Table 3.
Genome-wide QTL identification under deep-sowing condition in IBM Syn10 population.
| QTL Symbola | Chr | Position (cM) | Peak marker | LODb | R2c(%) | Additive | 2-LOD confidence interval | |||
|---|---|---|---|---|---|---|---|---|---|---|
| effectd | PCe start(Mb) | PC end(Mb) | GCf start(cM) | GC end(cM) | ||||||
| qDSGR1-1 | 1 | 1183.55 | chr01.2532.5 | 2.72 | 3.32 | −5.52 | 251.875 | 257.8 | 1167.45 | 1210.7 |
| qDSGR2-1 | 2 | 932.45 | chr02.2055.5 | 5.09 | 6.33 | −8.05 | 205.2 | 205.9 | 921.95 | 943.9 |
| qDSGR4-1 | 4 | 42.65 | chr04.28.5 | 3.1 | 3.82 | −6.21 | 2.4 | 3.4 | 29.75 | 72.7 |
| qDSGR4-2 | 4 | 193.3 | chr04.74.5 | 2.58 | 3.19 | −5.45 | 5.875 | 9.7 | 157 | 212.25 |
| qDSML2-1 | 2 | 646.85 | chr02.1280.5 | 2.92 | 3.58 | 0.31 | 104.45 | 136.9 | 621.5 | 654.35 |
| qDSML2-2 | 2 | 911.95 | chr02.2043.5 | 3.55 | 4.34 | −0.32 | 203.05 | 205.6 | 891.45 | 936.4 |
| qDSML5-1 | 5 | 223.2 | chr05.73.5 | 3.56 | 4.37 | −0.33 | 6.5 | 7.9 | 201.35 | 235.35 |
| qDSML7-1 | 7 | 423.6 | chr07.1280.5 | 2.85 | 3.47 | −0.29 | 125.55 | 129.8 | 408.5 | 432.5 |
| qDSCL1-1 | 1 | 841.45 | chr01.1955.5 | 3.5 | 4.17 | 0.12 | 194.55 | 195.8 | 828.2 | 849.7 |
| qDSCL2-1 | 2 | 974.7 | chr02.2099 | 2.85 | 3.38 | 0.1 | 207.5 | 210.725 | 958.55 | 992.25 |
| qDSCL3-1 | 3 | 771.6 | chr03.1827.5 | 2.54 | 3.21 | 0.1 | 180.95 | 185.25 | 751.95 | 805.25 |
| qDSCL4-1 | 4 | 893.2 | chr04.2021.5 | 3.58 | 4.27 | 0.13 | 200.6 | 216.5 | 883.5 | 913.2 |
| qDSCL5-1 | 5 | 1051.15 | chr05.2131.5 | 5.98 | 7.27 | 0.17 | 213 | 213.4 | 1046.85 | 1057.2 |
| qDSCL8-1 | 8 | 525.4 | chr08.1230.5 | 2.75 | 3.27 | −0.1 | 119.675 | 128.65 | 516.45 | 547.25 |
| qDSCL9-1 | 9 | 142.25 | chr09.81.5 | 2.84 | 3.55 | 0.11 | 7.8 | 8.4 | 125.4 | 156.95 |
| qDSPL2-1 | 2 | 1101 | chr02.2192 | 2.74 | 3.29 | 0.25 | 216.7 | 221.6 | 1075.6 | 1122.2 |
| qDSPL2-2 | 2 | 1282.4 | chr02.2342.5 | 2.99 | 3.4 | −0.26 | 232.8 | 234.7 | 1256.4 | 1295.6 |
| qDSPL3-1 | 3 | 818.45 | chr03.1873.5 | 6.42 | 7.55 | 0.39 | 184.6 | 188.7 | 802.35 | 829.9 |
| qDSPL4-1 | 4 | 508.65 | chr04.1083.5 | 2.52 | 2.86 | −0.24 | 76.4 | 140.1 | 492.2 | 535.8 |
| qDSPL8-1 | 8 | 345.25 | chr08.244.5 | 2.76 | 3.14 | 0.26 | 22.8 | 53.075 | 327.05 | 370.5 |
| qDSPL9-1 | 9 | 68.35 | chr09.44.5 | 3.91 | 5.03 | 0.37 | 4.4 | 5 | 60.85 | 73.1 |
| qDSPL9-2 | 9 | 98.2 | chr09.68 | 2.58 | 2.92 | −0.29 | 6.175 | 7.6 | 96.35 | 118.6 |
| qDSPL9-3 | 9 | 221.6 | chr09.116.5 | 4.29 | 4.89 | 0.31 | 10.975 | 12.8 | 206.55 | 230.2 |
| qDSPL10-1 | 10 | 301.1 | chr10.1044.5 | 6.65 | 7.8 | 0.4 | 94 | 111.3 | 297.55 | 309.7 |
| qDSSL2-1 | 2 | 932.45 | chr02.2055.5 | 3.21 | 3.87 | −0.43 | 203.6 | 205.9 | 905.1 | 943.9 |
| qDSSL4-1 | 4 | 510.8 | chr04.1198.5 | 3.77 | 4.55 | −0.44 | 82.25 | 127.075 | 498.25 | 521.9 |
| qDSSL4-2 | 4 | 626.6 | chr04.1623.5 | 2.67 | 3.2 | 0.39 | 158.1 | 165.475 | 609.45 | 636.25 |
| qDSSL7-1 | 7 | 423.25 | chr07.1279.5 | 3.23 | 3.88 | −0.42 | 125.55 | 130.5 | 406 | 444.3 |
a
DSGR, DSML, DSCL, DSPL, DSSL represents germination rate, mesocotyl length, coleoptile length, plumule length, and seedling length under 12.5 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.