Table 2 Single nucleotide polymorphisms (SNPs) associated with hundred seed weight of soybean and known QTL overlapped with peak SNP

HSW-3-1

E3

G:T

2.25

4.2

31.96

Seed weight per plant 5-3_40168335–42,675,829 (Kuroda et al. 2013);

Seed yield 27-4_40375902–41,065,116 (Kim et al. 2012);

Seed yield 30-4_40375902–41,065,116 (Kim et al. 2012);

HSW-4-1

E2

A:G

2.3

3.7

31.85

Seed width 1-10_32617784–45,860,827 (Salas et al. 2006)

HSW-4-2

E2

A:G

2.3

3.7

31.93

Seed width 1-10_32617784–45,860,827(Salas et al. 2006)

HSW-5-1

E2, E3

A:G

−1.68/− 1.61

4.15/3.97

32.33/32.11

HSW-5-2

E5

G:T

1.01

3.58

32.49

HSW-6-1

E6

G:T

1.59

3.77

34.19

HSW-6-2

E6

A:G

1.99

3.68

33.33

HSW-6-3

E5

G:T

1.77

3.79

32.85

HSW-8-1

E1, E2, E3

G:T

1.84/1.7/1.64

4.28/3.69/3.67

33.22/32.46/32.64

HSW-8-2

E2

A:G

−2.36

4.53

32.45

HSW-9-1

E2, E4, E5

G:T

1.8/2.05/1.98

4.73/4.14/4.84

30.85/31.95/31.18

HSW-10-1

E1

A:G

−1.64

4.12

33.4

Seed weight per plant 3-2_47716772–48,485,990 (Liu et al. 2011)

HSW-12-1

E1, E2, E3, E4

C:T

2.32/1.93/2.17/2.29

4.64/4.07/3.76/4.71

33.5/32.43/31.92/31.07

Seed weight 23–2_6653096–7,980,959 (Li et al. 2008)

HSW-12-2

E6

G:T

1.56

3.71

32.28

HSW-12-3

E1, E2

A:G

−1.92/−1.93

3.67/3.88

32.66/31.39

HSW-12-4

E1, E2, E4

A:C

−1.94/−2.15/−2.43

3.77/3.54/4.85

31.91/32.68/34.9

HSW-12-5

E5

A:T

1.31

3.85

33.03

HSW-13–1

E4

C:T

2.4

3.64

31.05

HSW-13 − 2

E3

A:C

1.31

3.64

30.71

Seed yield 28–11_29609521–32,196,800 (Rossi et al. 2013);

Seed weight 40-1_29609521–32,196,800 (Rossi et al. 2013);

Seed weight 49–13_29609521–31,661,129 (Teng et al. 2009)

HSW-13-3

E5

G:T

1.81

3.59

30.71

Seed weight 45-6_32,196,800–39,208,429 (Yan et al. 2014)

HSW-14–1

E3, E4

A:G

-2/−1.81

3.81/3.54

34.09

Seed weight 29–1_439027–971,657 (Liu et al. 2011)

HSW-16–1

E5

A:G

−2.11

4.34

34.6

Seed weight 30-6_16724085–27,167,274 (Kim et al. 2010)

HSW-16–3

E3, E4, E5, E6

G:T

1.94/1.66/1.6/1.76

4.96/3.84/4.18/4.68

35.54/35.39/34.04/33.33

HSW-17-1

E5

A:G

3

3.57

32.55

Seed weight 3–1_961346–2,201,427 (Mian et al. 1996)

HSW-17-2

E3

C:T

1.66

3.75

36.28

HSW-17-3

E1

A:G

−2.15

3.58

31.8

Seed weight 34–17_24110077–37,831,244(Han et al. 2012)

HSW-18–1

E5

G:T

−2.11

3.96

36.03

Seed weight per plant 6-7_22375695–48,185,138 (Yao et al. 2015)

HSW-18–2

E3

C:G

1.65

3.92

35.43

HSW-18-3

E3,E5

G:T

−1.65

4.18/3.97

34.42/31.38

HSW-19–1

E1

A:C

−2.27

4.91

36.31

HSW-20-1

E1

C:T

2.24

3.97

31.57

Seed yield 9–1_3903416–27,664,504 (Yao et al. 2015)

HSW-20-2

E3

C:T

−1.38

3.74

31.37

Seed yield 10–1_2716974–25,498,552 (Yao et al. 2015)

HSW-20-3

E3,E4

A:G

−1.11/− 1.07

3.57/3.67

32.63/37.25

Seed weight 36-5_34302228–46,787,225(Han et al. 2012)

HSW-20-4

E3

G:T

−1.95

3.57

31.62