Table 2 Phenotype, QTL position, allele frequencies and modes of allele inheritance.

From: Genetic control of tracheid properties in Norway spruce wood

Phenotype	QTL¹	SNP²	Region, Feature	Alleles (0/1)	Inclusion frequency	PVE (H²_QTL) (%)	2a³	d⁴	d/a
MFA_CORE	129,716	MA_10117352g0010_1285	Synonymous	T/C	0.548	1.47	0.403	0.168	0.836
MFA_OUTER	165,836	MA_10434903g0010_8217	Intron variant	T/A	0.600	1.03	0.190	− 0.002	− 0.025
TWr_EW	166,535	MA_10435070g0010_17636	Missense	T/C	0.627	3.16	0.349	− 0.053	− 0.304
TWr_LW	95,509	MA_336364g0010_6123	Missense	C/T	0.665	0.05	0.007	− 0.039	− 11.489
	12,016	MA_11172g0010_18275	Splice variant	A/G	0.579	0.01	0.051	− 0.078	− 3.058
	160,388	MA_10433459g0010_6695	Upstream	G/T	0.604	1.72	0.118	0.042	0.701
	44,384	MA_64438g0010_10851	Missense	A/C	0.546	0.03	0.395	0.024	0.123
	59,913	MA_96801g0010_10438	Synonymous	C/T	0.547	0.10	0.212	0.022	0.211
	116,013	MA_950574g0010_7132	Upstream	T/A	0.558	0.05	0.451	0.004	0.017
	120,168	MA_7460525g0010_2105	Upstream	G/A	0.561	2.27	0.140	0.045	0.642
TWt_EW	131,776	MA_10239556g0010_	Upstream	T/G	0.633	1.80	0.072	0.002	0.069
TWt_TW	171,180	MA_10436040g0010_61320	Upstream	G/A	0.661	2.13	0.003	− 0.039	− 24.638
TWt_Ring	171,180	MA_10436040g0010_61320	Upstream	G/A	0.566	3.79	0.019	− 0.046	− 4.646
WT_EW	51,296	MA_80033g0010_7384	Missense	T/C	0.541	0.01	0.047	0.0007	0.033
	65,505	MA_105586g0010_7132	Missense	T/C	0.536	0.10	0.032	− 0.002	− 0.114
	19,482	MA_17843g0010_11398	Missense	A/G	0.546	0.01	0.021	0.010	0.976
	103,329	MA_492000g0010_1672	Upstream	A/T	0.582	0.10	0.032	− 0.021	− 1.277
WT_LW	1	MA_5g0010_86525	Upstream	G/A	0.876	0.01	0.046	0.008	0.356
	9,848	MA_9125g0010_34791	Upstream	T/C	0.64	0.10	0.053	0.004	0.131
	112,677	MA_885527g0010_4213	Upstream	C/T	0.795	0.02	0.059	0.018	0.591
	126,271	MA_9357928g0010_1204	Upstream	G/A	0.567	0.02	0.060	− 0.024	− 0.809
	135,796	MA_10426383g0010_7358	Synonymous	A/G	0.61	1.57	0.097	− 0.0007	− 0.015
WT_Ring	103,326	MA_492000g0010_1596	Synonymous	T/C	0.726	1.78	0.038	− 0.003	− 0.163
	127,327	MA_9563494g0010_4010	Missense	G/T	0.509	0.01	0.084	− 0.019	− 0.464
	78,937	MA_138164g0010_2032	Downstream	C/T	0.529	1.25	0.007	0.001	0.442
C_EW	65,505	MA_105586g0010_7132	Missense	T/C	0.633	2.08	5.481	− 0.238	− 0.087
C_TW	96,993	MA_373300g0010_1844	Upstream	C/T	0.559	3.62	1.905	0.791	0.831
C_TW	135,796	MA_10426383g0010_7358	Synonymous	A/G	0.53	3.25	9.214	0.533	0.116
C_LW	16,320	MA_15229g0010_	Upstream	A/T	0.512	0.78	4.120	1.448	0.703
C_LW	135,796	MA_10426383g0010_7358	Synonymous	A/G	0.635	1.40	9.434	0.146	0.031

¹Bold QTLs indicate associations that have been detected across and within traits.
²SNP: The SNP name is composed of contig (MA_number) and SNP position on contig. As an example, the SNP MA_10117352g0010_1285 is located on contig MA_10117352 at position 1,285 bp. QTL is the value extracted after the Stability selection probability (SSP) has been performed to indicate the significant associations. This value then points to the significant SNP.
³Calculated as the difference between the phenotype means observed within each homozygous class (2a =|G_BB-G_bb|, where G_ij is the trait mean in the ijth genotype class).
⁴Calculated as the difference between the phenotypic mean observed within the heterozygous class and the average phenotypic mean across both homozygous classes [d = G_Bb-0.5(G_BB + G_bb), where Gij is the trait mean in the ijth genotypic class].

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Table 2 Phenotype, QTL position, allele frequencies and modes of allele inheritance.

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