Table 3.

A subset of SNPs significantly associated with 9 agronomic traits

Trait	Chr.a	Positionb	MAF	Allele	P value	R2(%)	XP-CLR	Known locic
Grain yield	1	55794390	0.06	T/C	2.38 × 10-6	2.6	1.60
	3	47136179	0.48	T/C	2.69 × 10-5	2.4	0.68	15-4
	4	43653965	0.10	T/C	1.59 × 10-6	2.7	18.20d	12-2
	8	39270868	0.21	T/C	5.50 × 10-8	4.5	4.25e
	14	46260055	0.07	A/G	3.80 × 10-7	3.2	17.01d	3-4
Protein content	7	7058915	0.11	T/C	1.46 × 10-7	3.2	3.55	24-4
	9	1195313	0.47	T/C	4.57 × 10-7	3.0	4.76e
	10	47656484	0.14	T/C	2.88 × 10-5	2.0	9.02e	5-4
	15	5312718	0.20	A/G	1.49 × 10-5	2.3	1.94	5-4
	20	36078120	0.06	T/G	1.62 × 10-5	2.1	7.63e	26-5
Oil content	1	52863692	0.30	A/G	6.66 × 10-6	2.5	8.45e	24-21
	6	14511997	0.08	A/G	1.23 × 10-5	2.4	8.93e	36-2
	10	6572950	0.08	A/G	2.29 × 10-5	2.6	10.37d
	11	1859395	0.06	T/C	7.63 × 10-6	2.3	2.10
	14	5340642	0.16	A/G	7.23 × 10-7	2.9	4.14	2-6
Lodging	2	7785541	0.19	T/C	3.81 × 10-5	2.6	7.90e	7-1
	10	44437412	0.13	A/C	4.96 × 10-6	2.3	9.02e
	10	44723907	0.12	A/G	5.06 × 10-7	2.8	7.35e	20-6
	10	44747924	0.12	A/G	1.85 × 10-6	2.6	7.35e	20-6
	19	47672198	0.39	T/C	8.14 × 10-6	2.4	0.227	4-3
Plant height	8	10789902	0.18	T/C	6.84 × 10-6	2.3	4.82e
	10	44444513	0.13	A/G	5.00 × 10-8	3.3	9.02e	E2
	13	37624457	0.36	T/C	3.13 × 10-5	2.3	3.79	17-1
	19	37391984	0.12	A/G	4.16 × 10-6	2.4	11.48d
	19	47392861	0.37	T/C	2.75 × 10-6	2.5	0.69	5-10
Maturity date	7	8270118	0.30	A/G	4.61 × 10-5	1.9	2.90	2-1
	10	5392194	0.21	T/C	7.56 × 10-6	2.3	0.81
	10	44753351	0.12	T/C	5.83 × 10-19	8.4	7.35e	E2
	18	59603446	0.06	A/G	5.9 × 10-5	1.9	0.19	29-8
	19	47390815	0.37	T/C	9.21 × 10-13	5.5	0.69	E3
Seed-coat color	3	42959913	0.21	G/A	6.97 × 10-6	5.0	1.25
	5	34734860	0.36	C/T	3.06 × 10-7	7.5	8.28e	CHS2
	8	7589397	0.14	A/G	1.15 × 10-16	19.3	11.18d	CHS
	8	8462762	0.12	T/G	1.30 × 10-19	23.3	7.52e	CHS
	13	7681784	0.07	A/C	1.35 × 10-5	4.7	12.24d
Pubescence color	3	47244893	0.18	A/G	3.46 × 10-7	8.3	0.00
	6	17567713	0.20	G/A	4.54 × 10-13	18.9	0.39
	6	18118558	0.40	T/C	1.08 × 10-28	48.2	0.00	T
	6	18583273	0.48	A/C	1.41 × 10-25	39.6	0.00
Flower color	13	2833623	0.44	T/C	1.37 × 10-11	12.2	0.00
	13	3301099	0.45	C/T	2.93 × 10-29	39.1	0.00
	13	3657853	0.44	G/A	7.63 × 10-35	46.4	0.19	W1
	13	4198124	0.50	C/A	3.62 × 10-28	35.6	0.00
	13	4559799	0.46	G/A	3.82 × 10-40	32.7	0.00

^aChr., chromosome; ^bPosition in base pairs for the peak SNP according to soybean reference sequence of Williams 82; ^cThe significant SNP located in one of the QTL intervals as reported in other studies (www.soybase.org) . ^dindicates a 1 % genome-wide cutoff level, ^eindicates a 5 % genome-wide cutoff level