Table 1 The significant QTNs for five rice yield-related traits detected simultaneously by using two or more multi-locus GWAS methods

Grain Length

qGL-1-1

1

16,255,794

3.57–6.37

0.29–1.91

1,2,3

qGL-3-1

3

8,800,352

3.43–4.15

1.71–3.56

4,5

qGL-3-2

3

16,182,203

3.42–5.81

1.92–2.23

1,3

qGL-3-3

3

16,699,322

3.68–4.70

2.78–7.54

1,4

GS3

qGL-3-4

3

16,717,839

3.47–3.51

2.68–6.97

2,3

GS3

qGL-3-5

3

16,911,337

4.01–4.76

3.49–9.75

1,5

GS3

qGL-3-6

3

35,509,618

3.22–7.14

2.79–3.68

1,3

qTGW3

qGL-5-1

5

5,371,587

4.23–4.92

1.25–2.28

2,5

GSE5/GW5

qGL-5-2

5

6,215,765

3.12–5.01

3.91–5.72

1,4

qGL-6-1

6

4,252,841

4.07–9.18

0.74–1.13

1,3

qGL-6-2

6

22,641,242

8.54–8.57

7.17–7.35

1,3

qGL-7-1

7

4,465,180

3.79–11.29

1.01–9.81

1,2,3

qGL-8-1

8

1,629,499

5.01–5.78

0.67–1.33

1,3

qGL-8-2

8

14,139,411

3.87–4.67

2.57–3.29

1,3,5

qGL-10-1

10

4,663,209

4.49–6.46

7.66–13.25

4,5

qGL-10-2

10

5,288,007

4.05–5.38

1.93–2.63

1,2

qGL-12–1

12

1,135,876

3.37–3.42

0.00–1.19

2,3

qGL-12-2

12

5,542,726

4.02–8.98

0.77–1.25

2,3

qGL-12-3

12

14,546,343

5.74–7.38

0.08–1.73

1,3

Grain Width

qGW-3-1

3

10,817,310

3.50–4.81

0.34–3.64

2,3

qGW-3-2

3

21,604,259

3.02–3.65

1.62–5.28

1,4

qGW-4-1

4

26,662,080

3.95–5.95

1.77–2.83

3,4

STRK1

qGW-5-1

5

5,359,498

4.12–6.93

1.68–6.34

2,4,5

GSE5/GW5

qGW-5-2

5

5,371,587

4.92–11.55

2.83–7.20

1,3,4,5

GSE5/GW5

qGW-9-1

9

191,910

3.59–5.35

2.30–2.68

3,4

qGW-9-2

9

1,318,664

6.74–7.74

5.97–13.97

3,4

BC12

qGW-10-1

10

22,500,927

3.31–4.41

1.04–1.50

2,4

OsCAO1

qGW-12–1

12

22,677,925

3.04–12.34

0.29–1.47

2,3

Grain Thickness

qGT-5-1

5

4,830,996

12.94–13.56

4.93–7.23

1,4

qGT-5-2

5

7,022,361

4.94–5.14

1.85–3.20

2,4

qGT-5-3

5

7,036,290

4.34–13.62

3.32–3.38

1,5

qGT-5-4

5

23,605,308

3.03–4.41

0.85–5.69

1,3

OsSNAT1

qGT-6-1

6

15,688,533

3.43–4.25

3.59–4.17

1,4

qGT-6-2

6

19,652,114

3.52–10.41

2.23–11.95

1,3

OsSPDS2

qGT-12–1

12

17,685,177

3.02–5.90

2.09–3.77

1,4

1000-Grain Weight

qTGW-1-1

1

4,853,002

6.27–6.60

1.97–2.11

1,4

GW5L

qTGW-1-2

1

33,427,348

3.19–4.48

0.60–1.57

3,4

qTGW-2-1

2

2,529,182

4.94–10.21

0.56–5.62

2,3

qTGW-3-1

3

16,776,481

6.15–7.49

0.89–2.76

1,3,4

GS3

qTGW-4-1

4

31,950,052

3.14–4.28

0.42–1.42

3,4

qTGW-4-2

4

32,409,784

4.54–5.22

1.47–2.41

2,4

FLO2

qTGW-5-1

5

4,859,527

7.33–8.91

0.86–3.90

1,3,4,5

qTGW-5-2

5

7,115,594

4.35–12.71

0.34–4.51

1,3,4,5

qTGW-7-1

7

18,639,992

3.57–11.64

1.39–6.37

3,4,5

qTGW-7-2

7

18,895,502

4.22–7.48

1.70–4.99

3,5

OsSPL13

qTGW-7-3

7

19,391,625

4.26–11.43

0.44–4.99

1,3,5

OsSPL13

qTGW-7-4

7

23,476,357

3.77–5.02

0.48–3.88

1,3

qTGW-7-5

7

26,928,988

3.89–7.12

0.60–1.40

3,4

qTGW-8-1

8

25,590,176

3.10–4.53

0.34–1.35

3,4,5

qTGW-8-2

8

26,309,952

5.51–6.94

1.06–1.95

1,3

GW8/OsSPL16/qGW8

qTGW-9-1

9

2,009,389

3.01–3.70

0.45–2.50

3,4

qTGW-10-1

10

2,107,100

5.81–11.33

1.29–5.77

3,4,5

qTGW-11–1

11

18,100,034

4.54–9.46

0.35–2.83

1,3,4

OsBDG1

qTGW-11–2

11

20,067,792

3.52–6.31

0.87–2.95

1,2,4

qTGW-11-3

11

25,914,037

3.04–7.25

0.88–1.53

3,5

qTGW-12–1

12

9,394,697

8.15–10.58

1.72–4.77

1,3

qTGW-12-2

12

16,332,104

3.01–4.30

0.13–0.89

3,4

Yield Per Plant

qYPP-2-1

2

26,731,138

3.01–3.80

1.13–3.13

4,5

qYPP-3-1

3

7,685,085

4.19–11.64

3.11–5.26

1,4,5

qYPP-4-1

4

513,812

4.81–5.88

2.67–3.98

1,5

qYPP-4-2

4

25,868,074

4.96–6.52

2.15–3.25

1,4,5

LABA1

qYPP-5-1

5

28,202

3.72–6.29

3.59–4.01

1,5

qYPP-5-2

5

25,806,082

4.43–8.85

1.17–6.77

3,4,5

OsRab7

qYPP-5-3

5

29,791,637

3.71–5.36

2.38–3.89

1,5

qYPP-6-1

6

15,037,982

5.50–6.92

3.75–3.87

4,5

qYPP-6-2

6

30,797,769

3.42–4.60

0.65–1.80

2,5

qYPP-7-1

7

337,826

8.93–9.51

1.86–5.81

1,3

qYPP-7-2

7

20,669,197

3.08–6.62

0.28–1.79

1,2,3,4,5

qYPP-8-1

8

79,975

4.58–5.62

1.65–1.86

2,5

qYPP-8-2

8

19,396,188

3.12–5.64

0.27–3.08

1,3

PAY1

qYPP-10-1

10

5,854,315

3.21–4.64

0.33–2.03

2,3,5

qYPP-10-2

10

20,388,038

3.81–12.61

0.57–6.99

2,3,4,5

qYPP-11–1

11

994,705

3.40–3.62

0.59–2.97

3,4

ONAC122

qYPP-12–1

12

10,578,786

3.15–4.20

1.65–3.60

4,5