Table 2 QTL associated with Cd accumulation identified by GWAS using different populations
QTLs | Chromosome | Linked SNP position a | P-value | Phenotype contribution (%) | Candidate gene |
|---|---|---|---|---|---|
Composite population | |||||
 qCd1 | 1 | 41,982,531 | 2.43E-06 | 4.66 | OsLCD |
 qCd2–1 | 2 | 2,060,980 | 6.01E-05 | 2.40 |  |
 qCd2–2 | 2 | 5,523,027 | 4.38E-05 | 3.47 |  |
 qCd2–3 | 2 | 23,732,572 | 6.88E-05 | 2.71 |  |
 qCd3–1 | 3 | 4,848,498 | 1.04E-05 | 4.06 |  |
 qCd3–2 | 3 | 5,635,117 | 2.78E-06 | 4.61 |  |
 qCd4 | 4 | 20,074,216 | 4.67E-05 | 2.53 |  |
 qCd7–1 | 7 | 7,186,204 | 1.69E-06 | 4.82 | OsHMA3 |
 qCd7–2 | 7 | 8,263,482 | 1.86E-06 | 4.78 | OsNRAMP1, OsNRAMP5 |
 qCd7–3 | 7 | 18,553,958 | 1.14E-05 | 4.02 |  |
 qCd8–1 | 8 | 902,085 | 3.25E-05 | 3.01 |  |
 qCd8–2 | 8 | 18,365,933 | 3.82E-06 | 4.48 |  |
 qCd8–3 | 8 | 27,463,194 | 3.12E-05 | 2.60 |  |
 qCd11 | 11 | 14,891,373 | 2.48E-05 |  |  |
Indica | |||||
 qCd_ind_1 | 1 | 41,982,531 | 8.89E-05 | 6.85 | OsLCD |
 qCd_ind_2–1 | 2 | 2,060,980 | 7.66E-04 | 5.00 |  |
 qCd_ind_2–2 | 2 | 4,986,931 | 2.27E-04 | 6.04 |  |
 qCd_ind_3 | 3 | 27,195,551 | 3.06E-04 | 5.78 |  |
 qCd_ind_4 | 4 | 20,368,258 | 1.34E-04 | 5.93 |  |
 qCd_ind_5 | 5 | 23,588,056 | 4.53E-04 | 5.45 |  |
 qCd_ind_8 | 8 | 899,377 | 1.93E-05 | 8.20 |  |
Japonica | |||||
 qCd_jap-2 | 2 | 23,666,135 | 5.23E-05 | 12.74 |  |
 qCd_jap-3 | 3 | 5,507,369 | 3.81E-04 | 9.63 |  |
 qCd_jap-7-1 | 7 | 7,451,789 | 3.52E-04 | 9.75 | OsHMA3 |
 qCd_jap-7-2 | 7 | 8,467,983 | 1.56E-04 | 11.01 | OsNRAMP1, OsNRAMP5 |
 qCd_jap-7-3 | 7 | 24,677,317 | 3.71E-05 | 13.29 |  |
 qCd_jap-7-4 | 7 | 27,037,840 | 6.24E-04 | 8.88 |  |
 qCd_jap-11 | 11 | 25,263,712 | 4.09E-04 | 9.52 |  |