Table 1. Genome-wide association of flowering time (FT) and seed size (SS) traits with domestication-related SNPs (bold) in soybean.

SNP		Domestication analysis			Genome-wide association study							Homologous gene in Arabidopsis
Chr.	Position (bp)	χ2 (−log10P)	U (−log10P)	FST	Trait	Allele	Frequency	Effect	−log10P	r2 (%)	Candidate gene	Gene	Reference
11	10957940	30.60(6.64)	−2.36(1.74)	0.4890	SS	T	0.45	−9.12 ~ −5.84	6.32 ~ 7.43	6.24 ~ 11.80	Glyma11g15300 Glyma11g15310
11	11100801				SS	G	0.58	−2.10 ~ −0.58	6.52 ~ 14.49	8.14 ~ 16.26	Glyma11g15480	NOT2A (AT1G07705)	49
11	11111516	38.40(8.34)	−2.53(1.95)	0.5069	SS	C	0.38	0.90 ~ 3.90	0.60 ~ 2.40	0.91 ~ 3.20	Glyma11g15480	NOT2A (AT1G07705)	49
11	11120981				SS	C	0.53	−23.59 ~ −18.40	6.19 ~ 10.59	6.50 ~ 14.42	Glyma11g15480	NOT2A (AT1G07705)	49
11	11121256				SS	G	0.51	4.40 ~ 18.40	6.11 ~ 9.91	5.96 ~ 16.85	Glyma11g15480	NOT2A (AT1G07705)	49
11	11121307				SS	T	0.56	−0.07 ~ 4.87	6.40 ~ 11.97	6.56 ~ 16.26	Glyma11g15480	NOT2A (AT1G07705)	49
11	15362036	45.45(9.87)	−2.43(1.82)	0.5656	FT	A	0.42	−10.11 ~ −4.87	1.51 ~ 2.61	1.32 ~ 2.17	Glyma11g18720	OTLD1 (AT2G27350)	46,47,48
12	5895633	37.23(8.08)	−3.73(3.71)	0.7344	FT	C	0.53	−12.96 ~ −5.21	7.63 ~ 8.65	6.16 ~ 7.00	Glyma12g08150 Glyma12g08160
12	5895655	38.04(8.26)	−4.30(4.78)	0.7830	FT	A	0.52	−13.05 ~ −5.20	6.53 ~ 7.61	5.32 ~ 6.34	Glyma12g08150 Glyma12g08160
12	5895785	38.74(8.41)	−4.19(4.55)	0.7938	FT	C	0.53	−4.54 ~ −1.30	8.14 ~ 9.33	6.44 ~ 7.32	Glyma12g08150 Glyma12g08160
12	5957099	30.47(6.62)	−2.78(2.27)	0.6017	FT	A	0.55	−12.93 ~ −9.17	6.54 ~ 7.11	5.61 ~ 5.92	Glyma12g08210 Glyma12g08230
15	39607166	32.10(6.97)	−3.89(3.40)	0.6496	FT	A	0.48	−14.97 ~ −10.93	1.11 ~ 1.74	1.06 ~ 1.54	Glyma15g35080	AREB3 (AT3G56850)	38
16	30207175	30.67(6.66)	−3.47(3.28)	0.5348	SS	G	0.35	−7.48 ~ −3.97	6.99	8.49	Glyma16g26030 Glyma16g26050
16	30207191				SS	T	0.44	−10.29 ~ −8.41	6.47 ~ 8.05	6.02 ~ 9.97	Glyma16g26030 Glyma16g26050
16	30210113	30.90(6.71)	−3.74(3.74)	0.6148	SS	C	0.37	−2.13 ~ 0.84	7.25 ~ 10.22	7.24 ~ 12.01	Glyma16g26030 Glyma16g26050