Table 6 List of candidate genes identified

1

Germination percentage, Days to emergence, Number of fruits per truss, Number of fruits per plant, Total leaf chlorophyll content

CH09_32797168

9

Solyc09g050070.1 (ITAG4.0)

NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic (AHRD V3.3 *** A0A2P1N7K1_9LAMI)

2

Germination percentage, Seedling vigor index, Duration of harvest

CH08_9528498

8

Solyc08g016796.1 (ITAG4.0)

UNKNOWN PROTEIN

3

Germination percentage

CH08_9481068

8

Solyc08g150109.1 (ITAG4.0)

UNKNOWN PROTEIN

4

Seedling vigor index, No of fruits per truss, Duration of harvest,

CH11_51779471

11

Solyc11g150146.1 (ITAG4.0)

Elongation factor 1-alpha (AHRD V3.3 *** A0A1U8EL12_CAPAN)

5

Seedling vigor index, Ascorbic acid, Lycopene content

CH11_2043421

11

Solyc11g007770.2 (ITAG4.0)

Glycosyltransferase family protein 64 protein C5 (AHRD V3.3 *** A0A2G2VEI7_CAPBA)

6

Seedling vigor index, Duration of harvest

CH08_45067778

8

Solyc08g061145.1 (ITAG4.0)

Geraniol 8-hydroxylase (AHRD V3.3 *-* A0A2G2W2C6_CAPBA)

7

Seedling vigor index

CH01_34883400

1

Solyc01g038232.1 (ITAG4.0)

UNKNOWN PROTEIN

8

Days to emergence, Average fruit weight

CH09_32800889

9

Solyc09g050070.1 (ITAG4.0)

NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic (AHRD V3.3 *** A0A2P1N7K1_9LAMI)

9

Days to emergence

CH07_66235223

7

Solyc07g064130.2 (ITAG4.0)

Polyubiquitin (AHRD V3.3 *** F1SY21_MESCR)

10

Days to emergence

CH08_45067768

8

Solyc08g061145.1 (ITAG4.0)

Geraniol 8-hydroxylase (AHRD V3.3 *-* A0A2G2W2C6_CAPBA)

11

Days to emergence, Seedling length at transplant

CH06_11575381

6

Solyc06g016760.3 (ITAG4.0)

Gamma-secretase subunit (AHRD V3.3 *-* AT5G09310.1)

12

Days to emergence

CH02_12004

2

Solyc02g004000.1 (ITAG4.0)

Regulator of rDNA transcription protein 15 (AHRD V3.3 *-* A0A2G2V0S9_CAPBA)

13

Days to emergence

CH06_8639002

6

Solyc06g150106.1 (ITAG4.0)

UNKNOWN PROTEIN

14

Days to emergence

CH08_9395894

8

Solyc08g016791.1 (ITAG4.0)

UNKNOWN PROTEIN

15

Days to emergence, Fruit yield per plant

CH08_9516336

8

Solyc08g016796.1 (ITAG4.0)

UNKNOWN PROTEIN

16

Days to emergence, Number of days to first harvest, Average fruit weight, Ascorbic acid.

CH11_51768254

11

Solyc11g150146.1 (ITAG4.0)

Elongation factor 1-alpha (AHRD V3.3 *** A0A1U8EL12_CAPAN)

17

Seedling length at transplant

CH05_26702700

5

Solyc05g021190.2 (ITAG4.0)

Photosystem II D2 protein (AHRD V3.3 *-* A0A2G2XVH6_CAPAN)

18

Seedling length at transplant, Fruit shape index, Total leaf chlorophyll content

CH11_8317802

11

Solyc11g017345.1 (ITAG4.0)

F-box/FBD/LRR-repeat protein (AHRD V3.3 *-* XP_010312830.1)

19

Seedling length at transplant, Fruit yield per plant

CH04_58505565

4

Solyc04g074580.1 (ITAG4.0)

Histone H3 (AHRD V3.3 *** A0A2K1J132_PHYPA)

20

Seedling length at transplant, Total soluble sugars

CH09_32793167

9

Solyc09g050069.1 (ITAG4.0)

NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic (AHRD V3.3 *-* A0A0U2L2P8_9MYRT)

21

Seedling length at transplant, Number of primary branches

CH04_30904930

4

Solyc04g024420.3 (ITAG4.0)

Proteasome subunit beta (AHRD V3.3 *** A0A2G2VMP0_CAPBA)

22

Seedling length at transplant

CH02_38534615

2

Solyc02g071000.1 (ITAG4.0)

Chlorophyll a-b binding protein, chloroplastic (AHRD V3.3 *** A0A2G3A7J8_CAPAN)

23

Seedling length at transplant, Plant height, Duration of harvest

CH02_11280

2

Solyc02g004000.1 (ITAG4.0)

Regulator of rDNA transcription protein 15 (AHRD V3.3 *-* A0A2G2V0S9_CAPBA)

24

Seedling length at transplant, Number of days to first fruit set, Total soluble sugars

CH11_47595957

11

Solyc11g063480.1 (ITAG4.0)

UNKNOWN PROTEIN

25

Number of flowers per truss, Number of fruits per truss, Number of fruits per plant, Fruit yield per plant, Ascorbic acid

CH03_2152187

3

Solyc03g007550.4 (ITAG4.0)

LIM domain protein (AHRD V3.3 *** AT5G52950.1)

26

Number of flowers per truss, Number of fruits per truss

CH08_9512856

8

Solyc08g016796.1 (ITAG4.0)

UNKNOWN PROTEIN

27

Number of flowers per truss

CH11_40366610

11

Solyc11g039880.2 (ITAG4.0)

Nucleoporin (DUF3414) (AHRD V3.3 *** F4JUG3_ARATH)

28

Number of flowers per truss, Number of days to first fruit set, Number of fruits per truss, Number of fruits per plant, Pollen viability and Ascorbic acid

CH12_49436823

12

Solyc12g038400.2 (ITAG4.0)

Acetyl-coenzyme A synthetase (AHRD V3.3 *** A4W5I5_ENT38)

29

Number of days to first fruit set

CH06_10446133

6

Solyc06g024320.1 (ITAG4.0)

UNKNOWN PROTEIN

30

Number of days to first fruit set, Number of days to first harvest

CH08_9570356

8

Solyc08g150111.1 (ITAG4.0)

UNKNOWN PROTEIN

31

Number of days to first fruit set, Malondialdehyde

CH11_13443107

11

Solyc11g021180.2 (ITAG4.0)

Protein TIC 214 (AHRD V3.3 *-* J7H3X3_CAPAN)

32

Number of days to first fruit set, Pollen viability, Malondialdehyde

CH02_22989441

2

Solyc02g022930.3 (ITAG4.0)

3-hydroxyisobutyrate dehydrogenase (AHRD V3.3 *** A0A1U8FBY0_CAPAN)

33

Number of fruits per truss, Fruit shape index and Number of primary branches

CH01_60016916

1

Solyc01g058470.1 (ITAG4.0)

UNKNOWN PROTEIN

34

Number of fruits per truss, Average fruit weight, Total phenols.

CH09_32765930

9

Solyc09g050061.1 (ITAG4.0)

UNKNOWN PROTEIN

35

Number of days to first harvest, Total soluble sugars

CH11_47631045

11

Solyc11g063577.1 (ITAG4.0)

Protein Ycf2 (AHRD V3.3 *-* A0A142DP97_9LAMI)

36

Number of days to first harvest

CH02_38613228

2

Solyc02g071110.3 (ITAG4.0)

Purine permease (AHRD V3.3 *** A0A2R6Q6Y9_ACTCH),Pfam:PF16913

37

Number of days to first harvest, Proline content

CH08_9395918

8

Solyc08g016791.1 (ITAG4.0)

UNKNOWN PROTEIN

38

Number of days to first harvest

CH08_9502536

8

Solyc08g016794.1 (ITAG4.0)

UNKNOWN PROTEIN

39

Number of days to first harvest

CH09_47357531

9

Solyc09g057860.1 (ITAG4.0)

UNKNOWN PROTEIN

40

Average fruit weight, Fruit yield per plant

CH07_67281689

7

Solyc07g065840.2 (ITAG4.0)

Molecular chaperone Hsp90-2

41

Average fruit weight

CH08_9514308

8

Solyc08g016796.1 (ITAG4.0)

UNKNOWN PROTEIN

42

Fruit shape index

CH04_61558849

4

Solyc04g078900.3 (ITAG4.0)

ABA 8'-hydroxylase

43

Fruit shape index

CH01_81577621

1

Solyc01g098950.3 (ITAG4.0)

Glyceraldehyde-3-phosphate dehydrogenase (AHRD V3.3 *** A0A2G3C9S8_CAPCH)

44

Fruit shape index, Number of primary branches, Plant height, Duration of harvest.

CH08_9792844

8

Solyc08g016806.1 (ITAG4.0)

UNKNOWN PROTEIN

45

Fruit shape index

CH09_47357555

9

Solyc09g057860.1 (ITAG4.0)

UNKNOWN PROTEIN

46

Number of fruits per plant, Ascorbic acid

CH10_64514613

10

Solyc10g086580.2 (ITAG4.0)

Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic (AHRD V3.3 *** RCA_SOLPN)

47

Fruit yield per plant

CH01_83040089

1

Solyc01g100860.3 (ITAG4.0)

ADP-ribosylation factor (AHRD V3.3 *** B4FP40_MAIZE)

48

Fruit yield per plant, Plant height

CH12_5896264

12

Solyc12g015880.2 (ITAG4.0)

Heat shock protein 90-1

49

Fruit yield per plant

CH11_47615653

11

Solyc11g063573.1 (ITAG4.0)

ATPase subunit 4 (AHRD V3.3 *** A0A0C5B288_HYONI)

50

Fruit yield per plant

CH08_9292962

8

Solyc08g016780.1 (ITAG4.0)

UNKNOWN PROTEIN

51

No of primary branches, Duration of harvest

CH02_23061139

2

Solyc02g023940.3 (ITAG4.0)

UNKNOWN PROTEIN

52

Pollen viability

CH04_64421176

4

Solyc04g082980.2 (ITAG4.0)

Tetratricopeptide repeat protein SKI3 (AHRD V3.3 *** A0A2G2ZSZ3_CAPAN)

53

Malondialdehyde

CH02_23029093

2

Solyc02g022935.1 (ITAG4.0)

Golgi-associated plant pathogenesis-related protein 1 (AHRD V3.3 --* A0A226DTU7_FOLCA)

54

Proline content

CH08_9435066

8

Solyc08g016792.1 (ITAG4.0)

UNKNOWN PROTEIN

55

Proline content, Total leaf chlorophyll content.

CH08_9484802

8

Solyc08g150109.1 (ITAG4.0)

UNKNOWN PROTEIN

56

Proline content

CH01_32207691

1

Solyc01g021620.3 (ITAG4.0)

Dirigent protein (AHRD V3.3 *** H8ZXA8_SOLTU)

57

Total leaf chlorophyll content, total phenols

CH10_42879486

10

Solyc10g048060.2 (ITAG4.0)

Hypothetical protein (AHRD V3.3 *-* ATMG00030.1)

58

Lycopene content

CH05_1507699

5

Solyc05g006830.3 (ITAG4.0)

Thioredoxin (AHRD V3.3 *** A0A2G2VM05_CAPBA)

59

Total phenols

CH02_23020130

2

Solyc02g022935.1 (ITAG4.0)

Golgi-associated plant pathogenesis-related protein 1 (AHRD V3.3 --* A0A226DTU7_FOLCA)

60

Total soluble sugars

CH11_17659987

11

Solyc11g051171.1 (ITAG4.0)

UNKNOWN PROTEIN