Table 3.
QTL mapping and genetic effect analysis
| Trait | LOD threshold | Position; interval (Chromosome; cM) |
QTL | Locus; size (peak bin; Kb) |
Lod | Add | Dom | D/[A] | R2(%) | Included QTLs/genes |
|---|---|---|---|---|---|---|---|---|---|---|
| PH | 3.2 | 1; 17.3-17.6 | qph1-1 | bin132; 14.6 | 2.35 | −2.64 | 1.49 | 0.57 | 1.4 | ph1.1 (Marri et al.2005) |
| 1; 22.7-23.2 | qph1-2 | bin172; 13.2 | 2.57 | −2.88 | 0.88 | 0.31 | 1.5 | |||
| 1; 131.0-131.5 | qph1-3 | bin807; 19.7 | 97.92 | 14.98 | 5.44 | 0.36 | 44.3 | sd-1 (Sasaki et al.2002) | ||
| 2.9 | 2; 87.5-87.7 | qph2-1 | bin1418; 34.0 | 2.98 | −2.71 | −2.65 | −0.98 | 1.8 | Sn2a (Tan et al.1996) | |
| 3.1 | 3; 48.3-50.7 | qph3-1 | bin1846; 10.9 | 6.15 | −4.31 | −0.5 | −0.12 | 3.6 | d88 (Gao et al.2009) | |
| 3; 70.7-71.1 | qph3-2 | bin1943; 40.9 | 3.3 | −3.29 | 0.17 | 0.05 | 2 | OsApx1 (Agrawal et al.2003) | ||
| 2.9 | 4; 121.9-122.4 | qph4-1 | bin2728; 106.0 | 2.83 | −1.21 | 3.83 | 3.17 | 1.7 | qPH1-4-1 (Cui et al.2004) | |
| 2.9 | 6; 26.6-27.1 | qph6-1 | bin3619; 57.6 | 19.37 | −7.42 | −2.58 | −0.35 | 10.9 | qPH2-6-1 (Cui et al.2004); ph6 (Xiao et al.1996) | |
| 6; 58.1-58.4 | qph6-2 | bin3845; 78.0 | 7.73 | −5.23 | 1.18 | 0.23 | 4.5 | qIN3-6 (Yamamoto et al.2001) | ||
| 2.8 | 9; 0.6-1.5 | qph9-1 | bin5195; 53.0 | 4.08 | −3.49 | 2.01 | 0.58 | 2.4 | ||
| 2.6 | 10; 47.2-48.0 | qph10-1 | bin5796; 88.3 | 10.73 | 5.32 | −2.89 | −0.54 | 6.2 | OsCesA7 (Tanaka et al.2003) | |
| 2.8 | 12; 66.8-68.0 | qph12-1 | bin6735; 107.2 | 3.58 | −3.15 | 2.49 | 0.79 | 2.1 | nd1 (Li et al.2009a) | |
| PL | 3.1 | 1; 131.3-131.7 | qpl1-1 | bin808; 23.3 | 6.41 | 0.7 | 0.4 | 0.57 | 3.8 | qp1-1 (Hittalmani et al.2002); p11.1 (Thomson et al.2003) |
| 3 | 2; 22.9-23.2 | qpl2-1 | bin1175; 25.2 | 5.04 | 0.63 | −0.39 | −0.62 | 3 | qph-2 (Ping et al.2003) | |
| 2.9 | 3; 48.3-50.7 | qpl3-1 | bin1846; 10.9 | 8.38 | −0.84 | 0.06 | 0.07 | 4.9 | d88 (Gao et al.2009) | |
| 3; 70.7-71.1 | qpl3-2 | bin1943; 40.9 | 6.48 | −0.74 | −0.07 | −0.09 | 3.8 | OsApx1 (Agrawal et al.2003) | ||
| 2.9 | 4; 77.7-78.2 | qpl4-1 | bin2570; 20.3 | 3.19 | 0.47 | 0.33 | 0.7 | 1.9 | pl4 (Zhuang et al.1997) | |
| 2.9 | 6; 26.6-27.1 | qpl6-1 | bin3619; 57.6 | 13.37 | −1.04 | −0.32 | −0.31 | 7.7 | qPH2-6-1 (Cui et al.2004); ph6 (Xiao et al.1996) | |
| 6; 52.7-53.4 | qpl6-2 | bin3807; 13.1 | 20.28 | −1.35 | 0.24 | 0.18 | 11.5 | OsIAA23 (Jun et al.2011); ph6 (Xiao et al.1996) | ||
| 2.9 | 8; 87.1-87.4 | qpl8-1 | bin5156; 37.6 | 9.7 | 0.89 | 0.11 | 0.12 | 5.7 | IPA1 (Jiao et al.2010) | |
| 2.6 | 10; 41.4-41.6 | qpl10-1 | bin5745; 268.2 | 5.1 | 0.59 | −0.45 | −0.76 | 3 | brd2 (Hong et al.2005) | |
| 2.8 | 12; 68.8-74.3 | qpl12-1 | bin6738; 11.9 | 3.14 | −0.46 | 0.47 | 1.03 | 1.9 | ||
| GN | 3.1 | 1; 18.4-18.7 | qgn1-1 | bin137; 13.4 | 23.01 | −37.07 | −5.39 | −0.15 | 12.9 | Gn1a (Ashikari et al.2005) |
| 1; 127.5-128.0 | qgn1-2 | bin784; 14.5 | 8.74 | 22.73 | 9.1 | 0.4 | 5.1 | qLVBTS1-1 (Cui et al.2003) | ||
| 3 | 2; 86.0-86.7 | qgn2-1 | bin1394; 189.6 | 3.29 | −15.64 | −2.96 | −0.19 | 2 | qPN2 (Yuan et al.2003) | |
| 3.2 | 3; 66.6-67.0 | qgn3-1 | bin1929; 16.9 | 2.36 | 12.6 | 13.61 | 1.08 | 1.4 | ||
| 3; 137.1-137.5 | qgn3-2 | bin2208; 23.2 | 2.2 | 12.05 | 1.01 | 0.08 | 1.3 | ps3 (Redona and Mackill1998) | ||
| 2.9 | 6; 9.7-10.2 | qgn6-1 | bin3519; 70.9 | 3.76 | −16.05 | 8.97 | 0.56 | 2.2 | TNSP6 (Zhuang et al.2001) | |
| 6; 26.2-26.5 | qgn6-2 | bin3612; 41.0 | 16.36 | −32.9 | −1.59 | −0.05 | 9.4 | tns6 (Lin et al.1995) | ||
| 6; 32.9-33.3 | qgn6-3 | bin3660; 135.5 | 15.62 | −31.37 | −5.62 | −0.18 | 8.9 | OsJMT1(Kim et al.2009) | ||
| 6; 36.5-36.8 | qgn6-4 | bin3685; 64.2 | 15.7 | −31.35 | −5.72 | −0.18 | 9 | gp6 (Hua et al.2002) | ||
| 2.7 | 8; 67.1-67.8 | qgn8-1 | bin5104; 14.8 | 18.73 | −33.28 | 15.65 | 0.47 | 10.6 | IPA1 (Jiao et al.2010) | |
| 2.7 | 11; 26.1-26.5 | qgn11-1 | bin6104; 17.2 | 3.01 | −14.04 | −0.43 | −0.03 | 1.8 | ||
| PBN | 3.2 | 1; 18.4-18.7 | qpbn1-1 | bin137; 13.4 | 5.55 | −0.82 | −0.12 | −0.15 | 3.3 | Gn1a (Ashikari et al.2005) |
| 3.1 | 2; 79.8-80.4 | qpbn2-1 | bin1364; 16.6 | 6.02 | −0.85 | −0.17 | −0.2 | 3.6 | np2.2 (Marri et al.2005) | |
| 2.9 | 6; 9.4-9.9 | qpbn6-1 | bin3517; 37.4 | 12.41 | −1.3 | 0.04 | 0.03 | 7.2 | qNPB6-1(Cui et al.2002) | |
| 6; 25.5-26.0 | qpbn6-2 | bin3607; 95.9 | 41.17 | −2.02 | −0.96 | −0.48 | 21.9 | Hd1 (Yano et al.2000) | ||
| 6; 36.5-36.8 | qpbn6-3 | bin3685; 64.2 | 31.76 | −1.8 | −0.8 | −0.44 | 17.4 | gp6 (Hua et al.2002) | ||
| 2.9 | 7; 65.3-65.7 | qpbn7-1 | bin4418; 71.0 | 2.55 | −0.39 | 0.57 | 1.48 | 1.5 | OsFOR1 (Jang et al.2003) | |
| 2.8 | 8; 68.0-68.4 | qpbn8-1 | bin5107; 45.0 | 14.26 | −1.33 | 0.45 | 0.34 | 8.2 | IPA1 (Jiao et al.2010) | |
| 2.6 | 10; 47.9-48.6 | qpbn10-1 | bin5798; 39.8 | 10.57 | 0.83 | −1.08 | −1.3 | 6.2 | Ehd1 (Doi et al.2004) | |
| SBN | 3.1 | 1; 18.4-18.7 | qsbn1-1 | bin137; 13.4 | 25.31 | −7.98 | −0.9 | −0.11 | 14.1 | Gn1a (Ashikari et al.2005) |
| 1; 127.5-128.0 | qsbn1-2 | bin784; 14.5 | 8.72 | 4.62 | 2.03 | 0.44 | 5.1 | qNSB1-1 (Cui et al.2002) | ||
| 3.1 | 3; 135.2-135.5 | qsbn3-1 | bin2186; 373.4 | 2.95 | 2.8 | 1.2 | 0.43 | 1.8 | ps3 (Redona and Mackill1998) | |
| 2.9 | 6; 26.2-26.5 | qsbn6-1 | bin3614; 107.2 | 10.21 | −5.46 | 0.9 | 0.16 | 5.9 | tns6 (Lin et al.1995) | |
| 6; 29.9-31.2 | qsbn6-2 | bin3649; 29.5 | 11.38 | −5.59 | −0.49 | −0.09 | 6.6 | qSPN-6 (He et al.2001) | ||
| 6; 36.5-36.8 | qsbn6-3 | bin3685; 64.2 | 10.76 | −5.44 | −0.53 | −0.1 | 6.3 | gp6 (Hua et al.2002) | ||
| 2.8 | 8; 67.1-67.8 | qsbn8-1 | bin5104; 14.8 | 22.34 | −7.55 | 2.62 | 0.35 | 12.6 | IPA1 (Jiao et al.2010) | |
| 2.9 | 11; 26.1-26.5 | qsbn11-1 | bin6104; 17.2 | 2.4 | −2.57 | −0.11 | −0.04 | 1.4 |
Note: LOD threshold was calculated using Mapqtl software with 1000 iterations of the arrangement test; R2: phenotypic variation rate, D/[A]: additive (d/a = 0-0.2), partially dominant (d/a = 0.2-0.8), dominant (d/a = 0.81-1.2), overdominant (d/a > 1.2); The bold and italic type of QTLs were represented new one.