Table 2.
Classification of detected variants of 28 flowering time-related genes by snpEff analysis
| Glyma ID | Description | Gene symbol | Number of variants in total | Number of novel variants | Number of known variants | Number of missense variants | Number of ‘high’ effect variants to gene functiona |
|---|---|---|---|---|---|---|---|
| Glyma.02G069500 | FLOWERING LOCUS T | GmFTL7 | 10 | 2 | 8 | 0 | 0 |
| Glyma.03G194700 | TERMINAL FLOWER 1 | GmTFL2 | 2 | 0 | 2 | 0 | 0 |
| Glyma.03G227300 | Phytochrome A | GmPHYA4 | 70 | 5 | 65 | 35 | 5 |
| Glyma.04G143300 | B3 domain-containing protein | E1Lb | 3 | 1 | 2 | 0 | 0 |
| Glyma.04G156400 | B3 domain-containing protein | E1La | 4 | 0 | 4 | 0 | 0 |
| Glyma.06G207800 | B3 domain-containing protein | E1 | 5 | 2 | 3 | 3 | 2 |
| Glyma.08G363100 | FLOWERING LOCUS T | GmFT4 | 9 | 2 | 7 | 0 | 0 |
| Glyma.08G363200 | FLOWERING LOCUS T | GmFT6 | 6 | 1 | 5 | 0 | 0 |
| Glyma.09G035500 | Phytochrome B | GmPHYB1 | 10 | 6 | 4 | 2 | 0 |
| Glyma.09G143500 | BROTHER OF FT AND TFL 1 | GmTFL4 | 1 | 1 | 0 | 0 | 0 |
| Glyma.10G141400 | Phytochrome A | 20 | 8 | 12 | 3 | 1 | |
| Glyma.10G221500 | GIGANTEA | E2 | 2 | 1 | 1 | 1 | 1 |
| Glyma.12G073900 | Two-component response regulator-like | 18 | 3 | 15 | 5 | 1 | |
| Glyma.15G140000 | Phytochrome B | 27 | 9 | 18 | 7 | 2 | |
| Glyma.16G044100 | FLOWERING LOCUS T | GmFT5a/GmFTL4 | 14 | 5 | 9 | 0 | 0 |
| Glyma.16G044200 | FLOWERING LOCUS T | GmFT3a/GmFTL1 | 8 | 2 | 6 | 1 | 0 |
| Glyma.16G150700 | FLOWERING LOCUS T | GmFT2a/GmFTL3 | 22 | 13 | 9 | 2 | 1 |
| Glyma.16G151000 | FLOWERING LOCUS T | GmFT2b/GmFTL5 | 9 | 3 | 6 | 1 | 0 |
| Glyma.16G196300 | BROTHER OF FT AND TFL 1 | GmTFL3 | 20 | 5 | 15 | 1 | 0 |
| Glyma.16G200700 | MADS box protein | 45 | 15 | 30 | 7 | 0 | |
| Glyma.17G052100 | WD repeat-containing protein 61 | WDR61 | 15 | 1 | 14 | 0 | 1 |
| Glyma.17G090500 | Achaete-scute transcription factor-related | 17 | 10 | 7 | 0 | 6 | |
| Glyma.19G108100 | FLOWERING LOCUS T | GmFT3b/GmFTL2 | 0 | 0 | 0 | 0 | 0 |
| Glyma.19G108200 | FLOWERING LOCUS T | GmFT5b/GmFTL6 | 11 | 3 | 8 | 1 | 0 |
| Glyma.19G194300 | TERMINAL FLOWER 1 | Dt1/GmTFL1 | 14 | 5 | 9 | 5 | 0 |
| Glyma.19G224200 | Phytochrome A | E3 | 16 | 8 | 8 | 5 | 3 |
| Glyma.19G260400 | Pseudo-response regulator 5 | 42 | 11 | 31 | 8 | 0 | |
| Glyma.20G090000 | Phytochrome A | E4 | 16 | 2 | 14 | 1 | 0 |
| Glyma.U034500 | Two-component response regulator-like | 26 | 26 | 0 | 5 | 7 |
a
High-impact variant to gene function includes criteria of stop lost, stop gained, and frameshift.