TABLE 1.

QTL clusters with elemental QTL, PC-QTL and aPC-QTL co-localized.

QTL cluster	Chr1	Genetic Position (cM)	Physical position (Kb)	Elemental QTL		PC-QTL		aPC-QTL		Candidate gene
				Element	Environment/tissue	PC	Top 5 elements2	aPC3	Top 5 elements2	ID	Annotation
1	1	28.704 ∼ 29.094	4151 ∼ 4469	P	03GF_Grain	06GF_PC2	P Mg Fe K S	F_03GF_aPC2	Mg Cu P As Cd	LOC_Os01g08660	Aquaporin protein (SIP1;1)
2	2	51.838 ∼ 54.839	4987 ∼ 5798	Cu	07GF_Grain	07GU_PC9	Cu Ni Fe	F_08GF2_aPC11	Cd As Mn Zn Rb	LOC_Os02g10290	Heavy metal-transporting P1B type ATPase (OsHMA4)
				Cu	08GF2_Grain	08GU1_PC10	As Cd	U_07GU_aPC6	Cu Fe Mo As Co
				Cu	08GU1_Grain		As Fe S Ni	FUGG_07GU_aPC14	Cu Mo K Mg As
				Cu	07GU_Grain		Zn	FUGG_11GGH_aPC14	Cu Mo K Mg As
				Cu	F_mean_Grain			FUGG_11GGH_aPC2	As Cu K Ni Cd
				Cu	U_mean_Grain			GRS_07GU_aPC13	Cu Co Cd As
				Cu	02-06_mean_Grain
				As	08GF2_Grain
3	2	79.626 ∼ 80.016	15571 ∼ 16509	Mg	08GU3_Grain	02GF_PC5	Mo Zn Mn Fe Rb	FUGG_08GU3_aPC15	Ni Mo P K Mn	LOC_Os02g26700	Cation transport regulator-like protein (OsARP)
4	2	106.137 ∼ 106.529	21244 ∼ 21828	Ca	06GF_Grain	08GF2_PC2	Sr Ca Mn P K	F_07GF_aPC1	Ni S As P K	LOC_Os02g36414	Transporter family protein Transporter family protein Transporter family protein
								FUGG_07GF_aPC3	Ca Mn Sr Cd As	LOC_Os02g36440
								GRS_08GF2_aPC6	Mn K P Zn Sr	LOC_Os02g36450
5	2	138.302 ∼ 138.497	28585 ∼ 29657	Cd	02GF_Grain	06GF_PC11	Mn Rb Ni Cd Zn	F_08GF2_aPC5	Co Rb Fe Cu S	LOC_Os02g46990	AAA-type ATPase family protein
				Cd	F_mean_Grain
6	3	0.783 ∼ 1.175	731 ∼ 1013	As	02GF_Grain	08GU1_PC2	Ca Mn Sr	GRS_08GU1_aPC1	Mo Fe S As Sr	LOC_Os03g02380	Major facilitator superfamily domain-containing protein (OsCd1)
				Rb	02GF_Grain		P Rb	GRS_08GU1_aPC3	Ni Rb P Mn
				Rb	08GU1_Grain			GRS_02GF_aPC4	Rb Ni Zn
								GRS_08GU1_aPC5	Mn Sr Zn Cd Co
								GRS_08GU1_aPC7	Zn Sr S Rb K
7	3	56.866 ∼ 57.061	13858 ∼ 14577	Fe	15SHH_Shoot	08GF2_PC9	Mn Rb Fe Ni Ca	FUGG_08GF2_aPC1	Mo P Mg Zn Fe	LOC_Os03g24860	Transporter family protein Transporter family protein
										LOC_Os03g24870
8	3	65.599 ∼ 66.185	15009 ∼ 15680	Sr	02GF_Grain	02GF_PC12	Sr Ca K Zn	F_02GF_aPC12	Sr S Ca As Zn	LOC_Os03g26650	Heavy metal-associated domain containing protein Heavy metal-associated domain containing protein
				Sr	03GF_Grain	07GF_PC16	Co	F_03GF_aPC12	Sr S Ca As Zn	LOC_Os03g27040
				Sr	08GU1_Grain	08GU1_PC15	Ca Sr As	F_03GF_aPC3	Sr Ca Cu P Mg
				Sr	02-06_mean_Grain		Mg Mo	U_08GU1_aPC13	K Mg Sr Ni S
				P	F_mean_Grain	07GU_PC14	Ca Sr Mn	U_08GU1_aPC15	Ca Mn Sr Ni Fe
							Mg As Sr	FUGG_02GF_aPC12	S Sr Ni K Rb
							K S	FUGG_03GF_aPC12	S Sr Ni K Rb
								FUGG_03GF_aPC4	Mg Rb Co Zn P
								FUGG_03GF_aPC5	Rb Sr As K Co
								FUGG_03GF_aPC6	Co Zn S K Rb
								FUGG_06GF_aPC11	Ca Sr Zn S As
								FUGG_08GU1_aPC11	Ca Sr Zn S As
								GRS_02GF_aPC9	Sr Mo Ka S Cu
								GRS_03GF_aPC9	Sr Mo Ka S Cu
9	3	67.38 ∼ 67.575	15630 ∼ 16243	Sr	06GF_Grain	06GF_PC5	Rb Cu Mo	F_03GF_aPC6	Mo Fe Mn Zn Co	LOC_Os03g27960	Sodium calcium exchanger protein Potassium channel protein
				Sr	07GF_Grain		Zn Mn	FUGG_02GF_aPC4	Mg Rb Co Zn P	LOC_Os03g28120
				Sr	F_mean_Grain			FUGG_03GF_aPC2	As Cu K Ni Cd
				Sr	U_mean_Grain			FUGG_08GU1_aPC12	S Sr Ni K Rb
								GRS_07GF_aPC9	Sr Mo K As Cu
10	3	72.964 ∼ 73.276	16895 ∼ 17416	Ca	03GF_Grain	03GF_PC3	Ca Sr S Mn	FUGG_02GF_aPC2	As Cu K Ni Cd	LOC_Os03g29850	Metal cation transporter
				Ca	F_mean_Grain		Cu	FUGG_03GF_aPC3	Ca Mn Sr Cd As
								GRS_03GF_aPC6	Mn K P Zn Sr
								GRS_03GF_aPC12	S Mo As
11	3	73.785 ∼ 74.097	17130 ∼ 17534	Ca	02GF_Grain	02GF_PC3	Sr Ca Mn Ni P	FUGG_02GF_aPC3	Ca Mn Sr Cd As	LOC_Os03g29920	Heavy metal transport/detoxification protein domain containing protein
12	3	173.329 ∼ 173.915	34655 ∼ 35388	Mg Mg	08GF2_Grain	07GF_PC1	Mg K P Rb	F_07GF_aPC2	Mg Cu P As Cd	LOC_Os03g61290	Cation/proton antiporter MATE efflux family protein
					U_mean_Grain		Zn	FUGG_06GF_aPC8	Fe Mg Cd P Mn	LOC_Os03g62270
13	7	51.187 ∼ 51.382	7007 ∼ 7904	Mn	08GU1_Grain	15SHH_PC9	Rb K Ni As Zn	GRS_08GU1_aPC5	Mn Sr Zn Cd Co	LOC_Os07g12900	Heavy metal-transporting P1B type ATPase (OsHMA3)
14	7	52.367 ∼ 52.756	8331 ∼ 9044	Mn	06GF_Grain	15SHH_PC16	Mn Cd Sr	F_06GF_aPC6	Mo Fe Mn Zn Co	LOC_Os07g15370	Natural resistance associated macrophage protein 5 (OsNRAMP5)
							Ca As	GRS_06GF_aPC6	Mn K P Zn Sr
15	11	83.595 ∼ 83.79	19351 ∼ 19879	Sr Zn	15SHH_Shoot	15SHH_PC1	Cd Mn Zn	GRS_15SHH_aPC5	Mn Sr Zn Cd Co	LOC_Os11g34350	ATP-binding cassette sub-family E member (OsABCE2)
					15SHH_Shoot		S As	GRS_15SHH_aPC6	Mn K P Zn Sr

¹: Chr, chromosome.

²: The elements with top 5 PC scores for corresponding PC or aPC were listed in order from highest loading to lowest loading. Only elements with the loading > 0.2 or < −0.2 are shown. The elements in bond were those corresponding to the elements controlled by elemental QTLs.

³: 02GF, 03GF, 06GF, 07GF and 07GU are grains (G) of RILs grown under flooded (F) or unflooded (U) conditions on 2002, 2003, 2006 and 2007, respectively; 08GF2, 08GU1 and 08GU3 are grains (G) of RILs grown under flooded (F) or unflooded (U) condition on 2008 in the field site number 2, 1 and 3; 11GGH is the grains (G) of RILs grown in a greenhouse (GH) condition on 2011; 15RTH and 15SHH are roots (RT) or shoots (SH) of RILs grown hydroponically (H) on 2015. F: 02GF+03GF+06GF+07GF+08GF2; U: 07GU+08GU1+08GU3; FUGG: F+U+11GGH; GRS: FUGG+15RTH+15SHH.