TABLE 4.

Single nucleotide polymorphisms (SNPs) significantly associated with height, spring phenology, and pathogen susceptibility traits under the additive genetic model, as identified by a two‐step approach based on mixed‐effects linear models (MLMs) implemented in Tassel and the Bayesian framework in BAMD (BMLMs)

Trait	SNP name	SNP motif	Site annotation	LG	MAF	MLMs			BMLMs
						F	p	R 2	Mean	Lower 95% CI	Upper 95% CI
Height	BX249583‐420	[A/G]	unk	1	0.266	7.383	0.001	0.027	3.956	1.162	6.762
	BX251999‐509	[A/T]	unk	9	0.296	6.576	0.002	0.024	2.749	0.262	5.255
	CT2714‐442	[T/A]	unk		0.381	5.683	0.004	0.021	−2.920	−5.335	−0.503
	F51TW9001AZG2W−933	[C/G]	unk	4	0.438	9.991	<0.001	0.036	3.480	0.931	6.083
	sp_v3.0_unigene17345‐1191	[T/G]	nc	9	0.344	5.977	0.003	0.022	3.232	0.588	5.871
bb2015	BX249218‐322	[A/C]	nc		0.315	6.499	0.002	0.03	7.230	2.107	12.440
	BX249671_307	[T/C]	unk	7	0.397	6.438	0.002	0.029	6.129	0.763	11.450
	BX253890‐151	[T/G]	nc	12	0.157	6.350	0.002	0.029	10.95	4.298	17.552
	CL2033CT1302CN1398‐513	[A/G]	nc	1	0.408	5.436	0.005	0.025	7.134	2.001	12.321
	CL544Contig1_03. Pipn−84	[T/G]	unk		0.135	9.107	<0.001	0.041	10.18	2.922	17.579
	FN692276‐550	[A/G]	unk	12	0.402	7.903	<0.001	0.036	5.667	0.664	10.774
	i13066s710	[A/C]	nc		0.242	6.107	0.002	0.028	8.365	2.328	14.407
	i16267s380	[A/G]	unk	2	0.411	7.388	0.001	0.033	−10.55	−15.885	−5.168
	LP3‐3–298	[C/G]	unk		0.143	5.538	0.004	0.025	8.510	1.696	15.302
bb2017	0_12730_01_contig1‐159	[A/C]	unk	12	0.379	9.749	<0.001	0.044	4.003	1.509	6.499
	AL750545‐695	[T/A]	non‐syn	1	0.487	5.754	0.003	0.026	4.131	1.375	6.800
	AL750773_910	[T/A]	unk	3	0.499	5.580	0.004	0.026	−4.048	−6.810	−1.339
	BX249816‐2143	[A/G]	non‐syn	7	0.269	5.783	0.003	0.026	5.787	2.792	8.839
	CT576106‐142	[C/G]	unk	1	0.180	7.147	0.001	0.032	5.590	2.165	9.029
	CT577489‐1569	[A/C]	unk		0.203	5.826	0.003	0.026	−4.606	−7.559	−1.602
	F7JJN6E01B7BCW−157	[A/G]	syn	5	0.117	5.591	0.004	0.025	7.708	3.801	11.533
	FM945796‐840	[T/G]	unk		0.213	6.284	0.002	0.028	−4.613	−7.748	−1.473
	i10996s1211	[T/C]	unk		0.301	8.281	<0.001	0.037	4.295	1.467	7.149
dbb2015	CL2507CT3369CN3610‐193	[T/A]	nc	1	0.387	5.406	0.005	0.025	8.981	2.203	15.730
	F51TW9001BWV4H−219	[T/C]	non‐syn		0.462	5.941	0.003	0.028	7.101	0.458	13.72
	F51TW9002FPGRE−170	[A/G]	nc		0.346	5.510	0.004	0.026	9.467	2.507	16.580
dbb2017	AL749850_679	[A/G]	unk		0.402	5.449	0.005	0.021	−4.992	−9.318	−0.654
	BX681656‐960	[A/C]	syn	5	0.481	8.050	<0.001	0.030	−6.416	−10.154	−2.669
	CT580064‐331	[A/G]	unk		0.442	6.236	0.002	0.024	−4.363	−7.934	−0.822
	CT582680‐451	[A/C]	unk		0.201	7.383	0.001	0.028	−10.48	−15.541	−5.470
	F51TW9001BAW7V−405	[A/G]	unk	12	0.163	9.088	<0.001	0.034	7.287	2.665	11.854
	i17647s350pg	[G/C]	unk		0.157	5.847	0.003	0.022	5.747	0.878	10.611
D. sapinea disc	BX679001‐1418	[T/C]	non‐syn	7	0.192	5.544	0.005	0.049	−0.054	−0.102	−0.006
	CT574726_30	[T/C]	unk		0.435	5.539	0.005	0.049	−0.051	−0.089	−0.014
	i11062s233	[G/C]	syn	7	0.293	5.596	0.005	0.050	−0.048	−0.090	−0.007
D. sapinea necrosis length	AL750492_595	[T/C]	unk	1	0.121	5.887	0.004	0.033	0.897	0.081	1.713
	F51TW9002FT2ZF−1060	[T/G]	unk	12	0.485	8.614	<0.001	0.048	−1.279	−1.992	−0.574
A. ostoyae necrosis length	F51TW9001AI9YZ_1847	[A/G]	unk	7	0.273	5.928	0.005	0.081	−0.735	−1.345	−0.129
	F51TW9001CXU1D_1264	[T/C]	unk	6	0.364	6.594	0.003	0.09	−0.997	−1.787	−0.225

Bayesian mean SNP effects and 95% credible intervals (CIs) were obtained from the distribution of the last 20,000 iterations in BAMD. Marker codes and linkage groups as reported in Plomion et al. (2016).

Abbreviations: bb, bud burst; dbb, duration of bud burst; disc, needle discoloration; LG, linkage group; MAF, minimum allele frequency; unk, unknown; nc, noncoding; non‐syn, non‐synonymous; syn, synonymous.