TABLE 4.

QTL associated by GWA with grain arsenic concentration (qAs) in the Rice Minicore Panel (RMC) arranged in chromosomal order. Overlaps with QTL for other traits within this study, and candidate genes are also noted. Panels for which QTL are listed include “all RMC” containing all RMC accessions, indica subspecies, japonica subspecies, IND subgroup, and AUS subgroup.

QTL	Chr	Start of QTL region (bp) a	End of QTL region (bp) a	QTL size (Mb)	Peak SNP location (bp) a	Panel QTL peak details from b	−log10(p)	Effect of most common allele c	Most common allele	Alter-nate allele	Nu. acc. with common allele	Nu. acc. with alt. allele	% panel having alt. allele	QTL overlaps among traits in this study	Co-location with QTL reported in literature	Candidate gene RAP ID d	Candidate gene symbol(s) or name(s) e
qAs1-1	1	1,34,61,779	1,36,17,444	0.156	1,35,33,400	all RMC	5.56	−0.26	C	T	60	46	43.4	DHD, PHT	–	–	–
qAs1-2	1	2,19,81,983	2,44,49,843	2.468	2,37,57,196	all RMC	5.17	−0.11	G	T	71	39	35.5	StHD, Si, DHD	Norton et al., 2014	LOC_Os01g41720	EnS-10
qAs1-3	1	3,14,52,607	3,42,20,812	2.768	3,16,77,916	all RMC	5.67	0.15	C	T	108	21	16.3	StHD, Si, Cu, DHD, PHT	–	LOC_Os01g56400	ABCI7
qAs2	2	2,15,23,027	2,17,30,651	0.208	2,15,75,358	all RMC	5.31	0.27	G	A	52	43	45.3	P, S	–	LOC_Os02g36570	ABC1-2
qAs3	3	2,82,21,674	2,84,16,354	0.195	2,83,66,354	all RMC	5.91	−0.34	A	G	65	54	45.4	–	Zhang et al., 2008; Liu et al., 2021	LOC_Os03g49440	phosphatase
qAs4	4	82,22,722	1,12,92,867	3.070	90,09,797	all RMC	5.75	0.21	A	T	85	9	9.6	Si	–	LOC_Os04g16450	PIP2;6
↓																LOC_Os04g17660	HAC1;2
qAs6-1	6	1,30,39,217	1,31,69,010	0.130	1,31,15,883	indica	6.09	−0.14	C	T	55	11	16.7	–	–	LOC_Os06g22960	TIP2;2
qAs6-2	6	1,76,19,751	1,92,18,461	1.599	1,90,23,908	all RMC	5.03	0.17	G	T	106	7	6.2	DHD, Cu	Zhang et al., 2008	LOC_Os06g29790	PHO1
↓																LOC_Os06g29844, LOC_Os06g29950, LOC_Os06g29994	Cluster of 3 MATE genes
↓
↓
qAs7-1	7	1,05,06,160	1,25,89,848	2.084	1,18,74,171	all RMC	6.13	0.18	G	A	89	11	11.0	S	Norton et al., 2014	─	─
qAs7-2	7	2,26,36,921	2,45,33,222	1.896	2,26,86,921	all RMC	5.42	−0.16	G	A	82	31	27.4	DHD, P	Norton et al., 2014	LOC_Os07g41310	Similar to Phytochelatin synthetase
qAs8	8	3,94,274	18,15,831	1.422	5,98,139	all RMC	6.24	−0.37	A	G	43	39	47.6	StHD	Norton et al., 2014; Liu et al., 2021	LOC_Os08g03020	transmembrane receptor protein
↓																LOC_Os08g03380	heat shock protein
↓
↓																LOC_Os08g03470 to LOC_03650	7 BTB-domain containing genes
↓
qAs10	10	2,09,14,520	2,11,45,930	0.231	2,10,12,106	AUS	5.24	−0.09	A	G	10	9	47.4	–	–	LOC_Os10g37920	MATE
↓																LOC_Os10g39980	Lsi3
qAs11-1	11	83,21,863	89,01,679	0.580	88,40,750	indica	6.23	0.20	C	T	42	7	14.3	S, Ca	–	–	–
qAs11-2	11	2,50,34,091	2,59,95,458	0.961	2,52,09,544	all RMC	5.35	0.17	G	A	116	9	7.2	DHD	Norton et al., 2014	–	–

^a O. sativa SNPs are identified by their physical location based on the Os-Nipponbare-Reference-IRGSP-1.0 assembly (Kawahara et al., 2013).

^bThe panels are defined as the complete Rice Minicore Diversity Panel (RMC, n = 166). The O. sativa subpopulation groups were tropical japonica (TRJ), temperate japonica (TEJ), aus (AUS), and indica (IND). The two O. sativa subspecies are indica, composed of IND and AUS combined, and japonica comprised TEJ and TRJ. QTL were often identified in GWA-mapping of more than one population (e.g., in INDAUS and AUS). Because alternate alleles became very rare in the smaller subpopulations, the table presents the results based on the entire RMC panel when the QTL was significant there.

^cA negative allele effect reflects a reduction in the trait associated with the most common allele.

^dRAP ID is the Rice Annotation Project identification locus identified for the candidate gene.

^eGene nomenclature followed the standardized nomenclature for rice genes used in Oryzabase (Yamazaki et al., 2010).