Table 3 QTLs for the three traits detected in the set of CSSLs in Shanghai and Hangzhou
Environment | Trait | QTL | Chromosome | Location (bin) | Location (Mb) | LOD | PVE (%)a | Addb | Known QTL/gene |
|---|---|---|---|---|---|---|---|---|---|
Shanghai | HD | qHD1-1 | chr01 | chr01_357 | 35.7–40.2 | 3.2 | 1.7 | − 1.7 | OsMADS51 |
Shanghai | HD | qHD4-2 | chr04 | chr04_196 | 18.5–22.0 | 14.1 | 9.3 | 3.4 |  |
Shanghai | HD | qHD6-1 | chr06 | chr06_10 | 1.0–3.0 | 41.7 | 52.3 | 11.2 | Hd3a/RFT1 |
Shanghai | HD | qHD8-1 | chr08 | chr08_41 | 3.9–4.6 | 22.9 | 18.4 | 8.1 | Ghd8 |
Shanghai | HD | qHD10-1 | chr10 | chr10_159 | 15.9–17.3 | 14.5 | 9.7 | 4.8 | Ehd1 |
Shanghai | PH | qPH1-1 | chr01 | chr01_357 | 35.7–40.2 | 34.5 | 71.7 | 19.2 | sd1 |
Shanghai | PH | qPH6-1 | chr06 | chr06_10 | 1.0–3.0 | 3.5 | 3.6 | 5.0 | Hd3a/RFT1 |
Shanghai | PL | qPL3-2 | chr03 | chr03_243 | 24.3–26.5 | 3.8 | 12.5 | − 0.9 |  |
Shanghai | PL | qPL10-1 | chr10 | chr10_174 | 15.9–19.0 | 3.0 | 9.8 | − 1.2 |  |
Hangzhou | HD | qHD4-1 | chr04 | chr04_185 | 18.5–22.0 | 9.6 | 3.8 | 1.8 |  |
Hangzhou | HD | qHD6-1 | chr06 | chr06_10 | 1.0–3.0 | 49.7 | 50.5 | 8.5 | Hd3a/RFT1 |
Hangzhou | HD | qHD7-1 | chr07 | chr07_0 | 0.0–5.1 | 10.9 | 4.4 | 4.3 |  |
Hangzhou | HD | qHD7-2 | chr07 | chr07_207 | 20.3–27.7 | 5.2 | 1.9 | 2.8 |  |
Hangzhou | HD | qHD8-1 | chr08 | chr08_41 | 3.9–4.6 | 18.4 | 8.8 | 4.3 | Ghd8 |
Hangzhou | HD | qHD10-1 | chr10 | chr10_159 | 15.9–17.3 | 15.5 | 7.0 | 3.2 | Ehd1 |
Hangzhou | HD | qHD10-2 | chr10 | chr10_195 | 19.5–22.3 | 5.2 | 1.9 | 2.0 |  |
Hangzhou | HD | qHD11-1 | chr11 | chr11_193 | 18.9–20.4 | 6.5 | 2.4 | 1.9 |  |
Hangzhou | HD | qHD11-2 | chr11 | chr11_288 | 28.8–28.9 | 6.5 | 2.4 | 1.9 |  |
Hangzhou | HD | qHD12-1 | chr12 | chr12_57 | 2.7–9.0 | 5.2 | 1.9 | 2.8 |  |
Hangzhou | HD | qHD12-2 | chr12 | chr12_91 | 8.0–20.4 | 15.8 | 7.2 | − 5.5 |  |
Hangzhou | HD | qHD12-3 | chr12 | chr12_204 | 20.4–21.1 | 43.4 | 37.5 | 7.3 |  |
Hangzhou | HD | qHD12-4 | chr12 | chr12_212 | 21.1–27.4 | 11.6 | 4.8 | − 4.5 |  |
Hangzhou | PH | qPH1-1 | chr01 | chr01_357 | 35.7–40.2 | 17.4 | 46.7 | 13.8 | sd1 |
Hangzhou | PH | qPH8-1 | chr08 | chr08_238 | 22.6–28.3 | 3.1 | 6.2 | 5.7 |  |
Hangzhou | PL | qPL3-1 | chr03 | chr03_130 | 12.8–26.5 | 3.9 | 14.0 | − 2.7 |  |