Table 3.
QTNs associated with PH via mrMLM in the SBL population.
| QTN | Chr | SNP | Allele | MAF | Position (bp) | Effecta | LOD scoreb | R2 | Known QTLc |
|---|---|---|---|---|---|---|---|---|---|
| qPH1-4-1d | 4 | Gm04_46680158 | T/C | 0.10 | 46680158 | -4.42 | 9.43 | 0.11 | 5-4 |
| qPH1-5-1 | 5 | Gm05_36588358 | G/A | 0.23 | 36588358 | 2.11 | 4.84 | 0.05 | 24-1 |
| qPH1-6-1 | 6 | Gm06_33125042 | T/C | 0.07 | 33125042 | 2.89 | 4.48 | 0.03 | 30-1 |
| qPH1-6-2 | 6 | Gm06_43710729 | G/A | 0.27 | 43710729 | -2.52 | 5.64 | 0.07 | 3-2,6-3 |
| qPH1-6-3 | 6 | Gm06_48441344 | A/G | 0.19 | 48441344 | 1.76 | 6.01 | 0.03 | 38-1 |
| qPH1-9-1 | 9 | Gm09_38680990 | C/T | 0.45 | 38680990 | 1.20 | 3.73 | 0.02 | |
| qPH1-10-1e | 10 | Gm10_44346474 | A/T | 0.41 | 44346474 | 3.04 | 14.99 | 0.13 | E2 |
| qPH1-13-5 | 13 | Gm13_41776586 | C/T | 0.05 | 41776586 | 3.04 | 4.11 | 0.03 | 39-1 |
| qPH1-14-1 | 14 | Gm14_1243675 | A/G | 0.21 | 1243675 | 1.92 | 4.59 | 0.04 | 34-6 |
| qPH1-18-1 | 18 | Gm18_7790416 | T/C | 0.34 | 7790416 | -0.91 | 3.61 | 0.01 | 23-6 |
| qPH1-18-2 | 18 | Gm18_51243803 | A/G | 0.22 | 51243803 | -1.66 | 3.26 | 0.03 | 26-12 |
| qPH2-6-4 | 6 | Gm06_13482496 | G/A | 0.36 | 13482496 | -1.37 | 3.40 | 0.03 | |
| qPH2-7-1 | 7 | Gm07_37502305 | T/C | 0.35 | 37502305 | 1.59 | 4.15 | 0.04 | 37-6 |
| qPH2-8-1 | 8 | Gm08_41977134 | G/A | 0.42 | 41977134 | 1.30 | 3.01 | 0.03 | |
| qPH2-9-2 | 9 | Gm09_7987471 | C/T | 0.23 | 7987471 | 1.60 | 5.16 | 0.03 | mqPH-009 |
| qPH2-9-3 | 9 | Gm09_41284917 | G/A | 0.05 | 41284917 | 2.42 | 3.55 | 0.02 | |
| qPH2-10-1 | 10 | Gm10_44346474 | A/T | 0.41 | 44346474 | 2.21 | 7.67 | 0.08 | E2 |
| qPH2-13-1 | 13 | Gm13_6859748 | A/G | 0.46 | 6859748 | 1.37 | 4.05 | 0.03 | 20-5 |
| qPH2-13-2 | 13 | Gm13_8246449 | T/C | 0.48 | 8246449 | 2.04 | 8.31 | 0.07 | 20-5 |
| qPH2-13-3 | 13 | Gm13_10898897 | T/C | 0.50 | 10898897 | -1.57 | 5.56 | 0.04 | 26-11 |
| qPH2-13-4 | 13 | Gm13_28457573 | T/G | 0.06 | 28457573 | -6.23 | 9.92 | 0.13 | 5-8,15-1 |
| qPH2-13-5 | 13 | Gm13_41776586 | C/T | 0.05 | 41776586 | 3.49 | 5.58 | 0.04 | 39-1 |
| qPH2-14-2 | 14 | Gm14_3056277 | T/C | 0.19 | 3056277 | 2.04 | 6.30 | 0.04 | 34-6 |
| qPH2-20-1 | 20 | Gm20_41211643 | G/T | 0.12 | 41211643 | 2.12 | 4.68 | 0.03 | 28-1 |
| qPH3-2-1 | 2 | Gm02_2328263 | C/A | 0.20 | 2328263 | -3.03 | 9.85 | 0.06 | 9-3 |
| qPH3-2-2 | 2 | Gm02_46786754 | C/T | 0.47 | 46786754 | -1.67 | 3.98 | 0.03 | 6-12 |
| qPH3-3-1 | 3 | Gm03_1920671 | A/G | 0.26 | 1920671 | 1.70 | 4.19 | 0.02 | |
| qPH3-3-2 | 3 | Gm03_6757344 | T/C | 0.26 | 6757344 | 1.63 | 6.27 | 0.02 | |
| qPH3-6-5 | 6 | Gm06_31222865 | C/T | 0.10 | 31222865 | 2.25 | 4.44 | 0.02 | 30-1 |
| qPH3-7-2 | 7 | Gm07_984279 | C/G | 0.09 | 984279 | 2.56 | 3.46 | 0.02 | |
| qPH3-7-1 | 7 | Gm07_37502305 | T/C | 0.35 | 37502305 | 1.88 | 3.21 | 0.04 | 37-6 |
| qPH3-8-2 | 8 | Gm08_18166829 | A/C | 0.46 | 18166829 | 1.46 | 5.53 | 0.02 | |
| qPH3-9-3 | 9 | Gm09_41284917 | G/A | 0.05 | 41284917 | 2.93 | 3.96 | 0.02 | |
| qPH3-10-2 | 10 | Gm10_34971279 | C/G | 0.13 | 34971279 | 2.99 | 8.06 | 0.04 | |
| qPH3-10-1 | 10 | Gm10_44346474 | A/T | 0.41 | 44346474 | 3.02 | 15.21 | 0.10 | E2 |
| qPH3-13-1 | 13 | Gm13_6859748 | A/G | 0.46 | 6859748 | 1.93 | 6.83 | 0.04 | 20-5 |
| qPH3-13-6 | 13 | Gm13_27311661 | G/C | 0.29 | 27311661 | 2.89 | 9.19 | 0.08 | 5-8,15-1 |
| qPH3-14-3 | 14 | Gm14_10617104 | A/G | 0.39 | 10617104 | 1.32 | 4.43 | 0.02 | 34-6 |
| qPH3-19-1 | 19 | Gm19_44938780 | C/T | 0.35 | 44938780 | -2.81 | 14.27 | 0.08 | Dt1 |
| qPH3-20-2 | 20 | Gm20_27547938 | G/A | 0.33 | 27547938 | 3.00 | 12.48 | 0.09 | 16-1 |
aQuantitative trait nucleotide effect. bLOD value, the significant threshold for the transformed P-value. cThe QTLs located in the same region of reported QTLs. dThe QTN identified for PH at the same stage by both methods are underlined in Table. eThe QTNs identified for PH at least two stages are displayed in bold in Table.