| Chlorophyll levels (control) | Quality/Components | 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 |
| Chlorophyll levels (control) | Quality/Components | 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 |
| stem color | Quality/Components | Lj3.0 | TM0225 | Lj3.0_chr2 | 16495426 | 16495545 | Lj3.0 | BM1626 | Lj3.0_chr2 | 18310832 | 18310982 | SC | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 26 | 36.9 | NA | 10.1139/G07-040 | t34305.T000079 |
| stem color | Quality/Components | Lj3.0 | TM0225 | Lj3.0_chr2 | 16495426 | 16495545 | Lj3.0 | BM1626 | Lj3.0_chr2 | 18310832 | 18310982 | SC | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 28 | 26.6 | NA | 10.1139/G07-040 | t34305.T000080 |
| Seed nutrient content(Ca) | Quality/Components | Lj3.0 | TM0832 | Lj3.0_chr0 | 140451547 | 140451676 | Lj3.0 | NA | NA | 0 | 0 | Ca-7 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr0 | 8.6 | 4.65 | NA | 10.1139/G09-039 | t34305.T000108 |
| Seed nutrient content(Cu) | Quality/Components | Lj3.0 | TM0178 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | Cu-5 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr0 | 20.1 | 4.07 | NA | 10.1139/G09-039 | t34305.T000111 |
| Seed nutrient concentration([Mg]) | Quality/Components | Lj3.0 | TM0632 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | [Mg]-3 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr0 | 23.6 | 3.23 | NA | 10.1139/G09-039 | t34305.T000112 |
| Seed nutrient content(Ca) | Quality/Components | Lj3.0 | TM0632 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | Ca-12 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr0 | 23.6 | 3.46 | NA | 10.1139/G09-039 | t34305.T000114 |
| Seed nutrient content(K) | Quality/Components | Lj3.0 | TM0632 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | K-9 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr0 | 23.6 | 3.94 | NA | 10.1139/G09-039 | t34305.T000115 |
| Seed nutrient concentration([P]) | Quality/Components | Lj3.0 | TM0616 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | [P]-3 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr0 | 69.8 | 4.85 | NA | 10.1139/G09-039 | t34305.T000116 |
| Seed nutrient concentration([S]) | Quality/Components | Lj3.0 | TM0088 | Lj3.0_chr1 | 217113 | 217274 | Lj3.0 | NA | NA | 0 | 0 | [S]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 0 | 15.16 | NA | 10.1139/G09-039 | t34305.T000117 |
| Seed nutrient concentration([S]) | Quality/Components | Lj3.0 | TM0088 | Lj3.0_chr1 | 217113 | 217274 | Lj3.0 | NA | NA | 0 | 0 | [S]-2 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 0 | 5.61 | NA | 10.1139/G09-039 | t34305.T000118 |
| Seed nutrient content(S) | Quality/Components | Lj3.0 | TM0088 | Lj3.0_chr1 | 217113 | 217274 | Lj3.0 | NA | NA | 0 | 0 | S-7 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 0 | 4.17 | NA | 10.1139/G09-039 | t34305.T000119 |
| Seed nutrient content(S) | Quality/Components | Lj3.0 | TM0027 | Lj3.0_chr1 | 10871784 | 10871961 | Lj3.0 | NA | NA | 0 | 0 | S-8 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 0 | 3.6 | NA | 10.1139/G09-039 | t34305.T000120 |
| Seed nutrient content(Mg) | Quality/Components | Lj3.0 | TM0372 | Lj3.0_chr1 | 23470662 | 23470768 | Lj3.0 | NA | NA | 0 | 0 | Mg-4 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 11.8 | 3.93 | NA | 10.1139/G09-039 | t34305.T000121 |
| Seed nutrient concentration([S]) | Quality/Components | Lj3.0 | TM0372 | Lj3.0_chr1 | 23470662 | 23470768 | Lj3.0 | NA | NA | 0 | 0 | [S]-3 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 17.3 | 4.73 | NA | 10.1139/G09-039 | t34305.T000122 |
| Seed nutrient content(Zn) | Quality/Components | Lj3.0 | TM0193 | Lj3.0_chr1 | 26962089 | 26962199 | Lj3.0 | NA | NA | 0 | 0 | Zn-3 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 18.3 | 2.9 | NA | 10.1139/G09-039 | t34305.T000123 |
| Seed nutrient content(Ca) | Quality/Components | Lj3.0 | TM0386 | Lj3.0_chr1 | 28671291 | 28671431 | Lj3.0 | NA | NA | 0 | 0 | Ca-3 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 21.7 | 2.79 | NA | 10.1139/G09-039 | t34305.T000124 |
| Seed nutrient concentration([Fe]) | Quality/Components | Lj3.0 | TM0101 | Lj3.0_chr1 | 30019246 | 30019380 | Lj3.0 | NA | NA | 0 | 0 | [Fe]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 24.4 | 4.41 | NA | 10.1139/G09-039 | t34305.T000125 |
| Seed nutrient concentration([Mn]) | Quality/Components | Lj3.0 | TM0101 | Lj3.0_chr1 | 30019246 | 30019380 | Lj3.0 | NA | NA | 0 | 0 | [Mn]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 24.4 | 5.39 | NA | 10.1139/G09-039 | t34305.T000126 |
| Seed nutrient concentration([Zn]) | Quality/Components | Lj3.0 | TM0101 | Lj3.0_chr1 | 30019246 | 30019380 | Lj3.0 | NA | NA | 0 | 0 | [Zn]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 24.4 | 6.5 | NA | 10.1139/G09-039 | t34305.T000127 |
| Seed nutrient content(Fe) | Quality/Components | Lj3.0 | TM0101 | Lj3.0_chr1 | 30019246 | 30019380 | Lj3.0 | NA | NA | 0 | 0 | Fe-4 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 24.4 | 3.42 | NA | 10.1139/G09-039 | t34305.T000128 |
| Seed nutrient concentration([Fe]) | Quality/Components | Lj3.0 | TM1635 | Lj3.0_chr1 | 31690752 | 31690891 | Lj3.0 | NA | NA | 0 | 0 | [Fe]-2 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 28.1 | 2.87 | NA | 10.1139/G09-039 | t34305.T000129 |
| Seed nutrient concentration([Cu]) | Quality/Components | Lj3.0 | TM0051 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | [Cu]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 29.3 | 5.97 | NA | 10.1139/G09-039 | t34305.T000130 |
| Seed nutrient concentration([Cu]) | Quality/Components | Lj3.0 | TM0051 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | [Cu]-2 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 29.3 | 3.38 | NA | 10.1139/G09-039 | t34305.T000131 |
| Seed nutrient concentration([K]) | Quality/Components | Lj3.0 | TM0051 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | [K]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 29.3 | 3.39 | NA | 10.1139/G09-039 | t34305.T000132 |
| Seed nutrient concentration([S]) | Quality/Components | Lj3.0 | TM0051 | NA | 0 | 0 | Lj3.0 | NA | NA | 0 | 0 | [S]-4 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 29.3 | 4.25 | NA | 10.1139/G09-039 | t34305.T000133 |
| Seed nutrient content(Ca) | Quality/Components | Lj3.0 | TM1168 | Lj3.0_chr1 | 34755807 | 34755930 | Lj3.0 | NA | NA | 0 | 0 | Ca-4 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 31.3 | 3.01 | NA | 10.1139/G09-039 | t34305.T000134 |
| Seed nutrient content(Ca) | Quality/Components | Lj3.0 | TM0113 | Lj3.0_chr1 | 38738303 | 38738438 | Lj3.0 | NA | NA | 0 | 0 | Ca-5 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 46.6 | 5.6 | NA | 10.1139/G09-039 | t34305.T000135 |
| Seed nutrient content(Mg) | Quality/Components | Lj3.0 | TM0805 | Lj3.0_chr1 | 42910317 | 42910477 | Lj3.0 | NA | NA | 0 | 0 | Mg-5 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 49.5 | 3.63 | NA | 10.1139/G09-039 | t34305.T000136 |
| Seed nutrient content(Ca) | Quality/Components | Lj3.0 | TM0222 | Lj3.0_chr1 | 46012439 | 46012589 | Lj3.0 | NA | NA | 0 | 0 | Ca-6 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 50.5 | 2.82 | NA | 10.1139/G09-039 | t34305.T000137 |
| Seed nutrient content(S) | Quality/Components | Lj3.0 | TM0122 | Lj3.0_chr1 | 58546864 | 58546987 | Lj3.0 | NA | NA | 0 | 0 | S-9 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 67.2 | 5.22 | NA | 10.1139/G09-039 | t34305.T000138 |
| Seed nutrient concentration([Ca]) | Quality/Components | Lj3.0 | TM0105 | Lj3.0_chr1 | 61873540 | 61873679 | Lj3.0 | NA | NA | 0 | 0 | [Ca]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 71 | 3.25 | NA | 10.1139/G09-039 | t34305.T000139 |
| Seed nutrient content(Cu) | Quality/Components | Lj3.0 | TM0105 | Lj3.0_chr1 | 61873540 | 61873679 | Lj3.0 | NA | NA | 0 | 0 | Cu-6 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 71 | 2.71 | NA | 10.1139/G09-039 | t34305.T000140 |
| Seed nutrient content(K) | Quality/Components | Lj3.0 | TM0105 | Lj3.0_chr1 | 61873540 | 61873679 | Lj3.0 | NA | NA | 0 | 0 | K-3 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 71 | 6.16 | NA | 10.1139/G09-039 | t34305.T000141 |
| Seed nutrient content(Mg) | Quality/Components | Lj3.0 | TM0105 | Lj3.0_chr1 | 61873540 | 61873679 | Lj3.0 | NA | NA | 0 | 0 | Mg-6 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr1 | 71 | 4.81 | NA | 10.1139/G09-039 | t34305.T000142 |
| Seed nutrient concentration([P]) | Quality/Components | Lj3.0 | TM0134 | Lj3.0_chr2 | 3625302 | 3625437 | Lj3.0 | NA | NA | 0 | 0 | [P]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 3.2 | 3.05 | NA | 10.1139/G09-039 | t34305.T000143 |
| Seed nutrient content(K) | Quality/Components | Lj3.0 | TM0134 | Lj3.0_chr2 | 3625302 | 3625437 | Lj3.0 | NA | NA | 0 | 0 | K-4 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 3.2 | 6.25 | NA | 10.1139/G09-039 | t34305.T000144 |
| Seed nutrient content(Mg) | Quality/Components | Lj3.0 | TM0134 | Lj3.0_chr2 | 3625302 | 3625437 | Lj3.0 | NA | NA | 0 | 0 | Mg-7 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 3.2 | 5.67 | NA | 10.1139/G09-039 | t34305.T000145 |
| Seed nutrient content(Mg) | Quality/Components | Lj3.0 | TM0134 | Lj3.0_chr2 | 3625302 | 3625437 | Lj3.0 | NA | NA | 0 | 0 | Mg-8 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 4.2 | 5.22 | NA | 10.1139/G09-039 | t34305.T000147 |
| Seed nutrient content(S) | Quality/Components | Lj3.0 | TM0134 | Lj3.0_chr2 | 3625302 | 3625437 | Lj3.0 | NA | NA | 0 | 0 | S-10 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 4.2 | 3.3 | NA | 10.1139/G09-039 | t34305.T000148 |
| Seed nutrient content(Zn) | Quality/Components | Lj3.0 | TM0134 | Lj3.0_chr2 | 3625302 | 3625437 | Lj3.0 | NA | NA | 0 | 0 | Zn-4 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 5.2 | 4.24 | NA | 10.1139/G09-039 | t34305.T000149 |
| Seed nutrient concentration([Ca]) | Quality/Components | Lj3.0 | TM0074 | Lj3.0_chr2 | 7041149 | 7041313 | Lj3.0 | NA | NA | 0 | 0 | [Ca]-2 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 6.2 | 2.73 | NA | 10.1139/G09-039 | t34305.T000150 |
| Seed nutrient content(K) | Quality/Components | Lj3.0 | TM0074 | Lj3.0_chr2 | 7041149 | 7041313 | Lj3.0 | NA | NA | 0 | 0 | K-5 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 6.2 | 2.91 | NA | 10.1139/G09-039 | t34305.T000151 |
| Seed nutrient concentration([Mn]) | Quality/Components | Lj3.0 | TM0383 | Lj3.0_chr2 | 7494969 | 7495079 | Lj3.0 | NA | NA | 0 | 0 | [Mn]-2 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 8.4 | 5.8 | NA | 10.1139/G09-039 | t34305.T000152 |
| Seed nutrient concentration([K]) | Quality/Components | Lj3.0 | TM0053 | Lj3.0_chr2 | 10514220 | 10514399 | Lj3.0 | NA | NA | 0 | 0 | [K]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 9.6 | 3.27 | NA | 10.1139/G09-039 | t34305.T000153 |
| Seed nutrient concentration([Ni]) | Quality/Components | Lj3.0 | TM0660 | Lj3.0_chr2 | 12827782 | 12827969 | Lj3.0 | NA | NA | 0 | 0 | [Ni]-1 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 12.8 | 3.24 | NA | 10.1139/G09-039 | t34305.T000154 |
| Seed nutrient concentration([Ni]) | Quality/Components | Lj3.0 | BM1626 | Lj3.0_chr2 | 18310832 | 18310982 | Lj3.0 | NA | NA | 0 | 0 | [Ni]-2 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr2 | 30.8 | 4.11 | NA | 10.1139/G09-039 | t34305.T000155 |
| Seed nutrient concentration([Ni]) | Quality/Components | Lj3.0 | TM0793 | Lj3.0_chr3 | 564251 | 564408 | Lj3.0 | NA | NA | 0 | 0 | [Ni]-3 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr3 | 0 | 3.91 | NA | 10.1139/G09-039 | t34305.T000156 |
| Seed nutrient content(Mg) | Quality/Components | Lj3.0 | TM0080 | Lj3.0_chr3 | 6144060 | 6144197 | Lj3.0 | NA | NA | 0 | 0 | Mg-9 | QTL analysis | Miyakojima MG-20 x Gifu B-129 | RIL | Miyakojima_MG-20_x_Gifu_B-129 chr3 | 16.5 | 3.71 | NA | 10.1139/G09-039 | t34305.T000157 |
