TABLE 3.
Details of the marker-trait associations (MTAs) mapped for grain Fe and Zn content at two different locations, New Delhi and Aduthurai.
| SNP | Allele | Chromosome | Position | Probability | Trait | Site | QTL | R2 | ai | Previous report | |
| Favorable allele | Alternate allele | ||||||||||
| AX-95918814 | A | G | 1 | 3,565,733 | 6.19E-08 | ZnMR | DEL | qZnMR1.1 | 9.3 | 1.7 | * |
| AX-95918814 | A | G | 1 | 3,565,733 | 6.19E-08 | ZnMR | ADT | qZnMR1.1 | 10.4 | 1.8 | * |
| AX-95934119 | T | C | 1 | 3,568,378 | 8.72E-15 | ZnBR | DEL | qZnBR1.1 | 12.4 | 3.4 | * |
| AX-95919006 | A | C | 1 | 15,673,604 | 8.88E-07 | ZnBR | DEL | qZnBR1.2a | 45.5 | 4.8 | Stangoulis et al., 2007 |
| AX-95917932 | G | A | 1 | 39,382,522 | 5.63E-08 | ZnBR | DEL | qZnBR1.2b | 40.1 | 4.3 | * |
| AX-95918225 | G | T | 1 | 41,121,295 | 3.33E-07 | ZnMR | DEL | qZnMR1.2 | 17.7 | 4.2 | IRO2 |
| AX-95921433 | C | A | 2 | 34,958,759 | 2.01E-07 | FeBR | DEL | qFeBR2.1 | 6.8 | 1.5 | Swamy et al., 2018 |
| AX-95965057 | A | G | 2 | 35,093,342 | 1.35E-06 | ZnBR | DEL | qZnBR2.1 | 26.4 | 5.0 | Swamy et al., 2018 |
| AX-95922070 | A | G | 3 | 10,164,543 | 1.06E-16 | FeBR | ADT | qFeBR3.1 | 53.3 | 4.1 | MIT, NAS1, NAS2 |
| AX-95962496 | A | C | 3 | 22,193,098 | 2.03E-10 | FeBR | ADT | qFeBR3.2 | 2.1 | 0.2 | * |
| AX-95921838 | G | T | 3 | 27,810,157 | 1.71E-08 | FeBR | ADT | qFeBR3.3 | 2.1 | 0.1 | * |
| AX-95923364 | C | T | 3 | 29,493,448 | 2.95E-07 | ZnBR | DEL | qZnBR3.1 | 39.9 | 4.0 | Anuradha et al., 2012a |
| AX-95921738 | T | G | 3 | 30,176,449 | 5.86E-07 | ZnMR | ADT | qZnMR3.1 | 18.3 | 3.3 | * |
| AX-95935621 | G | A | 3 | 32,326,592 | 4.79E-05 | FeMR | ADT | qFeMR3.1a | 12.8 | 0.4 | * |
| AX-95950999 | T | G | 3 | 32,335,075 | 4.13E-05 | FeMR | ADT | qFeMR3.1b | 12.9 | 0.4 | * |
| AX-95935460 | G | A | 3 | 32,374,286 | 8.90E-05 | FeMR | ADT | qFeMR3.1c | 12.3 | 0.4 | * |
| AX-95924055 | C | G | 3 | 32,380,341 | 8.90E-05 | FeMR | ADT | qFeMR3.1d | 12.3 | 0.4 | * |
| AX-95923317 | T | C | 3 | 32,380,432 | 2.61E-05 | FeMR | ADT | qFeMR3.1e | 13.7 | 0.4 | * |
| AX-95923159 | G | A | 3 | 32,380,964 | 2.61E-05 | FeMR | ADT | qFeMR3.1f | 13.7 | 0.4 | * |
| AX-95951158 | A | G | 4 | 32,811,874 | 5.24E-09 | ZnBR | DEL | qZnBR4.1 | 47.6 | 6.3 | ZIP3 |
| AX-95951158 | A | G | 4 | 32,811,874 | 4.86E-09 | ZnMR | DEL | qZnMR4.1 | 42.7 | 5.6 | ZIP3 |
| AX-95927387 | A | G | 6 | 11,840,203 | 8.42E-13 | ZnBR | ADT | qZnBR6.1 | 44.9 | 7.4 | * |
| AX-95928882 | C | A | 6 | 24,918,156 | 6.05E-07 | FeMR | DEL | qFeMR6.1 | 3.2 | 0.6 | * |
| AX-95956929 | A | G | 6 | 30,278,880 | 6.11E-07 | FeBR | DEL | qFeBR6.1 | 45.2 | 2.7 | NRAMP3 |
| AX-95915606 | A | T | 7 | 2,636,599 | 1.66E-07 | FeBR | ADT | qFeBR7.1 | 41.5 | 4.7 | * |
| AX-95929962 | T | G | 7 | 15,616,980 | 2.71E-09 | ZnBR | ADT | qZnBR7.1 | 16.5 | 3.4 | Anuradha et al., 2012a |
| AX-95929638 | T | A | 7 | 22,727,786 | 1.23E-06 | ZnBR | DEL | qZnBR7.2 | 33.4 | 6.6 | Anuradha et al., 2012a |
| AX-95930744 | C | A | 8 | 25,586,491 | 3.74E-08 | ZnBR | DEL | qZnBR8.1 | 2.3 | 0.6 | Garcia-Oliveira et al., 2009 |
| AX-95959928 | T | C | 9 | 849,821 | 4.76E-11 | ZnMR | ADT | qZnMR9.1 | 7.9 | 2.2 | * |
| AX-95932094 | A | G | 10 | 12,685,215 | 4.51E-08 | ZnBR | ADT | qZnBR10.1 | 6.8 | 1.7 | * |
SNP, single nucleotide polymorphic marker; DEL, New Delhi; ADT, Aduthurai; PVE, percentage variation explained; ai, additive effect of the favorable allele; FeBR, Fe content in brown rice; FeMR, Fe content in milled rice; ZnBR, Zn content in brown rice; ZnMR, Zn content in milled rice; asterisk indicates MTAs not reported so far.