Table 2.
Fruit ripening-related genes with low and moderate SNP impacts.
| Gene ID | Description | Function | Gene type | Chr | Variant ID | Effect | AA change |
|---|---|---|---|---|---|---|---|
| evm.model.supercontig_43.43 | Hydroxymethylbilane synthase | CCM | DEG | Ch6 | SNP_43.43[A/G]569749 | SV | Ser384Ser |
| evm.model.supercontig_92.51 | Magnesium-chelatase subunit chlh | CCM | DEG | Ch8 | SNP_92.51[G/A]470716 | SV | Leu675Leu |
| evm.model.supercontig_43.43 | Hydroxymethylbilane synthase | CCM | DEG | Ch6 | SNP_43.43[G/C]569757 | MV | Cys387Ser |
| evm.model.supercontig_151.20 | Glycosyl hydrolase 9B13 | CW | BLAST | Ch5 | SNP_151.20[G/C]175639 | SV | Ser435Ser |
| evm.model.supercontig_106.54 | Glycosyl hydrolase family protein | CW | DEG | Ch6 | SNP_106.54[C/T]643444 | SV | Pro679Pro |
| SNP_106.54[T/G]643459 | SV | Val674Val | |||||
| SNP_106.54[T/G]643531 | SV | Leu650Leu | |||||
| evm.model.supercontig_29.125 | Glycosyl hydrolases family 32 protein | CW | BLAST | Ch4 | SNP_29.125[G/A]1173309 | SV | Asp379Asp |
| evm.model.supercontig_508.5 | Major facilitator superfamily protein | CW | BLAST | Ch3 | SNP_508.5[C/T]19647 | SV | Thr486Thr |
| evm.model.supercontig_25.194 | Pectin methylesterase 3 | CW | BLAST | Ch4 | SNP_25.194[G/A]2039032 | SV | Tyr61Tyr |
| SNP_25.194[G/A]2039146 | SV | Ile23Ile | |||||
| evm.model.supercontig_82.65 | Sucrose synthase 4 | CW | DEG | Un | SNP_82.65[A/C]1098666 | SV | Ala803Ala |
| evm.model.supercontig_93.34 | Beta-galactosidase 12 | CW | DEG | Ch7 | SNP_93.34[T/C]879460 | MV | Val624Ala |
| evm.TU.contig_32583.1 | Beta-galactosidase 3 | CW | BLAST | Un | SNP_32583.1[C/T]2456 | MV | Gly233Ser |
| evm.model.supercontig_119.14 | Expansin A1 | CW | BLAST | Ch6 | SNP_119.14[G/A]71404 | MV | Arg225His |
| evm.model.supercontig_14.96 | Expansin A5 | CW | BLAST | X/Y | SNP_14.96[C/T]1096729 | MV | Ser17Asn |
| evm.model.supercontig_3.313 | Glycosyl hydrolases family 32 protein | CW | DEG | Ch9 | SNP_3.313[G/C]2180909 | MV | Glu637Gln |
| evm.model.supercontig_25.194 | Pectin methylesterase 3 | CW | BLAST | Ch4 | SNP_25.194[G/A]2039051 | MV | Ala55Val |
| evm.model.supercontig_151.32 | Ethylene response sensor 1 | PH | DEG | Ch5 | SNP_151.32[A/T]288630 | SV | Val331Val |
| evm.model.supercontig_6.74 | Auxin-responsive GH3 family protein | PH | BLAST | Ch4 | SNP_6.74[G/A]571741 | MV | Ala6Val |
| evm.model.supercontig_152.36 | WRKY family transcription factor | TF | BLAST | X/Y | SNP_152.36[C/T]269630 | SV | Ser551Ser |
| evm.model.supercontig_9.36 | WRKY DNA-binding protein 48 | TF | BLAST | Ch5 | SNP_9.36[A/T]151586 | MV | Gln308His |
AA amino acid, MV missense variant, SV synonymous variant, CW cell wall-related genes, CCM chlorophyll and carotenoid metabolism-related genes, PH plant hormone signal transduction pathway genes, TF transcription factor.