Table 3 Genes of horticultural interest

From: Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits

Gene

Trait

GeneID

Genomic location

No. of variants in the gene with predited effect

No. of variants in the gene with HIGH effect

No. of variants in the gene with MODERATE effect

No. of variants upstream/downstream of the gene with predicted effect

 

Cauliflower OR orange protein

Flesh color

Cp4.1LG13g00690

Cp4.1LG13:628,094–633,068

60

1

2

97

 

Ethylene-insensitive 3 (EIN3) (1)

Flowering

Cp4.1LG04g11790

Cp4.1LG04:8,670,547–8,672,394

8

1

2

0

 

Flowering time control protein (FPA)

Flowering

Cp4.1LG17g10910

Cp4.1LG17:8,241,363–8,252,364

339

4

86

201

 

Squamosa promoter binding protein-like (2)

Flowering

Cp4.1LG17g10620

Cp4.1LG17:8,083,301–8,086,452

81

1

7

167

 

Unusual floral organs

Flowering

Cp4.1LG20g02860

Cp4.1LG20:1,553,934–1,555,718

56

2

7

117

 

Protein IQ-DOMAIN (2)

Fruit morphology

Cp4.1LG03g08410

Cp4.1LG03:2,815,265–2,818,054

38

1

0

40

 

Tonneau recruiting motif

Fruit morphology

Cp4.1LG03g01040

Cp4.1LG03:1,235,448–1,237,683

40

1

10

76

 

Tonneau recruiting motif

Fruit morphology

Cp4.1LG03g06270

Cp4.1LG03:4,147,734–4,152,353

69

4

6

193

 

Tonneau recruiting motif

Fruit morphology

Cp4.1LG05g00950

Cp4.1LG05:499,361–506,004

71

1

9

94

*

Tonneau recruiting motif

Fruit morphology

Cp4.1LG08g10310

Cp4.1LG08:7,948,336–7,951,922

65

2

11

65

 

Tonneau recruiting motif

Fruit morphology

Cp4.1LG10g04070

Cp4.1LG10:1,593,038–1,598,092

54

1

4

119

 

Tonneau recruiting motif

Fruit morphology

Cp4.1LG12g10340

Cp4.1LG12:9,512,443–9,518,623

46

2

5

46

*

Tonneau recruiting motif

Fruit morphology

Cp4.1LG15g00200

Cp4.1LG15:105,059–109,560

60

2

10

23

*

Tonneau recruiting motif

Fruit morphology

Cp4.1LG15g01180

Cp4.1LG15:901,114–905,856

40

2

12

57

*

Tonneau recruiting motif

Fruit morphology

Cp4.1LG17g00460

Cp4.1LG17:325,022–334,267

93

1

9

103

 
  1. Selected genes, genomic locations, traits affected, number of changes predicted in total and with high and moderate effect, and number of changes 5 kb upstream or downstream of the genes that can have a potential effect are shown. For the TON1 recruiting motif proteins, asterisks identify those proteins that are phylogenetically close to TRM proteins of tomato known to interact with OVATE
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