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

^aPosition of SNP is base on rice reference sequence MSU V 7.0. (Kawahara et al. 2013)