Table 3. SNPs that met significance level of -log₁₀(P) > 4 for the GWAS of canopy wilting.

Locusa	Chr.b	Pos.c	SNP	-log10(P)	MAFd	Effecte	Envf	SoyBase QTLg
1	1	4015639	ss715579324	5.13	0.27	−1.62	KS-16
2	1	51961463	ss715580187	4.78	0.09	2.13	ALL
3	2	3165348	ss715581823	5.34	0.06	−3.65	GA-15	Canopy wilt 3-4, 3-8, 3-11, 6-1; mqCanopy wilt-001
4	2	42073473	ss715582842	4.73	0.37	1.97	GA-15	Canopy wilt 6-3
5	4	46096228	ss715588277	5.02	0.38	−1.97	GA-15
6	5	6207961	ss715592288	4.13	0.06	−3.19	GA-16	Canopy wilt 3-5
7	5	41387548	ss715591700	4.45	0.21	1.91	GA-15
8	6	13090474	ss715592991	7.05	0.06	2.97	GA-16
9	6	14258126	ss715593189	4.56	0.06	1.51	KS-15
10	6	47633030	ss715594738	6.75	0.28	−1.87	GA-16	Canopy wilt 3-12
11	6	49189084	ss715595012	5.94	0.37	1.50	ALL
12	7	11177483	ss715596171	4.40	0.32	0.71	KS-15
13	8	1699023	ss715599875	4.94	0.24	1.40	ALL
14	8	9837263	ss715602901	4.36	0.15	−1.42	ALL
15	8	34471238	ss715601484	4.14	0.20	1.79	KS-16
16	9	1769730	ss715603168	4.53	0.18	−1.93	KS-16
17	9	36942176	ss715603680	6.84	0.31	−2.01	GA-16
18	10	270252	ss715606054	6.63	0.47	1.81	KS-16
19	10	3598580	ss715606348	8.41	0.41	3.20	GA-15
20	10	23376136	ss715605804	8.26	0.27	−3.31	GA-16
21	10	30831897	ss715606157	5.41	0.15	3.43	GA-16
22	11	31929823	ss715610250	5.25	0.48	−1.45	GA-16
23	12	2053039	ss715611755	5.26	0.08	−1.38	KS-15
24	12	2839426	ss715612002	4.82	0.35	−1.43	KS-16
25	13	29459954	ss715614803	4.25	0.10	−1.89	GA-16
26	14	3078346	ss715618273	5.13	0.43	1.55	GA-16	Canopy wilt 1-2
27	14	10057919	ss715617366	4.15	0.07	2.76	GA-16
28	14	43597753	ss715618915	6.21	0.36	−0.90	KS-15
29	15	12437556	ss715620442	5.49	0.34	1.29	ALL
30	15	50499617	ss715622647	7.59	0.24	2.16	GA-16
31	15	51622014	ss715622805	4.60	0.23	−1.75	GA-15
32	16	164715	ss715623538	5.49	0.48	1.81	GA-15
	16	517535	ss715625192	5.04	0.09	−1.29	KS-15
33	17	9384325	ss715628378	5.12	0.43	0.75	KS-15	Canopy wilt 1-3, 3-10, 3-13; mqCanopy wilt-006
34	17	31794022	ss715626726	7.78	0.12	2.51	ALL	Canopy wilt 5-2
35	17	36227875	ss715626968	7.64	0.09	3.47	GA-16
36	18	46860521	ss715631153	5.78	0.13	−1.26	KS-15
37	18	54371258	ss715632037	5.31	0.09	1.47	KS-15
38	19	809326	ss715636293	4.04	0.28	−1.80	GA-15
39	19	38109922	ss715634688	7.73	0.15	−2.16	ALL	Canopy wilt 2-7, 4-3
	19	38109922	ss715634688	6.98	0.15	−3.05	GA-15	Canopy wilt 2-7, 4-3
40	19	45307395	ss715635460	4.61	0.34	1.47	GA-16	Canopy wilt 5-4, 6-2
41	20	294010	ss715637218	5.17	0.46	1.55	GA-16
42	20	39013106	ss715637991	5.03	0.36	−1.56	GA-15
43	20	46438247	ss715638748	4.30	0.46	−1.71	GA-15
44	20	47435005	ss715638900	4.65	0.48	−1.46	ALL

^aIf multiple SNPs were identified in the same linkage disequilibrium (LD) block they were deemed part of the same locus (genomic region).

^bChromosome.

^cGlyma.Wm82.a2 physical position.

^dMinor allele frequency.

^eAllelic effects were calculated by taking the difference in mean canopy wilting score between the two alleles at a particular SNP, and the direction, negative or positive, of the allelic effect estimates are relative to the alphabetical order of the nucleotides at each particular marker.

^fEnvironment written as location-year-population.

^gCanopy wilting QTL identified on SoyBase in which loci from our study are located within.