Table 2.
Quantitative trait nucleotides (QTNs) associated with PH and NN via CMLM in the SBL population.
| Trait | QTN | Chr | SNP | Position (bp) | Allele | MAF | -Log10 Pa | R2b | R2c | Effect | Known QTLSd |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PH | qPH1-4-1 | 4 | Gm04_46680158 | 46680158 | T/C | 0.10 | 4.35 | 0.35 | 0.38 | -3.71 | 5-4 |
| qPH1-6-1 | 6 | Gm06_43710729 | 43710729 | G/A | 0.27 | 4.15 | 0.35 | 0.38 | -3.08 | 3-2,6-3 | |
| qPH1-10-1 | 10 | Gm10_44226599 | 44226599 | A/C | 0.13 | 4.48 | 0.35 | 0.38 | 3.03 | 18-2,19-2 | |
| qPH1-10-2e | 10 | Gm10_44346474 | 44346474 | A/T | 0.41 | 9.26 | 0.35 | 0.42 | 3.57 | E2 | |
| qPH1-10-3 | 10 | Gm10_44550928 | 44550928 | C/T | 0.33 | 4.45 | 0.35 | 0.38 | -2.36 | 18-2,19-2 | |
| qPH1-10-4 | 10 | Gm10_45479097 | 45479097 | C/T | 0.11 | 4.13 | 0.35 | 0.38 | 3.31 | ||
| qPH1-14-1 | 14 | Gm14_926343 | 926343 | G/A | 0.21 | 4.29 | 0.35 | 0.38 | 2.40 | 34-6 | |
| qPH1-19-1 | 19 | Gm19_44544574 | 44544574 | A/G | 0.36 | 4.58 | 0.35 | 0.38 | -2.53 | 1-1 | |
| qPH2-4-1 | 4 | Gm04_46680158 | 46680158 | T/C | 0.10 | 4.04 | 0.29 | 0.32 | -3.36 | 5-4 | |
| qPH2-10-2 | 10 | Gm10_44346474 | 44346474 | A/T | 0.41 | 8.07 | 0.29 | 0.36 | 3.13 | E2 | |
| qPH2-10-3 | 10 | Gm10_44550928 | 44550928 | C/T | 0.33 | 4.45 | 0.29 | 0.32 | -2.24 | 18-2,19-2 | |
| qPH3-10-2 | 10 | Gm10_44346474 | 44346474 | A/T | 0.41 | 8.52 | 0.25 | 0.33 | 3.80 | E2 | |
| qPH3-19-2 | 19 | Gm19_44938780 | 44938780 | C/T | 0.35 | 6.39 | 0.25 | 0.31 | 3.74 | Dt1 | |
| qPH3-19-3 | 19 | Gm19_45721414 | 45721414 | G/T | 0.33 | 4.25 | 0.25 | 0.29 | -2.62 | 3-1,4-2,6-1 | |
| qPH3-20-1 | 20 | Gm20_41211643 | 41211643 | G/T | 0.12 | 4.02 | 0.25 | 0.29 | 3.03 | 28-1 | |
| NN | qNN1-4-1 | 4 | Gm04_46680158 | 46680158 | T/C | 0.10 | 4.33 | 0.34 | 0.37 | -0.46 | |
| qNN1-6-1 | 6 | Gm06_31222865 | 31222865 | C/T | 0.10 | 4.85 | 0.34 | 0.38 | -0.52 | 4-2 | |
| qNN1-10-1 | 10 | Gm10_44346474 | 44346474 | A/T | 0.41 | 7.99 | 0.34 | 0.40 | 0.41 | E2 | |
| qNN1-14-1 | 14 | Gm14_926343 | 926343 | G/A | 0.21 | 4.35 | 0.34 | 0.37 | 0.30 | ||
| qNN1-18-1 | 18 | Gm18_3716679 | 3716679 | T/C | 0.21 | 4.32 | 0.34 | 0.37 | 0.39 | ||
| qNN1-19-1 | 19 | Gm19_45415096 | 45415096 | C/A | 0.20 | 4.30 | 0.34 | 0.37 | -0.34 | ||
| qNN2-4-1 | 4 | Gm04_46680158 | 46680158 | T/C | 0.10 | 4.53 | 0.29 | 0.33 | -0.27 | ||
| qNN2-6-1 | 6 | Gm06_31222865 | 31222865 | C/T | 0.10 | 4.08 | 0.29 | 0.32 | -0.28 | 4-2 | |
| qNN2-10-1 | 10 | Gm10_44346474 | 44346474 | A/T | 0.41 | 6.95 | 0.29 | 0.35 | 0.22 | E2 | |
| qNN2-10-2 | 10 | Gm10_45479097 | 45479097 | C/T | 0.11 | 4.44 | 0.29 | 0.33 | 0.25 | ||
| qNN2-13-1 | 13 | Gm13_38510582 | 38510582 | T/G | 0.13 | 4.84 | 0.29 | 0.33 | 0.21 | ||
| qNN2-14-1 | 14 | Gm14_926343 | 926343 | G/A | 0.21 | 4.02 | 0.29 | 0.32 | 0.17 | ||
| qNN3-10-1 | 10 | Gm10_44346474 | 44346474 | A/T | 0.41 | 6.83 | 0.25 | 0.31 | 0.11 | E2 | |
| qNN3-13-2 | 13 | Gm13_31053641 | 31053641 | T/C | 0.25 | 4.09 | 0.25 | 0.29 | -0.09 | 1-8 | |
| qNN3-13-1 | 13 | Gm13_38510582 | 38510582 | T/G | 0.13 | 4.46 | 0.25 | 0.29 | 0.10 | ||
| qNN3-19-2 | 19 | Gm19_44558007 | 44558007 | C/A | 0.34 | 4.77 | 0.25 | 0.29 | -0.09 | ||
| qNN3-19-3 | 19 | Gm19_44938780 | 44938780 | C/T | 0.35 | 7.36 | 0.25 | 0.32 | 0.13 | Dt1 | |
| qNN3-19-4 | 19 | Gm19_45295148 | 45295148 | C/G | 0.39 | 4.61 | 0.25 | 0.29 | 0.09 | ||
| qNN3-19-1 | 19 | Gm19_45384848 | 45384848 | A/G | 0.40 | 4.10 | 0.25 | 0.29 | -0.08 | ||
| qNN3-19-5 | 19 | Gm19_45727395 | 45727395 | G/A | 0.39 | 4.48 | 0.25 | 0.29 | -0.09 | ||
aNegative log10-transformed P-value of the suggestive. bThe contribution rate of the model without SNP. cThe contribution rate of the model with SNP. dBased on the QTL list on SoyBase (www.soybase.org). eThe QTNs shown in bold indicate that they reach the significance threshold based on the Bonferroni correction.