Table 2.
Selected candidate genes identified within selective sweep regions for the traits studied
| Trait | Gene ID | ROD 5% | XPCLR 1% | Annotation | Note |
|---|---|---|---|---|---|
| Fruit pigmentation | SMEL4_01g014380.1 | Yes | No | ABCC4: ABC transporter C family member 4 | Homolog of Vitis ABCC1 |
| SMEL4_01g014110.1 | Yes | No | PER64: Peroxidase 64 | Homolog of Vitis Peroxidase 31 | |
| SMEL4_01g014400.1 | Yes | No | ABCC4: ABC transporter C family member 4 | Homolog of Vitis ABCC1 | |
| SMEL4_03g030370.1 | Yes | No | Flavonol synthase/flavanone 3‐hydroxylase (Fragment) | Homolog of Arabidopsis FLS | |
| SMEL4_04g017830.1 | Yes | No | PER9: Peroxidase 9 | Homolog of Vitis Peroxidase 31 | |
| SMEL4_05g001480.1 | No | Yes | CHI3: Probable chalcone–flavonone isomerase 3 | Homolog to Arabidopsis CHI3 | |
| SMEL4_05g019980.1 | No | Yes | PER46: Peroxidase 46 | Homolog of Vitis Peroxidase 31 | |
| SMEL4_07g024990.1 | Yes | No | ABCC3: ABC transporter C family member 3 | Homolog of Vitis ABCC1 | |
| SMEL4_10g010780.1 | Yes | No | CHI: Chalcone–flavonone isomerase | Homolog of petunia CHI | |
| SMEL4_10g014610.1 | Yes | No | MYB14: Transcription factor MYB14 | Homolog of Medicago MYB14 | |
| SMEL4_10g021500.1 | No | Yes | DTX21: Protein DETOXIFICATION 21 | Homolog of Vitis MATE1 | |
| SMEL4_11g013090.1 | Yes | No | Putative anthocyanidin reductase | Homolog of Vitis ANR | |
| SMEL4_11g015550.1 | Yes | No | DFR1: Dihydroflavonol 4‐reductase (fragment) | Homolog of Medicago DFR | |
| SMEL4_10g010780.1 | Yes | No | CHI: Chalcone–flavonone isomerase | Ortholog of Arabidopsis TT5 | |
| SMEL4_10g026990.1 | Yes | No | MYB4: Transcription repressor MYB4 (AtMYBL2) | Eggplant MYBL1 | |
| SMEL4_12g004430.1 | No | Yes | DTX29: Protein DETOXIFICATION 29 | Homolog of Vitis MATE1 | |
| Prickliness | SMEL4_06g026690.1 | Yes | No | NUDT19: Nudix hydrolase 19 chloroplastic | PI locus |
| SMEL4_06g026740.1 | Yes | No | GATA11: GATA transcription factor 11 | PI locus | |
| SMEL4_06g026750.1 | Yes | No | ARF18: Auxin response factor 18 | PI locus | |
| SMEL4_07g003480.1 | Yes | No | MYB82: Transcription factor MYB82 | Homolog of Arabidopsis Gl1 | |
| SMEL4_07g003490.1 | Yes | No | MYB82: Transcription factor MYB82 | Homolog of Arabidopsis Gl1 | |
| SMEL4_11g010530.1 | Yes | No | GIS2: Zinc finger protein GIS2 | Homolog of Arabidopsis GLS2 | |
| Fruit shape | SMEL4_01g002640.1 | Yes | No | PCR2: Protein PLANT CADMIUM RESISTANCE 2 | Homolog of tomato FW2.2 |
| SMEL4_02g003540.1 | No | Yes | CNR1: Cell number regulator 1 | Ortholog of tomato FW2.2 | |
| SMEL4_02g008010.1 | No | Yes | OFP7: Transcription repressor OFP7 | Ortholog to tomato ovate | |
| SMEL4_02g010610.1 | No | Yes | WUS: Protein WUSCHEL | Ortholog of tomato LC/WUS | |
| SMEL4_02g013940.1 | No | Yes | PCR1: Protein PLANT CADMIUM RESISTANCE 1 | Homolog of tomato FW2.2 | |
| SMEL4_02g015770.1 | No | Yes | WOX9: WUSCHEL‐related homeobox 9 | Homolog of tomato LC/WUS | |
| SMEL4_02g015780.1 | No | Yes | WOX8: WUSCHEL‐related homeobox 8 | Homolog of tomato LC/WUS | |
| SMEL4_04g004380.1 | No | Yes | IQD1: Protein IQ‐DOMAIN 1 | Homolog of tomato SUN | |
| SMEL4_06g012950.1 | No | Yes | IQD14: Protein IQ‐DOMAIN 14 | Homolog of tomato SUN | |
| SMEL4_06g026430.1 | Yes | No | YAB2: Putative axial regulator YABBY 2 | Homolog of tomato FAS | |
| SMEL4_08g003660.1 | Yes | Yes | YAB4: Protein YABBY 4 | Homolog of tomato FAS | |
| SMEL4_08g014200.1 | No | Yes | IQD1: Protein IQ‐DOMAIN 1 | Homolog of tomato SUN | |
| SMEL4_09g010770.1 | Yes | No | FAF3: Protein FANTASTIC FOUR 3 | Homolog of tomato CSR | |
| SMEL4_10g009740.1 | No | Yes | OFP2: Transcription repressor OFP2 | Ortholog of tomato suppressor of ovate | |
| SMEL4_10g026030.1 | No | Yes | PCR12: Protein PLANT CADMIUM RESISTANCE 9 | Homolog of tomato FW2.2 | |
| SMEL4_11g016380.1 | Yes | No | IQD1: Protein IQ‐DOMAIN 1 | Homolog of tomato SUN |