Table 4 SNPs identified in a single environment or when using the BLUPs from both environments for carbon and nitrogen related traits that met the significance threshold level of -log₁₀(P) > 4

Locus^a

Chr^b

Pos^c

SNP ID

-log₁₀(P)

MAF^d

Effect^e

Env^f

1

1

33,203,133

ss715578992

7.11

0.27

−0.12

Both

2

4

3,418,112

ss715587736

5.36

0.44

−0.09

GA-15

4

3,425,900

ss715587739

6.90

0.46

−0.10

Both

3

4

46,166,265

ss715588297

4.40

0.45

0.06

GA-15

4

4

47,373,969

ss715588481

4.23

0.19

0.10

GA-15

4

47,376,582

ss715588482

4.11

0.19

0.10

GA-15

5

5

37,563,155

ss715591464

5.44

0.42

−0.09

GA-16

6

6

6,576,054

ss715595435

5.61

0.47

0.08

Both

7

6

9,451,023

ss715595676

7.29

0.09

−0.18

GA-15

8

7

38,213,845

ss715597738

4.96

0.19

0.10

Both

9

8

19,267,914

ss715600198

6.65

0.19

−0.13

GA-15

10

8

19,518,756

ss715600277

5.87

0.32

0.11

GA-15

11

10

4,260,367

ss715607234

8.65

0.36

0.10

Both

12

10

21,586,075

ss715605850

5.49

0.47

0.10

GA-16

13

11

4,875,880

ss715610795

5.67

0.41

−0.11

GA-16

14

11

8,151,411

ss715611206

5.42

0.13

0.13

GA-16

15

12

458,748

ss715613097

5.79

0.45

−0.09

GA-16

16

12

38,049,740

ss715612828

6.25

0.21

−0.12

GA-16

17

13

28,776,094

ss715614695

4.89

0.36

−0.07

GA-15

18

14

12,079,082

ss715617567

4.45

0.47

−0.07

GA-15

19

14

47,854,709

ss715619453

5.15

0.43

−0.09

GA-15

20

15

40,841,088

ss715621829

4.25

0.12

−0.10

GA-15

21

15

47,257,859

ss715622121

6.99

0.07

−0.19

Both

22

15

47,349,730

ss715622149

7.93

0.12

−0.16

GA-15

23

16

3,557,974

ss715624794

4.71

0.33

0.08

Both

16

3,566,872

ss715624799

5.15

0.37

0.09

Both

24

16

6,706,066

ss715625333

5.68

0.48

−0.08

Both

25

16

35,166,856

ss715624733

8.21

0.23

−0.12

Both

26

17

15,380,811

ss715626252

4.86

0.24

−0.12

GA-15

27

17

38,826,185

ss715627535

4.06

0.10

−0.12

GA-16

28

18

5,429,903

ss715631531

4.52

0.39

−0.08

GA-16

29

18

20,093,832

ss715629730

6.62

0.18

−0.12

GA-15

30

18

21,021,784

ss715629903

4.07

0.19

−0.12

GA-16

31

18

51,704,746

ss715631722

6.61

0.42

−0.09

Both

32

19

45,240,169

ss715635451

6.39

0.26

0.10

Both

Locus

Chr

Pos

SNP ID

-log₁₀(P)

MAF

Effect

Env

1

1

1,756,948

ss715578613

7.63

0.50

−0.05

Both

2

1

2,126,801

ss715578694

7.97

0.30

−0.10

GA-16

3

4

6,329,113

ss715589139

6.84

0.28

0.05

GA-15

4

6

21,606,676

ss715593886

5.99

0.12

0.07

GA-15

5

7

2,811,470

ss715597004

5.31

0.29

−0.05

Both

6

7

15,036,339

ss715596324

5.19

0.14

0.10

GA-16

7

9

3,732,795

ss715603834

8.26

0.22

−0.06

GA-15

8

9

45,017,460

ss715604529

7.87

0.32

−0.13

GA-16

9

10

2,699,011

ss715606028

5.10

0.08

−0.14

GA-16

10

10

7,565,702

ss715608519

6.18

0.20

−0.06

GA-15

11

13

7,212,966

ss715617100

5.54

0.07

0.08

GA-15

12

13

16,630,119

ss715616751

5.09

0.15

0.05

Both

13

14

30,072,552

ss715618124

9.22

0.11

0.11

Both

14

15

1,121,373

ss715620300

4.46

0.09

0.05

GA-15

15

15

13,304,091

ss715620571

4.71

0.23

−0.05

Both

16

15

49,446,994

ss715622476

6.61

0.33

0.04

GA-15

17

16

1,675,623

ss715623543

5.40

0.14

0.07

Both

18

17

11,003,712

ss715625747

4.24

0.34

−0.03

GA-15

19

18

8,504,254

ss715632791

4.11

0.20

−0.08

GA-16

20

19

39,924,653

ss715634905

7.68

0.49

−0.04

GA-15

21

19

45,292,930

ss715635458

4.44

0.37

0.08

GA-16

19

45,292,930

ss715635458

5.35

0.37

0.06

Both

22

20

4,645,190

ss715638934

5.01

0.35

0.04

Both

23

20

39,218,472

ss715638011

4.19

0.24

−0.06

GA-16

Locus

Chr

Pos

SNP ID

-log₁₀(P)

MAF

Effect

Env

1

1

51,706,358

ss715580153

5.08

0.09

−1.14

GA-16

2

2

1,482,658

ss715581317

4.16

0.24

0.62

GA-16

3

2

1,864,987

ss715581422

4.93

0.05

1.46

GA-16

4

3

2,475,142

ss715584877

5.60

0.45

−0.61

GA-15

5

3

2,945,818

ss715585023

8.03

0.15

−1.10

Both

6

3

37,336,737

ss715585803

8.25

0.27

−0.94

GA-15

7

6

16,421,594

ss715593518

9.09

0.28

−1.09

GA-15

8

6

16,706,510

ss715593613

4.49

0.27

−0.63

GA-15

9

7

4,232,510

ss715598067

7.40

0.15

1.16

GA-15

10

7

7,433,625

ss715598611

4.01

0.38

−0.56

GA-16

11

8

11,126,044

ss715599253

4.64

0.45

−0.58

GA-15

12

9

28,739,753

ss715603408

5.06

0.22

−0.79

GA-16

13

10

45,301,855

ss715607477

4.01

0.22

0.63

GA-15

14

11

34,311,552

ss715610522

4.50

0.33

0.58

GA-15

11

34,311,552

ss715610522

4.14

0.33

0.53

Both

15

12

4,839,133

ss715613118

8.74

0.24

1.01

Both

16

12

8,677,962

ss715613605

5.53

0.10

1.05

GA-16

17

13

17,044,187

ss715616699

8.69

0.49

0.95

GA-16

13

17,062,998

ss715616695

4.69

0.42

−0.55

Both

18

16

5,223,380

ss715625193

5.37

0.30

0.64

Both

19

16

8,026,492

ss715625562

5.89

0.17

−0.91

Both

20

16

32,772,447

ss715624545

7.06

0.46

0.99

GA-16

21

16

37,144,699

ss715624944

5.31

0.11

−1.17

GA-16

22

18

49,000,413

ss715631434

5.19

0.18

−0.84

GA-15

23

19

179,420

ss715635206

6.10

0.45

0.70

Both

24

19

48,043,481

ss715635757

4.57

0.38

0.68

Both

25

19

50,357,367

ss715636025

4.67

0.36

−0.66

GA-16

26

20

39,264,651

ss715638016

9.63

0.14

−1.33

GA-15