Table 4.
Genome-wide QTL identification under standard-germination condition in IBM Syn10 population.
| QTL Symbola | Chr | Position (cM) | Peak marker | LODb | R2c (%) | Additive effectd | 2-LOD confidence interval | |||
|---|---|---|---|---|---|---|---|---|---|---|
| PCe start (Mb) | PC end (Mb) | GCf start (cM) | GC end (cM) | |||||||
| qSGGR1-1 | 1 | 107.35 | chr01.56.5 | 2.63 | 2.97 | −4.56 | 5 | 6.4 | 83.6 | 119.15 |
| qSGGR4-1 | 4 | 260.95 | chr04.115.5 | 2.53 | 2.86 | 4.49 | 11.1 | 13.4 | 250.9 | 284.2 |
| qSGGR9-1 | 9 | 680.45 | chr09.1431.5 | 2.86 | 3.23 | −4.99 | 142.7 | 144.2 | 657.95 | 696.25 |
| qSGGR10-1 | 10 | 0.05 | chr10.0.5 | 3.91 | 4.47 | −5.52 | 0.025 | 0.3 | 0.05 | 7.2 |
| qSGML2-1 | 2 | 501.6 | chr02.351.5 | 3.87 | 4.06 | 0.26 | 30.4 | 39.5 | 479.75 | 520.55 |
| qSGML3-1 | 3 | 754.45 | chr03.1810.5 | 4.35 | 4.72 | 0.28 | 180.2 | 182.575 | 743.7 | 771.6 |
| qSGML4-1 | 4 | 170.05 | chr04.61.5 | 3.43 | 3.64 | −0.25 | 5.2 | 7.8 | 136.8 | 196.5 |
| qSGML4-2 | 4 | 401.85 | chr04.276.5 | 2.85 | 3.1 | −0.22 | 23.45 | 34.4 | 382.15 | 430.05 |
| qSGML4-3 | 4 | 614.1 | chr04.1595.5 | 2.84 | 2.97 | 0.24 | 157.25 | 167.6 | 602.65 | 654.85 |
| qSGML5-1 | 5 | 159.85 | chr05.54.5 | 4.35 | 4.93 | 0.28 | 4.725 | 5.8 | 138.7 | 169.55 |
| qSGML6-1 | 6 | 221.6 | chr06.925.5 | 3.46 | 3.64 | −0.25 | 90.725 | 93.15 | 210.9 | 239.15 |
| qSGML6-2 | 6 | 493.3 | chr06.1288 | 5.18 | 5.53 | 0.34 | 128.1 | 129.65 | 487.95 | 499.35 |
| qSGML10-1 | 10 | 304.7 | chr10.1096.5 | 4.66 | 4.92 | 0.29 | 97.15 | 116.7 | 298.25 | 321.1 |
| qSGCL1-1 | 1 | 1258.35 | chr01.2654.5 | 2.76 | 2.81 | −0.13 | 260.575 | 269.275 | 1239.05 | 1275.15 |
| qSGCL1-2 | 1 | 1582.8 | chr01.2935.5 | 2.85 | 2.91 | −0.13 | 292.725 | 295.8 | 1558.85 | 1605.8 |
| qSGCL3-1 | 3 | 349.1 | chr03.152 | 5.13 | 5.35 | 0.17 | 14.65 | 17.6 | 341.6 | 362.0 |
| qSGCL4-1 | 4 | 171.1 | chr04.63 | 4.18 | 4.32 | −0.16 | 5.875 | 7.2 | 152.0 | 190.4 |
| qSGCL4-2 | 4 | 659.1 | chr04.1699 | 3.4 | 3.49 | 0.14 | 166.975 | 172.275 | 641.6 | 687.4 |
| qSGCL5-1 | 5 | 445.8 | chr05.443 | 2.85 | 3.01 | 0.13 | 39.5 | 52.875 | 433.65 | 457.2 |
| qSGCL6-1 | 6 | 229.15 | chr06.932.5 | 3.82 | 3.93 | −0.15 | 91.9 | 93.15 | 217.7 | 239.15 |
| qSGCL6-2 | 6 | 734.55 | chr06.1582.5 | 2.52 | 2.69 | −0.12 | 155.45 | 159.2 | 697.15 | 756.05 |
| qSGCL7-1 | 7 | 39.55 | chr07.28.5 | 6.06 | 6.36 | 0.19 | 2.7 | 2.8 | 33.1 | 54.55 |
| qSGCL9-1 | 9 | 181.15 | chr09.95.5 | 2.65 | 2.8 | −0.12 | 8.3 | 13.4 | 151.6 | 247.0 |
| qSGCL10-1 | 10 | 312.9 | chr10.1131.5 | 5.32 | 5.55 | 0.18 | 111.3 | 115.075 | 309.7 | 317.55 |
| qSGPL2-1 | 2 | 1145.45 | chr02.2239.5 | 3.81 | 3.78 | 0.31 | 221.325 | 225.2 | 1120.45 | 1153.3 |
| qSGPL3-1 | 3 | 578.75 | chr03.1607 | 3.23 | 3.29 | 0.27 | 158.5 | 162.1 | 549.7 | 590.9 |
| qSGPL6-1 | 6 | 229.15 | chr06.932.5 | 4.73 | 5 | −0.39 | 92.95 | 93.15 | 223.4 | 236.65 |
| qSGPL7-1 | 7 | 862.05 | chr07.1728 | 3.41 | 3.37 | 0.27 | 171.525 | 172.875 | 845.6 | 871.45 |
| qSGPL9-1 | 9 | 181.15 | chr09.95.5 | 3.47 | 3.52 | −0.27 | 8.5 | 11.1 | 164.35 | 210.55 |
| qSGPL10-1 | 10 | 55.3 | chr10.26.5 | 2.56 | 2.51 | −0.25 | 2.4 | 2.6 | 43.45 | 65.3 |
| qSGSL1-1 | 1 | 1188.55 | chr01.2533.5 | 2.68 | 2.78 | −0.38 | 252.95 | 258.05 | 1172.8 | 1220.1 |
| qSGSL1-2 | 1 | 1589.65 | chr01.2951.5 | 3.26 | 3.43 | −0.43 | 293.5 | 295.8 | 1575.3 | 1605.8 |
| qSGSL3-1 | 3 | 824.15 | chr03.1884.5 | 3.73 | 4.09 | 0.47 | 187.2 | 191.325 | 816.3 | 841.7 |
| qSGSL4-1 | 4 | 171.1 | chr04.63 | 3.49 | 3.68 | −0.45 | 5.875 | 7.4 | 154.5 | 193.3 |
| qSGSL4-2 | 4 | 940.75 | chr04.2284.5 | 3.20 | 3.37 | 0.46 | 225.25 | 229.4 | 931.1 | 963.65 |
| qSGSL5-1 | 5 | 439.7 | chr05.403.5 | 3.93 | 4.16 | 0.51 | 39.5 | 48.05 | 433.65 | 449.0 |
| qSGSL10-1 | 10 | 304.7 | chr10.1096.5 | 7.13 | 7.73 | 0.67 | 90.9 | 110.125 | 294.7 | 307.2 |
a
SGGR, SGML, SGCL, SGPL, SGSL represents germination rate, mesocotyl length, coleoptile length, plumule length and seedling length under 2 cm sowing depth, respectively.
b
LOD: Log10-likelihood value.
c
R2: The coefficient of determination, which represents the percentage of phenotypic variance explained by a putative QTL.
d
Additive effect: The positive value means that the allele from B73 is positive contributor.
e
PC: Physical coordinates refer to B73_RefGen_v3.
f
GC: Genetic coordinates.