Table 4.

Summary of quantitative trait loci identified for grain As concentrations in rice.

Locus	Dataset	Chr.a	SSNb	Peak SNPc	Location	Alleled	MAFe	Effectf	P-value
qGAS1	ALL	1	8	SNP-1.32110595	32111640	T/G	0.34	0.06	3.55 × 10-8
qGAS2	ALL	2	1	SNP-2.8547163	8547165	T/A	0.08	0.07	7.53 × 10-6
qGAS3	ALL	2	1	SNP-2.10953257	10953261	A/G	0.07	0.07	6.02 × 10-6
qGAS4	ALL	4	1	SNP-4.31609708	31794816	T/C	0.07	0.07	4.98 × 10-6
qGAS5	ALL	5	2	id5007352	18449575	A/G	0.09	0.08	2.43 × 10-6
qGAS6	ALL	5	1	SNP-5.24080444	24143026	C/T	0.10	0.06	4.14 × 10-6
qGAS7	ALL	5	4	SNP-5.27975384	28038030	A/G	0.06	0.09	2.34 × 10-6
qGAS8	ALL	9	4	SNP-9.21119182	21119664	T/C	0.21	0.06	5.88 × 10-8
qGAS9	ALL	11	2	SNP-11.7798060	7802316	A/G	0.06	0.08	2.20 × 10-6
qGAS10	ALL	12	1	SNP-12.3668397	3669399	G/A	0.06	0.08	6.96 × 10-6
qGAS11	AUS	5	1	SNP-5.6897684	6897743	A/T	0.13	0.13	5.41 × 10-6
qGAS12	AUS	5	2	SNP-5.21487581	21550141	T/C	0.30	0.10	4.89 × 10-6
qGAS13	AUS	7	4	SNP-7.20773328	20774322	A/G	0.15	0.15	5.92 × 10-6
qGAS14	AUS	7	1	SNP-7.27175857	27176852	C/T	0.29	0.09	2.15 × 10-6
qGAS15	IND	3	1	SNP-3.13827874	13829158	T/C	0.23	0.07	9.12 × 10-6
qGAS16	IND	5	1	SNP-5.18389617	18450132	G/A	0.26	-0.07	6.03 × 10-6
qGAS17	IND	6	1	SNP-6.27927466	27928465	T/G	0.13	0.08	7.82 × 10-6
qGAS18	IND	11	1	SNP-11.24643782	25109943	C/T	0.24	0.07	3.43 × 10-6
qGAS19	TRJ	3	1	SNP-3.10935433	10936716	G/A	0.08	0.09	8.26 × 10-6
qGAS20	TRJ	3	1	SNP-3.16460269	16461625	C/T	0.08	0.10	1.38 × 10-6
qGAS21	TRJ	11	1	id11007895	21030105	C/T	0.06	0.10	5.51 × 10-6
qGAS22	TRJ	11	1	SNP-11.24623164	25089325	C/T	0.08	0.10	1.39 × 10-6

Threshold for significance, P-value < 1.00 × 10^-5 (<2.62 × 10^-7 for AUS subpopulation). ^aChr., chromosome. ^bSSN, significant SNP number. ^cSNP with the best P value. ^dAllele, minor/major alleles. ^eMAF, minor allele frequency. ^fEffect, allele effect with respect to the minor allele.