Molecular Dissection of Seedling Salinity Tolerance in Rice (Oryza sativa L.) Using a High-Density GBS-Based SNP Linkage Map

De Leon, Teresa B.; Linscombe, Steven; Subudhi, Prasanta K.

doi:10.1186/s12284-016-0125-2

Rice

Table 4 Additive QTLs for traits related to seedling-stage salt tolerance in Bengal/Pokkali F₆ RIL population identified by IM and ICIM methods

From: Molecular Dissection of Seedling Salinity Tolerance in Rice (Oryza sativa L.) Using a High-Density GBS-Based SNP Linkage Map

Phenotype	QTL	Chr^a	Position (cM)	Left Marker	Right Marker	QTL Interval Size (bp)	LOD	PVE (%)	Additive Effect	Parental Source of Increasing Allele Effect^b	No. of genes in QTL interval
Na⁺ concentration-IM	qNa2.7	2	48	S2_7769844	S2_7939496	169,652	2.2969	5.55	-66.59	P	24
	qNa6.5	6	34	S6_5269698	S6_5533752	264,054	2.399	5.97	69.15	B	34
	qNa12.18	12	60	S12_18687038	S12_18741493	54,455	2.2496	5.51	-66.36	P	5
Na⁺ concentration-ICIM	qNa2.7	2	48	S2_7769844	S2_7939496	169,652	2.2969	5.55	-66.59	P	24
	qNa6.5	6	34	S6_5269698	S6_5533752	264,054	2.399	5.97	69.15	B	34
	qNa12.18	12	60	S12_18687038	S12_18741493	54,455	2.2496	5.51	-66.36	P	5
K⁺ concentration-IM	qK1.8	1	63	S1_8656025	S1_8901503	245,478	5.7933	13.65	-46.34	P	33
	qK1.11	1	71	S1_11529325	S1_11581799	52,474	5.9263	13.66	-45.13	P	6
	qK1.38	1	173	S1_38794029	S1_39047133	253,104	3.5096	8.30	-33.32	P	40
	qK5.4	5	31	S5_4699921	S5_5326365	626,444	2.2496	5.51	-27.00	P	86
	qK6.4	6	31	S6_4890290	S6_5269698	379,408	3.333	8.21	-32.92	P	61
K⁺ concentration-ICIM	qK1.11	1	71	S1_11529325	S1_11581799	52,474	7.7414	16.08	-48.95	P	6
	qK1.38	1	173	S1_38794029	S1_39047133	253,104	5.3793	10.71	-37.86	P	40
NaK ratio-IM	qNaK1.11	1	71	S1_11529325	S1_11581799	52,474	4.154	9.83	0.29	B	6
	qNaK6.2	6	15	S6_2927160	S6_2962502	35,342	3.5777	8.46	0.26	B	7
	qNaK6.5	6	33	S6_5269698	S6_5533752	264,054	5.1164	13.21	0.32	B	34
NaK ratio-ICIM	qNaK1.11	1	71	S1_11529325	S1_11581799	52,474	2.6375	5.66	0.22	B	6
	qNaK6.5	6	33	S6_5269698	S6_5533752	264,054	3.7097	8.85	0.26	B	34
Salt injury score-IM	qSIS2.8	2	50	S2_8730258	S2_8927908	197,650	3.5375	8.58	-0.06	P	25
	qSIS2.19	2	81	S2_19331684	S2_19454952	123,268	3.2133	7.66	-0.06	P	14
	qSIS2.28	2	131	S2_28239596	S2_28274467	34,871	2.6449	6.37	-0.05	P	8
	qSIS5.03	5	1	S5_312457	S5_329699	17,242	2.8257	6.74	0.06	B	4
	qSIS5.1a	5	12	S5_1686924	S5_1707475	20,551	2.8266	6.76	0.06	B	5
	qSIS5.24	5	106	S5_24057323	S5_24281632	224,309	3.1266	7.51	0.06	B	39
	qSIS6.2	6	15	S6_2927160	S6_2962502	35,342	2.0824	5.04	0.05	B	7
	qSIS6.5	6	37	S6_5848568	S6_5905669	57,101	3.0401	7.23	0.06	B	11
	qSIS6.7	6	48	S6_7646442	S6_7661883	15,441	3.1238	7.41	0.06	B	3
	qSIS6.20	6	90	S6_20929261	S6_20929283	22	3.9605	9.44	0.07	B	1
	qSIS11.2	11	18	S11_2838776	S11_3716306	877,530	2.664	8.36	0.06	B	136
Salt injury score-ICIM	qSIS5.1b	5	11	S5_1441967	S5_1454837	12,870	9.7068	13.33	0.08	B	2
	qSIS6.2b	6	9	S6_2123411	S6_2242943	119,532	3.5933	4.46	0.05	B	23
	qSIS6.21	6	92	S6_21253244	S6_21256132	2888	6.9204	9.11	0.07	B	1
	qSIS7.14	7	57	S7_14598897	S7_14625841	26,944	3.6209	4.50	0.05	B	7
	qSIS8.24	8	93	S8_24763939	S8_25110888	346,949	2.6235	3.28	0.04	B	47
	qSIS9.8	9	13	S9_8608506	S9_9070610	462,104	7.09	9.19	0.07	B	51
	qSIS11.2	11	21	S11_2838776	S11_3716306	877,530	2.336	3.53	0.04	B	136
Chlorophyll content-IM	qCHL11.1	11	5	S11_1086712	S11_1293020	206,308	2.1922	5.41	-1.00	P	34
	qCHL11.2	11	14	S11_2666525	S11_2724222	57,697	2.0172	4.86	-0.95	P	7
Chlorophyll content-ICIM	qCHL2.20	2	86	S2_20258450	S2_20346560	88,110	3.6938	7.44	1.18	B	7
	qCHL2.30	2	143	S2_30353435	S2_30402468	49,033	2.3418	4.69	-0.94	P	7
	qCHL3.26	3	136	S3_26705619	S3_26709038	3419	3.2263	6.42	-1.10	P	1
Shoot length-IM	qSHL1.1	1	11	S1_1708228	S1_1747144	38,916	2.0367	5.03	-1.42	P	7
	qSHL1.7a	1	48	S1_7259818	S1_7296346	36,528	3.9307	9.26	-1.95	P	7
	qSHL1.38	1	168	S1_38286772	S1_38611845	325,073	25.3529	48.03	-4.43	P	52
	qSHL3.34	3	185	S3_34720589	S3_35060080	339,491	2.361	5.65	1.54	B	69
	qSHL5.4	5	29	S5_4565557	S5_4699921	134,364	2.3239	5.64	-1.52	P	23
	qSHL5.6	5	44	S5_6356744	S5_6433933	77,189	2.0324	4.96	-1.41	P	13
Shoot length-ICIM	qSHL1.7b	1	50	S1_7520182	S1_7569628	49,446	6.2678	5.86	-1.57	P	5
	qSHL1.38	1	168	S1_38286772	S1_38611845	325,073	36.9075	51.64	-4.59	P	52
	qSHL2.18	2	77	S2_18806154	S2_18937362	131,208	3.0049	2.71	1.04	B	25
	qSHL3.34	3	185	S3_34720589	S3_35060080	339,491	4.3994	3.96	1.29	B	69
	qSHL5.3	5	25	S5_3353753	S5_3506138	152,385	7.0797	6.79	-1.66	P	21
	qSHL12.25	12	93	S12_25709174	S12_25887173	177,999	2.246	2.05	0.91	B	30
Root length-IM	qRTL1.26	1	121	S1_26421289	S1_26447134	25,845	2.7346	6.52	0.32	B	6
	qRTL2.24	2	114	S2_24961302	S2_24961342	40	4.1447	9.72	0.39	B	0
	qRTL2.26	2	120	S2_26028043	S2_26070191	42,148	4.2053	9.91	0.39	B	9
	qRTL2.33	2	160	S2_33573567	S2_33614297	40,730	3.9359	9.50	0.39	B	7
	qRTL3.6	3	36	S3_6011601	S3_6027452	15,851	3.4683	8.23	0.36	B	2
	qRTL3.7	3	44	S3_7130220	S3_7209963	79,743	4.4685	10.70	0.41	B	15
	qRTL3.10	3	57	S3_10116591	S3_10132745	16,154	5.0358	11.99	0.43	B	2
	qRTL4.10	4	24	S4_10625625	S4_10726368	100,743	2.0131	4.88	0.28	B	14
	qRTL8.4	8	37	S8_4558562	S8_4858127	299,565	2.121	5.34	0.36	B	41
	qRTL8.19	8	59	S8_19884635	S8_19898432	13,797	3.272	7.75	0.41	B	2
	qRTL8.27	8	109	S8_27238050	S8_27304101	66,051	2.1036	5.13	-0.28	P	9
	qRTL9.14	9	39	S9_14960521	S9_14976723	16,202	2.6572	6.45	-0.36	P	3
Root length-ICIM	qRTL1.22	1	102	S1_22666852	S1_22677418	10,566	2.2657	3.54	0.23	B	2
	qRTL1.26	1	121	S1_26421289	S1_26447134	25,845	2.1764	3.41	0.23	B	6
	qRTL3.9	3	56	S3_9853159	S3_9891061	37,902	4.2907	7.59	0.34	B	7
Dry weight-IM	qDWT1.21	1	97	S1_21707357	S1_21733437	26,080	2.3413	5.60	-0.01	P	6
	qDWT4.32	4	126	S4_32367131	S4_32367159	28	2.3915	5.73	-0.01	P	1
	qDWT5.2	5	15	S5_2116055	S5_2167880	51,825	4.6334	10.80	-0.01	P	4
	qDWT5.4	5	29	S5_4565557	S5_4699921	134,364	6.5783	15.04	-0.01	P	23
	qDWT5.5	5	42	S5_5997340	S5_6196044	198,704	6.5368	15.47	-0.01	P	32
	qDWT6.13	6	72	S6_13046472	S6_13097774	51,302	2.0119	5.16	0.00	P	10
	qDWT6.20	6	90	S6_20929261	S6_20929283	22	3.7538	8.95	-0.01	P	1
	qDWT6.23	6	102	S6_23812023	S6_24039384	227,361	3.7054	8.91	-0.01	P	32
	qDWT11.2	11	10	S11_2379158	S11_2402109	22,951	2.4389	6.03	-0.01	P	3
Dry weight-ICIM	qDWT1.40	1	185	S1_40372283	S1_40412316	40,033	2.0722	3.13	0.00	P	6
	qDWT4.32	4	126	S4_32367131	S4_32367159	28	3.6566	5.93	-0.01	P	1
	qDWT5.4	5	29	S5_4565557	S5_4699921	134,364	7.5727	12.98	-0.01	P	23
	qDWT6.06	6	3	S6_692773	S6_782975	90,202	3.7128	6.02	-0.01	P	13
	qDWT6.24	6	104	S6_24107596	S6_24228831	121,235	4.4604	7.46	-0.01	P	19
Shoot-root ratio-IM	qSRR1.7	1	50	S1_7520182	S1_7569628	49,446	3.7944	9.09	-0.38	P	5
	qSRR1.29	1	135	S1_29561423	S1_29568978	7555	3.1151	7.42	-0.33	P	2
	qSRR1.36	1	159	S1_36158467	S1_36189206	30,739	5.8447	13.42	-0.45	P	5
	qSRR1.382	1	170	S1_38286772	S1_38611845	325,073	10.3107	23.01	-0.59	P	52
	qSRR2.28	2	133	S2_28317911	S2_28375704	57,793	4.7052	10.96	-0.41	P	7
	qSRR2.31	2	146	S2_31037977	S2_31043939	5962	3.2045	7.62	-0.34	P	1
	qSRR2.33	2	160	S2_33573567	S2_33614297	40,730	4.1813	9.90	-0.39	P	7
	qSRR2.34	2	168	S2_34660774	S2_35085922	425,148	2.9367	7.37	-0.33	P	68
	qSRR3.8	3	49	S3_8327882	S3_8353264	25,382	2.6453	6.32	-0.31	P	6
	qSRR3.10	3	57	S3_10116591	S3_10132745	16,154	2.6902	6.58	-0.31	P	2
	qSRR3.11	3	70	S3_11848358	S3_11865689	17,331	2.4751	5.93	-0.30	P	1
	qSRR4.10	4	24	S4_10625625	S4_10726368	100,743	2.438	5.91	-0.30	P	14
	qSRR8.19	8	59	S8_19884635	S8_19898432	13,797	2.3793	5.70	-0.35	P	2
Shoot root ratio-ICIM	qSRR1.7	1	50	S1_7520182	S1_7569628	49,446	6.9282	8.73	-0.37	P	5
	qSRR1.386	1	171	S1_38636497	S1_38768787	132,290	15.6449	22.43	-0.59	P	22
	qSRR2.33	2	160	S2_33573567	S2_33614297	40,730	8.5304	10.92	-0.41	P	7
	qSRR3.9	3	56	S3_9853159	S3_9891061	37,902	4.3278	5.25	-0.28	P	7
	qSRR8.26	8	107	S8_26716230	S8_26744324	28,094	2.533	3.01	0.21	B	5

^a Chromosome where the QTL was located. ^bParental source of increasing allele effect was either Pokkali (P) or Bengal (B)

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