Table 3 Significant genome-wide associations robustly detected in two environments for morphological, agronomic and root traits using a compressed mixed linear model. For each trait, chromosomal position (in bp), main statistic and effects of each association, corresponding annotated gene or close annotated gene are shown

Growth Habit

8

47,571,836

23.94

1.31E-06

C/T

0.12

−3.2

Solyc08g061750.1.1

0.0 kb

Adenylate isopentenyltransferase

Inflorescence

11

53,260,458

16.85

8.57E-08

G/C

0.56

2.78

Solyc11g071840.2.1

0.0 kb

SUN-like protein 31

Style Position

1

34,753,298

13.98

1.27E-06

A/G

0.31

−1.39

Solyc01g034213.1.1

+ 23.60 kb

Unknown protein

1

47,749,676

14.03

1.20E-06

C/T

0.26

−2.64

Solyc01g056485.2.1

−21.89 kb

sentrin-specific protease 1-like

5

11,580,510

15.08

4.49E-07

T/C

0.06

0.11

Solyc05g015610.3.1

+ 4.98 kb

Histidine kinase 3

5

11,580,511

14.63

6.87E-07

G/A

0.06

0.09

Solyc05g015610.3.1

+ 4.98 kb

Histidine kinase 3

5

11,580,560

15.08

4.49E-07

G/T

0.06

0.11

Solyc05g015610.3.1

+ 5.02 kb

Histidine kinase 3

5

11,580,572

15.08

4.49E-07

T/A

0.06

0.11

Solyc05g015610.3.1

+ 5.03 kb

Histidine kinase 3

5

11,580,755

15.08

4.49E-07

A/G

0.06

1.11

Solyc05g015610.3.1

+ 5.22 kb

Histidine kinase 3

11

53,260,458

17.81

3.51E-08

G/C

0.35

−0.25

Solyc11g071840.2.1

0.0 kb

SUN-like protein 31

Fruit shape

8

9,391,514

21.53

1.01E-06

C/T

0.07

2.15

Solyc08g016791.1.1

−0.73 kb

Unknown protein

Green shoulder

10

1,855,401

14.69

6.48E-07

G/A

0.28

−0.27

Solyc10g007720.4.1

+ 0.42 kb

Conserved oligomeric Golgi complex subunit 5

12

41,393,666

14.22

1.00E-06

G/A

0.10

− 0.86

Solyc12g035620.2.1

−48.38 kb

Polynucleotidyl transferase

Fruit Colour

1

70,208,801

12.36

1.10E-06

A/G

0.01

−0.52

Solyc01g068280.3.1

0.0 kb

CHROMATIN REMODELING 24

Puffiness Appearance

4

14,315,417

14.89

5.40E-07

G/T

0.13

0.78

Solyc04g028560.5.1

+ 179.117 kb

Lysine-specific demethylase REF6

4

14,315,418

14.89

5.40E-07

A/C

0.13

0.77

Solyc04g028560.5.1

+ 179.118 kb

Lysine-specific demethylase REF6

5

21,484,118

14.27

9.62E-07

A/G

0.06

1.04

Solyc05g160290.1.1

−81.983 kb

Zinc-finger homeodomain protein 3

5

21,484,211

14.27

9.62E-07

G/A

0.06

1.04

Solyc05g160290.1.1

−81.890 kb

Zinc-finger homeodomain protein 3

8

2,778,672

38.57

1.14E-09

C/T

0.06

1.19

Solyc08g008340.4.1

+ 2.75 kb

Nucleoside diphosphate kinase

8

2,783,032

31.66

3.13E-08

G/A

0.06

1.69

Solyc08g008350.3.1

0.0 kb

ribosome maturation factor

8

2,782,603

16.04

1.81E-07

G/A

0.08

0.98

Solyc08g008350.3.1

0.0 kb

ribosome maturation factor

8

3,626,105

27.14

6.83E-12

G/A

0.06

1.36

Solyc08g014080.4.1

−14.64 kb

RING/FYVE/PHD zinc finger superfamily protein

8

9,290,304

32.58

2.01E-08

C/T

0.00

4.20

Solyc08g016790.1.1

−37.40 kb

Unknown protein

11

26,261,071

18.47

1.91E-08

T/G

0.11

−5.44

Solyc11g160970.1.1

+ 192.90 kb

Polyprotein

11

26,877,894

20.87

2.07E-09

A/G

0.10

−6.03

Solyc11g045670.3.1

+ 98.82 kb

S-acyltransferase

11

33,544,861

23.64

1.62E-10

G/T

0.07

−6.68

Solyc11g042710.3.1

+ 4.51 kb

(+)-neomenthol dehydrogenase-like

12

23,114,935

43.24

1.28E-10

C/T

0.004

5.79

Solyc12g026360.1.1

−76.66 kb

Unknown protein

Ribbing at Calyx End

11

53,260,458

37.78

6.07E-16

G/C

0.35

0.95

Solyc11g071840.2.1

0.0 kb

SUN-like protein 31

Concentric Cracking

4

18,063,194

14.08

1.16E-06

C/A

0.12

−2.54

Solyc04g026150.2.1

−11.09 kb

homeobox-leucine zipper protein ROC8-like

10

12,292,223

17.98

3.02E-08

G/A

0.08

−3.69

Solyc10g160680.1.1

+ 5.34 kb

GrpE protein homolog

12

1,284,242

13.95

1.30E-06

A/G

0.07

0.69

Solyc12g006850.2.1

+ 15.65 kb

LELKT1GEN L.esculentum potassium channel

Blossomendrot

10

57,291,816

14.20

1.02E-06

A/G

0.20

−1.67

Solyc10g074680.2.1

+ 19.26 kb

Protein SCARECROW

Fruit fasciation

11

53,260,458

24.33

8.81E-11

G/C

0.35

0.69

Solyc11g071840.2.1

0.0 kb

SUN-like protein 31

Locules number

11

53,189,222

13.82

1.30E-06

G/A

0.43

−0.36

Solyc11g071710.2.2

0.0 kb

Thylakoid lumenal P17.1 protein

11

53,189,305

14.71

6.34E-07

G/A

0.49

−0.53

Solyc11g071710.2.1

0.0 kb

Thylakoid lumenal P17.1 protein

11

53,260,458

43.58

4.30E-18

G/C

0.35

3.93

Solyc11g071840.2.1

0.0 kb

SUN-like protein 31

Fruit weight

4

8,517,135

15.39

3.37E-07

A/C

0.12

16.29

Solyc04g017860.1.1

−16.52 kb

Aminotransferase-like

4

29,500,083

13.89

1.28E-06

C/A

0.11

−198.71

Solyc04g024530.3.1

+ 46.73 kb

Actin-related protein

5

36,583,094

17.72

3.80E-08

A/G

0.06

275.06

Solyc05g025770.1.1

+ 1685.55 kb

asparagine-rich protein-like

5

38,204,910

17.77

3.61E-08

T/C

0.07

− 183.23

Solyc05g025920.3.1

+ 22.06 kb

Auxin responsive SAUR protein

11

15,470,616

14.55

7.34E-07

T/C

0.10

−52.13

Solyc11g160550.1.1

−11.30 kb

Peptidyl-prolyl cis-trans isomerase PASTICCINO1

11

36,433,332

15.86

2.18E-07

A/G

0.11

−114.62

Solyc11g040390.2.1

−14.99 kb

Aspartokinase-homoserine dehydrogenase

11

53,260,458

32.51

5.93E-14

G/C

0.35

152.71

Solyc11g071840.2.1

0.0 kb

SUN-like protein 31

Soluble Solids

2

43,609,921

14.64

6.77E-07

A/T

0.05

1.33

Solyc02g081820.3.1

0.0 kb

Haloacid dehalogenase-like hydrolase

Diametre of Main Root

5

23,364,578

23.41

2.07E-10

T/A

0.10

−1.52

Solyc05g018743.1.1

−139.73 kb

Retrovirus-related Pol polyprotein from transposon TNT 1–94

11

19,987,778

37.05

2.41E-09

G/T

0.06

−1.11

Solyc11g028270.1.1

+ 50.96 kb

Bidirectional sugar transporter SWEET

12

18,088,359

17.94

3.08E-08

T/G

0.43

−0.76

Solyc12g082795.1.1

+ 19.66 kb

Unknown protein