Table 5 GWAS results for FEh, TGW, GNS, HD and PH. Information of haplotypes/SNPs physical location, frequency in the collection and effect direction, P values in each environment and the colocated traits

FEh

Chr1A-B32-Hap4

1A

482.3

487.0

6+

*

ns

*

*

**

-

ns

ns

ns

ns

ns

Chr2A-B19-Hap3

2A

70.2

72.9

12+

*

ns

*

*

ns

-

**

ns

*

ns

ns

Chr2A-B23-Hap1

2A

83.8

84.5

52-

*

*

*

*

ns

-

*

ns

ns

*

*

Chr2A-B26-Hap3

2A

102.0

102.7

36+

*

**

**

*

ns

-

ns

ns

ns

ns

*

Chr2A-B30-Hap4

2A

165.8

182.1

7+

**

ns

*

*

ns

-

ns

*

ns

ns

ns

Chr2A-B49-Hap2

2A

704.8

705.8

15+

*

*

*

**

*

-

ns

ns

ns

ns

ns

GNS

AX-94874921

2A

707.1

-

16+

ns

ns

ns

ns

ns

-

**

ns

*

*

*

Chr2A-B55-Hap1

2A

716.8

718.9

12+

*

***

**

*

*

-

ns

ns

ns

ns

ns

Chr3B-B14-Hap4

3B

23.0

24.0

6+

ns

ns

**

*

*

-

**

ns

ns

*

ns

AX-94869767

4A

606.4

-

18+

*

ns

*

*

ns

-

*

*

ns

*

*

Chr4A-B35-Hap3

4A

625.7

625.9

23+

**

*

**

*

*

-

ns

ns

ns

ns

ns

Chr5A-B33-Hap4

5A

445.2

445.2

7+

**

*

*

*

ns

-

ns

ns

ns

ns

ns

PH

Chr5A-B43-Hap1

5A

476.4

476.7

15+

*

ns

*

*

ns

-

ns

**

ns

*

ns

Chr6A-B24-Hap2

6A

205.1

233.3

17+

***

*

*

ns

ns

-

ns

ns

ns

ns

*

TGW

Chr6A-B28-Hap4

6A

448.7

454.6

9-

*

*

*

**

*

-

*

ns

ns

ns

ns

Chr6A-B29-Hap2

6A

455.6

467.0

25+

***

ns

*

*

ns

-

ns

ns

*

ns

*

Chr7A-B36-Hap2

7A

119.0

126.0

10+

*

ns

*

**

*

-

ns

ns

ns

ns

*

TGW

Chr2D-B5-Hap3

2D

17.6

18.2

7-

*

*

ns

ns

ns

-

ns

ns

*

*

**

Chr3A-B12-Hap3

3A

46.7

52.6

5-

ns

*

ns

*

*

-

**

*

*

ns

ns

AX-95257035

3A

686.8

-

11+

ns

ns

ns

ns

ns

-

*

ns

***

**

*

Chr3B-B111-Hap4

3B

817.4

817.8

11+

ns

ns

ns

*

ns

-

**

ns

*

*

ns

PH

AX-94459169

6A

0.6

-

30+

ns

**

*

ns

ns

-

ns

*

***

***

**

Chr6A-B20-Hap3

6A

63.8

74.0

21-

ns

ns

*

ns

ns

-

ns

ns

*

**

*

Chr6A-B21-Hap3

6A

74.5

101.3

20-

ns

ns

*

ns

ns

-

ns

ns

*

**

*

Chr6A-B24-Hap2

6A

205.1

233.3

17-

ns

ns

**

ns

ns

-

*

ns

*

***

*

FEh

Chr7B-B38-Hap3

7B

626.1

627.6

5+

ns

***

**

ns

ns

-

ns

*

*

ns

**

Chr7B-B60-Hap2

7B

702.3

703.7

27+

ns

ns

ns

*

ns

-

*

*

**

*

*

Chr7B-B60-Hap3

7B

702.3

703.7

15+

ns

ns

*

ns

ns

-

*

*

**

**

**

GNS

Chr2A-B49-Hap2

2A

704.8

705.8

15+

*

ns

*

**

**

-

ns

ns

*

ns

ns

FEh

Chr4A-B19-Hap5

4A

231.0

349.3

13+

*

**

ns

ns

ns

-

**

*

*

ns

*

HD

Chr1B-B76-Hap2

1B

643.1

645.7

35+

*

**

ns

ns

ns

**

*

*

ns

*

*

Chr1B-B84-Hap3

1B

667.2

667.8

17-

ns

ns

**

**

*

ns

*

*

*

ns

ns

Chr1B-B89-Hap4

1B

676.8

678.0

6-

ns

ns

*

**

*

*

*

ns

*

*

ns

Chr2B-B40-Hap4

2B

162.9

166.9

10+

*

**

ns

ns

ns

ns

*

ns

*

*

ns

Chr2B-B62-Hap1

2B

564.2

569.0

10+

*

**

ns

ns

ns

*

ns

ns

ns

*

ns

Ppd-D1 sensitive

2D

34

-

42+

*

*

*

*

*

**

***

**

***

***

**

Chr3A-B31-Hap1

3A

504.8

507.5

59-

ns

ns

*

ns

*

**

*

*

*

*

*

Chr3A-B49-Hap3

3A

631.2

633.1

12-

**

ns

*

*

ns

*

*

ns

*

**

*

Chr3A-B59-Hap3

3A

695.5

695.7

19+

ns

*

ns

ns

ns

**

*

**

*

*

ns

Chr3A-B60-Hap4

3A

699.4

700.6

10+

ns

**

ns

ns

ns

**

*

***

**

*

ns

Chr3D-B7-Hap1

3D

518.2

560.1

54-

*

*

ns

ns

ns

*

*

**

*

*

*

Chr5B-B75-Hap4

5B

597.2

601.4

11-

*

ns

ns

ns

ns

*

*

ns

*

**

ns

AX-94610041

6A

13.8

-

46+

*

*

**

*

*

**

ns

*

*

*

ns

Chr6A-B43-Hap1

6A

591.7

592.5

61-

ns

**

ns

ns

ns

*

*

**

*

*

*

Chr6B-B26-Hap3

6B

157.6

157.8

11+

*

**

ns

ns

ns

ns

ns

ns

*

*

**

PH

Chr7A-B24-Hap2

7A

68.0

70.2

8+

ns

ns

*

**

*

*

ns

**

*

*

ns

PH

Chr1A-B38-Hap3

1A

508.6

510.4

16+

*

**

ns

ns

ns

*

ns

ns

*

ns

ns

Chr1B-B17-Hap4

1B

121.0

124.0

5+

*

*

*

**

*

***

*

*

*

*

**

AX-94510167

1B

548.7

-

21+

ns

*

ns

**

*

**

ns

ns

*

ns

ns

Chr1B-B54-Hap1

1B

580.5

581.2

43-

*

**

ns

*

*

*

ns

ns

***

***

ns

Lr10

1D

8.6

-

10+

*

*

**

ns

*

ns

*

ns

*

*

ns

Chr1D-B5-Hap4

1D

11.6

11.9

19-

*

**

ns

*

*

*

ns

*

*

*

*

Chr1D-B10-Hap4

1D

31.1

32.5

10+

*

ns

***

*

ns

*

*

ns

ns

ns

ns

Chr2A-B39-Hap1

2A

611.2

611.9

70-

**

ns

**

ns

ns

*

ns

*

ns

ns

*

Chr2A-B48-Hap3

2A

701.0

702.1

15-

*

***

*

ns

*

*

ns

ns

*

*

ns

Chr2B-B56-Hap4

2B

469.2

476.6

6+

ns

*

**

*

ns

*

ns

*

ns

**

*

Chr2B-B79-Hap3

2B

664.2

664.9

5+

*

ns

**

*

ns

**

ns

*

ns

**

*

AX-94687989

2B

702.2

-

52+

ns

**

ns

ns

ns

ns

*

ns

**

*

ns

Chr2B-B97-Hap1

2B

719.5

719.5

38-

ns

**

ns

ns

ns

ns

*

ns

**

*

*

Chr2B-B114-Hap4

2B

762.0

763.9

8+

**

*

*

ns

*

ns

ns

ns

*

ns

ns

AX-94585596

2B

776.4

-

15+

*

**

ns

ns

*

**

*

*

*

ns

ns

AX-94624485

2B

776.8

-

10+

*

*

*

ns

ns

**

*

*

ns

ns

ns

Chr2B-B122-Hap3

2B

777.1

777.2

6+

*

*

*

ns

*

***

**

*

*

*

ns

Chr3A-B22-Hap2

3A

391.5

393.4

53+

*

*

ns

*

ns

*

**

*

*

ns

*

AX-95090222

3A

700.6

-

18+

**

ns

ns

*

ns

ns

**

ns

*

ns

ns

AX-95083205

3A

743.9

-

46+

**

*

ns

ns

*

ns

ns

*

*

ns

ns

Chr3B-B6-Hap1

3B

16.4

17.1

65-

*

*

*

ns

*

ns

*

*

**

**

*

Chr3B-B55-Hap4

3B

511.1

513.6

6-

**

*

ns

ns

*

ns

ns

ns

ns

*

*

Chr3B-B60-Hap6

3B

541.5

544.5

5+

*

ns

*

*

ns

**

*

*

*

*

ns

Chr3B-B109-Hap2

3B

796.0

799.1

9-

*

**

*

ns

ns

ns

ns

ns

ns

*

*

Chr3B-B111-Hap4

3B

817.4

817.8

11+

***

ns

*

*

**

***

*

**

*

*

*

TGW

Chr4A-B57-Hap6

4A

738.7

739.7

9-

*

ns

ns

**

ns

**

ns

ns

ns

*

ns

Chr4B-B28-Hap5

4B

612.2

613.2

6+

*

**

*

*

*

*

*

*

*

*

ns

Chr4B-B36-Hap2

4B

650.7

650.7

57-

**

*

*

*

ns

*

**

**

ns

*

ns

Chr5A-B16-Hap4

5A

33.0

33.2

5+

*

*

*

*

*

**

**

ns

ns

ns

ns

Chr5A-B33-Hap4

5A

445.2

445.2

7-

ns

***

*

ns

ns

*

ns

ns

ns

*

*

FEh

Chr5A-B54-Hap3

5A

516.1

527.9

5+

ns

*

*

**

**

***

ns

ns

*

*

*

Chr5A-B82-Hap2

5A

611.6

613.5

10+

*

ns

*

ns

ns

*

***

ns

*

ns

*

Chr5B-B26-Hap2

5B

430.7

430.7

17+

**

*

ns

*

*

*

*

ns

ns

ns

*

AX-94550178

5B

455.7

-

46+

ns

ns

***

*

*

*

ns

ns

*

ns

ns

Chr5B-B92-Hap4

5B

683.5

684.0

5+

*

ns

*

*

ns

**

*

*

*

ns

**

Chr6A-B2-Hap5

6A

0.6

0.8

5+

*

ns

**

**

*

ns

ns

ns

*

*

ns

Chr6A-B4-Hap2

6A

2.2

2.7

26+

*

ns

*

*

**

ns

*

ns

ns

*

ns

Chr6A-B4-Hap3

6A

2.2

2.7

17-

**

*

*

ns

*

ns

*

ns

*

**

*

Chr6A-B16-Hap1

6A

48.6

49.8

57+

ns

ns

ns

*

ns

*

*

ns

**

*

**

Chr6A-B17-Hap3

6A

50.3

51.4

33-

ns

*

*

*

ns

**

ns

*

*

**

ns

Chr6A-B54-Hap5

6A

610.0

610.2

6+

ns

ns

*

*

ns

***

ns

**

ns

ns

ns

Chr6B-B7-Hap2

6B

19.8

20.7

82-

**

***

**

*

ns

*

***

*

*

*

*

Chr6B-B20-Hap4

6B

124.4

126.1

6+

*

ns

ns

ns

ns

**

*

*

ns

*

*

Chr6B-B25-Hap4

6B

151.4

156.4

25-

*

**

*

*

**

ns

ns

ns

*

*

ns

Chr6B-B26-Hap3

6B

157.6

157.8

11-

*

***

ns

*

ns

*

*

*

ns

*

***

HD

Chr6B-B31-Hap2

6B

195.3

197.8

5+

*

ns

**

**

*

**

ns

ns

*

*

*

AX-94943227

6B

234.8

-

17+

**

***

**

*

*

*

***

*

*

*

*

Chr6B-B47-Hap3

6B

480.4

491.6

24-

ns

ns

ns

*

**

ns

ns

ns

*

ns

*

AX-94476474

7A

561.6

-

14+

**

*

*

ns

ns

ns

ns

**

*

*

ns

Chr7B-B14-Hap4

7B

59.6

61.6

22-

***

ns

ns

ns

*

ns

*

ns

ns

*

ns

Chr7B-B76-Hap3

7B

743.5

743.6

10-

**

***

*

*

ns

*

ns

*

**

**

*