Table 2.
Summary of QTL based on a skeleton map derived from the 2846 loci data set.
| Trait, QTL number and QTL interaction | Chrom. | QTL peak position | 2-LOD confidence interval | Morphological and/or cloned genes within 2 LOD conf. interval | LOD | Additive effect | R2* | LOD threshold | MIM R2** | H2 |
|---|---|---|---|---|---|---|---|---|---|---|
| Final leaf number | 3.0 | 0.47 | 0.87 | |||||||
| 1 | 1H | 158 | (154-158) | 6.9 | -0.9 | 0.17 | ||||
| 2 | 4H | 118 | (117-120) | VRN-H2 | 4.6 | 0.7 | 0.10 | |||
| 3 | 5H | 157 | (154-161) | VRN-H1 | 3.5 | -0.7 | 0.09 | |||
| 4 | 7H | 29 | (26-36) | 3.6 | 0.7 | 0.08 | ||||
| Plant height | 3.1 | 0.82 | 0.94 | |||||||
| 1 | 1H | 131 | (120-136) | 7.1 | -6.7 | 0.06 | ||||
| 2 | 2H | 156 | (155-158) | ZEO1 | 32.1 | -22.8 | 0.67 | |||
| 3 | 3H | 51 | (43-60) | 6.1 | 6.3 | 0.05 | ||||
| 4 | 6H | 100 | (74-104) | 6.0 | 5.7 | 0.05 | ||||
| Spike number | 2.9 | 0.50 | 0.63 | |||||||
| 1 | 2H | 99 | (95-102) | VRS1 | 13.3 | 3.5 | 0.38 | |||
| 2 | 5H | 43 | 2.4 | -1.3 | 0.05 | |||||
| 3 | 6H | 80 | 2.7 | 1.3 | 0.06 | |||||
| Spike length | 3.1 | 0.93 | 0.98 | |||||||
| 1 | 1H | 158 | (152-158) | 6.7 | -0.5 | 0.00 | ||||
| 2 | 2H | 156 | (155-159) | ZEO1 | 45.8 | -3.0 | 0.81 | |||
| 3 | 3H | 20 | (13-23) | 5.0 | -0.5 | 0.04 | ||||
| 4 | 5H | 138 | (137-144) | 3.8 | -0.3 | 0.02 | ||||
| 5 | 6H | 95 | (93-100) | 4.5 | 0.4 | 0.02 | ||||
| 1 × 2 | 0.5 | 0.05 | ||||||||
| Floret number | 3.0 | 0.87 | 0.97 | |||||||
| 1 | 1H | 156 | (150-158) | 9.4 | -5.8 | 0.06 | ||||
| 2 | 2H | 99 | (97-101) | VRS1 | 40.3 | -21.6 | 0.79 | |||
| 3 | 3H | 36 | 2.9 | -2.9 | 0.01 | |||||
| 4 | 4H | 120 | (112-127) | VRN-H2 | 3.6 | 3.3 | 0.02 | |||
| 5 | 6H | 91 | (73-103) | 4.6 | 3.7 | 0.02 | ||||
| Grain number | 3.0 | 0.74 | 0.92 | |||||||
| 1 | 1H | 151 | (142-156) | 3.9 | -4.9 | 0.01 | ||||
| 2 | 2H | 99 | (99-101) | VRS1 | 20.1 | -12.3 | 0.46 | |||
| 3 | 2H | 156 | (150-163) | ZEO1 | 10.4 | -7.3 | 0.18 | |||
| 1 × 2 | 2.9 | 0.04 | ||||||||
| 2 × 3 | 3.4 | 0.05 | ||||||||
| Hundred grain weight | 2.9 | 0.66 | 0.78 | |||||||
| 1 | 2H | 99 | (97-101) | VRS1 | 19.9 | 0.5 | 0.53 | |||
| 2 | 6H | 60 | (54-61) | 3.5 | -0.1 | 0.04 | ||||
| 3 | 7H | 103 | (96-111) | 4.2 | 0.2 | 0.05 | ||||
| Grain yield | 3.1 | 0.29 | 0.49 | |||||||
| 1 | 1H | 157 | (153-158) | 4.4 | -2.9 | 0.11 | ||||
| 2 | 2H | 160 | (150-165) | ZEO1 | 8.1 | -4,1 | 0.23 | |||
***Proportion of phenotypic the variance explained by individual QTL
**R2 of the multi-locus model that includes QTL and their significant interactions calculated with MIM
The QTLs in italics and underlined showed a trend in the RAD-only map but did not reach the LOD threshold.