Table 3.

Percentage explained variance (%Var), phenotypic means of SNP alleles, and significant (P < 0.05) marker-trait associations

Candidate gene	Site position1	%Var	P -value	Means of SNP alleles2 (accession classes)
BLZ1	Flowering time [days after sowing]
	1733	6.46	0.0033	A: 67.96	C: 69.87
	1825	7.38	0.0031	G: 67.96	A: 69.91
	1888	6.46	0.0033	C: 67.96	T: 69.87
	1890	7.10	0.0017	G: 67.50	A: 69.54
	2038	7.52	0.0011	Del: 67.62	AT: 69.68
	2520	7.10	0.0017	G: 67.50	A: 69.54
	2562	6.46	0.0033	C: 67.96	T: 69.87
	2774	7.10	0.0017	T: 67.50	C: 69.54
BPBF	Crude protein content [%]
	-368	6.65	0.0003	G: 14.85	A: 15.63
	-315	5.40	0.0003	T: 14.85	C: 15.63
	-303	6.50	0.0003	T: 14.87	A: 15.63
	-215	6.86	0.0002	C: 14.86	G: 15.63
	-209	6.19	0.0004	A: 14.88	G: 15.63
	-166	6.07	0.0003	A: 14.87	G: 15.64
	-101	5.38	0.0004	T: 14.88	C: 15.64
	-27	4.94	0.0003	C: 14.88	T: 15.65
	-3	6.76	0.0002	T: 14.82	C: 15.64
	62	4.02	<.0001	T: 14.79	C: 15.66
	579	12.40	0.0003	T: 14.90	C: 15.66
	586	3.34	0.0025	G: 14.93	A: 15.58
	618	3.42	0.0019	A: 14.91	G: 15.58
	713	5.45	0.0008	A: 14.88	G: 15.60
	797	4.06	0.0029	G: 14.94	T: 15.58
	972	4.40	0.0016	G: 14.91	A: 15.59
	1026	7.91	0.0019	T: 14.98	G: 15.62
	1075	3.51	0.0007	A: 14.91	G: 15.63
	1129	5.57	0.0007	C: 14.92	A: 15.63
	Starch content [%]
	-368	4.44	0.0004	A: 55.58	G: 56.74
	-315	7.30	0.0007	C: 55.57	T: 56.66
	-303	5.39	0.0002	A: 55.56	T: 56.77
	-215	4.41	0.0004	G: 55.58	C: 56.73
	-209	4.84	0.0003	G: 55.57	A: 56.74
	-166	5.12	0.0001	G: 55.55	A: 56.78
	-101	4.79	0.0001	C: 55.53	T: 56.78
	-27	4.22	0.0001	T: 55.55	C: 56.79
	-3	3.27	0.0008	C: 55.61	T: 56.72
	62	0.16	0.0009	C: 55.56	T. 56.70

1: Positions refer to the sequence alignment given in additional file 3

2: All differences between classes for a given site position are significant at P = 0.05