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Table 3 QTLs for the three traits detected in the set of CSSLs in Shanghai and Hangzhou

From: Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice

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  
  1. aThe percentage of phenotypic variation explained (PVE) by the detected QTL; b Additive effects (Add), the positive value suggests that alleles from BAS increase the effect