Table 4 Results of the genetic analyses performed on the WOSR (A) or DH (B) populations for [a] the genotypic estimates extracted from the multi-environment model (\( {\boldsymbol{P}}_{\boldsymbol{i}\boldsymbol{jklm}} = \boldsymbol{\mu} +\underline {{\boldsymbol{G}}_{\boldsymbol{i}}} + {\boldsymbol{N}}_{\boldsymbol{j}} + \underline {{\boldsymbol{T}}_{\boldsymbol{l}}}+\underline {{\boldsymbol{T}}_{\boldsymbol{l}}\left({\boldsymbol{R}}_{\boldsymbol{k}}\right)} + \underline {{\boldsymbol{G}}_{\boldsymbol{i}}\times {\boldsymbol{N}}_{\boldsymbol{j}}}+\underline {{\boldsymbol{G}}_{\boldsymbol{i}} \times {\boldsymbol{T}}_{\boldsymbol{l}}} + \underline {{\boldsymbol{G}}_{\boldsymbol{i}}\times {\boldsymbol{N}}_{\boldsymbol{j}}\times {\boldsymbol{T}}_{\boldsymbol{l}}} + \underline {{\boldsymbol{e}}_{\boldsymbol{i}\boldsymbol{jklm}}} \) (model 1)) and [b] the ecovalence values calculated using the G × N or G × T model (\( {\boldsymbol{W}}_{\boldsymbol{i}} = {\displaystyle \sum_{\boldsymbol{i}}}\left({\boldsymbol{Y}}_{\boldsymbol{i}\boldsymbol{j}}-{\boldsymbol{Y}}_{\boldsymbol{i}.}-{\boldsymbol{Y}}_{.\boldsymbol{j}}+{\boldsymbol{Y}}_{..}\ \right)2 \) (model 8))

Model (a)

Trait

LG

Marker (b)

Position (cM) (c)

Position (bp) (d)

MAF (e)

FDR (f)

R² (g)

CI (cM) (h)

CI (bp) (i)

Favorable allele (j)

Additivity (k)

G [a]

SY

A1

Bn-A01-p1000115

3.0

617,658

0.18

0.08

0.13

1.73

234,187

T

0.25

Bn-A01-p5480514

36.4

5,042,546

0.43

0.10

0.13

1.50

158,442

G

0.18

Bn-A01-p20990218

65.3

17,795,523

0.21

0.10

0.12

0.30

370,421

C

0.23

Bn-A01-p24697185

74.6

20,465,114

0.40

0.10

0.12

5.70

184,781

G

0.20

A3

Bn-A03-p766322

1.1

634,722

0.39

0.14

0.11

4.70

400,479

A

0.20

Bn-C3-p15411996

64.8

9,973,043

0.10

0.13

0.12

72.10

315,568

T

0.27

A4

Bn-A04-p11510797

22.1

12,567,132

0.10

0.02

0.21

0.65

323,361

A

0.39

A5

Bn-A05-p4108818

32.1

3,986,210

0.32

0.15

0.11

6.00

608,673

A

0.20

Bn-A05-p6897871

48.8

6,348,806

0.07

0.03

0.17

7.10

1,584,822

A

0.40

Bn-A05-p23166612

99.8

21,325,804

0.19

0.02

0.18

6.15

2,427,395

C

0.30

A8

Bn-A08-p14156050

17.9

11,851,743

0.42

0.15

0.11

2.30

390,921

C

0.19

Bn-A08-p16125811

28.2

13,582,310

0.06

0.15

0.11

3.35

370,297

G

0.31

A9

Bn-A09-p3024539

20

2,944,505

0.49

0.02

0.22

32.53

5,529,615

T

0.28

Bn-A08-p9226756

65.5

14,301,186

0.09

0.15

0.11

0.00

1,533,647

T

0.29

A10

Bn-A10-p9052583

13.5

10,444,212

0.10

0.12

0.12

6.80

1,679,566

A

0.29

C1

Bn-C1-p5199797

31.5

5,036,240

0.31

0.09

0.13

0.00

410,741

A

0.21

Bn-C1-p37170472

77.4

34,962,509

0.17

0.09

0.13

0.00

1,141,921

A

0.23

C2

Bn-C2-p50647994

125.4

44,768,073

0.40

0.06

0.15

39.00

5,044,117

C

0.22

C5

Bn-C5-p45854218

117.0

42,566,107

0.29

0.07

0.14

1.50

230,043

A

0.20

C6

Bn-C6-p19300068

42.9

18,948,227

0.12

0.06

0.14

8.20

1,201,949

G

0.30

Bn-C6-p8469110

65.9

28,380,973

0.37

0.15

0.11

9.50

5,946,818

C

0.21

C7

Bn-C7-p32630456

41.0

32,902,306

0.22

0.02

0.21

0.70

3,328,120

T

0.31

Bn-C7-p37740616

57.8

34,843,632

0.22

0.02

0.20

3.68

1,113,132

A

0.32

C8

Bn-C8-p21614432

31.8

20,898,335

0.28

0.11

0.12

6.40

545,619

G

0.21

C9

Bn-C9-p2006237

16.3

872,443

0.49

0.03

0.17

12.80

3,275,350

G

0.26

O

A5

Bn-A02-p26656981

103.2

22,149,643

0.20

0.12

0.21

2.86

976,652

G

0.84

A9

Bn-A09-p1989556

15.6

1,964,619

0.33

0.12

0.27

12.60

2,168,340

A

0.84

Bn-A09-p6950255

50.4

5,891,565

0.37

0.12

0.24

0.55

329,763

A

0.74

C1

Bn-C1-p5199797

31.5

5,036,240

0.31

0.12

0.23

3.14

1,808,094

A

0.78

C7

Bn-C7-p36749441

53.6

33,959,826

0.20

0.12

0.23

10.22

3,157,954

A

0.93

Bn-C7-p38504198

59.9

35,328,335

0.32

0.14

0.20

2.75

651,737

T

0.73

O/Pr

A9

Bn-A09-p3051349

20.3

2,971,796

0.46

0.13

0.24

4.80

745,210

G

0.13

G × N [b]

O

A5

Bn-A02-p26656981

103.2

22,149,643

0.20

0.12

0.21

2.86

976,653

G

0.32

A9

Bn-A09-p1989556

15.6

1,964,619

0.33

0.12

0.27

12.60

2,168,341

A

0.32

Bn-A09-p6950255

50.4

5,891,565

0.37

0.12

0.24

0.55

329,762

A

0.28

C1

Bn-C1-p5195180

31.5

5,031,632

0.31

0.12

0.23

3.14

1,771,001

T

0.30

C7

Bn-C7-p35762591

51.0

33,046,261

0.20

0.12

0.23

10.22

3,825,530

G

0.35

G × T [b]

SY

A1

Bn-A01-p3005793

22.7

2,717,050

0.12

0.15

0.20

25.00

467,612

T

1.42

Bn-A01-p19929280

62.9

16,718,048

0.07

0.15

0.19

1.20

953,751

G

1.67

Bn-A01-p23321507

70.1

19,192,316

0.06

0.06

0.31

5.40

2,053,778

C

2.38

A3

Bn-A03-p3795299

31.7

3,348,503

0.07

0.15

0.20

1.00

142,079

A

1.69

Bn-A03-p19897251

108

18,786,539

0.08

0.15

0.20

1.80

309,561

A

1.71

A4

Bn-A04-p8348806

11.2

9,654,868

0.06

0.06

0.30

0.30

290,373

T

2.52

A7

Bn-A07-p10750190

27.6

11,956,021

0.08

0.15

0.23

13.35

2,016,127

A

1.80

Bn-A07-p13485722

45.2

15,490,316

0.07

0.09

0.26

0.90

179,009

T

1.95

C6

Bn-C6-p10394225

64.7

26,530,886

0.07

0.15

0.21

3.00

2,341,718

C

1.73

Bn-C6-p4142963

74.6

32,815,121

0.13

0.15

0.19

5.58

855,273

A

1.30

O

A3

Bn-A03-p3857752

32.2

3,414,578

0.12

0.03

0.36

1.50

243,919

C

407.71

Bn-A03-p19897251

108

18,786,539

0.08

0.00

0.56

8.20

1,991,427

A

646.30

A5

Bn-A05-p5372015

39.9

5,159,907

0.06

0.05

0.32

9.80

1,033,840

T

527.86

Bn-A05-p23876386

104.6

22,847,000

0.17

0.13

0.28

2.60

397,014

T

333.29

A8

Bn-A08-p10270998

5.3

8,220,334

0.06

0.06

0.31

14.40

7,267,401

A

518.40

Bn-A08-p14375712

20.3

12,062,255

0.07

0.15

0.27

0.90

299,176

G

435.05

C4

Bn-C4-p1583238

7.5

1,269,444

0.12

0.04

0.34

0.00

543

G

406.32

Bn-C4-p9031482

47.8

8,359,826

0.06

0.05

0.32

3.30

643,168

C

527.86

Pr

A3

Bn-A03-p3862928

32.2

3,422,213

0.10

0.06

0.34

1.40

73,710

C

96.42

Bn-A03-p11364656

68.3

10,465,900

0.07

0.11

0.27

0.60

120,617

G

99.10

Bn-A03-p19897251

108

18,786,539

0.08

0.02

0.45

6.10

1,665,096

A

126.30

O/Pr

A1

Bn-A01-p1409723

6.7

1,006,909

0.07

0.10

0.29

1.24

148,550

A

2.21

Bn-A01-p3378332

24.8

3,044,540

0.10

0.15

0.25

0.00

131,684

A

1.84

A3

Bn-A03-p3851195

32.2

3,406,943

0.12

0.08

0.31

2.00

212,147

T

1.85

Bn-A03-p11364656

68.3

10,475,189

0.07

0.12

0.28

0.90

223,645

G

2.16

Bn-A03-p19897251

108

18,786,539

0.08

0.00

0.55

8.20

1,991,427

A

3.03

A7

Bn-A07-p16965943

67.1

18,885,532

0.06

0.07

0.35

2.00

190,634

T

2.71

Model(l)

Population

Trait

LG

Marker (m)

Position (cM) (n)

Position (bp) (o)

LOD (p)

R² (q)

CI (cM) (r)

CI (bp) (s)

Favorable allele (t)

Additivity (u)

G [a]

AM-DH

DTF

A1

Bn-A01-p821328

0.9

449,990

10.48

0.19

1.8

157,286

Aviso

1.67

A2

Bn-A02-p10621504

31.6

7,486,332

10.73

0.20

2

1,268,217

Aviso

1.34

C2

Bn-C2-p2374956

22

-

12.51

0.24

4.5

2,829,279

Aviso

1.38

C6

Bn-C6-p4847689

54

32,036,565

12.08

0.23

7.4

4,825,658

Montego

1.58

SY

A5

BS005820

30.7

3,536,588

7.2

0.21

5.8

577,487

Montego

0.92

C3

Bn-C3-p1719357

8.2

1,592,799

5.72

0.16

5.1

749,919

Aviso

0.84

SN

A1

Bn-A01-p2884934

22.4

2,388,770

4.76

0.15

19.6

2,415,980

Montego

1513.74

A5

BS006984

44.4

8,910,408

4.43

0.14

39.8

17,132,188

Montego

1794.32

TSW

C3

BS010983

136.7

51,428,020

3.57

0.11

20

7,091,270

Aviso

0.05

C4

BS009060

0

834,581

3.66

0.11

22.4

11,856,417

Aviso

0.07

C5

Bn-C5-p41401139

66.3

38,568,003

4.15

0.12

10

3,714,187

Montego

0.06

DK-DH

DTF

A2

BS006299

44

375,658

12.87

0.28

7.4

3,335,785

Express

1.67

A10

BS010793

50

2,137,761

6.59

0.12

3.8

651,272

Express

1.18

C6

Bn-C6-p8468434

63.7

28,381,646

16.92

0.41

1.6

82,072

Tenor

2.32

TSW

A5

BS038657

83.7

-

3.57

0.12

18

1,623,621

Express

0.05

A6

Bn-A06-p3184395

37.1

3,059,935

4.98

0.17

11

591,264

Tenor

0.06

C2

Bn-C2-p7577094

12

-

5.1

0.17

10

8,848,115

Tenor

0.07

O/Pr

C2

Bn-Scaffold00285-p518297

42.9

39,511,111

3.45

0.17

15.7

7,299,924

Express

0.01

Pr

C2

Bn-Scaffold00285-p518297

42.9

39,511,111

4.07

0.20

24

7,170,032

Tenor

0.11

G × N [b]

AM-DH

SN

A1

Bn-A01-p2841043

22.4

2,350,106

4.93

0.16

15.6

936,796

Montego

9.0.10⁵

A5

Bn-A05-p15236669

45.3

11,713,855

4.79

0.16

39.8

8,839,936

Montego

8.8.10⁵

TSW

A1

Bn-A01-p2841043

22.4

2,350,106

3.89

0.07

11.8

1,358,912

Aviso

0.01

A4

BS009059

0

834,628

8.2

0.17

8.9

5,557,003

Aviso

0.01

A7

Bn-A07-p10635069

21.7

11,816,784

3.83

0.07

14.3

2,286,113

Aviso

0.01

A9

Bn-A09-p32257776

109.2

30,105,456

5.09

0.10

10

36,978

Montego

0.01

C3

Bn-C3-p55422785

136.7

51,342,596

5.82

0.11

5.1

1,520,491

Aviso

0.01

C5

Bn-C5-p41401139

66.3

38,568,003

5.91

0.12

4

1,265,089

Montego

0.01

O

C1

Bn-C1-p7004482

44.6

6,770,122

3.56

0.14

22

4,433,568

Montego

0.35

Pr

A1

BS010224

69.5

19,925,267

3.49

0.14

48

18,210,785

Aviso

0.28

O/Pr

A2

Bn-A02-p26398002

74.4

24,112,871

3.66

0.13

16

1,091,767

Montego

1.82.10⁻³

C3

Bn-C3-p579321

1

520,340

3.81

0.14

2.8

441,719

Aviso

1.90.10⁻³

DK-DH

DTF

A2

Bn-A02-p9506103

43.7

6,320,247

14.1

0.30

4

2,927,770

Express

14.1

A10

BS010815

44.9

15,547,512

5.63

0.09

8

651,272

Express

5.63

C6

Bn-C6-p8468434

63.7

28,381,646

17.41

0.41

1.3

790,491

Express

17.41

TSW

A5

Bn-A05-p21375514

83.7

19,544,037

4.14

0.14

20

1,334,758

Express

4.14

A6

Bn-A06-p3184395

37.1

3,059,935

4.57

0.16

9.7

162,861

Express

4.57

C2

Bn-Scaffold01089-p23965

11.5

6,472,037

4.47

0.15

12.3

2,436,439

Express

4.47

Pr

C2

Bn-Scaffold00285-p518297

42.9

39,511,111

4.35

0.21

15.6

7,299,924

Express

4.35

O/Pr

A6

Bn-A06-p18634396

85

19,998,443

4.61

0.14

15.3

1,358,110

Express

1.88.10⁻⁵

A8

Bn-A08-p14799839

21.3

12,362,293

3.77

0.11

10

999,231

Tenor

1.93.10⁻⁵

C2

Bn-C3-p24936161

39.5

36,232,623

6.23

0.20

7

1,632,362

Express

2.18.10⁻⁵

G × T [b]

AM-DH

DTF

A1

Bn-A01-p1150857

5.2

754,478

7.55

0.13

7

537,061

Aviso

55

A2

Bn-A02-p7892272

31.6

4,878,455

10.63

0.20

3.6

2,645,488

Aviso

59.93

C2

Bn-C2-p2054626

19

246,359

10.27

0.19

6.8

202,734

Aviso

49.08

C6

Bn-C6-p8905311

47.2

27,985,250

9.79

0.18

7.3

298,022

Montego

48.73

SN

A1

Bn-A01-p2069488

13.3

1,561,728

4.74

0.19

19.2

1,921,336

Montego

2.34.10⁸

Pr

A1

Bn-A01-p2538180

17.3

2,035,020

3.12

0.11

16.8

1,601,066

Aviso

2.6

A9

Bn-C9-p17562068

54.4

9,942,680

4.49

0.16

15.4

17,290,961

Aviso

3.28

DK-DH

DTF

A2

Bn-A02-p9506103

43.7

6,320,247

13.09

0.29

4.2

2,152,190

Express

13.09

A10

A10_BS010815

44.9

15,547,512

5.14

0.09

7.8

651,272

Express

41.43

C6

Bn-C6-p8468434

63.7

28,381,646

16.43

0.40

1.3

790,491

Tenor

84.49

TSW

C2

Bn-C2-p17324647

19.1

13,977,345

4.92

0.24

11.5

16,386,686

Tenor

0.34

Pr

C2

Bn-Scaffold00285-p518297

42.9

39,511,111

4.01

0.20

15.6

7,299,924

Tenor

6.7

O/Pr

C2

Bn-Scaffold00285-p518297

42.9

39,511,111

3.26

0.16

13.9

6,363,073

Express

0.24