Table 1.
QTL identified from the analysis of the rice recombinant inbred lines
| Trait | LOD thresholda | QTL | Chr. | LOD | LOD peak position (cM) | R 2 (%)b | Additive effectc | 95% CI (cM)d | QTL region (Mb)e | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Recombination bins | Simulation of 2,330 markers | Simulation of 238 markers | |||||||||
| Heading date | 3.33 | qHD-3 | 3 | 5.40 | 3.7 | 11.0 | 4.03 | 3.1–4.7 | 0.6–1.3 | 0.572–1.392 | 0.8–8.8 |
| Culm diameter | 3.37 | qCD-2 | 2 | 5.71 | 135.5 | 10.4 | 0.38 | 135.2–137.1 | 33.4–34.2 | 33.372–34.356 | 31.2–34.4 |
| qCD-4 | 4 | 4.13 | 94.9 | 7.3 | 0.30 | 93.6–96.6 | 30.1–31.3 | 29.764–31.404 | 28.0–32.8 | ||
| qCD-12 | 12 | 5.47 | 74.9 | 9.9 | 0.36 | 73.9–75.9 | 18.6–20.0 | 18.448–20.088 | 18.4–23.2 | ||
| Plant height | 3.46 | qPH-1 | 1 | 17.18 | 191 | 30.0 | −13.10 | 190.0–193.2 | 40.0–40.6 | 40.096–40.752 | 39.2–40.8 |
| qPH-2 | 2 | 8.00 | 136.4 | 11.9 | 7.90 | 136.1–137.7 | 33.9–34.6 | 33.700–34.356 | 31.2–36.0 | ||
| qPH-3 | 3 | 5.27 | 138.5 | 7.6 | 6.21 | 137.6–139.7 | 32.6–33.3 | 32.224–33.536 | |||
| qPH-12 | 12 | 4.61 | 88.4 | 6.5 | 5.89 | 86.2–91.2 | 22.4–22.9 | 22.056–23.204 | 21.6–23.2 | ||
| Flag leaf length | 3.43 | qFLL-2 | 2 | 3.32 | 109.9 | 7.0 | 2.68 | 107.6–112.2 | 25.7–27.3 | 25.664–27.304 | 24.8–29.6 |
| qFLL-5 | 5 | 3.07 | 115.8 | 6.4 | −1.96 | 112.2–118.3 | 27.5–29.0 | 27.468–29.272 | |||
| qFLL-12 | 12 | 3.73 | 35.4 | 7.8 | 2.21 | 34.7–36.5 | 6.2–7.0 | 6.148–7.132 | 4.0–8.8 | ||
| Flag leaf width | 3.48 | qFLW-1 | 1 | 3.48 | 45.3 | 6.0 | 0.66 | 43.5–47.7 | 4.9–5.4 | 4.836–5.656 | |
| qFLW-4 | 4 | 8.68 | 100.7 | 16.4 | −1.01 | 99.0–101.2 | 31.3–31.8 | 31.240–31.896 | 31.2–34.4 | ||
| qFLW-7 | 7 | 4.34 | 80.4 | 7.4 | 0.67 | 74.4–82.2 | 24.4–25.6 | ||||
| qFLW-8 | 8 | 3.89 | 1.0 | 6.8 | 0.66 | 0.0–2.0 | 0.0–0.3 | 0.080–0.736 | |||
| Tiller angle | 3.37 | qTA-2 | 2 | 3.72 | 118.7 | 4.7 | −0.34 | 114.1–121.3 | 27.8–30.0 | 27.468–30.256 | 26.4–31.2 |
| qTA-6 | 6 | 3.22 | 32.2 | 4.1 | −0.38 | 31.3–33.5 | 5.3–5.8 | 4.0–7.2 | |||
| qTA-9 | 9 | 24.57 | 81.8 | 46.0 | 1.03 | 81.1–82.9 | 21.3–21.7 | 21.236–21.892 | 20.0–23.2 | ||
| Tiller number | 2.85 | qTN-5 | 5 | 4.01 | 115.5 | 8.8 | 1.92 | 114.5–116.8 | 27.9–28.7 | ||
| Panicle length | 3.37 | qPL-2 | 2 | 3.27 | 137.4 | 5.1 | 0.96 | 135.9–139.6 | 33.9–34.9 | 33.864–35.012 | 32.8–36.0 |
| qPL-6a | 6 | 4.13 | 3.9 | 6.5 | −0.99 | 2.3–5.6 | 0.8–1.5 | 0.900–1.556 | |||
| qPL-6b | 6 | 4.09 | 62.7 | 6.4 | 1.07 | 62.3–64.1 | 13.1–17.6 | 13.036–17.628 | |||
| qPL-12a | 12 | 4.39 | 99.0 | 7.1 | 1.09 | 97.2–99.7 | 23.6–24.2 | 23.532–24.352 | |||
| qPL-12b | 12 | 3.14 | 32.2 | 4.9 | 0.94 | 30.3–33.5 | 5.4–5.8 | 4.0–7.2 | |||
| Awn length | 3.30 | qAL-1 | 1 | 7.40 | 152.6 | 13.7 | 5.71 | 150.7–154.9 | 29.1–30.8 | 26.648–30.420 | 28.0–31.2 |
| qAL-3 | 3 | 6.98 | 77.8 | 12.9 | 5.62 | 77.6–80.2 | 16.7–17.4 | 16.152–17.464 | 15.2–18.4 | ||
| qAL-4a | 4 | 4.75 | 86.3 | 8.4 | −4.57 | 86.3–87.6 | 28.1–28.4 | 27.960–28.616 | 26.4–29.6 | ||
| qAL-4b | 4 | 3.25 | 53.0 | 5.6 | −4.02 | 48.9–55.9 | 19.6–20.7 | 19.596–20.744 | |||
| Grain length | 3.35 | qGL-1 | 1 | 5.81 | 149.7 | 8.1 | 0.29 | 147.6–150.4 | 27.7–29.1 | 26.976–29.764 | 26.4–29.6 |
| qGL-3 | 3 | 10.51 | 78.8 | 16.1 | 0.41 | 78.5–81.3 | 16.8–17.5 | 16.644–17.464 | 16.8–18.4 | ||
| qGL-6 | 6 | 4.12 | 32.2 | 5.7 | 0.28 | 30.8–34.5 | 5.2–5.9 | 5.164–5.984 | |||
| qGL-10 | 10 | 4.45 | 59.1 | 6.1 | 0.23 | 54.2–65.1 | 19.0–20.9 | 18.776–21.236 | |||
| Grain width | 3.26 | qGW-2a | 2 | 4.18 | 41.4 | 4.3 | −0.07 | 41.1–44.3 | 9.0–9.8 | 8.936–9.920 | |
| qGW-2b | 2 | 3.21 | 112.1 | 3.2 | −0.06 | 111.5–113.4 | 27.1–27.5 | ||||
| qGW-3 | 3 | 7.02 | 82.2 | 7.3 | −0.09 | 78.5–83.7 | 16.8–17.9 | 16.644–18.120 | 15.2–18.4 | ||
| qGW-5 | 5 | 12.61 | 25.1 | 14.6 | −0.15 | 25.1–26.4 | 5.1–5.5 | 4.672–5.656 | 4.0–5.6 | ||
| qGW-6 | 6 | 5.32 | 60.4 | 5.5 | −0.09 | 59.7–62.3 | 11.5–13.1 | 11.396–13.200 | 10.4–18.4 | ||
| Grain thickness | 3.35 | qGT-5 | 5 | 4.77 | 23.0 | 9.2 | −0.04 | 22.6–25.5 | 4.7–5.3 | 4.672–5.328 | |
| qGT-6 | 6 | 3.91 | 61.4 | 7.4 | −0.04 | 60.1–62.5 | 11.6–16.9 | 11.560–16.972 | 10.4–20.0 | ||
| qGT-10 | 10 | 4.73 | 78.7 | 9.2 | −0.04 | 77.2–82.2 | 22.4–23.2 | 22.384–23.204 | |||
| qGT-11 | 11 | 3.73 | 45.9 | 7.1 | 0.03 | 45.6–47.3 | 10.6–11.0 | 10.248–11.068 | |||
| 1,000-grain weight | 3.35 | qTGW-5a | 5 | 3.29 | 9.1 | 6.7 | −1.08 | 7.9–9.7 | 1.3–2.2 | ||
| qTGW-5b | 5 | 3.14 | 110.4 | 5.8 | −0.96 | 107.8–111.5 | 27.0–27.4 | 26.812–27.468 | |||
| qTGW-8 | 8 | 4.27 | 106.7 | 8.8 | 1.23 | 104.9–108.1 | 25.9–26.4 | 26.320–27.304 | 24.8–28.0 | ||
| qTGW-10 | 10 | 4.26 | 21.9 | 9.7 | −1.28 | 21.2–23.1 | 11.7–11.9 | 10.740–12.052 | 2.4–12.0 | ||
| Spikelet number | 3.43 | qSN-1a | 1 | 4.63 | 37.3 | 8.8 | 18.98 | 35.0–40.9 | 3.5–4.4 | 3.360–3.852 | 36.0–40.8 |
| qSN-1b | 1 | 5.08 | 181.2 | 9.8 | −18.78 | 179.8–182.1 | 37.1–37.5 | 36.980–37.636 | |||
| qSN-6 | 6 | 5.09 | 60.4 | 10.0 | 19.81 | 58.8–62.4 | 11.2–16.9 | 11.068–16.972 | 10.4–21.6 | ||
| qSN-8 | 8 | 4.36 | 18.3 | 8.3 | 16.99 | 16.7–20.0 | 2.3–3.0 | 2.376–3.196 | 0.8–4.0 | ||
aThresholds determined by 1,000 permutation
bPercentage of phenotypic variation explained
cPositive and negative values indicated additive effect contributed by the alleles of 93-11 and Nipponbare, respectively
dChromosome regions corresponding to the 95% confidence interval for the detected QTL
eRegions between flanking bins or simulated markers of identified QTLs using high-throughput genotyping method (re-sequencing), 2,330 simulated markers, and 238 simulated markers by their physical locations, respectively. Blank spaces represent no overlapped QTL