Table 3 QTLs identified for agronomic, yield, and grain Fe and Zn concentration in two RILs populations using inclusive composite interval mapping and interval mapping.

From: Deciphering the genetic basis of agronomic, yield, and nutritional traits in rice (Oryza sativa L.) using a saturated GBS-based SNP linkage map

QTL	Chr	Marker interval	Interval (bp)	LOD	PVE (%)	Additive	Allele	Season	Pop’n	Mapping	Previous report
QTL	Chr	Marker interval	Interval (bp)	LOD	PVE (%)	Effect	Allele	Season	Pop’n	Method	Previous report
qDF_2.1	2	S2_11105185–S2_11117489	12304	7.1	9.1	2.4	IR95040	18DS	P1	CIM
qDF_2.2	2	S2_11190409–S2_11324529	134120	3.6	13.6	2.9	IR95040	17DS	P1	CIM
qDF_2.3	2	S2_16536936–S2_16600692	63756	7.2	11	3.9	IR95040	17WS	P1	CIM
qDF_4.1	4	S4_12594329–S4_13303827	709498	3.3–5.0	7.5, 7.5	−2.5, −2.3	Kaliboro	17DS	P2	IM, CIM
qDF_6.1	6	S6_7218361–S6_7231743	13382	5	6.2	−2.8	Kaliboro	18DS	P1	CIM
qDF_10.1	10	S10_18745977–S10_18962117	216140	3.3	5.2	−5.3	Kaliboro	18DS	P1	IM
qDF_10.2	10	S10_19142624–S10_19342582	199958	4.8	7.3	−2.7	Kaliboro	17WS	P1	CIM
qDF_10.3	10	S10_22498821–S10_22942320	443499	6	8.1	−3.9	Kaliboro	18DS	P1	CIM
qDF_12.1	12	S12_19691458–S12_19805138	113680	3.1	5.8	−2.3	Kaliboro	18DS	P2	CIM
qPH_1.1	1	S1_42035412–S1_42409666	374254	5.3	6.1	−16.2	Kaliboro	17WS	P1	CIM
*qPH*_1.2	1	S1_39641602–S1_40129302	487700	3.1–5.1	5.0–10.3	−13.2 to −15.9	Kaliboro	17DS,17WS,18DS	P2	IM, CIM, MPP	Zaw et al.¹⁹
											Descalsota et. al.³¹
											Swamy et al.¹⁸
											Yadav et al.¹³
qPH_2.1	2	S2_21183199–S2_21259490	76291	7.7	8.4	17.1	IR95040	17WS	P1	CIM
qPH_4.1	4	S4_3653327–S4_3873522	220195	3.1–3.4	5.7–7.2	−11.3, −12.3	Kaliboro	17WS	P2	IM, CIM
qPH_4.2	4	S4_20627686–S4_20750130	122444	3.2–5.3	5.0–8.9	−10.9, −14.6	Kaliboro	18DS	P2	IM,CIM
qPH_4.3	4	S4_20964478–S4_21048868	84390	3.3	5.3	−13	Kaliboro	17WS	P2	IM
qPH_4.4	4	S4_22012189–S4_22028419	16230	3.9	9	−12.5	Kaliboro	17DS	P2	CIM
qPH_4.5	4	S4_32219091–S4_32219139	48	6.6	8.8	17.9	IR95040	17DS	P1	CIM
qPH_6.1	6	S6_20146062–S6_21730677	1584615	10.6	12.1	−21.2	Kaliboro	17WS	P1	CIM
qPH_6.2	6	S6_27973551–S6_28801387	827836	4.7	10.6	−15	Kaliboro	18DS	P1	CIM
qPH_7.2	7	S7_25094623–S7_25127435	32812	3.2	5.8	−12.8	Kaliboro	18DS	P1	CIM
qPH_8.1	8	S8_10629469–S8_10725490	96021	5.5	8.3	−16	Kaliboro	17DS	P1	CIM
qPH_10.1	10	S10_19466453–S10_19657592	191139	4.2	6.5	−22.5	Kaliboro	18DS	P1	IM
qPH_10.2	10	S10_21447674–S10_21850052	402378	5.5	7.3	−18.8	Kaliboro	17DS	P1	CIM
qPH_10.3	10	S10_22498821–S10_22942320	443499	5.7	10.2	−22	Kaliboro	18DS	P1	CIM
qNT_3.1	3	S3_26839242–S3_27333736	494494	4.2	7.6	−2.1	Kaliboro	17DS	P1	CIM
qNT_3.2	3	S3_27333736–S3_27887110	553374	4.2	7.6	−2	Kaliboro	17DS	P1	CIM
qNT_4.1	4	S4_16985534–S4_17003608	18074	3.8, 3.5	7.7, 8.3	−2.6, −2.2	Kaliboro	17WS	P2	IM, CIM
qNT_5.1	5	S5_5522854–S5_5890485	367631	12.1	16.6	−2.3	Kaliboro	17WS	P1	CIM
qNT_7.1	7	S7_13238545–S7_13402264	163719	42.4	7.3	−3.9	Kaliboro	18DS	P2	CIM
qNT_7.2	7	S7_17515406–S7_17515417	11	3.6, 4.1	5.8, 6.5	−1.1, −1.2	Kaliboro	17WS	P2	IM, CIM
qNT_7.3	7	S7_19517257–S7_19575858	58601	4	5.2	−1.3	Kaliboro	17DS	P1	CIM
qNP_2.2	2	S2_24011710–S2_24404464	392754	3	5	−3.8	Kaliboro	17WS	P1	CIM
qNP_2.3	2	S2_34569951–S2_34585333	15382	3	5.3	−3.5	Kaliboro	17WS	P1	CIM
qNP_3.1	3	S3_26839242–S3_27333736	494494	4.6	7.6	−2.32	Kaliboro	17DS	P1	CIM
qNP_3.2	3	S3_27333736–S3_27887110	553374	4.6	7.5	−2.23	Kaliboro	17DS	P1	CIM
qNP_4.1	4	S4_16985534–S4_17003608	18074	3.8, 3.6	7.8, 8.4	−2.6, −2.2	Kaliboro	17WS	P2	IM, CIM
qNP_7.1	7	S7_13238545–S7_13402264	163719	43.6	8.5	−3.9	Kaliboro	18DS	P2	CIM
qNP_7.2	7	S7_17515406–S7_17515417	11	3.4, 3.9	5.6, 6.3	−1.1, −1.2	Kaliboro	17WS	P2	IM, CIM
qNP_7.3	7	S7_21486117–S7_21534773	48656	5.8	9.3	−2.5	Kaliboro	17WS	P1	CIM
qPL_2.1	2	S2_16248951–S2_16282542	33591	3.8	5.8	−1.3	Kaliboro	17WS	P1	CIM
qPL_2.3	2	S2_34569951–S2_34585333	15382	4.4	7.2	1.4	IR95040	17WS	P1	CIM
qPL_3.1	3	S3_14554124–S3_14647645	93521	8.5	13.5	2.2	IR95097	18DS	P2	CIM
qPL_3.2	3	S3_14758220–S3_14764507	6287	3.3	5.8	1.21	IR95097	17DS	P2	CIM
qPL_4.1	4	S4_20353816–S4_20391410	37594	4.7, 3.7	7.8, 6.2	1.2, 1.3	IR95040	17WS	P1	IM, CIM
*qPL*_4.2	4	S4_20627686–S4_20750130	122444	5.5, 5.6	9.4, 5.9	−1.6, −1.3	Kaliboro	17DS, 18DS	P2	IM,CIM, MPP	Wang et al.⁵³
*qPL*_4.2	4	S4_20627686–S4_20750130	122444	5.5, 5.6	9.4, 5.9	−1.6, −1.3	Kaliboro	17DS, 18DS	P2	IM,CIM, MPP	Jia et al.⁵⁴
qPL_6.1	6	S6_7422892–S6_7422981	89	3.6	6.4	1.4	IR95040	17WS	P1	IM
qPL_7.1	7	S7_17727140–S7_18807779	1080639	5.8	7.7	−1.4	Kaliboro	17DS	P1	CIM
qPL_8.1	8	S8_22220043–S8_22959293	739250	3.2	7	1.5	IR95097	17DS	P2	IM,
qPL_8.2	8	S8_25335668–S8_25374117	38449	4.6, 4.7	10.9, 10.9	1.3, 1.3	IR95097	17WS	P2	IM, CIM
qPL_8.3	8	S8_27607492–S8_27667551	60059	3.1	8.4	1.3	IR95040	18DS	P1	CIM
qYLD_4.1	4	S4_12594329–S4_13303827	709498	4.3, 7.0	9.6, 14.8	−475.5, −922.7	Kaliboro	17DS,18DS	P2	IM, CIM
qYLD_4.2	4	S4_20420516–S4_20622080	201564	3.4	7	425.9	IR95040	17WS	P1	CIM
qYLD_4.3	4	S4_20927114–S4_20963995	36881	4.4	7	823.4	IR95040	17DS	P1	CIM
qYLD_6.1	6	S6_14222757–S6_14416117	193360	3.1	8	1111.9	IR95040	18DS	P1	CIM
qYLD_7.1	7	S7_9317551–S7_9491729	174178	4.8,3.8	5.0, 7.4	823.8, 566.7	IR95040	17DS	P1	IM, CIM
qTGW_1.1	1	S1_42035412–S1_42409666	374254	5.2, 3.9	10.7, 8.5	−2.3, −2.2	Kaliboro	17WS	P1	IM, CIM
qTGW_4.1	4	S4_28885650–S4_28885760	110	4.9, 3.8	9.1, 5.1	−2.3, −2.2	Kaliboro	17WS	P2	IM, CIM
qTGW_6.1	6	S6_11624477–S6_12259317	634840	3.2	5.4	−1.5	Kaliboro	17WS	P1	CIM
qTGW_12.1	12	S12_3322264–S12_4645838	1323574	3	7.5	−2.4	Kaliboro	17WS	P2	IM
qGL_2.1	2	S2_3255415–S2_3264434	9019	3.1,3.2	7.9, 7.9	0.2, 0.3	IR95097	17WS	P2	IM, CIM
qGL_2.2	2	S2_21183199–S2_21259490	76291	3.7	10.4	0.3	IR95040	17WS	P1	IM
qGL_4.1	4	S4_20391410–S4_20398230	6820	3.1	9.1	0.2	IR95040	17DS	P1	CIM
qGL_4.2	4	S4_32417638–S4_32458506	40868	3.1	9.7	0.2	IR95040	17DS	P1	CIM
qGL_10.1	10	S10_18988329	19655	3.6	10.6	0.3	IR95040	17WS	P1	CIM
qGW_2.1	2	S2_3255415–S2_3264434	9019	3.3	5.4	−0.08	Kaliboro	17WS	P2	CIM
qGW_2.2	2	S2_14997215–S2_14997217	2	3.5	9	−0.05	Kaliboro	17DS	P1	CIM
qGW_2.3	2	S2_15116074–S2_15197689	81615	3.4	5.9	−0.05	Kaliboro	17DS	P1	IM
qGW_3.1	3	S3_248218–S3_453338	205120	3.2	5.4	−0.03	Kaliboro	17DS	P1	IM
qGW_4.1	4	S4_11640949–S4_11739616	98,667	3.4, 3.0	5.3, 5.2	0.2, 0.2	IR95097	17DS,17WS	P2	IM, CIM
qGW_4.2	4	S4_12594329–S4_13303827	709498	5.1–6.9,	5.5–11.6	0.12, 0.15,	IR95097	17DS,17WS	P2	IM, CIM
qGW_4.3	4	S4_17934582–S4_18157390	222808	5.1, 3.5	7.9,5.8	−0.2, −0.1	Kaliboro	17DS,17WS	P2	IM, CIM
qGW_4.5	4	S4_32219091–S4_32219139	48	7.6, 3.5	13.8 5.9	−0.08, −0.04	Kaliboro	17WS	P1	IM, CIM
qGW_6.1	6	S6_26737593–S6_26824877	87284	5.3, 5.3	8.8, 9.8	−0.1, −0.2	Kaliboro	17WS,17DS	P2	IM, CIM
qGW_7.1	7	S7_26653449–S7_26833996	180547	3.8	7.7	−0.07	Kaliboro	17WS	P1	CIM
qGW_10.1	10	S10_19078485–S10_19088946	10461	3.5, 4.5	6.0, 9.6	−0.04, −0.04	Kaliboro	17DS	P1	IM, CIM
qFe_4.1	4	S4_32219091–S4_32219139	48	4.4	9.4	−0.43	Kaliboro	18DS	P1	CIM
qFe_6.1	6	S6_14049331–S6_14095906	46575	3.5	7.6	−0.42	Kaliboro	17DS	P1	CIM
qFe_6.2	6	S6_27973551–S6_28801387	827836	3.5	7.5	0.31	IR95040	18DS	P1	CIM
qFe_9.1	9	S9_16360525–S9_16603135	242610	3	6.9	−0.79	Kaliboro	17DS	P1	IM
qFe_11.1	11	S11_28325418–S11_28416009	90591	3.4	7.2	−0.91	Kaliboro	17DS	P1	IM
qZn_3.1	3	S3_11569043–S3_11591292	22249	3.6, 3.5	7.4, 6.0	−2.2, −1.3	Kaliboro	17DS, 17WS	P1	IM, CIM	Hu et al.⁵⁵
											Mohiuddin et al.⁵⁶
											Nawaz et al.⁵⁷
											Anuradha et al.⁵⁸
qZn_4.1	4	S4_12594329–S4_13303827	709498	7.5–10.8	7.4–18.3	2.4 to 3.3	IR95097	17DS,17WS,18DS	P2	IM, CIM	Islam et al.⁵⁹
											Hu et al.⁵⁵
											Palanog et al.¹⁶
qZn_4.2	4	S4_22682312—S4_22824314	142002	3.5	5.2	2.76	IR95097	17DS	P2	IM
*qZn*_5.2	5	S5_24658994–S5_27563777	2904783	3.6	6.4,	−2.2,	Kaliboro	18DS	P2	CIM, MPP	Palanog et al.¹⁶
											Zaw et al.¹⁹
											Yu et al.⁶⁰
qZn_6.1	6	S6_20146062–S6_21730677	1584615	4.7	8	−1.7	Kaliboro	17WS	P1	CIM
qZn_6.2	6	S6_28982499–S6_29062391	79892	4	11.6	−2.8	Kaliboro	17WS	P2	CIM
qZn_6.3	6	S6_31285864–S6_31396406	110542	3.6,3.6	5.2,7.8	−3.1,−2.8	Kaliboro	17DS	P2	IM
qZn_7.1	7	S7_24855163–S7_24902559	47396	3.9	7.1	−2.1	Kaliboro	17WS	P1	CIM
qZn_7.2	7	S7_25971002–S7_26035985	64983	4.2	6.5	−2.5	Kaliboro	18DS	P1	CIM
qZn_7.3	7	S7_28866595–S7_29116717	250122	3.2–4.8	8.4	−2.1 to −2.6	Kaliboro	18DS,17DS,17WS	P1	CIM	Bollinedi et al.⁶¹
											Anuradha et al.⁵⁸
											Hu et al.⁵⁵
											Mohiuddin et al.⁵⁶
											Zhang et al.⁶²
											Zaw et al.¹⁹
											Descalsota et. al.³¹
qZn_8.1	8	S8_23062176–S8_23182047	119871	3.1,3.4	5.1,6.0	−1.92, −3.1	Kaliboro	17WS,17DS	P2	CIM	Sahu et al.⁶³
											Bollinedi et al.⁶¹
											Garcia-Oliveira et al.⁶⁴
											Xu et al.⁶⁵
qZn_10.1	10	S10_19135519–S10_19140574	5055	5.2 –10.6	10.6–6.5	−1.9 to −3.1	Kaliboro	18DS,17DS,17WS	P1	CIM	Ishikawa et al.⁶⁶
											Hu et al.⁵⁵
											Palanog et al.¹⁶
qZn_12.1	12	S12_13088982–S12_13118577	29595	4.5	8.4	−3.8	Kaliboro	18DS	P2	CIM

LOD logarithm of the odds, PVE phenotypic variance explained, DS dry season, WS wet season, IM interval mapping, ICIM inclusive composite interval mapping, MPP multi-parent population mapping.
Bold: consistent/stable QTLs identified in two to three seasons.

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Table 3 QTLs identified for agronomic, yield, and grain Fe and Zn concentration in two RILs populations using inclusive composite interval mapping and interval mapping.

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