Table 4.
Details of the genes identified through combined genome-wide association and transcriptome analysis
| Gene | Chr | Start position | End position | Trait | Distance from the SNP (kb) | Largest LD Block size (kb) | Functional annotation |
|---|---|---|---|---|---|---|---|
| VaccDscaff2-snap-gene-267.44 | 2 | 26,724,956 | 26,726,221 | NDVI | -210.8 | 425 | Transcription termination factor MTERF6, chloroplastic/mitochondrial-like |
| VaccDscaff4-augustus-gene-93.28 | 3 | 9,296,804 | 9,300,766 | Fv/Fm | -21.7 | 425 | Rhomboid-like protein 14, mitochondrial |
| VaccDscaff4-processed-gene-93.2 | 3 | 9,322,227 | 9,325,671 | Fv/Fm | - | 425 | Receptor-like protein 12 |
| VaccDscaff6-processed-gene-123.1 | 4 | 12,328,383 | 12,329,624 | SR | -92.7 | 418 | Ethylene-responsive transcription factor ERF054-like |
| VaccDscaff13-augustus-gene-24.20 | 8 | 2,465,456 | 2,468,582 | SR | -70.6 | 261 | Protein OPI10 homolog |
| VaccDscaff13-augustus-gene-52.35 | 8 | 5,259,424 | 5,263,977 | ABS/RC | 37.5 | 261 | Zinc finger protein 511 |
| VaccDscaff13-snap-gene-322.19 | 8 | 32,248,523 | 32,249,662 | SR | -43.7 | 261 | E3 ubiquitin-protein ligase ATL42-like |
| VaccDscaff17-augustus-gene-331.40 | 9 | 33,150,482 | 33,153,445 | ABS/RC | 58.6 | 243 | NAC domain-containing protein 72-like |
| VaccDscaff17-augustus-gene-331.41 | 9 | 33,170,705 | 33,171,852 | ABS/RC | 78.8 | 243 | NAC domain-containing protein 72-like |
| VaccDscaff20-processed-gene-127.33 | 10 | 12,751,584 | 12,754,015 | NDVI | 92.9 | 255 | 3-ketoacyl-CoA synthase 6 |
| VaccDscaff22-augustus-gene-28.24 | 12 | 2,813,459 | 2,815,662 | SR | 10.0 | 194 | Small heat shock protein, chloroplastic-like isoform X2 |