Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)

Murugaiyan, Varunseelan; Ali, Jauhar; Mahender, Anumalla; Aslam, Umair M.; Jewel, Zilhas Ahmed; Pang, Yunlong; Marfori-Nazarea, Corinne M.; Wu, Lin-Bo; Frei, Michael; Li, Zhikang

doi:10.1186/s12284-019-0321-y

Rice

Table 2 QTLs associated with As-related traits after 18 days of 10 ppm As stress in WTR1× Hao-an-nong population by single marker regression

From: Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)

QTL^a	Trait	Chr	Position^b	Associated marker^c	-log p(F)^d	R² (%)^e	Additive effect^f	Tolerance allele^g
qRChlo1	Relative chlorophyll content	1	39.2829	66SNP_1_39282883	3.7781	8.6216	4.0676	WTR1
		1	39.3692	67SNP_1_39369209	3.7781	8.6216	4.0676	WTR1
		1	39.4208	68SNP_1_39420824	3.7781	8.6216	4.0676	WTR1
qAsR8.1	Arsenic content root	8	6.0577	487SNP_8_6057678	4.652	10.5069	− 11.7883	WTR1
qAsR8.2	Arsenic content root	8	7.854	492SNP_8_7854002	3.821	8.7155	−10.6686	WTR1
qAsS2	Arsenic content shoot	2	4.3429	88SNP_2_4342883	4.3275	9.8119	−1.1264	WTR1
		2	4.9307	89SNP_2_4930742	4.1432	9.4147	−1.1015	WTR1
		2	5.8303	90SNP_2_5830265	4.0335	9.1768	−1.0944	WTR1
		2	6.4799	91SNP_2_6479920	4.1741	9.4812	−1.1054	WTR1
		2	7.0233	92SNP_2_7023295	4.1741	9.4812	−1.1054	WTR1
		2	7.0767	93SNP_2_7076671	4.332	9.8214	−1.1248	WTR1
		2	7.1037	94SNP_2_7103684	4.332	9.8214	−1.1248	WTR1
		2	7.1708	95SNP_2_7170842	4.332	9.8214	−1.1248	WTR1
		2	7.2388	96SNP_2_7238793	4.332	9.8214	−1.1248	WTR1
		2	7.2775	97SNP_2_7277487	4.1741	9.4812	−1.1054	WTR1
qAsS5.1	Arsenic content shoot	5	10.8863	287SNP_5_10886331	3.7203	8.4964	−1.0489	WTR1
		5	13.3255	288SNP_5_13325546	3.7203	8.4964	−1.0489	WTR1
		5	13.7687	289SNP_5_13768744	3.7203	8.4964	−1.0489	WTR1
		5	14.0797	290SNP_5_14079677	3.7203	8.4964	−1.0489	WTR1
		5	14.644	291SNP_5_14643984	4.1216	9.3682	−1.1564	WTR1
qAsS5.2	Arsenic content shoot	5	15.4693	292SNP_5_15469279	4.0303	9.1701	−1.0871	WTR1
		5	15.556	293SNP_5_15556017	4.0303	9.1700	−1.0871	WTR1
		5	16.4598	294SNP_5_16459802	4.0303	9.1701	−1.0871	WTR1
		5	16.5851	295SNP_5_16585060	4.0303	9.1700	−1.0871	WTR1
		5	16.8086	296SNP_5_16808642	5.6649	12.6433	−1.3646	WTR1
qAsS6	Arsenic content shoot	6	0.4008	329SNP_6_400753	4.1072	9.3372	1.3763	Hao-an-nong
		6	0.6469	330SNP_6_646915	4.4046	9.9782	1.4682	Hao-an-nong
		6	0.8342	332SNP_6_834170	4.1072	9.3372	1.3763	Hao-an-nong
		6	1.5219	335SNP_6_1521855	3.5808	8.1922	1.3782	Hao-an-nong
		6	1.768	336SNP_6_1768006	5.323	11.929	1.4867	Hao-an-nong
		6	1.9284	337SNP_6_1928403	4.0138	9.1355	1.2804	Hao-an-nong
		6	1.9783	338SNP_6_1978288	4.0138	9.1355	1.2804	Hao-an-nong
		6	2.0107	339SNP_6_2010737	4.5116	10.208	1.3335	Hao-an-nong
		6	2.0256	340SNP_6_2025629	4.5116	10.208	1.3335	Hao-an-nong
qAsS9.1	Arsenic content shoot	9	18.3666	551SNP_9_18366555	3.884	8.8531	−1.085	WTR1
		9	18.3891	552SNP_9_18389054	3.884	8.8531	−1.085	WTR1
		9	19.2081	553SNP_9_19208050	3.7654	8.5948	−1.0579	WTR1
qAsS9.2	Arsenic content shoot	9	20.587	555SNP_9_20587039	3.9802	9.0617	−1.0806	WTR1
		9	21.2154	557SNP_9_21215424	3.6667	8.379	−1.0403	WTR1
		9	21.3489	558SNP_9_21348882	4.368	9.8987	−1.1294	WTR1

^aClosely linked markers are assumed as the same QTL. ^bPhysical position of markers on chromosomes
^cMarker associated with QTL. ^dF-statistical analysis indicates association between markers and trait
^eProportion of phenotypic variance explained. ^fPositive/negative values indicate that WTR1/ Hao-an-nong can increase trait values
^gTolerance allele provided by parental line

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