,430,898

C/T

0.46

3.11E-12

1.26E-07

0.19

Flour protein

S4B_63121316

4B

63,121,316

C/T

0.10

2.21E-06

9.95E-03

0.22

Flour protein

S5D_135645455

5D

135,645,455

G/A

0.35

2.28E-08

1.85E-04

-0.17

Flour protein

S7A_32805734

7A

32,805,734

G/A

0.27

1.27E-06

6.46E-03

-0.16

Flour protein

S7A_730416426

7A

730,416,426

G/A

0.21

1.06E-05

4.00E-02

0.13

Flour protein

S7D_507227865

7D

507,227,865

G/T

0.05

1.09E-05

4.00E-02

-0.32

Flour protein

SUN_351152321

UN

351,152,321

A/G

0.31

1.35E-07

9.13E-04

-0.19

SDS sedimentation

S1A_5326555

1A

5326,555

G/A

0.30

1.59E-06

8.65E-03

-0.37

SDS sedimentation

S1B_561712520

1B

561,712,520

G/A

0.40

8.53E-14

3.45E-09

0.48

SDS sedimentation

S1D_121990680

1D

121,990,680

T/G

0.07

1.08E-06

7.26E-03

-0.67

SDS sedimentation

S1D_223797230

1D

223,797,230

C/A

0.05

1.78E-06

8.65E-03

-0.75

SDS sedimentation

S1D_411063068

1D

411,063,068

T/A

0.14

1.95E-10

3.95E-06

0.65

SDS sedimentation

S2B_155110438

2B

155,110,438

A/G

0.42

2.14E-06

8.65E-03

-0.33

SDS sedimentation

S3A_697202279

3A

697,202,279

T/C

0.09

7.40E-06

2.50E-02

0.47

SDS sedimentation

S3B_723505334

3B

723,505,334

T/G

0.43

1.18E-09

1.59E-05

-0.42

SDS sedimentation

S5A_585018041

5A

585,018,041

A/G

0.44

1.97E-06

8.65E-03

0.33

SDS sedimentation

S5A_633105837

5A

633,105,837

C/A

0.06

3.25E-06

1.20E-02

-0.75

SDS sedimentation

S5B_539075483

5B

539,075,483

A/G

0.11

7.34E-08

7.44E-04

0.61

SDS sedimentation

S7A_108785365

7A

108,785,365

G/A

0.07

1.06E-05

3.32E-02

0.93

SDS sedimentation

S7A_675198728

7A

675,198,728

C/T

0.11

1.42E-07

1.15E-03

-0.57

Water SRC

S1B_547973154

1B

547,973,154

C/T

0.10

5.59E-08

3.78E-04

0.60

Water SRC

S1B_653681752

1B

653,681,752

G/T

0.14

1.25E-10

5.08E-06

0.92

Water SRC

S2A_613720768

2A

613,720,768

T/C

0.06

2.02E-07

1.02E-03

-0.74

Water SRC

S2B_66559534

2B

66,559,534

C/A

0.08

5.49E-07

2.22E-03

0.69

Water SRC

S3A_24993876

3A

24,993,876

C/T

0.08

1.49E-07

8.61E-04

0.74

Water SRC

S5A_382294123

5A

382,294,123

G/A

0.24

2.88E-08

2.33E-04

-0.46

Water SRC

S5A_673550305

5A

673,550,305

C/G

0.37

1.18E-09

1.59E-05

-0.45

Water SRC

S6B_29771821

6B

29,771,821

G/C

0.35

2.97E-07

1.34E-03

-0.36

Water SRC

S7A_709765148

7A

709,765,148

G/T

0.12

9.56E-10

1.59E-05

0.69

Water SRC

S7B_539196288

7B

539,196,288

A/G

0.07

1.35E-08

1.37E-04

0.72

Water SRC

S7D_327690580

7D

327,690,580

G/A

0.26

8.76E-06

3.23E-02

-0.38

FSV

S1A_534055653

1A

534,055,653

G/T

0.05

1.70E-06

8.40E-03

0.74

FSV

S1B_6678732

1B

6,678,732

A/C

0.28

8.90E-09

3.60E-04

-0.38

FSV

S2A_705583892

2A

705,583,892

T/C

0.10

2.86E-06

9.65E-03

0.44

FSV

S2B_7653964

2B

7,653,964

C/T

0.19

2.28E-06

8.40E-03

0.43

FSV

S2B_31382050

2B

31,382,050

G/C

0.48

1.74E-06

8.40E-03

-0.27

FSV

S3D_266839264

3D

266,839,264

A/G

0.29

2.21E-06

8.40E-03

0.31

FSV

S3D_601013637

3D

601,013,637

A/G

0.13

4.77E-07

3.22E-03

0.49

FSV

S4A_12168393

4A

12,168,393

C/T

0.33

3.61E-07

3.22E-03

-0.33

FSV

S4B_541252759

4B

541,252,759

A/G

0.15

2.04E-06

8.40E-03

-0.44

FSV

S5D_86308878

5D

86,308,878

C/A

0.05

4.10E-08

8.31E-04

0.80

FSV

S7A_200608114

7A

20,060,8114

G/T

0.18

1.28E-05

3.71E-02

0.45

FSV

S7A_583357214

7A

583,357,214

G/A

0.05

4.20E-07

3.22E-03

0.73

FSV

S7B_540056850

7B

540,056,850

C/T

0.06

6.71E-08

9.06E-04

0.66

FSV

S7D_38000037

7D

38,000,037

C/T

0.06

5.62E-06

1.75E-02

-0.63

  1. aWater SRC, water solvent retention capacity; FSV, flour swelling volume
  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 FSV and lower phenotypic values for flour protein, SDS sedimentation, and water SRC)
  5. eMinor allele frequency of the SNP
  6. fP value of the significant SNP
  7. gFalse discovery rate of the significant SNP
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