Table 2.
QTLs identified for seed dormancy measured as germination rates (GR) under three different treatments using a rice diversity panel.
| QTL | Treatment | Chr. | Peak SNP | Effect | SE | p-Value | R 2 | Germination Indicator Used in Previous Study | References |
|---|---|---|---|---|---|---|---|---|---|
| qGR1-1 | DH | 1 | 2,998,209 | 1.0 | 3.8 | 2.49 × 10−5 | 10.8% | T50 (time to reach 50% germination of the total number of germinated seeds). U8416 (time interval between 84% and 16% of viable seed to germinate). Intact seed harvested on 35 day after flowering. | [28] |
| qGR1-2 | GA | 1 | 23,870,065 | 18.4 | 5.3 | 6.68 × 10−5 | 16.8% | GR of intact seed (35 day after heading (DAH)) at day seven. | [41] |
| qGR2-1 | GA | 2 | 4,193,857 | 23.8 | 6.5 | 2.04 × 10−5 | 13.8% | - | - |
| qGR2-2 | DH | 2 | 23,728,701 | −15.5 | 5.9 | 3.31 × 10−5 | 9.3% | - | - |
| qGR3 | GA | 3 | 28,515,163 | −24.0 | 6.8 | 5.69 × 10−5 | 18.7% | - | - |
| qGR4-1 | GA | 4 | 4,523,405 | 19.3 | 5.5 | 1.00 × 10−5 | 17.8% | - | - |
| qGR4-2 | DH | 4 | 4,662,452 | 17.2 | 6.8 | 7.07 × 10−5 | 8.7% | - | - |
| qGR4-3 | GA | 4 | 8,563,180 | −18.3 | 6.4 | 5.97 × 10−5 | 14.8% | - | - |
| qGR4-4 | WDB control | 4 | 10,123,838 | 27.7 | 7.1 | 8.32 × 10−5 | 17.5% | - | - |
| GA | 4 | 10,123,838 | 27.7 | 7.1 | 5.79 × 10−5 | 14.8% | - | - | |
| qGR4-5 | GA | 4 | 10,352,980 | −24.0 | 9.1 | 1.66 × 10−5 | 16.9% | - | - |
| WDB control | 4 | 10,355,218 | 20.6 | 7.3 | 7.79 × 10−5 | 20.4% | - | - | |
| qGR4-6 | GA | 4 | 10,726,116 | −23.8 | 7.2 | 1.95 × 10−5 | 16.6% | - | - |
| qGR4-7 | GA | 4 | 10,981,781 | 24.0 | 9.1 | 1.66 × 10−5 | 16.9% | - | - |
| qGR4-8 | GA | 4 | 14,056,148 | 6.6 | 6.6 | 7.05 × 10−5 | 14.5% | - | - |
| qGR5-1 | DH | 5 | 2,322,980 | 1.0 | 5.1 | 1.85 × 10−5 | 9.8% | - | - |
| qGR5-2 | DH | 5 | 13,914,542 | 7.7 | 4.1 | 5.21 × 10−5 | 8.9% | - | - |
| qGR6-1 | DH | 6 | 1,484,749 | 3.8 | 3.6 | 9.29 × 10−5 | 9.6% | - | - |
| qGR6-2 | GA | 6 | 13,120,454 | 27.6 | 7.2 | 1.95 × 10−5 | 16.6% | GR at day seven. GR at day three. T50. U8416. AUC (area under the germination curve). GI (germination index). GR of after-ripened intact seed (32 DAH) at day seven. | [28,34] |
| qGR8 | DH | 8 | 8,040,564 | 24.5 | 11.6 | 5.68 × 10−5 | 8.9% | GR at day three. T50. | [28] |
| GA | 8 | 8,073,758 | −30.7 | 7.5 | 8.14 × 10−5 | 14.3% | |||
| qGR9-1 | DH | 9 | 6,327,905 | −29.9 | 9.5 | 3.27 × 10−5 | 10.5% | - | - |
| qGR9-2 | DH | 9 | 6,672,606 | 5.2 | 5.2 | 6.01 × 10−5 | 8.8% | - | - |
| qGR9-3 | DH | 9 | 11,261,867 | 10.2 | 10.6 | 6.80 × 10−5 | 8.7% | GR of intact seed and de-hulled seed (30 DAH) at day seven. | [42] |
| qGR9-4 | WDB control | 9 | 18,641,166 | −24.8 | 7.3 | 4.53 × 10−5 | 15.4% | - | - |
| qGR10 | DH | 10 | 11,242,705 | 0.7 | 4.5 | 7.28 × 10−5 | 8.6% | - | - |
| qGR11-1 | DH | 11 | 9,730,691 | −3.0 | 7.6 | 6.57 × 10−5 | 7.3% | GR of intact seed (30–40 DAH) at ten days. GR of intact seed (effective cumulative temperature reached 600° after heading) at day seven. | [2,29] |
| qGR11-2 | DH | 11 | 10,370,801 | −9.4 | 5.1 | 8.89 × 10−5 | 9.6% | - | - |
| qGR11-3 | DH | 11 | 10,544,254 | 10.2 | 5.6 | 6.75 × 10−5 | 9.9% | - | - |
| qGR11-4 | WDB control | 11 | 19,263,268 | −23.5 | 9.0 | 2.84 × 10−5 | 16.3% | GR of after-ripened intact seed (32 DAH) at day seven. GR of intact seed (30 DAH) at day seven. | [34,42] |
| DH | 11 | 19,313,112 | −6.4 | 6.6 | 1.23 × 10−5 | 10.1% | |||
| GA | 11 | 19,313,112 | −6.4 | 6.6 | 2.44 × 10−5 | 20.2% | |||
| qGR11-5 | DH | 11 | 20,619,141 | 19.9 | 9.1 | 2.97 × 10−5 | 9.4% | GR of de-hulled seed (60 DAH) at day seven. | [42] |
| qGR11-6 | DH | 11 | 23,872,614 | 4.6 | 4.4 | 9.96 × 10−5 | 9.5% | GR of intact seed (30 and 60 DAH) at day seven. | [42] |
| qGR11-7 | DH | 11 | 24,096,053 | −1.9 | 3.8 | 2.52 × 10−5 | 10.7% | GR of intact seed (30 and 60 DAH) at day seven. | [42] |
WDB control, without dormancy breaking as a control treatment. DH, dry heating treatment. GA, gibberellic acid treatment. SE, standard error.