Table 2. GWA scan results for protein and oil.

MS-1996 (728)a			MS-2000 (934)			IL-1964 (619)			IL-1966 (977)			Huang et al. 2014 (214)
SNP	-log (p-value)b	Allelic Effect Estimate	SNP	-log (p-value)	Allelic Effect Estimate	SNP	-log (p-value)	Allelic Effect Estimate	SNP	-log (p-value)	Allelic Effect Estimate	SNP	-log (p-value)	Allelic Effect Estimate
% Protein (43.45 [43.50])c ; H2 = 0.65 (MS-1966), 0.80 (MS-2000), 0.52 (IL-1964), 0.79 (IL-1966), 0.88 (Hwang 2014)
12_38378352d,e	4.85 (4.69)	0.6	20_31972955	10.63 (10.43)	1.38	8_44632488	4.4 (4.37)	0.44	13_24858209	4.75 (4.12)	0.39	20_31610452	5.99 (5.98)	1.49
17_2678979	4.03 (4.61)	0.63	12_34729290	4.94 (4.11)	0.66				11_37932701	4.68 (5.08)	0.41
									15_3919945	4.35 (4.24)	0.28

% Oil (18.60 [18.45]); H2 = 0.66 (MS-1966), 0.88 (MS-2000), 0.73 (IL-1964), 0.78 (IL-1966), 0.91 (Hwang 2014)
15_12490330	6.43 (6.9)	0.34	20_31150279	13.33 (15.02)	1.06	20_613396	6.51 (6.56)	0.46	12_39580013	6.32 (5.6)	0.22	20_31150279	5.27 (5.2)	0.71
6_46040638	4.72 (5.32)	0.28	15_3919945	8.15 (8.04)	0.48	15_3702534	7.83 (5.8)	0.72	6_10324739	4.67 (4.5)	0.28	16_7253088	4.54 (4.64)	0.62
7_35214966	5.11 (4.6)	0.57	5_38495217	6.74 (8.39)	0.78	11_11633102	4.56 (5.78)	0.61	4_2052748	4.51 (4.61)	0.33
5_38495217	4.88 (4.6)	0.28	6_42907701	5.7 (4.31)	0.26	14_10300717	4.49 (4.33)	0.36
16_510565	4.64 (4.81)	0.44				8_2969485	4.45 (5.1)	0.5
						15_3828587	4.49 (4.33)	0.36
						4_9617727	4.22 (4.42)	0.51

^aPopulation used; value in parentheses is the number of genotypes used.

^bValue from MLMM; parenthetical value from CMLM.

^cMean values for combined populations are in parentheses with median values in brackets.

^dBold font indicates that the marker (or a marker within 4 Mbp) was associated with the trait in two or more environment–population datasets.

^eItalic font indicates that the marker (or a marker within 4 Mbp) was also associated with another trait in the study.