| 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 |
| 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 |
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
| 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 |
| 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 |
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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