Table 4.
Major loci associated with traits in non-flooded and flooded conditions.
| Trait | Locus abbr. | Chr | Position | Class† | -log10 (P-value) | r2 | |
|---|---|---|---|---|---|---|---|
| GERMINATION RATE | |||||||
| Non-flooded | Pv01/49.8 | 1 | 49,760,345 | NF | 4.07 | 13.33 | |
| Pv04/6.4 | 4 | 6,446,043 | NF | 4.12 | 12.40 | ||
| Pv05/36.5 | 5 | 36,523,875 | NF | 5.12 | 15.68 | ||
| Pv09/33.4 | 9 | 33,436,855 | NF | 4.92 | 16.33 | ||
| 36.26 | |||||||
| Flooded | Pv04/45.7 | 4 | 45,724,128 | F | 5.19 | 13.03 | |
| Pv06/16.0 | 6 | 16,034,362 | F | 5.47 | 14.31 | ||
| Pv08/3.2 | 8 | 3,260,637 | F | 5.48 | 14.30 | ||
| 20.59 | |||||||
| TOTAL WEIGHT | |||||||
| Non-flooded | Pv08/7.5 | 8 | 7,494,340 | NF | 5.28 | 16.51 | |
| Flooded | Pv05/1.2 | 5 | 1,163,339 | both ‡ | 5.41 | 15.89 | |
| Pv08/59.1 | 8 | 59,069,546 | F | 5.25 | 15.35 | ||
| 22.17 | |||||||
| SHOOT WEIGHT | |||||||
| Non-flooded | Pv08/7.5 | 8 | 7,494,340 | NF | 5.20 | 15.77 | |
| Flooded | Pv05/1.2 | 5 | 1,163,367 | both | 5.21 | 15.89 | |
| Pv08/59.1 | 8 | 59,069,546 | F | 5.11 | 15.58 | ||
| 21.34 | |||||||
| ROOT WEIGHT | |||||||
| Non-flooded | Pv01/28.5 | 1 | 28,497,505 | NF | 4.77 | 17.11 | |
| Pv02/32.0 | 2 | 32,055,514 | NF | 4.80 | 18.02 | ||
| Pv05/1.3 | 5 | 1,296,877 | NF | 4.53 | 16.86 | ||
| Pv06/14.9 | 6 | 14,869,116 | NF | 4.66 | 17.46 | ||
| Pv10/1.0 | 10 | 1,023,101 | NF | 4.93 | 17.41 | ||
| 36.97 | |||||||
| Flooded | Pv08/62.3 | 8 | 62,282,561 | F | 4.95 | 12.90 | |
| Pv09/13.5 | 9 | 13,549,503 | F | 5.04 | 15.26 | ||
| 21.64 | |||||||
| HYPOCOTYL LENGTH | |||||||
| Non-flooded | Pv04/0.2 | 4 | 177,101 | NF | 4.37 | 12.09 | |
| Pv05/13.9 | 5 | 13,923,936 | NF | 4.82 | 12.63 | ||
| Pv05/35.7 | 5 | 35,759,769 | NF | 4.42 | 11.54 | ||
| Pv10/0.4 | 10 | 384,405 | NF | 4.23 | 11.02 | ||
| Pv11/52.9 | 11 | 52,955,904 | both | 4.50 | 11.77 | ||
| 39.75 | |||||||
| Flooded | Pv03/46.9 | 3 | 46,914,727 | F | 3.82 | 10.31 | |
| Pv07/24.4 | 7 | 24,450,920 | F | 6.00 | 17.22 | ||
| Pv09/7.8 | 9 | 7,809,795 | F | 4.25 | 11.62 | ||
| Pv11/52.9 | 11 | 52,955,972 | both | 4.72 | 13.29 | ||
| 33.05 | |||||||
| SPAD INDEX | |||||||
| Non-flooded | Pv01/3.9 | 1 | 3,931,202 | NF | 4.89 | 13.74 | |
| Pv03/50.0 | 3 | 50,059,460 | NF | 4.03 | 10.73 | ||
| Pv07/38.3 | 7 | 38,274,271 | NF | 4.39 | 12.44 | ||
| Pv09/11.5 | 9 | 11,514,939 | NF | 4.51 | 9.86 | ||
| 29.94 | |||||||
| Flooded | Pv06/24.3 | 6 | 24,294,817 | F | 3.73 | 12.21 | |
| Pv07/8.1 | 7 | 8,083,989 | F | 4.04 | 10.04 | ||
| Pv08/61.1 | 8 | 61,080,306 | F | 4.51 | 11.41 | ||
| 27.74 | |||||||
| ADVENTITIOUS ROOTS § | |||||||
| Flooded | Pv07/28.7 | 7 | 28,690,630 | F | 3.78 | 9.70 | |
| Pv08/62.3 | 8 | 62,270,633 | F | 4.26 | 10.24 | ||
| Pv09/13.5 | 9 | 13,549,503 | F | 4.49 | 11.47 | ||
| Pv09/20.2 | 9 | 20,230,630 | F | 4.01 | 10.30 | ||
| 33.60 | |||||||
| SURVIVAL SCORE | |||||||
| Flooded | Pv02/47.3 | 2 | 47,348,500 | F | 3.65 | 10.73 | |
| Pv04/46.8 | 4 | 46,852,214 | F | 4.56 | 12.15 | ||
| Pv07/4.7 | 7 | 4,735,092 | F | 4.65 | 13.73 | ||
| Pv09/19.1 | 9 | 19,108,550 | F | 3.62 | 6.02 | ||
| Pv10/1.5 | 10 | 1,471,633 | F | 4.66 | 13.06 | ||
| 37.82 | |||||||
*
Classification was based on detection of QTL in each treatment. NF = QTL only detected in the non-flooded condition. F = QTL detected in flooding condition and both = QTL were detected in both treatments (non-flooded vs. flooded). ‡ The QTL on Pv05/1.2 associated with total and shoot weight was identified in both flooded and non-flooded conditions. Under the non-flooded condition, the significant markers are falling between 0.01 and 0.1 percentile tail of the empirical distribution of P-values, however in flooded condition, it passes the 0.01 percentile. For more clarifications, refer to Figure 5. § Adventitious root was observed only in flooded condition.