| Total primary shoot length (control) | Stress | Lj3.0 | TM0113 | Lj3.0_chr1 | 38738303 | 38738438 | Lj3.0 | TM0805 | Lj3.0_chr1 | 42910317 | 42910477 | Total primary shoot length | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr1 | 45 | 4.84 | <0.0001 | 10.1111/pce.12268 | t34305.T000035 |
| Total primary shoot length (waterlogging) | Stress | Lj3.0 | TM0113 | Lj3.0_chr1 | 38738303 | 38738438 | Lj3.0 | TM0805 | Lj3.0_chr1 | 42910317 | 42910477 | Total primary shoot length | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr1 | 45 | 2.4 | 0.0069 | 10.1111/pce.12268 | t34305.T000036 |
| Primary shoot number (waterlogging) | Stress | Lj3.0 | TM0805 | Lj3.0_chr1 | 42910317 | 42910477 | Lj3.0 | TM0222 | Lj3.0_chr1 | 46012439 | 46012589 | Primary shoot number | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr1 | 51 | 8.04 | <0.0001 | 10.1111/pce.12268 | t34305.T000037 |
| Primary shoot number (control) | Stress | Lj3.0 | TM0222 | Lj3.0_chr1 | 46012439 | 46012589 | Lj3.0 | TM0009 | Lj3.0_chr1 | 49389836 | 49389985 | Primary shoot number | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr1 | 54 | 7.47 | <0.0001 | 10.1111/pce.12268 | t34305.T000038 |
| Root dry mass (waterlogging) | Stress | Lj3.0 | TM0009 | Lj3.0_chr1 | 49389836 | 49389985 | Lj3.0 | TM0295 | Lj3.0_chr1 | 52855524 | 52855640 | Root dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr1 | 61 | 3.53 | 0.0009 | 10.1111/pce.12268 | t34305.T000039 |
| Root dry mass (control) | Stress | Lj3.0 | TM0295 | Lj3.0_chr1 | 52855524 | 52855640 | Lj3.0 | TM0122 | Lj3.0_chr1 | 58546864 | 58546987 | Root dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr1 | 64 | 1.68 | 0.0363 | 10.1111/pce.12268 | t34305.T000040 |
| Pod dry mass (waterlogging) | Stress | Lj3.0 | TM0122 | Lj3.0_chr1 | 58546864 | 58546987 | Lj3.0 | TM0105 | Lj3.0_chr1 | 61873540 | 61873679 | Pod dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr1 | 71 | 2.43 | 0.005 | 10.1111/pce.12268 | t34305.T000041 |
| Chlorophyll levels (control) | Stress | Lj3.0 | TM0120 | Lj3.0_chr2 | 19868663 | 19868765 | Lj3.0 | TM1150 | Lj3.0_chr2 | 21552345 | 21552501 | Chlorophyll levels | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr2 | 40.2 | 2.49 | 0.0057 | 10.1111/pce.12268 | t34305.T000042 |
| Root dry mass (control) | Stress | Lj3.0 | TM0426 | Lj3.0_chr3 | 15411177 | 15411300 | Lj3.0 | TM0087 | Lj3.0_chr4 | 24444265 | 24444405 | Root dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr3 | 27 | 1.7 | 0.0344 | 10.1111/pce.12268 | t34305.T000043 |
| Number of secondary branches (waterlogging) | Stress | Lj3.0 | TM0426 | Lj3.0_chr3 | 15411177 | 15411300 | Lj3.0 | TM0087 | Lj3.0_chr4 | 24444265 | 24444405 | Number of secondary branches | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr3 | 28 | 2.8 | 0.003 | 10.1111/pce.12268 | t34305.T000044 |
| Total primary shoot length (control) | Stress | Lj3.0 | TM0035 | Lj3.0_chr3 | 14526694 | 14526804 | Lj3.0 | TM0110 | Lj3.0_chr3 | 22755676 | 22755812 | Total primary shoot length | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr3 | 29 | 2.52 | 0.0053 | 10.1111/pce.12268 | t34305.T000045 |
| Total primary shoot length (waterlogging) | Stress | Lj3.0 | TM0035 | Lj3.0_chr3 | 14526694 | 14526804 | Lj3.0 | TM0110 | Lj3.0_chr3 | 22755676 | 22755812 | Total primary shoot length | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr3 | 29 | 2.28 | 0.0089 | 10.1111/pce.12268 | t34305.T000046 |
| Shoot dry mass (control) | Stress | Lj3.0 | TM0035 | Lj3.0_chr3 | 14526694 | 14526804 | Lj3.0 | TM0110 | Lj3.0_chr3 | 22755676 | 22755812 | Shoot dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr3 | 30 | 2.67 | 0.0034 | 10.1111/pce.12268 | t34305.T000047 |
| Shoot dry mass (waterlogging) | Stress | Lj3.0 | TM0035 | Lj3.0_chr3 | 14526694 | 14526804 | Lj3.0 | TM0110 | Lj3.0_chr3 | 22755676 | 22755812 | Shoot dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr3 | 30 | 2.35 | 0.0068 | 10.1111/pce.12268 | t34305.T000048 |
| Primary shoot number (waterlogging) | Stress | Lj3.0 | TM0194 | Lj3.0_chr4 | 13253314 | 13253436 | Lj3.0 | TM0281 | Lj3.0_chr4 | 18526673 | 18526806 | Primary shoot number | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr4 | 23 | 3.12 | 0.0015 | 10.1111/pce.12268 | t34305.T000049 |
| Number of secondary branches (control) | Stress | Lj3.0 | TM0281 | Lj3.0_chr4 | 18526673 | 18526806 | Lj3.0 | TM0426 | Lj3.0_chr3 | 15411177 | 15411300 | Number of secondary branches | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr4 | 24.6 | 4.27 | 0.0001 | 10.1111/pce.12268 | t34305.T000050 |
| Shoot dry mass (waterlogging) | Stress | Lj3.0 | TM0186 | Lj3.0_chr5 | 20644864 | 20644999 | Lj3.0 | TM0341 | Lj3.0_chr5 | 18517193 | 18517309 | Shoot dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 37.2 | 3.73 | 0.0004 | 10.1111/pce.12268 | t34305.T000051 |
| Stomatal conductance (waterlogging) | Stress | Lj3.0 | TM0341 | Lj3.0_chr5 | 18517193 | 18517309 | Lj3.0 | TM0657 | Lj3.0_chr5 | 11119564 | 11119695 | Stomatal conductance | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 42.2 | 4.08 | 0.0001 | 10.1111/pce.12268 | t34305.T000052 |
| Stomatal conductance (control) | Stress | Lj3.0 | TM0341 | Lj3.0_chr5 | 18517193 | 18517309 | Lj3.0 | TM0657 | Lj3.0_chr5 | 11119564 | 11119695 | Stomatal conductance | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 43.2 | 5.13 | <0.0001 | 10.1111/pce.12268 | t34305.T000053 |
| Shoot dry mass (control) | Stress | Lj3.0 | TM0341 | Lj3.0_chr5 | 18517193 | 18517309 | Lj3.0 | TM0657 | Lj3.0_chr5 | 11119564 | 11119695 | Shoot dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 43.2 | 4.54 | 0.0001 | 10.1111/pce.12268 | t34305.T000054 |
| Chlorophyll levels (control) | Stress | Lj3.0 | TM0657 | Lj3.0_chr5 | 11119564 | 11119695 | Lj3.0 | TM0428 | Lj3.0_chr5 | 7127906 | 7128049 | Chlorophyll levels | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 45.2 | 3.6 | 0.0006 | 10.1111/pce.12268 | t34305.T000055 |
| Pod dry mass (control) | Stress | Lj3.0 | TM0657 | Lj3.0_chr5 | 11119564 | 11119695 | Lj3.0 | TM0428 | Lj3.0_chr5 | 7127906 | 7128049 | Pod dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 48.1 | 2.13 | 0.0108 | 10.1111/pce.12268 | t34305.T000056 |
| Pod dry mass (waterlogging) | Stress | Lj3.0 | TM0657 | Lj3.0_chr5 | 11119564 | 11119695 | Lj3.0 | TM0428 | Lj3.0_chr5 | 7127906 | 7128049 | Pod dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 48.1 | 2.23 | 0.0079 | 10.1111/pce.12268 | t34305.T000057 |
| Root absorption surface (control) | Stress | Lj3.0 | TM0034 | Lj3.0_chr5 | 4130584 | 4130767 | Lj3.0 | TM0146 | Lj3.0_chr5 | 581656 | 581803 | Root absorption surface | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 53.2 | 5.25 | <0.0001 | 10.1111/pce.12268 | t34305.T000058 |
| Number of secondary branches (control) | Stress | Lj3.0 | TM0034 | Lj3.0_chr5 | 4130584 | 4130767 | Lj3.0 | TM0146 | Lj3.0_chr5 | 581656 | 581803 | Number of secondary branches | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr5 | 55.2 | 5.41 | <0.0001 | 10.1111/pce.12268 | t34305.T000059 |
| Root dry mass (waterlogging) | Stress | Lj3.0 | TM1417 | Lj3.0_chr6 | 1055655 | 1055825 | Lj3.0 | TM0095 | Lj3.0_chr5 | 25291632 | 25291802 | Root dry mass | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr6 | 18.2 | 2.27 | 0.0112 | 10.1111/pce.12268 | t34305.T000060 |
| Total primary shoot length (waterlogging) | Stress | Lj3.0 | TM0013 | Lj3.0_chr6 | 14155490 | 14155696 | Lj3.0 | TM0880 | Lj3.0_chr6 | 16717630 | 16717805 | Total primary shoot length | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr6 | 42.3 | 2.42 | 0.0066 | 10.1111/pce.12268 | t34305.T000061 |
| Total primary shoot length (control) | Stress | Lj3.0 | TM0756 | Lj3.0_chr6 | 21783429 | 21783556 | Lj3.0 | TM0336 | Lj3.0_chr6 | 24123928 | 24124092 | Total primary shoot length | QTL analysis | Gifu B-129 x Miyakojima MG-20 | RIL | Gifu_B-129_x_Miyakojima_MG-20 chr6 | 53.3 | 3.91 | 0.0003 | 10.1111/pce.12268 | t34305.T000062 |
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