Table 3 Genome-wide significant associations for coleoptiles phenotype under anaerobic germination (AG) using MLM

CD-AN2d

S1_ 39674301

1

39674301

1.48E-10

9.83

A/C

0.2

Hsu and Tung 2015; qCD-1(ES) (Yang et al. 2019a, 2019b)

S2_ 21568963

2

21568963

3.14E-09

8.5

C/T

0.2

S2_ 35360509

2

35376690

7.98E-11

10.1

A/G

0.2

S5_ 7135836

5

7135836

2.32E-11

10.63

C/T

0.1

S5_ 22190175

5

22190175

2.69E-11

10.57

G/A

0.2

S6_ 20797781

6

20797781

8.49E-12

11.07

G/A

0.1

Hsu and Tung 2015

S8_ 13123867

8

13123867

2.65E-11

10.58

G/T

0.1

S8_ 11595732

8

11595732

5.64E-10

9.25

A/T

0.1

CD-AN3d

S5_ 27918754

5

27918754

1.69E-09

8.77

A/G

0.4

Hsu and Tung 2015

CD-AN4d

S1_ 32866906

1

32866906

1.24E-09

8.91

G/A

0.2

S3_ 27854371

3

27854371

5.11E-16

15.29

A/G

0.3

S3_ 2828271

3

2828271

4.16E-11

10.38

A/G

0.2

S3_ 28290634

3

28290634

3.02E-10

9.52

G/A

0.1

S3_ 32459722

3

32459722

1.20E-09

8.92

C/T

0.5

S3_ 7243651

3

7243651

4.89E-09

8.31

C/A

0.2

S3_ 15571447

3

15571447

2.23E-08

7.65

G/T

0.3

S5_ 27918754

5

27918754

1.72E-11

10.76

A/G

0.4

Hsu and Tung 2015

S5_ 18621890

5

18621890

9.76E-11

10.01

A/C

0.1

S5_ 21585755

5

21585755

1.21E-08

7.92

T/A

0.2

S7_ 18722403

7

18722403

3.45E-09

8.46

T/C

0.2

qAG 7.2 (Septiningsih et al. 2013; Hsu and Tung 2015)

S8_ 22721012

8

22721012

1.31E-09

8.88

A/G

0.2

S8_ 9946213

8

9946213

2.51E-08

7.6

T/A

0.2

Hsu and Tung 2015

S11_ 19165397

11

19165397

4.62E-09

8.34

C/A

0.3

qAG 11(Jiang et al. 2006; Angaji et al. 2009; Zhang et al. 2017)

CL-AN3d

S3_ 24689629

3

24689629

4.71E-08

7.33

T/C

0.4

CL-AN4d

S1_ 25099585

1

25099585

1.73E-08

7.76

G/A

0.2

S3_ 24689629

3

24689629

1.83E-08

7.74

T/C

0.4