Table 3.
Summary of the QTL identified by GWAS mapping for five different rice seedling chilling tolerance indices.
| QTL | Trial no.† | p-value (x 10-3) | LOD value‡ | Chromosome | Position (Mb) | Associated marker | Marker R2 (%)# |
|---|---|---|---|---|---|---|---|
| Low temperature germinability (LTG) | |||||||
| qLTG1 | 1 | 0.74 | 3.13 | 1 | 29.5 | RM1231 | 11.90 |
| 3 | 2.73 | 2.57 | 1 | 29.5 | RM1231 | 10.44 | |
| combined | 1.13 | 2.95 | 1 | 29.5 | RM1231 | 11.45 | |
| qLTG6 | 3 | 1.63 | 2.79 | 6 | 22.3 | RM3827 | 12.97 |
| combined | 1.35 | 2.87 | 6 | 22.3 | RM3827 | 13.20 | |
| qLTG7 | 2 | 2.81 | 2.55 | 7 | 28.3 | RM1335 | 11.25 |
| qLTG10-1 | 2 | 3.77 | 2.42 | 10 | 19.1 | RM171 | 6.30 |
| combined | 10.53ˆ! | 1.98 | 10 | 19.1 | RM171 | 5.15 | |
| qLTG10-2 | 3 | 4.00 | 2.40 | 10 | 21.1 | RM484 | 5.99 |
| combined | 6.44 | 2.19 | 10 | 21.1 | RM484 | 5.48 | |
| qLTG12 | 2 | 0.26 | 3.58 | 12 | 5.1 | RM5746 | 9.47 |
| Plumule growth rate after cold germination (PGCG) | |||||||
| qPGCG1 | 1 | 4.53 | 2.34 | 1 | 0.2 | RM495 | 5.38 |
| qPGCG9-1 | 1 | 3.55 | 2.45 | 9 | 6.3 | RM23869 | 7.91 |
| qPGCG9-2 | 1 | 6.71 | 2.17 | 9 | 14.4 | RM409 | 5.98 |
| qPGCG9-3 | 1 | 7.04 | 2.15 | 9 | 22.2 | RM6816 | 3.58 |
| qPGCG11 | 1 | 6.98 | 2.16 | 11 | 11.9 | RM5857 | 13.34 |
| Low temperature seedling survivability (LTSS) | |||||||
| qLTSS2 | 4 | 6.56 | 2.22 | 2 | 19.4 | RM341 | 5.81 |
| qLTSS3-1 | 1 | 0.15 | 3.82 | 3 | 7.1 | RM14643 | 9.28 |
| qLTSS3-2 | 1 | 4.68 | 2.33 | 3 | 15.8 | RM15123 | 12.56 |
| 2 | 8.61 | 2.07 | 3 | 15.8 | RM15123 | 10.89 | |
| qLTSS3-3 | 2 | 7.51 | 2.12 | 3 | 24.9 | RM5626 | 5.55 |
| combined | 0.29 | 3.54 | 3 | 24.9 | RM5626 | 5.56 | |
| qLTSS3-4 | combined | 10.43ˆ! | 1.98 | 3 | 35.3 | RM514 | 6.21 |
| qLTSS4-1 | 1 | 0.15 | 3.84 | 4 | 13.6 | RM3317 | 12.32 |
| 2 | 0.30 | 3.52 | 4 | 13.6 | RM3317 | 10.75 | |
| combined | 0.93 | 3.03 | 4 | 13.6 | RM3317 | 8.51 | |
| qLTSS4-2 | 2 | 7.55 | 2.12 | 4 | 30.1 | RM3217 | 6.45 |
| qLTSS4-3 | combined | 2.72 | 2.57 | 4 | 34.7 | RM124 | 3.95 |
| qLTSS6 | 1 | 6.45 | 2.19 | 6 | 28.6 | RM340 | 8.51 |
| qLTSS7-1 | 3 | 7.33 | 2.14 | 7 | 2.7 | RM427 | 1.98 |
| qLTSS7-2 | 4 | 5.61 | 2.25 | 7 | 9.0 | RM1186 | 6.31 |
| qLTSS8-1 | combined | 4.87 | 2.31 | 8 | 5.7 | RM22559 | 4.87 |
| qLTSS8-2 | 2 | 6.64 | 2.18 | 8 | 15.4 | RM404 | 11.04 |
| 5 | 0.64 | 2.20 | 8 | 15.4 | RM404 | 5.07 | |
| qLTSS8-3 | 4 | 4.50 | 2.35 | 8 | 21.0 | RM284 | 6.04 |
| qLTSS9-1 | 5 | 0.54 | 2.27 | 9 | 9.4 | RM24011 | 8.14 |
| qLTSS9-2 | combined | 10.85ˆ! | 1.97 | 9 | 14.4 | RM409 | 4.25 |
| qLTSS9-3 | 4 | 7.77 | 2.11 | 9 | 21.9 | RM6971 | 10.77 |
| qLTSS10-1 | 2 | 9.16 | 2.04 | 10 | 5.4 | RM216 | 6.27 |
| combined | 5.68 | 2.25 | 10 | 5.4 | RM216 | 4.65 | |
| qLTSS10-2 | 1 | 0.64 | 3.19 | 10 | 11.6 | RM25289 | 9.98 |
| qLTSS11-1 | 4 | 3.15 | 2.50 | 11 | 5.7 | RM116 | 5.09 |
| qLTSS11-2 | 2 | 3.35 | 2.48 | 11 | 11.9 | RM5857 | 13.00 |
| qLTSS11-3 | 1 | 8.51 | 2.07 | 11 | 19.2 | RM5349 | 8.35 |
| qLTSS12-1 | 4 | 10.81ˆ! | 1.97 | 12 | 23.2 | RM3726 | 9.04 |
| combined | 0.70 | 3.15 | 12 | 23.2 | RM3726 | 10.80 | |
| qLTSS12-2 | 3 | 0.37 | 3.43 | 12 | 25.0 | RM3739 | 3.91 |
| combined | 9.55 | 2.02 | 12 | 25.0 | RM3739 | 5.40 | |
| Plumule recovery growth after cold exposure (PGC) | |||||||
| qPGC3-1 | combined | 10.51ˆ! | 1.98 | 3 | 15.8 | RM15123 | 10.65 |
| qPGC3-2 | combined | 2.51 | 2.60 | 3 | 17.2 | RM3400 | 11.41 |
| qPGC6-1 | combined | 9.91 | 2.00 | 6 | 1.8 | Ex_6 | 2.96 |
| qPGC6-2 | combined | 4.81 | 2.32 | 6 | 6.8 | NPBR | 3.57 |
| qPGC6-3 | combined | 1.48 | 2.83 | 6 | 28.6 | RM340 | 10.02 |
| Low temperature survival (LTS) | |||||||
| qLTS3-1 | 2 | 9.13 | 2.04 | 3 | 2.5 | RM231 | 8.79 |
| qLTS3-2 | 1 | 5.85 | 2.23 | 3 | 24.9 | RM5626 | 6.40 |
| combined | 2.39 | 2.62 | 3 | 24.9 | RM5626 | 7.09 | |
| qLTS4 | 1 | 2.14 | 2.67 | 4 | 34.7 | RM124 | 5.86 |
| combined | 0.01 | 5.00 | 4 | 34.7 | RM124 | 10.00 | |
| qLTS5 | 1 | 5.04 | 2.30 | 5 | 7.5 | RM169 | 10.64 |
| qLTS7 | combined | 10.71ˆ! | 1.97 | 7 | 2.7 | RM427 | 4.21 |
| qLTS8 | combined | 0.46 | 3.34 | 8 | 15.4 | RM404 | 16.55 |
| qLTS9 | 1 | 6.52 | 2.19 | 9 | 22.8 | RM1013 | 4.86 |
| qLTS12 | combined | 3.58 | 2.45 | 12 | 25.0 | RM3739 | 7.30 |
All QTL below the p-value = 0.01 are included. †QTL identified from the individual trials or combined across all trials for the particular index. ‡The LOD value is the logarithm of odds (-log10p). #Marker effects as identified by TASSEL 3.0 (Bradbury et al., 2007). !Value very close to p = 0.01 cutoff.