Table 4 Description of significant SNP loci, MAF, r², %variance estimates, additive and dominance effects

SNP Locus	Trait	SNP ^a	MAF	r^2b	% Phenotypic variance explained by SNP	Additive effect a^c	Standard error of the additive effect	Dominance effect d^d	Standard error of the dominance effect	d/a
0_14415_01_190	Ht	[T/A]	0.35	0.06	<0.01	−1.28	0.84	−3.99^*	1.19	3.13
0_17030_01_94	Δ¹³C	[A/G]	0.05	0.08	0.4	0.83^*	0.15	−0.79^*	0.16	−0.95
0_8304_02_414	Δ¹³C	[A/G]	0.11	0.06	<0.01	0.34^*	0.08	−0.27^*	0.09	−0.79
0_17543_01_196	Δ¹³C	[A/G]	0.08	0.06	<0.01	0.51^*	0.11	−0.47	0.12	−0.92
0_10921_01_353	Δ¹³C	[A/G]	0.06	0.05	0.2	0.47^*	0.11	−0.48	0.12	−1.03
2_1501_01_109	Δ¹³C	[A/G]	0.02	0.05	NE^e	NE	NE	NE	NE	NE
CL599Contig1_07_109	Δ¹³C	[G/C]	0.11	0.05	2.7	0.28^*	0.06	−0.28^*	0.07	−1.01
0_3648_01_357	Δ¹³C	[G/A]	0.09	0.04	3.8	0.24^*	0.07	0.31^*	0.08	1.30
UMN_6338_01_99	%N	[A/T]	0.06	0.09	<0.01	−0.10^*	0.02	0.11^*	0.02	−1.09
2_7865_01_156	%N	[A/G]	0.06	0.08	NA	−0.10^*	0.02	0.09^*	0.02	−0.95
2_1087_01_86	%N	[G/A]	0.05	0.07	<0.01	−0.06	0.01	0.05^*	0.01	−0.80
CL1074Contig1_03_101	%N	[A/G]	0.03	0.07	<0.01	0.04^*	0.02	<−0.01	0.02	−0.01
0_17195_01_417	%N	[A/C]	0.04	0.06	7.0	−0.06^*	0.01	0.04^*	0.01	−0.75
2_4191_01_104	%N	[G/A]	0.08	0.05	<0.01	−0.05^*	0.01	0.05^*	0.01	−1.04

Abbreviations: MAF, minor allele frequencies; SNP, single nucleotide polymorphism.
^aSNPs are listed in order of common allele/minor allele for each locus.
^br-square of the markers from the single marker models regressed on Clonal BLUP values.
^cAdditive effect is significantly different from zero from ANOVA (P<0.05).
^dDominance effect is significantly different from zero from ANOVA (P<0.05).
^eNE (Not Estimated) indicates the SNP locus did not meet criteria of three genotypic classes and/or departed from Hardy Weinberg Equilibrium.

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