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Table 3 SNPs signifcantly associated with the four yield-related traits and previously reported QTLs at similar genome regions

From: Genome-wide association study of four yield-related traits at the R6 stage in soybean

Traits

SNPa

MAFb

Physical position

Significant region

Meanc

Effectd

Enve

Known QTLsf

Chr.

Position

Start

End

-Log10(P)

R2(%)

   

PFW

AX-90490395

0.34

2

46,440,530

46,321,460

46,559,600

6.41

27.72

3.81

15,16,mean

seed weight 50–12

AX-90483564

0.27

3

36,787,728

36,668,658

36,906,798

6.60

29.19

4.57

15,16,mean

 

AX-90435834

0.18

4

1,402,717

1,283,647

1,521,787

6.08

25.12

11.06

15,16,mean

Seed weight per plant 6–2; Seed weight 47–3; Seed height 1–12, Seed length 1–13

AX-90328574

0.11

9

39,625,218

39,506,148

39,744,288

6.52

27.10

11.46

15,16,mean

Seed weight 50–5; Seed yield 31–10

AX-90481424

0.24

14

5,733,475

5,614,405

5,852,545

6.52

27.22

4.58

15,16,mean

Seed weight 36–14

AX-90512978

0.14

14

45,661,649

45,542,579

45,780,719

6.49

27.16

15.43

15,16,mean

Seed yield 31–1

AX-90496773

0.07

16

1,617,227

1,498,157

1,736,297

7.03

29.99

16.33

15,16,mean

Seed yield 23–6; Pod maturity 19–6; Pod maturity 9–1

AX-90370125

0.08

16

5,791,933

5,672,863

5,911,003

7.54

33.61

0.53

15,16,mean

Seed yield 29–2

AX-90519309

0.35

17

4,197,693

4,078,623

4,316,763

7.34

32.14

8.22

15,16,mean

Seed weight 21–2; Seed weight 22–3; Seed weight 22–4

SFW

AX-90490395

0.34

2

46,440,530

46,321,460

46,559,600

6.26

26.86

0.64

15,16,mean

Seed weight 50–12

AX-90481424

0.24

14

5,733,475

5,614,405

5,852,545

6.45

26.54

0.75

15,16,mean

Seed weight 36–14

AX-90370125

0.08

16

5,791,933

5,672,863

5,911,003

6.37

27.80

0.01

15,16,mean

Seed yield 29–2

AX-90519309

0.35

17

4,197,693

4,078,623

4,316,763

6.35

27.47

1.74

15,16,mean

Seed weight 21–2;, Seed weight 22–3, Seed weight 22–4

SDW

AX-90505318

0.12

1

50,248,686

50,129,616

50,367,756

7.31

17.69

3.71

15,16,mean

Seed weight 15–2; Seed weight 45–2

AX-90395822

0.14

1

50,267,101

50,148,031

50,386,171

7.12

19.42

3.79

15,16,mean

Seed weight 15–2; Seed weight 45–2

AX-90328574

0.11

9

39,625,218

39,506,148

39,744,288

5.84

16.24

0.48

15,16,mean

Seed weight 50–5; Seed yield 31–10

AX-90501040

0.05

14

42,496,533

42,377,463

42,615,603

9.58

24.87

5.81

15,16,mean

Seed yield 32–3; Pod maturity 27–3

AX-90367415

0.05

14

42,696,630

42,577,560

42,815,700

6.58

18.05

3.69

15,16,mean

Seed yield 32–3; Pod maturity 27–3

AX-90480993

0.05

14

42,700,090

42,581,020

42,819,160

6.58

18.05

3.69

15,16,mean

Seed yield 32–3; Pod maturity 27–3

AX-90496773

0.07

16

1,617,227

1,498,157

1,736,297

6.16

17.29

0.60

15,16,mean

Seed yield 23–6; Pod maturity 19–6; Pod maturity 9–1

AX-90421382

0.09

16

5,520,943

5,401,873

5,640,013

5.51

13.46

2.76

15,16,mean

Seed yield29–2

MCFS

AX-90441957

0.46

5

41,791,118

41,672,048

41,910,188

7.38

19.52

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90371675

0.47

5

41,797,554

41,678,484

41,916,624

7.36

19.32

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90525251

0.46

5

41,807,238

41,688,168

41,926,308

7.38

19.52

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90320946

0.47

5

41,807,727

41,688,657

41,926,797

7.36

19.32

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90347760

0.46

5

41,808,982

41,689,912

41,928,052

7.38

19.52

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90335134

0.46

5

41,815,650

41,696,580

41,934,720

7.38

19.52

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90418462

0.47

5

41,818,004

41,698,934

41,937,074

7.36

19.32

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90492796

0.47

5

41,818,197

41,699,127

41,937,267

7.36

19.32

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90363684

0.47

5

41,818,450

41,699,380

41,937,520

7.36

19.32

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90392895

0.46

5

41,828,027

41,708,957

41,947,097

7.38

19.52

3.39

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90333199

0.46

5

41,831,486

41,712,416

41,950,556

7.18

18.99

3.36

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90344127

0.44

5

41,833,722

41,714,652

41,952,792

7.64

20.59

3.36

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90494650

0.46

5

41,853,747

41,734,677

41,972,817

7.36

19.32

3.36

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90424180

0.47

5

41,866,507

41,747,437

41,985,577

7.75

20.30

3.47

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90335974

0.46

5

41,882,999

41,763,929

42,002,069

7.00

20.68

3.51

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90435701

0.47

5

41,903,235

41,784,165

42,022,305

7.34

21.56

3.51

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90460290

0.47

5

41,927,984

41,808,914

42,047,054

8.19

21.56

3.51

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90337409

0.47

5

41,932,683

41,813,613

42,051,753

8.09

21.17

3.47

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90391337

0.48

5

41,947,344

41,828,274

42,066,414

7.36

19.34

3.37

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

AX-90415951

0.48

5

41,955,229

41,836,159

42,074,299

7.36

19.34

3.37

15,16,mean

Seed thickness 1–3; Seed arabinose plus galactose 1–1; Seed yield 15–3

  1. aThe significant SNP ID, bMinor allele frequency for each associated marker, cThe average across two years was used to association analysis -Log10(P) and R2 were listed, dPhenotypic differences between different genotypes classified on alleles of associated markers, e15 and 16 represented the environments of years 2015 and 2016, respectively. “mean” represented associations detected with the mean values across two years, fComparision of trait-marker associations identified in this study with QTLs identified in previous studies. Based on the QTL list on SoyBase (http://www.soybase.org), The underlined SNPs were common markers detected in two traits